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A: New Tools and Methods in Experiment and Theory

Computational Insights into the Adsorption of Ligands on Gold Nanosurfaces
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The Journal of Physical Chemistry A

Cite this: J. Phys. Chem. A 2023, 127, 48, 10282–10294
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https://doi.org/10.1021/acs.jpca.3c05560
Published November 22, 2023

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Abstract

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We study the adsorption process of model peptides, nucleobases, and selected standard ligands on gold through the development of a computational protocol based on fully atomistic classical molecular dynamics (MD) simulations combined with umbrella sampling techniques. The specific features of the interface components, namely, the molecule, the metallic substrate, and the solvent, are taken into account through different combinations of force fields (FFs), which are found to strongly affect the results, especially changing absolute and relative adsorption free energies and trends. Overall, noncovalent interactions drive the process along the adsorption pathways. Our findings also show that a suitable choice of the FF combinations can shed light on the affinity, position, orientation, and dynamic fluctuations of the target molecule with respect to the surface. The proposed protocol may help the understanding of the adsorption process at the microscopic level and may drive the in-silico design of biosensors for detection purposes.

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1. Introduction

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The understanding, at the molecular level, of the interaction between ligands and nanostructured surfaces is very important in the current research, especially because it can drive the design of novel sensing devices for the detection and identification of chemical and biological agents, ranging from small drugs to viruses and bacteria. (1) In many different multidisciplinary areas of nanoscience and nanotechnology, (2,3) systems composed of a target molecule, an inorganic substrate, and an aqueous solvent are gaining increasing attention due to their potential applications. For instance, noble metals and graphene-based engineered materials provide a powerful tool to combine tunable spectral selectivity and enhanced sensitivity, which can be exploited in the growing fields of biosensing. (4−9) Nevertheless, the design and optimization of nanotechnological applications benefit from understanding the molecular factors that drive the recognition and binding of the molecule on the nanosurface. Notably, the investigation of the structural, dynamic, and interaction features of molecule-inorganic surface-water systems is challenging both experimental and theoretical research fields.
The intrinsic complexity of molecule–surface assemblies, which span a wide range of time and length scales, can only be partially investigated by means of experimental measurements. In fact, in the protein case, experiments aimed at probing the interface between the protein and the surface in an aqueous environment are extremely demanding and provide indirect information at nanometer resolution, leading to uncertainty on the location and orientation of the adsorbed biomolecules and on the role played by polyelectrolytes and surfactants at the aqueous interface. (10,11) In addition, experimental techniques like surface plasmon resonance spectroscopy and quartz crystal microbalance can provide adsorption free energies of peptides on gold surfaces, (12,13) but they are still limited to single molecules. Similarly, other techniques like single-molecule force microscopy (SMFM) and isothermal titration calorimetry afford valuable information that can be used to indirectly estimate adsorption free energies (AFE) based on desorption forces and thermodynamic measurements and provide a preliminary comparison with direct experimental and computational data. (14)
Due to the lack of (direct) experimental data for the majority of molecular species, computational techniques can effectively complement experimental studies to atomistically investigate molecule/surface/water interfaces and evaluate the binding affinity to nanosurfaces. (11,12,15,16) A great effort in this direction is already underway, and computational chemistry offers new insights into recognition and binding processes and explains how molecules, especially biomolecules, interact with different kinds of surfaces. (17,18) However, as pointed out by Martin et al., (19) “there are no proven models for describing biointerfaces” because of the lack of experimental information to validate results, and this translates into always newly developed methodologies for the simulation of molecule–surface interactions trying to better describe and predict adsorption phenomena.
Simulating water-solvated molecules in the presence of inorganic surfaces requires an accurate description of each component of the system and a robust sampling method. (20,21) Extensive sampling methodologies are currently being developed and applied to explore the complex phase space of (bio)molecules/surfaces. Classical molecular dynamics (MD) simulations are by far the most used and suitable method to reveal the interesting dynamical features of this kind of aqueous system and to gain insight into adsorption events on a molecular scale. In this regard, consistent force fields (FFs) have been built to describe the properties of adsorbates and plasmonic surfaces in water, both separately and as a whole. (20,21) Until now, there are few computational protocols (16) able to model and simulate molecules of different natures and sizes interacting with various inorganic surfaces in solution.
In this work, we propose a computational strategy to study, at an atomistic level, the adsorption of small- and medium-sized molecules on nanostructured plasmonic surfaces in an aqueous environment. To that end, we used MD trajectories of the adsorption process of several adsorbates on gold and estimated the AFEs. We focus on the parameters affecting the molecule–surface interaction, i.e., the average distance of the molecule from the surface, its orientation once it is adsorbed on it, and the nature of the interaction, as mediated by the surrounding water molecules. Such a computational protocol may help the understanding of the adsorption process at the microscopic level and the in silico design of (bio)sensors for detection purposes. (22−24)

2. Methods

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The simulation of interfacial systems requires the application of a computational strategy based on three main aspects. First, a realistic representation of the structure of the molecule, the surface, and the solvent can be achieved by adopting fully atomistic approaches. Second, the necessity of using classical approaches for the description of the physicochemical properties of these systems. (21) Indeed, dealing with their complexity, which covers a broad range of time and length/size scales, going from femtoseconds to milliseconds and from nanometers to micrometers, prevents the use of quantum mechanical methods. Within this framework, a suitable set of parameters is needed to properly reproduce the atomic properties of each component and its interaction with the others. Third, the exploration of the conformational phase space of the molecule and the surrounding solvent upon the surface by means of a robust sampling method, for instance, MD simulations. The thermodynamic description of adsorption processes thus benefits from the combination of accurately parametrized FFs and well-sampled configurations, which account for enthalpic and entropic contributions to adsorption.
Potential of mean force (PMF) methods like umbrella sampling (US) (25) can be applied to such systems to recover information for the travel of the molecule from the bulk solution to the surface and to obtain adsorption free energies. US is used as a benchmark reference for evaluating the performance of other free-energy computational protocols (26−28) and has also been employed in the study of adsorption processes. (29) Despite its practical application, the usage of the US is often limited by its elevated computational cost since various overlapping windows, sufficiently equilibrated, must be prepared.
In this section, the next steps are addressed: a short description of the chosen FFs to treat each part of the system, the building of the system in relation to its characteristic features, and the computational procedure to be followed in MD and US simulations.

2.1. Force Fields for the Gold Surface

In the literature, different FFs are available to describe gold surfaces, and most of them rely on classical Lennard-Jones (LJ) potentials to include nonelectrostatic interactions.
Among the first optimized sets of LJ parameters developed to model mixed interfaces, there is the parametrization proposed by Heinz et al., incorporated in the INTERFACE FF (IFF) for inorganic nanostructures. (30,31) Within IFF, the face-centered cubic (fcc) metal consists of charge-neutral atoms with repulsive and dispersive van der Waals interactions. Therefore, they can rearrange their positions, thus allowing the modeling of different crystallographic facets and shape constructs. The model comprises just one atom type for the metal atoms; that is, only one set of LJ parameters for each metal. IFF parameters are the result of a parameter validation process only involving properties of pure metal and nonbonded interactions. Therefore, the interaction of the surface with other components of the interface is considered to be mainly dictated by the metal itself. Such parameters are transferable since the functional form of the energy is compatible with a broad range of “organic” FFs (AMBER, (32) CHARMM, (33) and OPLS/AA (34) among them), thus implying that standard combination rules are sufficient to deal with interfaces of various kinds. (20,35) In its original formulation, IFF lacks the inclusion of explicit metal polarization effects, since the parametrization against experimental data should, in principle, make them implicitly accounted for. Nevertheless, Heinz et al. have recently introduced a core–electron polarizable LJ potential to describe gold surfaces, whose effectiveness has been proven in the specific case of charged ions and peptides. (36)
GolP FF, (37) related to the previously established OPLS/AA FF, and GolP-CHARMM, (38) developed on the basis of the widely used CHARMM family of FFs, economically incorporate polarization effects using the rigid-rod model proposed and implemented by Iori and Corni (39) in 2008. GolP was specifically developed for Au(111) surfaces, whereas GolP-CHARMM was extended to treat also Au(100). (40) Unlike IFF, GolP and GolP-CHARMM do not include intrasurface Au–Au interaction terms. As a result, the gold surface is kept frozen, which disables any potential gold lattice deformation and prevents the evaluation of the surface energies or intrinsic properties of the metal. An important aspect of GolP FFs is the introduction, for each gold atom, of two LJ virtual sites occupying the hollow sites of the gold surface that favor on-top adsorption, as suggested by DFT calculations. (37) With respect to the IFF, GolP FFs contain specific parameters to describe the interactions between the adsorbate and gold. This aspect prevents transferability to other bio-oriented FFs.
GolP and GolP-CHARMM FFs have been specifically parametrized so as to give a balanced description of the gold-molecule versus gold–water interactions, which is essential since the adsorption of a molecule on a surface is actually a competition between the molecule and the water molecules for that surface. Then, special attention has been paid to the modeling of water molecules adsorbed on gold, given that water structuring and layering above both Au(111) and Au(100) surfaces can strongly affect the adsorption of biomolecules. (41)
In this work, nonpolarizable and polarizable IFF, as well as GolP and GolP-CHARMM, have been tested to study the adsorption processes on Au(111).

2.2. System Preparation and Simulation Setup

We have investigated the adsorption on gold nanostructures of the seven molecules shown in Figure 1: alanine dipeptide (ALD) as a representative of peptide structures, the four DNA nucleobases [adenine (ADE), guanine (GUA), cytosine (CYT), and thymine (THY)], and two nonstandard ligands [pyridine (PYR) and doxorubicin (DOX)].

Figure 1

Figure 1. Structures and atom numberings of the adsorbates studied in this work.

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The gold nanostructure is here modeled as a planar surface under the assumption that neglecting the curvature of the nanoparticle/nanoaggregate represents a good approximation of the experimental setup. Among the various crystal surfaces, we have selected Au(111) facets, which are the most stable and therefore the most abundant in nanoparticles. (42) The gold slabs are generated using the atomic simulation environment (ASE) Python module, (43) which sets up the lattice constant, the crystal packing (fcc111 in this case), the required dimensions, and hence the number of layers.
Optimized structures (at the DFT level, B3LYP/DZP) of the seven molecules are taken as the starting point to obtain parameters and charges compatible with the FFs employed to describe the gold surface. To this aim, LigParGen (44) and CGenFF (45,46) web servers are used, respectively, to generate OPLS/AA parameters to be joined with IFF and GolP FFs and CHARMM parameters to be used with IFF and GolP-CHARMM. This procedure allows us to test the performance of different combinations of existing force fields for the molecule and the gold surface and avoid expensive and time-consuming manual reparameterization. The standard nonpolarizable SPC (47) and the TIP3P (48) water models for the solvent are employed with OPLS/AA and CHARMM FFs, respectively.

2.3. Molecular Dynamics

MD simulations are performed in the GROMACS 2020.4 software. (49) A 4.4 × 4.1 × 1.0 nm metal slab (5 layers thick so as to mimic the structure of a metal nanoparticle) is enclosed in a simulation box of 5 nm (7 nm in the DOX case) height. The metal slab comprises 1200 real lattice atoms that correspond to simulating 1200 particles within the nonpolarizable IFF, 2400 within its polarizable version, and 3360 in the GolP and GolP-CHARMM cases. The studied molecule is placed in the center of a 3D simulation box at 1 nm (1.5 nm for doxorubicin) from the top of the surface in a random initial conformation (see Figure 2a). The molecule/surface system is solvated with more than 2000 water molecules, and sodium and chloride ions are included in the box to neutralize the system and attain a physiological 0.154 M concentration. The solvated system is then subjected to steepest-descent energy minimization in order to remove clashes between the atoms and ensure starting from a reasonable structure in terms of geometry and solvent orientation. After the energy was minimized, a 2 ns simulation was performed to adjust the water density in the NPT ensemble at a pressure of 1 bar. Afterward, a 15 ns MD production is conducted in the NVT ensemble (time step of 2 fs) at 300 K using a Nosé–Hoover thermostat (50) with a coupling constant of 2 ps. During these steps, the bond lengths of hydrogen atoms are constrained using the LINCS (51) algorithm. Particle Mesh Ewald (52) electrostatic summation is cutoff at 10 Å, and a force-switched cutoff starting at 9 Å and ending at 10 Å is used for LJ nonbonded interactions. Periodic boundary conditions are adopted in all simulations.

Figure 2

Figure 2. (a) Initial and (b) final configurations of guanine on gold. The system is enclosed in a 3D simulation box (blue lines). Water molecules and ions have been omitted for clarity. In the favorable adsorption geometries, all molecules studied here (see Figure 1) are adsorbed parallel (slightly tilted) to the surface.

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2.4. Umbrella Sampling

For the purpose of estimating the AFEs, the 1D US technique is applied during the adsorption/desorption processes of each adsorbate. Notice that, for some systems, like molecules embedded in lipid bilayers, it is important to consider the conformational freedom of the solute to guarantee proper sampling. As exposed by Jambeck and Lyubartsev (53) and also in earlier works, (54−56) this can be done by exploring more than one collective variable/coordinate, which is, indeed, the philosophy of 2D US calculations. Notwithstanding, such techniques are more computationally demanding than the standard 1D US.
In this work, starting configurations of each system for 1D US are sampled through steered MD simulations, in which the molecule is pulled away along the z-direction, i.e., perpendicular to the gold surface, from the previously obtained adsorbed state to the free state in solution with a rate of 0.5 nm per ns. 30–50 configurations are extracted along the trajectory and equilibrated at 300 K. Finally, each window is simulated for 5 ns in the NVT ensemble, restraining the center of mass (COM) of the molecule in the z-direction with a harmonic constant of k = 2000 kJ mol–1 nm–2, but allowing it to explore the xy-plane. Additional configurations and/or differently restrained windows are added whenever needed to improve the sampling. The weighted histogram analysis method (WHAM), (57) implemented in GROMACS, is used as a postprocessing method to obtain the adsorption Helmholtz free energy profile, taking the free molecule in solution as the reference state and using a bootstrapping method (N = 100) to estimate error bars. 2D US test calculations for the adsorption of DOX indicated that even if the sampling is done with further degrees of freedom, the conformation of the molecule in the adsorption minima remains unaltered with the anthraquinone rings parallel to the surface while the rest of the molecule freely moves.
To further investigate the possible molecular basis of the adsorption mechanism, key points are extracted from the adsorption profiles, and non-covalent interaction (NCI) (58) plots are constructed from the promolecular densities using the NCIPLOT4 program. (59)

3. Results

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In this section, we report the results obtained with the methods explained in Section 2. Briefly summarized, the adsorption process of the set of molecules in Figure 1 on a gold surface was studied through 15 ns MD simulations. Example structures for GUA in its initial and final configurations are presented in Figure 2. Starting from the “adsorbed” configuration, the binding energies were calculated by using the US technique in a path normal to the metal surface, mimicking the deattachment procedure until the molecule was free again. The obtained adsorption energies, ΔEads, and the minimum distance values, dmin, are collected in Tables 1 and S1, and for the sake of comparison, they are plotted in Figure 3. Overall, all molecules present an affinity to the surface (ΔEads < 0), and each one lies horizontally (at around 0.30–0.40 nm) with respect to the surface, revealing some kind of strong interactions with the metal that are further studied by means of NCI analyses. In what follows, we will comment on the findings for every particular subset: alanine dipeptide, nucleobases, and nonstandard ligands.
Table 1. Computed Average Adsorption Free Energies, ΔEads, and Minimum Distances, dmin, for Adsorbed Molecule/Au(111) Systems of Figure 1, Using OPLS/AA for Each Molecule and IFF and GolP for the Gold Surfacea
LigandIFFGolPother works
 ΔEadsdminΔEadsdmin 
 (kJ/mol)(nm)(kJ/mol)(nm) 
ALD–79.4 ± 1.90.31–27.9 ± 1.10.37–21.9 ± [1.6–3.5]b
     –25.0 ± 0.5 (0.37)c
     ≈ −70d
     –8.7 ± 1.0e
ADE–89.9 ± 1.60.28–35.0 ± 0.40.33–30.6 (0.33)f, 131.4g, −35.4 ± 1.8h
CYT–70.2 ± 1.30.28–29.4 ± 0.60.32–30.0 (0.29)f, 131.8g, −18.5 ± 1.0h
GUA–104.5 ± 2.50.28–40.6 ± 0.40.33–40.7 (0.33)f, 142.3g, −34.6 ± 1.1h
THY–78.7 ± 2.40.28–31.1 ± 0.60.32–20.1 (0.35)f, 111.7g, −18.3 ± 0.5h
PYR–38.3 ± 0.70.28–18.3 ± 0.30.33 
DOX–135.0 ± 5.60.34–79.6 ± 2.30.44 
a

Standard deviations obtained from the bootstrap analysis and reference values taken from the literature are also listed.

b

Value obtained through thermodynamic integration in ref (60).

c

Values obtained through metadynamics in ref (61).

d

Values obtained through well-tempered metadynamics in ref (62).

e

Values obtained through well-tempered metadynamics in ref (63).

f

Values obtained through well-tempered metadynamics in ref (64). Numbers in parentheses refer to reported minimum distances.

g

Values obtained in ref (65).

h

Values obtained through well-tempered metadynamics in ref (14).

Figure 3

Figure 3. Performance of each combination of force fields for the seven studied molecules in estimating minimum distances from the gold surface, dmin (top clustered histogram), and adsorption free energies, ΔEads (bottom clustered histogram), with the corresponding error bars.

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3.1. Alanine Dipeptide for Validation

Since amino acids constitute the building blocks of proteins, their adsorption on metal surfaces has been widely studied in recent years. (66−68) In particular, capped amino acids have been employed as model structures to mimic the behavior of longer peptides. (60,62,69) For this reason, we selected alanine dipeptide to test our computational strategy against previously published computational results.
Concerning the adsorption dynamics, we plotted in Figure 4a the time evolution of the minimum distance of ALD parametrized with OPLS/AA. The corresponding plots using the CHARMM FF are given in the Supporting Information (Figure S1). Figure 4a shows that ALD rapidly approaches the gold surface and, once adsorbed, it remains bound to it, mainly with the methyl lateral group pointing up toward the bulk water in agreement with descriptions of previous works. (38) Exceptionally, in the GolP-CHARMM case (see Figure S1 in Supporting Information), ALD desorbs a couple of times, suggesting that there is a competitive effect for the interactions with the water molecules in the vicinity and with the gold surface; this behavior is expected, being a known feature of this FF. (40) It can be noticed that the structural disposition of the adsorbate allows for a more flat orientation that favors the contact of the majority of its atoms, especially heteroatoms, with the gold surface. (38,63) Even when ALD desorbs in some intervals of the MD run, it then returns to the metal in the same orientation as before. It is worth mentioning that our computed minimum distance agrees better with the simulation works in the GolP case (0.37 nm in Table 1), and it is shorter (0.31 nm) when IFF is used to describe the gold surface. Despite having found longer minimum distances with GolP FFs, there are no water layers between the molecule and the surface in the adsorbed state.

Figure 4

Figure 4. (a) Evolution of the time of the minimum distance and (b) free energy profiles along the reaction coordinate for the adsorption of the alanine dipeptide on a gold surface. FF: IFF/OPLS and GolP.

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Now we move on to comment on the outcomes of the PMF profiles obtained by the US technique. The overlapping of the umbrella windows for the GolP case is shown as a set of histograms in Figure S2 in the Supporting Information. As highlighted in Table 1, our results on adsorption free energy are in line with other works. The value obtained by using IFF (−79.4 kJ/mol) agrees with ≈−70 kJ/mol reported by Shao and Hall (62) from well-tempered metadynamics calculations on gold nanoparticles of varying size. Discrepancies may arise from the use of a different FF to treat ALD (GROMOS vs OPLS/AA), from the mobility of gold atoms (the authors of ref (62) kept the positions of gold atoms fixed), or from the specific facet involved in the binding process. GolP results can be compared with those provided by Hoefling et al. (60) and Bellucci and Corni, (61) who used two diverse pathway-based methods to compute adsorption free energies for alanine dipeptide. Clearly, the agreement is good in terms of both minimum distance and adsorption free energy. In the case of GolP-CHARMM, the value is similar to the one reported in ref (63).
By looking at the shape of the free energy profiles in Figure 4b, we note that OPLS-derived profiles are smooth and do not present evident barriers for adsorption. In contrast, those profiles coming from CHARMM FF, in particular from GolP-CHARMM (Figures S1 and S3 in Supporting Information), exhibit a small barrier of 2.3 kJ/mol around 0.5 nm; similarly to ref (63), energy barriers are more pronounced and better evidence the three steps of the adsorption process. (60) In general, our data indicate that the adsorption process of ALD on gold is very sensitive to the FFs used to describe the surface and the molecule; adsorption free energy values can range from −5.3 to −79.4 kJ/mol, as can be seen in the bottom panel of Figure 3. Notwithstanding, the assessment of such values requires a direct comparison with experimental data that, to the best of our knowledge, are not available in the literature. A more in-depth discussion of the diverse performance of the FFs employed here is given below.
For the sake of completeness, we performed additional MD and US simulations to evaluate the effect of gold polarization within the IFF model (pol IFF) on the adsorption dynamics and energetics of the alanine dipeptide. The results, which are depicted in Figure S4 in the Supporting Information, show that the inclusion of polarization effects within IFF leads to negligible differences in both minimum distances and adsorption free energy profiles, regardless of the usage of OPLS/AA or CHARMM FF to describe the molecule.

3.2. Performance of FFs: Nucleobases

The biomolecular adsorption of nucleobases on nanoscale surfaces, especially concerning gold, is a mature topic at present. Studies range from DFT calculations (70,71) to classical MD simulations that can include enhanced sampling techniques. (64,65,72,73) We assessed how the description of the DNA bases and the gold provides diverse nuances in the understanding of the adsorption process. Regardless of the initial orientation, after adsorption, every nucleobase lies parallel to the surface (horizontal, slightly tilted orientation), as can be seen in panel b of Figure 2, and in line with the configurations reported by Rosa et al. (64) In these preferred adsorption geometries, molecule-surface distances from Tables 1 and S1 are around 0.28 and 0.33 nm and have almost the same value independently of the nucleobase, allowing no water molecules in between, similarly to ALD. A comparison of the minimum distances in Figure 3 evinces that nucleobases adsorb at longer distances from the Au(111) surface when GolP and GolP-CHARMM are used. In addition, there is a fair agreement with distances reported by previous works (0.29–0.35 nm). (64,72) Plots for the evolution of the minimum distances along the trajectory are shown in Figure S5 in Supporting Information. As a general rule, we found that once the purine or pyrimidine is adsorbed on the surface, it does not desorb during the entire MD simulation, implying a preference for the adsorbed configuration in agreement with previous works, (73) except for ADE and CYT in GolP-CHARMM, which adsorb and desorb multiple times. Also, Figure S5 highlights an important feature related to two possible accommodations of the nucleobases: one at the dmin written in Tables 1 and S1 and another one at a longer distance, ≈0.5 nm, where each nucleobase is adsorbed with the plane of the molecule in a parallel orientation with respect to the substrate surface but with solvent molecules mediating the interaction. An example of both configurations is included in panels e and f in Figure 6 (see below). Notice that all of the data listed in Tables 1 and S1 are associated with the most favorable conditions (orientation and distance) for each interface.
Experimental studies providing structural information on nucleobases adsorbed to surface interactions are currently limited, and in the past, findings were based on the study of the changes of vibrational modes and supported a certain extent of tilt. (74) Tilted orientations were also found in several simulations using MD. (64) Concerning energies, we refer to values obtained from two indirect experimental techniques. First, ref (14) reports the following inferred AFEs for the nucleobases: ADE = 36 ± 11 kJ/mol, GUA = 29 ± 3, CYT = 28 ± 2, and THY = 21 ± 7 kJ/mol from SMFS experiments that measure the desorption force of the four ssDNA oligomers from the aqueous Au(111) interface. Second, there are available values of heats of desorption from temperature-programmed desorption (TPD) experiments, which detail a G > A > C > T trend for DNA monolayer bases acting as adsorbates on gold, (75) but carried out in dried samples. The same trend was then confirmed in the experimental work of ref (74). Computational works by Rosa et al. (64) and Rapino and Zerbetto (65) reproduced the trend (ref (65) also replicates the values in the gas phase) employing computations by means of well-tempered metadynamics or calculating adsorption free energies from the energies of the optimized cell and fragments (Au surface and molecule), respectively. Data in Table 1 shows that with GolP/OPLS, we obtained AFE values similar to those reported in refs (14) and (64), except for THY, which is no longer the nucleobase that interacts more weakly with the gold surface. Indeed, that is the reason our trend differs from the experimentally reported one.
Moreover, Table 1 shows that when the gold surface is described by the IFF, larger adsorption energies are found and thus more similar values to desorption enthalpies in ref (65) and in vacuo free energies in ref (64). This observation again highlights the fact that the level of treatment for the solvent and the inclusion of dynamic/entropic effects might eventually alter the individual values of the AFE. However, it is difficult to establish whether there is a systematic overestimation of these IFF-calculated adsorption energies in the absence of experimental data for the adsorption of single ADE, CYT, GUA, and THY molecules on hydrated Au(111).
Figure S6 reports the free energy landscape for the formation of an interface between each nucleobase and Au(111) in a water solution as a function of the nucleobase COM-surface distance. To compare the energy profiles obtained for the four nucleobases with the different FFs, curves are plotted together in Figures 5 and S7 for the GolP family FFs (GolP and GolP-CHARMM) and IFF, respectively. From these results, it is clear that OPLS gives rise to the G > A > T > C trend, whereas CHARMM provides G > T > A > C, both orderings differing from that of the experimental propensity to desorb. (75) Beyond the sensitivity of the AFE values to the different FF mixtures, the two panels in Figure 5 illustrate the existence of lowest-free-energy global minima in all cases (for GUA it is displayed in Figure 6f) with their corresponding equivalent equilibrium distances, 0.28 and 0.33 nm, when GolP/OPLS and GolP/CHARMM are used to treat the surface/molecule, respectively.

Figure 5

Figure 5. Adsorption free energy profiles of the four nucleobases modeled with OPLS/AA on the left and CHARMM on the right by using GolP FFs.

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Figure 6

Figure 6. Analysis of the interactions occurring during the adsorption of guanine on the gold surface (GolP-CHARMM FF). Left: evolution in time of the number of contacts with the surface and water molecules surrounding guanine. Right: NCI plots of guanine in its in-solution state, local minimum, transition state, and global minimum (top and lateral view) configurations. Water molecules within 0.3 nm of guanine are shown. Similar plots using the IFF/CHARMM FF are displayed in Figure S10 in the Supporting Information.

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When looking at the energetics of the whole adsorption process, we can recognize the presence of a second minimum in each profile (for GUA, it is displayed in Figure 6d for GolP-CHARMM and Figure S10d for IFF-CHARMM), holding a water layer between the gold substrate and the adsorbate and located in the 0.50–0.70 nm interval from the surface as suggested by the plots of the minimum distances (Figure S5 in Supporting Information). These two minima are connected by a transition state (TS). For GUA, in the GolP-CHARMM case, the TS is characterized by the NH2 group pointing toward the surface and several water molecules located at the same distance from the metal, as displayed in Figure 6, panel e. In the IFF-CHARMM case, GUA directly interacts with gold atoms through the hydrogen linked to atom C8 (see the numbering in Figure 1).
The energy barriers are exacerbated in the CHARMM-derived profiles, as can be seen in the right panel of Figure 5. The appearance of TS configurations agrees with the reported findings when computing the free energy of the interaction of nucleobases on Au using PMF in conjunction with the GolDNA-AMBER force field. (73) According to the authors, the barrier exists because of a water displacement from the interface in the competing process, at that distance, between the adsorbate and the solvent for the surface, in line with what we found here for the nucleobases, which must displace the water molecules before getting closer to the gold substrate.
The DNA base interactions on the gold surface and with the water molecules are further analyzed in Figures 6 and S10, which display the number of contacts and the noncovalent interaction (NCI) plots for GUA while getting adsorbed on the surface. According to Figure 6, panel a, the number of waters at the beginning of the trajectory is slightly higher since the adsorption process reveals that the molecule spent some time immersed in bulk water before being adsorbed just above the surface. However, there are always at least 11 waters in the vicinity that keep interactions with the nucleobase. Such interactions are confirmed by the blue lentils and small green NCI surfaces that appear in Figure 6, panel b, to indicate the formation of hydrogen bonds (HB) with the solvent. The maximization of the GUA···water contacts when the molecule is far from the gold coincides with the null number of interactions with the metal (see the curve in the first ns in Figure 6, panel c. NCI surfaces for GUA in its minima (local and global) and its TS are plotted in panels d,e of Figure 6. It can be noticed that the energetic difference between both minima is related to the green NCI (attractive) surfaces that are more spread when GUA is adsorbed onto the surface and follow the shape of the aromatic rings just after adsorption. In the latter position, there are up to 14 atom pairs that fall within 0.35 nm, a threshold chosen based on the minimum distance plots of Figure 3. When performing the same comprehensive analysis for GUA/gold/water using the IFF-CHARMM combination, we observed notable differences with respect to the GolP-CHARMM adsorption pathway. Specifically, IFF-CHARMM resulted in a higher number of GUA/gold contacts compared to the GolP-CHARMM-adsorbed configuration, as highlighted in Figure S10 panel c. This increased interaction between guanine and the gold surface is reflected in a 2-fold value of the NCI integral in the global minimum, as outlined in Table S2. By further comparing the integral values for the NCI surfaces reported in Table S2, we note that GolP-CHARMM gives, in contrast, a stronger interaction with the solvent when guanine is present in the bulk.

3.3. Further Applications: Nonstandard Ligands

To showcase the applicability of our methodology, we performed a complete analysis of two nonstandard ligands, pyridine and doxorubicin, that have been widely used in surface enhanced Raman scattering (SERS) experiments. (76−87)
As expected, both PYR and DOX, whenever adsorbed, assume an orientation with the aromatic rings lying almost parallel to the surface, likewise the nucleobases. Clustering analysis for DOX in Figure S8 in Supporting Information shows that irrespectively of the FF, there are around five structural families, whose representative structures differ from each other in the flexibility of the anchor (substituent in the anthraquinone ring) and the daunosamine, the latter known to be involved in the groove binding when DOX is intercalated into DNA. This flexibility has already been reported in other works for free, solvated, and intercalated DOX. (88−91) As a matter of fact and unlike previous MD for DOX, (89,92,93) with the IFF/OPLS combination, one of the hydroxyl groups attached to the ring C (see Figure S8) rotates during the MD simulation, breaking the standard strong intramolecular interaction and being oriented toward the oxygen atom that bridges the sugar group, forming a new O–H···O HB.
The evolution of minimum distance molecule···surface and AFE profiles is displayed in Figure 7. Minimum distances for PYR have the same value, 0.28 nm, when IFF is used, regardless of the FF employed to describe the molecule, while GolP-derived distances are longer, as reported in Tables 1 and S1. Longer distances are also seen for DOX: GolP parametrization allows the molecule to stay up to 1 Å farther (0.34 vs 0.44 nm in Figure 3) with respect to the gold surface than IFF one, even if there are no water molecules mediating the interactions with gold atoms.

Figure 7

Figure 7. Minimum distance and adsorption free energy plots for PYR (left) and DOX (right) for all of the possible combinations of force fields.

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As can be appreciated in the right panel in Figure 7, when GolP-CHARMM is used, there is a jump resulting in a reduction of the minimum distance, a feature shared also with the other adsorbates. In fact, at around 0.5 nm from the gold surface, i.e., before jumping to the final adsorbed configuration, there seems to be an initial favorable position for DOX, in which the daunosamine portion is located, such that it diminishes the possible steric hindrance for the rings to be positioned parallel to the substrate. At that distance, some water molecules surround DOX, mediating the interaction with the gold surface, as shown in the NCI plot in Figure S13 in Supporting Information.
In contrast to the permanent adsorption of DOX, the time evolution of PYR···Au minimum distances in Figure 7, left panel, highlights the difficulty of this molecule in adsorbing and remaining adsorbed, which is further underlined by the corresponding adsorption free energy profiles. PYR AFE profiles exhibit diverse energy barriers, suggesting, in turn, different transition states. For example, in the IFF cases, one of these energy barriers, with ≈5.7 kJ/mol, lies above the zero reference. Then, pyridine in the transition state is perpendicular with respect to gold (around 90°, better between 60 and 120°), and in the umbrella window, the nitrogen atom stays most of the time directly above gold atoms. In spite of the barriers, the adsorption process still occurs for IFF/OPLS, IFF/CHARMM, and GolP, as opposed to the GolP-CHARMM AFE profile, where there are shallow minima (the lowest-energy one has a −2.13 kJ/mol value in Table S1). In addition, the GolP-CHARMM PMF curve is almost entirely above the zero reference, thus confirming the tendency of PYR to remain in bulk water.
Concerning DOX, as in the previous cases, adsorption free energy values are found to be very sensitive to the combination of the FFs, up to 4-fold different (−47.6 vs −163.1 kJ/mol). By looking at Figure 3, we notice that DOX is the only adsorbate that alters the trend of the predicted adsorption free energies with the tested FF combinations, which we find to be in absolute values AFEIFF/OPLS > AFEIFF/CHARMM > AFEGolP > AFEGolP-CHARMM. We speculate that since DOX is a medium-sized, more complex molecule than the other adsorbates studied here, the different sorting for the AFE values could be related to the diverse geometries that DOX presents in the minimum of the profiles. Figure S9 superimposes DOX structures in the adsorbed configurations with the four FFs. It is clear that the DOX structure comes from the combinations that change the trend, i.e., IFF/OPLS and IFF/CHARMM are those that are more bent, and in particular, IFF/OPLS (in goldenrod) exhibits the hydroxyl group rotation mentioned above.

3.4. Discussion

So far, we have seen that structural properties and AFE values are quite sensitive to the FF choice. One of the desirable features of any FF is that it should be system-independent, and indeed, our results are an attempt to contribute to the answer to the ever-open question in the literature about what FF to employ when modeling molecule-surface interactions. In this respect, there are a few approaches: (i) specifically parametrize interfacial FFs to describe different molecular moieties on gold surfaces; (ii) take a FF rigorously parametrized to tune specific interfacial interactions (e.g, GolP and GolP-CHARMM) and use it as it is; or (iii) combine existing FFs for the different components of the system (e.g., IFF/CHARMM). Surely, the former strategy is the most expensive but also accurate for describing the specific interaction occurring at the interface. (17,19,35,94,95)
Resorting to the transferability principle, in our protocol, we have used the second and third options, and from our findings summarized in Figure 3, the strength of the adsorption is affected by the FFs chosen for both the molecule and the gold, but it seems that the FF of the molecule determines the shape of the profile, so the adsorption pathway and relative trends of affinity (see nucleobases case in Figure 5), while the FF for treating the surface more strongly determines the minimum distance molecule···Au and thus the absolute AFE values. In particular, the GolP-CHARMM combination returns detailed shapes of the profiles, e.g., energy barriers, whereas IFF in any combination permits the molecule to get closer to the gold surface and to adsorb faster and stronger.
In the end, the selection of one of the three above-mentioned options is conditioned by the details that one is interested in exploring. For example, concerning an application in the sensing field, the most interesting things are whether the molecule remains adsorbed along the time or not, the molecule-surface distance, and the orientation. Therefore, a FF combination like GolP/OPLS could be a good balance between cost-effectiveness and accuracy in providing such information.
It is worth mentioning the role of the solvent as a third component of the interface. Water mediates molecule-surface interactions, and its accurate treatment could influence the final results. The selection becomes challenging since the FF used to represent water molecules must be coupled to those for the adsorbate and the surface. We used SPC and TIP3P FFs for OPLS and CHARMM, respectively. The use of OPLS/SPC and CHARMM/TIP3P is a common practice when simulating organic molecules, peptides, and biomolecules, and both have been proven to afford reliable results in interfacial cases with metals. (16,41) However, the combination of OPLS/TIP3P can in principle be used and, in our case, can lead to non-negligible differences in adsorption free energies, whose reliability should be checked and validated. (95)
To unravel the influence of the FF used to model the solvent, we performed further MDs for water/gold, representing the situation without molecular adsorption. Our analyses, supported by NCI indexes listed in Table S3 and displayed in Figures S11 and S12, suggest that TIP3P water molecules engage in intensified competition with ligands for adsorption on the surface, thereby giving rise to more dynamic phenomena. In fact, the greater affinity of water molecules for gold when modeled with the TIP3P FF results in a more dense hydration layer over the Au(111) surface, regardless of the FF employed to describe it, which is clearly visible when examining Figures S11 and S12. As a consequence, this competition challenges the entry of adsorbates across the hydration layer to reach the surface. Conversely, in the case of SPC water models, the adsorbed molecule finds it comparatively easier to reach the metal surface, even though water molecules are in closer proximity to the surface.
The interaction strength between the water layer and the gold surface, as determined by the combination of water/surface force fields (FFs), significantly influences the predicted AFE values of the adsorbed molecules. We have consistently observed a trend wherein SPC water models yield stronger AFE values compared to TIP3P when using the same FF for gold. Importantly, as shown in Figures S11 and S12, the use of IFF for gold surfaces results in a higher number of water molecules (ca. 200 vs 160) at the same threshold value of 0.35 nm. Additionally, IFF affords close proximity between the adsorbate and the gold surface, as highlighted in the plot of Figure S10c. Ultimately, these proximal contacts, water···gold and adsorbate···gold, enhance the overall affinity.
Hence, our findings, as summarized in Figure 3, suggest that distinct water models result in varying binding affinities, and these disparities are further accentuated by the selection of force fields used for the ligand and the surface.

4. Conclusions

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In this work, we have studied the adsorption process and the absolute and relative binding affinities of seven adsorbates, namely, alanine dipeptide, the four DNA nucleobases, and a couple of nonstandard ligands, pyridine and doxorubicin, on the Au(111) surface. Notably, an accurate description of the system’s components depends on the choice of force fields for the molecule, solvent, and gold substrate. Hence, in order to understand the role played by the parametrization of the molecule-surface interactions, we have carried out a comparison between different combinations of FFs: IFF/OPLS, IFF/CHARMM, GolP/OPLS, and GolP-CHARMM.
Our classical MD simulations provide valuable insight into these complex systems’ dynamic features, thanks to an effective sampling of the phase space of the molecule in close proximity to the nanosurface while also accounting for solvation effects. The AFE values, calculated by means of an umbrella sampling procedure, indicate that for the entire set of molecules, adsorption on gold is favorable, with pyridine and doxorubicin having the lowest and highest affinities, respectively, although the values depend on the FF combination used. Minimum molecule-surface distances revealed that guanine is the adsorbate that gets closer to Au atoms, but in general, dmin < 0.44 nm for all molecules. Despite these apparently long distances and the slightly tilted orientations, in the adsorbed configurations, there are no water molecules mediating the molecule-surface interactions in each studied system. Concerning the adsorption pathway, each FF combination leads to different results that have to be interpreted based on the final scope. For example, if there is any interest in the sensing field, GolP/OPLS offers information more in agreement with that available in both experimental and computational works, in terms of both AFE values and minimum distances. On the other hand, GolP-CHARMM gives more detailed free energy profiles that present energy barriers and transition state configurations.
After monitoring the trajectories, there is a switch in the interactions that take place: first, molecule/water when the molecule is immersed in the bulk solution far from the surface, then molecule/water/gold in the transition state with a layer of water between, and then water/molecule/gold with the molecule in direct contact with the surface. All these interfaces are the result of a series of hydrogen bonds and weak van der Waals interactions that appeared as noncovalent interaction surfaces when characterized by NCI plots. The eventual formation of covalent bonds between Au and N atoms is out of the scope of this work and should be analyzed with reactive FFs. (96−99)
Lastly, our computational protocol allows collecting information on the distances, orientations, and energetics of molecules with respect to a nanosurface that is essential in view of subsequent spectroscopic applications, such as SERS. In addition, the in silico design of plasmonic sensors and the foreseen extension of the modeling to the simulation of spectral signals may lead to an improvement in the performance of detection techniques for small molecules. Indeed, we plan to investigate that in future works.

Data Availability

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All adsorbate structures have been optimized by using the AMS code (version 2020.202, http://www.scm.com). Gold slabs have been generated using the atomic simulation environment (ASE) Python module (https://wiki.fysik.dtu.dk/ase/). MD simulations and umbrella sampling calculations of the different adsorbate/water/gold nanosurfaces have been performed by using Gromacs version 2020.4 (https://www.gromacs.org). NCI calculations have been performed by using NCIPLOT4 (https://www.lct.jussieu.fr/pagesperso/contrera/nciplot.html).

Supporting Information

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The Supporting Information is available free of charge at https://pubs.acs.org/doi/10.1021/acs.jpca.3c05560.

  • Adsorption free energies and minimum distances of the seven studied molecules with IFF/CHARMM and GolP-CHARMM; plots of minimum distances and adsorption free energy profiles for alanine dipeptide and the four nucleobases; NCI analyses; and clustered structures of doxorubicin (PDF)

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Most electronic Supporting Information files are available without a subscription to ACS Web Editions. Such files may be downloaded by article for research use (if there is a public use license linked to the relevant article, that license may permit other uses). Permission may be obtained from ACS for other uses through requests via the RightsLink permission system: http://pubs.acs.org/page/copyright/permissions.html.

Author Information

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  • Corresponding Author
  • Authors
    • Sveva Sodomaco - Scuola Normale Superiore, Classe di Scienze, Piazza dei Cavalieri 7, 56126 Pisa, Italy
    • Sara Gómez - Scuola Normale Superiore, Classe di Scienze, Piazza dei Cavalieri 7, 56126 Pisa, Italy;  Orcidhttps://orcid.org/0000-0002-5430-9228
    • Tommaso Giovannini - Scuola Normale Superiore, Classe di Scienze, Piazza dei Cavalieri 7, 56126 Pisa, Italy;  Orcidhttps://orcid.org/0000-0002-5637-2853
  • Notes
    The authors declare no competing financial interest.

Acknowledgments

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This work has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 818064). We gratefully acknowledge the Center for High Performance Computing (CHPC) at SNS for providing the computational infrastructure. Computing facilities provided by CINECA (Iscra C projects “SCOOPS” and “SENSORS”) are also acknowledged.

References

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    Paria, D.; Kwok, K. S.; Raj, P.; Zheng, P.; Gracias, D. H.; Barman, I. Label-free spectroscopic SARS-CoV-2 detection on versatile nanoimprinted substrates. Nano Lett. 2022, 22, 3620– 3627,  DOI: 10.1021/acs.nanolett.1c04722
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    8
    Label-free spectroscopic SARS-CoV-2 detection on versatile nanoimprinted substrates
    Paria, Debadrita; Kwok, Kam Sang; Raj, Piyush; Zheng, Peng; Gracias, David H.; Barman, Ishan
    Nano Letters (2022), 22 (9), 3620-3627CODEN: NALEFD; ISSN:1530-6984. (American Chemical Society)
    Widespread testing and isolation of infected patients is a cornerstone of viral outbreak management, as underscored during the ongoing COVID-19 pandemic. Here, we report a large-area and label-free testing platform that combines surface-enhanced Raman spectroscopy and machine learning for the rapid and accurate detection of SARS-CoV-2. Spectroscopic signatures acquired from virus samples on metal-insulator-metal nanostructures, fabricated using nanoimprint lithog. and transfer printing, can provide test results within 25 min. Not only can our technique accurately distinguish between different respiratory and nonrespiratory viruses, but it can also detect virus signatures in physiol. relevant matrixes such as human saliva without any addnl. sample prepn. Furthermore, our large area nanopatterning approach allows sensors to be fabricated on flexible surfaces allowing them to be mounted on any surface or used as wearables. We envision that our versatile and portable label-free spectroscopic platform will offer an important tool for virus detection and future outbreak preparedness.
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  9. 9
    Premachandran, S.; Haldavnekar, R.; Das, S.; Venkatakrishnan, K.; Tan, B. DEEP Surveillance of Brain Cancer Using Self-Functionalized 3D Nanoprobes for Noninvasive Liquid Biopsy. ACS Nano 2022, 16, 17948– 17964,  DOI: 10.1021/acsnano.2c04187
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    9
    DEEP Surveillance of Brain Cancer Using Self-Functionalized 3D Nanoprobes for Noninvasive Liquid Biopsy
    Premachandran, Srilakshmi; Haldavnekar, Rupa; Das, Sunit; Venkatakrishnan, Krishnan; Tan, Bo
    ACS Nano (2022), 16 (11), 17948-17964CODEN: ANCAC3; ISSN:1936-0851. (American Chemical Society)
    Brain cancers, one of the most fatal malignancies, require accurate diagnosis for guided therapeutic intervention. However, conventional methods for brain cancer prognosis (imaging and tissue biopsy) face challenges due to the complex nature and inaccessible anatomy of the brain. Therefore, deep anal. of brain cancer is necessary to (i) detect the presence of a malignant tumor, (ii) identify primary or secondary origin, and (iii) find where the tumor is housed. In order to provide a diagnostic technique with such exhaustive information here, we attempted a liq. biopsy-based deep surveillance of brain cancer using a very minimal amt. of blood serum (5μL) in real time. We hypothesize that holistic anal. of serum can act as a reliable source for deep brain cancer surveillance. To identify minute amts. of tumor-derived material in circulation, we synthesized an ultrasensitive 3D nanosensor, adopted SERS as a diagnostic methodol., and undertook a DEEP neural network-based brain cancer surveillance. Detection of primary and secondary tumor achieved 100% accuracy. Prediction of intracranial tumor location achieved 96% accuracy. This modality of using patient sera for deep surveillance is a promising noninvasive liq. biopsy tool with the potential to complement current brain cancer diagnostic methodologies.
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  10. 10
    Curry, D.; Cameron, A.; MacDonald, B.; Nganou, C.; Scheller, H.; Marsh, J.; Beale, S.; Lu, M.; Shan, Z.; Kaliaperumal, R. Adsorption of doxorubicin on citrate-capped gold nanoparticles: insights into engineering potent chemotherapeutic delivery systems. Nanoscale 2015, 7, 19611– 19619,  DOI: 10.1039/c5nr05826k
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    10
    Adsorption of doxorubicin on citrate-capped gold nanoparticles: insights into engineering potent chemotherapeutic delivery systems
    Curry, Dennis; Cameron, Amanda; MacDonald, Bruce; Nganou, Collins; Scheller, Hope; Marsh, James; Beale, Stefanie; Lu, Mingsheng; Shan, Zhi; Kaliaperumal, Rajendran; Xu, Heping; Servos, Mark; Bennett, Craig; MacQuarrie, Stephanie; Oakes, Ken D.; Mkandawire, Martin; Zhang, Xu
    Nanoscale (2015), 7 (46), 19611-19619CODEN: NANOHL; ISSN:2040-3372. (Royal Society of Chemistry)
    Gold nanomaterials have received great interest for their use in cancer theranostic applications over the past two decades. Many gold nanoparticle-based drug delivery system designs rely on adsorbed ligands such as DNA or cleavable linkers to load therapeutic cargo. The heightened research interest was recently demonstrated in the simple design of nanoparticle-drug conjugates wherein drug mols. are directly adsorbed onto the as-synthesized nanoparticle surface. The potent chemotherapeutic, doxorubicin often serves as a model drug for gold nanoparticle-based delivery platforms; however, the specific interaction facilitating adsorption in this system remains understudied. Here, for the first time, we propose empirical and theor. evidence suggestive of the main adsorption process where (1) hydrophobic forces drive doxorubicin towards the gold nanoparticle surface before (2) cation-π interactions and gold-carbonyl coordination between the drug mol. and the cations on AuNP surface facilitate DOX adsorption. In addn., biol. relevant compds., such as serum albumin and glutathione, were shown to enhance desorption of loaded drug mols. from AuNP at physiol. relevant concns., providing insight into the drug release and in vivo stability of such drug conjugates.
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  11. 11
    Brancolini, G.; Corazza, A.; Vuano, M.; Fogolari, F.; Mimmi, M. C.; Bellotti, V.; Stoppini, M.; Corni, S.; Esposito, G. Probing the influence of citrate-capped gold nanoparticles on an amyloidogenic protein. ACS Nano 2015, 9, 2600– 2613,  DOI: 10.1021/nn506161j
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    11
    Probing the Influence of Citrate-Capped Gold Nanoparticles on an Amyloidogenic Protein
    Brancolini, Giorgia; Corazza, Alessandra; Vuano, Marco; Fogolari, Federico; Mimmi, Maria Chiara; Bellotti, Vittorio; Stoppini, Monica; Corni, Stefano; Esposito, Gennaro
    ACS Nano (2015), 9 (3), 2600-2613CODEN: ANCAC3; ISSN:1936-0851. (American Chemical Society)
    Nanoparticles (NPs) are known to exhibit distinct phys. and chem. properties compared with the same materials in bulk form. NPs have been repeatedly reported to interact with proteins, and this interaction can be exploited to affect processes undergone by proteins, such as fibrillogenesis. Fibrillation is common to many proteins, and in living organisms, it causes tissue-specific or systemic amyloid diseases. The nature of NPs and their surface chem. is crucial in assessing their affinity for proteins and their effects on them. Here the authors present the first detailed structural characterization and mol. mechanics model of the interaction between a fibrillogenic protein, β2-microglobulin, and a NP, 5 nm hydrophilic citrate-capped gold nanoparticles. NMR measurements and simulations at multiple levels (enhanced sampling mol. dynamics, Brownian dynamics, and Poisson-Boltzmann electrostatics) explain the origin of the obsd. protein perturbations mostly localized at the amino-terminal region. The protein-NP interaction is weak in the physiol.-like, conditions and do not induce protein fibrillation. Simulations reproduce these findings and reveal instead the role of the citrate in destabilizing the lower pH protonated form of β2-microglobulin. The results offer possible strategies for controlling the desired effect of NPs on the conformational changes of the proteins, which have significant roles in the fibrillation process.
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  12. 12
    Tang, Z.; Palafox-Hernandez, J. P.; Law, W.-C.; Hughes, Z. E.; Swihart, M. T.; Prasad, P. N.; Knecht, M. R.; Walsh, T. R. Biomolecular recognition principles for bionanocombinatorics: an integrated approach to elucidate enthalpic and entropic factors. ACS Nano 2013, 7, 9632– 9646,  DOI: 10.1021/nn404427y
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    12
    Biomolecular Recognition Principles for Bionanocombinatorics: An Integrated Approach To Elucidate Enthalpic and Entropic Factors
    Tang, Zhenghua; Palafox-Hernandez, J. Pablo; Law, Wing-Cheung; E. Hughes, Zak; Swihart, Mark T.; Prasad, Paras N.; Knecht, Marc R.; Walsh, Tiffany R.
    ACS Nano (2013), 7 (11), 9632-9646CODEN: ANCAC3; ISSN:1936-0851. (American Chemical Society)
    Bionanocombinatorics is an emerging field that aims to use combinations of positionally encoded biomols. and nanostructures to create materials and devices with unique properties or functions. The full potential of this new paradigm could be accessed by exploiting specific noncovalent interactions between diverse palettes of biomols. and inorg. nanostructures. Advancement of this paradigm requires peptide sequences with desired binding characteristics that can be rationally designed, based upon fundamental, mol.-level understanding of biomol.-inorg. nanoparticle interactions. Here, the authors introduce an integrated method for building this understanding using exptl. measurements and advanced mol. simulation of the binding of peptide sequences to gold surfaces. From this integrated approach, the importance of entropically driven binding is quant. demonstrated, and the first design rules for creating both enthalpically and entropically driven nanomaterial-binding peptide sequences are developed. The approach presented here for gold is now being expanded in the authors' labs. to a range of inorg. nanomaterials and represents a key step toward establishing a bionanocombinatorics assembly paradigm based on noncovalent peptide-materials recognition.
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  13. 13
    Corni, S.; Hnilova, M.; Tamerler, C.; Sarikaya, M. Conformational Behavior of Genetically-Engineered Dodecapeptides as a Determinant of Binding Affinity for Gold. J. Phys. Chem. C 2013, 117, 16990– 17003,  DOI: 10.1021/jp404057h
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    13
    Conformational Behavior of Genetically-Engineered Dodecapeptides as a Determinant of Binding Affinity for Gold.
    Corni, Stefano; Hnilova, Marketa; Tamerler, Candan; Sarikaya, Mehmet
    Journal of Physical Chemistry C (2013), 117 (33), 16990-17003CODEN: JPCCCK; ISSN:1932-7447. (American Chemical Society)
    Genetically engineered solid binding peptides, because of their unique affinity and specificity for solid materials, represent a promising mol. toolbox for nanoscience and nanotechnol. Despite their potential, the physicochem. determinants of their high affinity for surfaces remain, in most cases, poorly understood. Here the authors present exptl. data and classical atomistic mol. dynamics simulations for two gold binding dodecapeptides (AuBP1 and AuBP2) and a control peptide that does not bind to gold, to unravel the key microscopic differences among them. In particular, by extensive sampling via replica exchange simulations, the authors show here that the conformational ensemble of the three peptides in soln. and on the gold surface can be examd., and that the role played by their different conformational flexibility can be analyzed. The authors found, specifically, that AuBP1 and AuBP2 are much more flexible than the control peptide, which allows all the potential Au-binding amino acids present in these AuBPs to concurrently bind to the gold surface. On the contrary, the potential Au-binding amino acids in the rigid control peptide cannot contact the surface all at the same time, hampering the overall binding. The role of conformational flexibility has been also analyzed in terms of the configurational entropy of the free and adsorbed peptides. Such anal. suggests a possible route to improve upon current flexible gold binding peptides.
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  14. 14
    Hughes, Z. E.; Wei, G.; Drew, K. L.; Colombi Ciacchi, L.; Walsh, T. R. Adsorption of DNA fragments at aqueous graphite and Au (111) via integration of experiment and simulation. Langmuir 2017, 33, 10193– 10204,  DOI: 10.1021/acs.langmuir.7b02480
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    Adsorption of DNA Fragments at Aqueous Graphite and Au(111) via Integration of Experiment and Simulation
    Hughes, Zak E.; Wei, Gang; Drew, Kurt L. M.; Colombi Ciacchi, Lucio; Walsh, Tiffany R.
    Langmuir (2017), 33 (39), 10193-10204CODEN: LANGD5; ISSN:0743-7463. (American Chemical Society)
    The authors combine single mol. force spectroscopy measurements with all-atom metadynamics simulations to study the cross-materials binding strength trends of DNA fragments adsorbed at the aq. graphite C(0001) and Au(111) interfaces. The authors' simulations predict this adsorption at the level of the nucleobase, nucleoside, and nucleotide. Despite challenges in making clear, careful connections between the exptl. and simulation data, reasonable consistency between the binding trends between the two approaches and two substrates was evident. On C(0001), the authors' simulations predict a binding trend of dG > dA ≈ dT > dC, which broadly aligns with the exptl. trend. On Au(111), the simulation-based binding strength trends reveal stronger adsorption for the purines relative to the pyrimidines, with dG ≈ dA > dT ≈ dC. Moreover, the authors' simulations provide structural insights into the origins of the similarities and differences in adsorption of the nucleic acid fragments at the two interfaces. In particular, the authors' simulation data offer an explanation for the differences obsd. in the relative binding trend between adenosine and guanine on the two substrates.
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  15. 15
    Cohavi, O.; Corni, S.; De Rienzo, F.; Di Felice, R.; Gottschalk, K. E.; Hoefling, M.; Kokh, D.; Molinari, E.; Schreiber, G.; Vaskevich, A. Protein–surface interactions: challenging experiments and computations. J. Mol. Recognit. 2010, 23, 259– 262,  DOI: 10.1002/jmr.993
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    Protein-surface interactions: challenging experiments and computations
    Cohavi, Ori; Corni, Stefano; De Rienzo, Francesca; Di Felice, Rosa; Gottschalk, Kay E.; Hoefling, Martin; Kokh, Daria; Molinari, Elisa; Schreiber, Gideon; Vaskevich, Alexander; Wade, Rebecca C.
    Journal of Molecular Recognition (2010), 23 (3), 259-262CODEN: JMORE4; ISSN:0952-3499. (John Wiley & Sons Ltd.)
    Protein-surface interactions are fundamental in natural processes, and have great potential for applications ranging from nanotechnol. to medicine. A recent workshop highlighted the current achievements and the main challenges in the field. Copyright © 2009 John Wiley & Sons, Ltd.
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    Brancolini, G.; Kokh, D. B.; Calzolai, L.; Wade, R. C.; Corni, S. Docking of ubiquitin to gold nanoparticles. ACS Nano 2012, 6, 9863– 9878,  DOI: 10.1021/nn303444b
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    Docking of Ubiquitin to Gold Nanoparticles
    Brancolini, Giorgia; Kokh, Daria B.; Calzolai, Luigi; Wade, Rebecca C.; Corni, Stefano
    ACS Nano (2012), 6 (11), 9863-9878CODEN: ANCAC3; ISSN:1936-0851. (American Chemical Society)
    Protein-nanoparticle assocns. have important applications in nanoscience and nanotechnol. such as targeted drug delivery and theranostics. However, the mechanisms by which proteins recognize nanoparticles and the determinants of specificity are still poorly understood at the microscopic level. Gold is a promising material in nanoparticles for nanobiotechnol. applications because of the ease of its functionalization and its tunable optical properties. Ubiquitin is a small, cysteine-free protein (ubiquitous in eukaryotes) whose binding to gold nanoparticles has been characterized recently by NMR (NMR). To reveal the mol. basis of these protein-nanoparticle interactions, we performed simulations at multiple levels (ab initio quantum mechanics, classical mol. dynamics and Brownian dynamics) and compared the results with exptl. data (CD and NMR). The results provide a model of the ensemble of structures constituting the ubiquitin-gold surface complex, and insights into the driving forces for the binding of ubiquitin to gold nanoparticles, the role of nanoparticle surfactants (citrate) in the assocn. process, and the origin of the perturbations in the NMR chem. shifts.
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    Charchar, P.; Christofferson, A. J.; Todorova, N.; Yarovsky, I. Understanding and designing the gold–bio interface: Insights from simulations. Small 2016, 12, 2395– 2418,  DOI: 10.1002/smll.201503585
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    Understanding and Designing the Gold-Bio Interface: Insights from Simulations
    Charchar, Patrick; Christofferson, Andrew J.; Todorova, Nevena; Yarovsky, Irene
    Small (2016), 12 (18), 2395-2418CODEN: SMALBC; ISSN:1613-6810. (Wiley-VCH Verlag GmbH & Co. KGaA)
    A review. Gold nanoparticles (AuNPs) are an integral part of many exciting and novel biomedical applications, sparking the urgent need for a thorough understanding of the physicochem. interactions occurring between these inorg. materials, their functional layers, and the biol. species they interact with. Computational approaches are instrumental in providing the necessary mol. insight into the structural and dynamic behavior of the Au-bio interface with spatial and temporal resolns. not yet achievable in the lab., and are able to facilitate a rational approach to AuNP design for specific applications. A perspective of the current successes and challenges assocd. with the multiscale computational treatment of Au-bio interfacial systems, from electronic structure calcns. to force field methods, is provided to illustrate the links between different approaches and their relation to expt. and applications.
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    Brancolini, G.; Bellucci, L.; Maschio, M. C.; Di Felice, R.; Corni, S. The interaction of peptides and proteins with nanostructures surfaces: a challenge for nanoscience. Curr. Opin. Colloid Interface Sci. 2019, 41, 86– 94,  DOI: 10.1016/j.cocis.2018.12.003
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    The interaction of peptides and proteins with nanostructures surfaces: a challenge for nanoscience
    Brancolini, Giorgia; Bellucci, Luca; Maschio, Maria Celeste; Di Felice, Rosa; Corni, Stefano
    Current Opinion in Colloid & Interface Science (2019), 41 (), 86-94CODEN: COCSFL; ISSN:1359-0294. (Elsevier Ltd.)
    A review. The impact of nanotechnologies in biomedicine and biotechnol. is becoming more and more evident. It imposes practical challenges, for instance, raising specific issues on the biocompatibility of nanostructures. Nanoparticles are characterized by a high surface-to-vol. ratio, which makes them reactive to foreign species. Thus, when proteins or peptides approach an inorg. nanoparticle, as well as a flat surface, they are likely to interact with the substrate to some extent. This interaction is crucial for applications in drug delivery, imaging, diagnostics, implants, and other medical devices. Specifically, gold nanoparticles are highly versatile and particularly appealing. It is widely accepted that the surfaces of nanoparticles adsorb proteins either transiently in the soft corona layer or permanently in the hard corona layer. As a consequence, the protein structure and/or function may undergo profound adjustments or remain conserved. Detailing the interaction of different inorg. substrates with proteins and peptides at the at. level, and designing ways to control the interaction, is the key for biomedical applications of nanoparticles, both from a fundamental viewpoint and for practical implementations. In the last decade, we have addressed protein-nanoparticle interactions, focusing on interfaces of gold surfaces and nanoparticles with amyloidogenic peptides and protein models. We have developed classical force fields, performed advanced mol. dynamics simulations, and compared computational outcomes with data from NMR expts. Protein-gold complexes with differently coated gold nanoparticles have been modeled to explore the effects of charge and size on the protein structure. Our work unravels that a complex interplay between surface properties and characteristics of the biol. adsorbate dets. whether peptide conformation is influenced and whether protein aggregation is accelerated or inhibited by the presence of the substrate. General guidelines to cope with amyloidogenic proteins could be inferred: these can be essentially summarized with the necessity of balancing the hydrophobic and electrostatic interactions that the amyloidogenic proteins establish with the coating moieties.
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    Martin, L.; Bilek, M. M.; Weiss, A. S.; Kuyucak, S. Force fields for simulating the interaction of surfaces with biological molecules. Interface Focus 2016, 6, 20150045,  DOI: 10.1098/rsfs.2015.0045
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    Force fields for simulating the interaction of surfaces with biological molecules
    Martin Lewis; Bilek Marcela M; Kuyucak Serdar; Weiss Anthony S
    Interface focus (2016), 6 (1), 20150045 ISSN:2042-8898.
    The interaction of biomolecules with solid interfaces is of fundamental importance to several emerging biotechnologies such as medical implants, anti-fouling coatings and novel diagnostic devices. Many of these technologies rely on the binding of peptides to a solid surface, but a full understanding of the mechanism of binding, as well as the effect on the conformation of adsorbed peptides, is beyond the resolution of current experimental techniques. Nanoscale simulations using molecular mechanics offer potential insights into these processes. However, most models at this scale have been developed for aqueous peptide and protein simulation, and there are no proven models for describing biointerfaces. In this review, we detail the current research towards developing a non-polarizable molecular model for peptide-surface interactions, with a particular focus on fitting the model parameters as well as validation by choice of appropriate experimental data.
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    Latour, R. A. Molecular simulation of protein-surface interactions: Benefits, problems, solutions, and future directions (Review). Biointerphases 2008, 3, FC2– FC12,  DOI: 10.1116/1.2965132
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    Molecular simulation of protein-surface interactions: benefits, problems, solutions, and future directions (review)
    Latour, Robert A.
    Biointerphases (2008), 3 (3), FC2-FC12CODEN: BJIOBN; ISSN:1559-4106. (AVS-Science and Technology of Materials, Interfaces and Processing)
    A review. While the importance of protein adsorption to materials surfaces is widely recognized, little is understood at this time regarding how to design surfaces to control protein adsorption behavior. All-atom empirical force field mol. simulation methods have enormous potential to address this problem by providing an approach to directly investigate the adsorption behavior of peptides and proteins at the at. level. As with any type of technol., however, these methods must be appropriately developed and applied if they are to provide realistic and useful results. Three issues that are particularly important for the accurate simulation of protein adsorption behavior are the selection of a valid force field to represent the at.-level interactions involved, the accurate representation of solvation effects, and system sampling. In this article, each of these areas is addressed and future directions for continued development are presented.
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    Ozboyaci, M.; Kokh, D. B.; Corni, S.; Wade, R. C. Modeling and simulation of protein-surface interactions: Achievements and challenges. Q. Rev. Biophys. 2016, 49, e4  DOI: 10.1017/s0033583515000256
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    Modeling and simulation of protein-surface interactions: achievements and challenges
    Ozboyaci, Musa; Kokh, Daria B.; Corni, Stefano; Wade, Rebecca C.
    Quarterly Reviews of Biophysics (2016), 49 (), e4/1-e4/87CODEN: QURBAW; ISSN:0033-5835. (Cambridge University Press)
    Understanding protein-inorg. surface interactions is central to the rational design of new tools in biomaterial sciences, nanobiotechnol. and nanomedicine. Although a significant amt. of exptl. research on protein adsorption onto solid substrates has been reported, many aspects of the recognition and interaction mechanisms of biomols. and inorg. surfaces are still unclear. Theor. modeling and simulations provide complementary approaches for exptl. studies, and they have been applied for exploring protein-surface binding mechanisms, the determinants of binding specificity towards different surfaces, as well as the thermodn. and kinetics of adsorption. Although the general computational approaches employed to study the dynamics of proteins and materials are similar, the models and force-fields (FFs) used for describing the phys. properties and interactions of material surfaces and biol. mols. differ. In particular, FF and water models designed for use in biomol. simulations are often not directly transferable to surface simulations and vice versa. The adsorption events span a wide range of time- and length-scales that vary from nanoseconds to days, and from nanometers to micrometers, resp., rendering the use of multi-scale approaches unavoidable. Further, changes in the at. structure of material surfaces that can lead to surface reconstruction, and in the structure of proteins that can result in complete denaturation of the adsorbed mols., can create many intermediate structural and energetic states that complicate sampling. In this review, we address the challenges posed to theor. and computational methods in achieving accurate descriptions of the phys., chem. and mech. properties of protein-surface systems. In this context, we discuss the applicability of different modeling and simulation techniques ranging from quantum mechanics through all-atom mol. mechanics to coarse-grained approaches. We examine uses of different sampling methods, as well as free energy calcns. Furthermore, we review computational studies of protein-surface interactions and discuss the successes and limitations of current approaches.
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    Aliaga, A. E.; Ahumada, H.; Sepúlveda, K.; Gomez-Jeria, J. S.; Garrido, C.; Weiss-López, B. E.; Campos-Vallette, M. M. SERS, molecular dynamics and molecular orbital studies of the MRKDV peptide on silver and membrane surfaces. J. Phys. Chem. C 2011, 115, 3982– 3989,  DOI: 10.1021/jp1107153
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    SERS, Molecular Dynamics and Molecular Orbital Studies of the MRKDV Peptide on Silver and Membrane Surfaces
    Aliaga, Alvaro E.; Ahumada, Hernan; Sepulveda, Karen; Gomez-Jeria, Juan S.; Garrido, Carlos; Weiss-Lopez, Boris E.; Campos-Vallette, Marcelo M.
    Journal of Physical Chemistry C (2011), 115 (10), 3982-3989CODEN: JPCCCK; ISSN:1932-7447. (American Chemical Society)
    The MRKDV peptide, structurally assocd. with an immunomodulatory protein, was studied using surface enhanced Raman scattering (SERS), mol. dynamics (MD) simulations, and quantum chem. calcns. The SERS spectrum of the MRKDV peptide adsorbed on the silver surface is dominated by signals coming from the guanidinium moiety of the arginine amino acid (R). Guanidinium is the intrinsic probe that drives the orientation of the peptide onto the silver surface. Mol. mechanics and extended Hueckel calcns. of a model of MRKDV interacting with a silver surface support the exptl. results. MD calcns. representing the evolution of the peptide toward a model membrane were also performed. The guanidinium moiety interacts with the phospholipid membrane surface. A hydrophobic C-terminal modification favors the peptide membrane affinity.
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    Thimes, R. L.; Santos, A. V. B.; Chen, R.; Kaur, G.; Jensen, L.; Jenkins, D. M.; Camden, J. P. Using Surface-Enhanced Raman Spectroscopy to Unravel the Wingtip-Dependent Orientation of N-Heterocyclic Carbenes on Gold Nanoparticles. J. Phys. Chem. Lett. 2023, 14, 4219– 4224,  DOI: 10.1021/acs.jpclett.3c00588
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    23
    Using Surface-Enhanced Raman Spectroscopy to Unravel the Wingtip-Dependent Orientation of N-Heterocyclic Carbenes on Gold Nanoparticles
    Thimes, Rebekah L.; Santos, Alyssa V. B.; Chen, Ran; Kaur, Gurkiran; Jensen, Lasse; Jenkins, David M.; Camden, Jon P.
    Journal of Physical Chemistry Letters (2023), 14 (18), 4219-4224CODEN: JPCLCD; ISSN:1948-7185. (American Chemical Society)
    N-Heterocyclic carbenes (NHCs) are an attractive alternative to thiol ligands when forming self-assembled monolayers on noble-metal surfaces; however, relative to the well-studied thiol monolayers, comparatively little is known about the binding, orientation, and packing of NHC monolayers. Herein, we combine surface-enhanced Raman spectroscopy (SERS) and first-principles theory to investigate how the alkyl "wingtip" groups, i.e., those attached to the nitrogens of N-heterocyclic carbenes, affect the NHC orientation on gold nanoparticles. Consistent with previous literature, smaller wingtip groups lead to stable flat configurations; surprisingly, bulkier wingtips also have stable flat configurations likely due to the presence of an adatom. Comparison of exptl. SERS results with the theor. calcd. spectra for flat and vertical configurations shows that we are simultaneously detecting both NHC configurations. In addn. to providing information on the adsorbate geometry, this study highlights the extreme SERS enhancement of vibrational modes perpendicular to the surface.
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    Dutta, S.; Corni, S.; Brancolini, G. Atomistic simulations of functionalized nano-materials for biosensors applications. Int. J. Mol. Sci. 2022, 23, 1484,  DOI: 10.3390/ijms23031484
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    Atomistic Simulations of Functionalized Nano-Materials for Biosensors Applications
    Dutta, Sutapa; Corni, Stefano; Brancolini, Giorgia
    International Journal of Molecular Sciences (2022), 23 (3), 1484CODEN: IJMCFK; ISSN:1422-0067. (MDPI AG)
    A review. Nanoscale biosensors, a highly promising technique in clin. anal., can provide sensitive yet label-free detection of biomols. The spatial and chem. specificity of the surface coverage, the proper immobilization of the bioreceptor as well as the underlying interfacial phenomena are crucial elements for optimizing the performance of a biosensor. Due to exptl. limitations at the microscopic level, integrated cross-disciplinary approaches that combine in silico design with exptl. measurements have the potential to present a powerful new paradigm that tackles the issue of developing novel biosensors. In some cases, computational studies can be seen as alternative approaches to assess the microscopic working mechanisms of biosensors. Nonetheless, the complex architecture of a biosensor, assocd. with the collective contribution from "substrate-receptor-analyte" conjugate in a solvent, often requires extensive atomistic simulations and systems of prohibitive size which need to be addressed. In silico studies of functionalized surfaces also require ad hoc force field parameterization, as existing force fields for biomols. are usually unable to correctly describe the biomol./surface interface. Thus, the computational studies in this field are limited to date. In this review, we aim to introduce fundamental principles that govern the absorption of biomols. onto functionalized nanomaterials and to report state-of-the-art computational strategies to rationally design nanoscale biosensors. A detailed account of available in silico strategies used to drive and/or optimize the synthesis of functionalized nanomaterials for biosensing will be presented. The insights will not only stimulate the field to rationally design functionalized nanomaterials with improved biosensing performance but also foster research on the required functionalization to improve biomol.-surface complex formation as a whole.
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    Kästner, J. Umbrella sampling. Wiley Interdiscip. Rev. Comput. Mol. Sci. 2011, 1, 932– 942,  DOI: 10.1002/wcms.66
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    Baştuğ, T.; Chen, P.-C.; Patra, S. M.; Kuyucak, S. Potential of mean force calculations of ligand binding to ion channels from Jarzynski’s equality and umbrella sampling. J. Chem. Phys. 2008, 128, 04B614,  DOI: 10.1063/1.2904461
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    Bochicchio, D.; Panizon, E.; Ferrando, R.; Monticelli, L.; Rossi, G. Calculating the free energy of transfer of small solutes into a model lipid membrane: Comparison between metadynamics and umbrella sampling. J. Chem. Phys. 2015, 143, 10B612_1,  DOI: 10.1063/1.4932159
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    Noh, S. Y.; Notman, R. Comparison of umbrella sampling and steered molecular dynamics methods for computing free energy profiles of aromatic substrates through phospholipid bilayers. J. Chem. Phys. 2020, 153, 034115,  DOI: 10.1063/5.0016114
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    Comparison of umbrella sampling and steered molecular dynamics methods for computing free energy profiles of aromatic substrates through phospholipid bilayers
    Noh, Sang Young; Notman, Rebecca
    Journal of Chemical Physics (2020), 153 (3), 034115CODEN: JCPSA6; ISSN:0021-9606. (American Institute of Physics)
    Understanding the permeation of mols. through lipid membranes is fundamental for predicting the cellular uptake of solutes and drug delivery mechanisms. In mol. simulations, the usual approach is to compute the free energy (FE) profile of a mol. across a model lipid bilayer, which can then be used to est. the permeability of the mol. Umbrella Sampling (US), which involves carrying out a series of biased simulations along a defined reaction coordinate (usually the bilayer normal direction), is a popular method for the computation of such FE profiles. However, US can be challenging to implement because the results are dependent on the strength of the biasing potential and the spacing of windows along the reaction coordinate, which, in practice, are usually optimized by an inefficient trial and error approach. The Steered Mol. Dynamics implementation of the Jarzynski Equality (JE-SMD) has been identified as an alternative to equil. sampling methods for measuring the FE change across a reaction coordinate. In the JE-SMD approach, equil. FE values are evaluated from the av. of rapid non-equil. trajectories, thus avoiding the practical issues that come with US. Here, the authors use three different corrections of the JE-SMD method to calc. the FE change for the translocation of two arom. substrates, phenylalanine and toluene, across a lipid bilayer and compare the accuracy and computational efficiency of these approaches to the results obtained using US. The authors show evidence that when computing the free energy profile, the JE-SMD approach suffers from insufficient sampling convergence of the bilayer environment and is dependent on the characteristic of the arom. substrate itself. Despite its drawbacks, US remains the more viable approach of the two for computing the FE profile. (c) 2020 American Institute of Physics.
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    Wei, Q.; Zhao, W.; Yang, Y.; Cui, B.; Xu, Z.; Yang, X. Method evaluations for adsorption free energy calculations at the solid/water interface through metadynamics, umbrella sampling, and jarzynski’s equality. ChemPhysChem 2018, 19, 690– 702,  DOI: 10.1002/cphc.201701241
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    29
    Method Evaluations for Adsorption Free Energy Calculations at the Solid/Water Interface through Metadynamics, Umbrella Sampling, and Jarzynski's Equality
    Wei, Qichao; Zhao, Weilong; Yang, Yang; Cui, Beiliang; Xu, Zhijun; Yang, Xiaoning
    ChemPhysChem (2018), 19 (6), 690-702CODEN: CPCHFT; ISSN:1439-4235. (Wiley-VCH Verlag GmbH & Co. KGaA)
    Considerable interest in characterizing protein/peptide-surface interactions has prompted extensive computational studies on calcns. of adsorption free energy. However, in many cases, each individual study has focused on the application of free energy calcns. to a specific system; therefore, it is difficult to combine the results into a general picture for choosing an appropriate strategy for the system of interest. Herein, three well-established computational algorithms are systemically compared and evaluated to compute the adsorption free energy of small mols. on two representative surfaces. The results clearly demonstrate that the characteristics of studied interfacial systems have crucial effects on the accuracy and efficiency of the adsorption free energy calcns. For the hydrophobic surface, steered mol. dynamics exhibits the highest efficiency, which appears to be a favorable method of choice for enhanced sampling simulations. However, for the charged surface, only the umbrella sampling method has the ability to accurately explore the adsorption free energy surface. The affinity of the water layer to the surface significantly affects the performance of free energy calcn. methods, esp. at the region close to the surface. Therefore, a general principle of how to discriminate between methodol. and sampling issues based on the interfacial characteristics of the system under investigation is proposed.
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  30. 30
    Heinz, H.; Vaia, R. A.; Farmer, B. L.; Naik, R. R. Accurate simulation of surfaces and interfaces of face-centered cubic metals using 12–6 and 9–6 Lennard-Jones potentials. J. Phys. Chem. C 2008, 112, 17281– 17290,  DOI: 10.1021/jp801931d
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    Accurate Simulation of Surfaces and Interfaces of Face-Centered Cubic Metals Using 12-6 and 9-6 Lennard-Jones Potentials
    Heinz, Hendrik; Vaia, R. A.; Farmer, B. L.; Naik, R. R.
    Journal of Physical Chemistry C (2008), 112 (44), 17281-17290CODEN: JPCCCK; ISSN:1932-7447. (American Chemical Society)
    Mol. dynamics and Monte Carlo simulations often rely on Lennard-Jones (LJ) potentials for nonbond interactions. The authors present 12-6 and 9-6 LJ parameters for several fcc. metals (Ag, Al, Au, Cu, Ni, Pb, Pd, Pt) which reproduce densities, surface tensions, interface properties with H2O and (bio)org. mols., as well as mech. properties in quant. (<0.1%) to good qual. (25%) agreement with expt. under ambient conditions. Deviations assocd. with earlier LJ models were reduced by 1 order of magnitude due to the precise fit of the new models to densities and surface tensions under std. conditions, which also leads to significantly improved results for surface energy anisotropies, interface tensions, and mech. properties. The performance is comparable to tight-binding and embedded atom models at up to a million times lower computational cost. The models extend classical simulation methods to metals and a variety of interfaces with biopolymers, surfactants, and other nanostructured materials through compatibility with widely used force fields, including AMBER, CHARMM, COMPASS, CVFF, OPLS-AA, and PCFF. Limitations include the neglect of electronic structure effects and the restriction to noncovalent interactions with the metals.
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    Heinz, H.; Lin, T.-J.; Kishore Mishra, R.; Emami, F. S. Thermodynamically consistent force fields for the assembly of inorganic, organic, and biological nanostructures: the INTERFACE force field. Langmuir 2013, 29, 1754– 1765,  DOI: 10.1021/la3038846
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    Thermodynamically Consistent Force Fields for the Assembly of Inorganic, Organic, and Biological Nanostructures: The INTERFACE Force Field
    Heinz, Hendrik; Lin, Tzu-Jen; Kishore Mishra, Ratan; Emami, Fateme S.
    Langmuir (2013), 29 (6), 1754-1765CODEN: LANGD5; ISSN:0743-7463. (American Chemical Society)
    A review. The complexity of the mol. recognition and assembly of biotic-abiotic interfaces on a scale of 1 to 1000 nm can be understood more effectively using simulation tools along with lab. instrumentation. We discuss the current capabilities and limitations of atomistic force fields and explain a strategy to obtain dependable parameters for inorg. compds. that has been developed and tested over the past decade. Parameter developments include several silicates, aluminates, metals, oxides, sulfates, and apatites that are summarized in what we call the INTERFACE force field. The INTERFACE force field operates as an extension of common harmonic force fields (PCFF, COMPASS, CHARMM, AMBER, GROMACS, and OPLS-AA) by employing the same functional form and combination rules to enable simulations of inorg.-org. and inorg.-biomol. interfaces. The parametrization builds on an in-depth understanding of phys.-chem. properties on the at. scale to assign each parameter, esp. at. charges and van der Waals consts., as well as on the validation of macroscale phys.-chem. properties for each compd. in comparison to measurements. The approach eliminates large discrepancies between computed and measured bulk and surface properties of up to 2 orders of magnitude using other parametrization protocols and increases the transferability of the parameters by introducing thermodn. consistency. As a result, a wide range of properties can be computed in quant. agreement with expt., including densities, surface energies, solid-water interface tensions, anisotropies of interfacial energies of different crystal facets, adsorption energies of biomols., and thermal and mech. properties. Applications include insight into the assembly of inorg.-org. multiphase materials, the recognition of inorg. facets by biomols., growth and shape preferences of nanocrystals and nanoparticles, as well as thermal transitions and nanomechanics. Limitations and opportunities for further development are also described.
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  32. 32
    Cornell, W. D.; Cieplak, P.; Bayly, C. I.; Gould, I. R.; Merz, K. M.; Ferguson, D. M.; Spellmeyer, D. C.; Fox, T.; Caldwell, J. W.; Kollman, P. A. A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. J. Am. Chem. Soc. 1995, 117, 5179– 5197,  DOI: 10.1021/ja00124a002
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    A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules
    Cornell, Wendy D.; Cieplak, Piotr; Bayly, Christopher I.; Gould, Ian R.; Merz, Kenneth M., Jr.; Ferguson, David M.; Spellmeyer, David C.; Fox, Thomas; Caldwell, James W.; Kollman, Peter A.
    Journal of the American Chemical Society (1995), 117 (19), 5179-97CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)
    The authors present the derivation of a new mol. mech. force field for simulating the structures, conformational energies, and interaction energies of proteins, nucleic acids, and many related org. mols. in condensed phases. This effective two-body force field is the successor to the Weiner et al. force field and was developed with some of the same philosophies, such as the use of a simple diagonal potential function and electrostatic potential fit atom centered charges. The need for a 10-12 function for representing hydrogen bonds is no longer necessary due to the improved performance of the new charge model and new van der Waals parameters. These new charges are detd. using a 6-31G* basis set and restrained electrostatic potential (RESP) fitting and have been shown to reproduce interaction energies, free energies of solvation, and conformational energies of simple small mols. to a good degree of accuracy. Furthermore, the new RESP charges exhibit less variability as a function of the mol. conformation used in the charge detn. The new van der Waals parameters have been derived from liq. simulations and include hydrogen parameters which take into account the effects of any geminal electroneg. atoms. The bonded parameters developed by Weiner et al. were modified as necessary to reproduce exptl. vibrational frequencies and structures. Most of the simple dihedral parameters have been retained from Weiner et al., but a complex set of .vphi. and ψ parameters which do a good job of reproducing the energies of the low-energy conformations of glycyl and alanyl dipeptides was developed for the peptide backbone.
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  33. 33
    MacKerell, A. D.; Bashford, D.; Bellott, M.; Dunbrack, R. L.; Evanseck, J. D.; Field, M. J.; Fischer, S.; Gao, J.; Guo, H.; Ha, S. All-atom empirical potential for molecular modeling and dynamics studies of proteins. J. Phys. Chem. B 1998, 102, 3586– 3616,  DOI: 10.1021/jp973084f
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    All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins
    MacKerell, A. D., Jr.; Bashford, D.; Bellott, M.; Dunbrack, R. L.; Evanseck, J. D.; Field, M. J.; Fischer, S.; Gao, J.; Guo, H.; Ha, S.; Joseph-McCarthy, D.; Kuchnir, L.; Kuczera, K.; Lau, F. T. K.; Mattos, C.; Michnick, S.; Ngo, T.; Nguyen, D. T.; Prodhom, B.; Reiher, W. E., III; Roux, B.; Schlenkrich, M.; Smith, J. C.; Stote, R.; Straub, J.; Watanabe, M.; Wiorkiewicz-Kuczera, J.; Yin, D.; Karplus, M.
    Journal of Physical Chemistry B (1998), 102 (18), 3586-3616CODEN: JPCBFK; ISSN:1089-5647. (American Chemical Society)
    New protein parameters are reported for the all-atom empirical energy function in the CHARMM program. The parameter evaluation was based on a self-consistent approach designed to achieve a balance between the internal (bonding) and interaction (nonbonding) terms of the force field and among the solvent-solvent, solvent-solute, and solute-solute interactions. Optimization of the internal parameters used exptl. gas-phase geometries, vibrational spectra, and torsional energy surfaces supplemented with ab initio results. The peptide backbone bonding parameters were optimized with respect to data for N-methylacetamide and the alanine dipeptide. The interaction parameters, particularly the at. charges, were detd. by fitting ab initio interaction energies and geometries of complexes between water and model compds. that represented the backbone and the various side chains. In addn., dipole moments, exptl. heats and free energies of vaporization, solvation and sublimation, mol. vols., and crystal pressures and structures were used in the optimization. The resulting protein parameters were tested by applying them to noncyclic tripeptide crystals, cyclic peptide crystals, and the proteins crambin, bovine pancreatic trypsin inhibitor, and carbonmonoxy myoglobin in vacuo and in a crystal. A detailed anal. of the relationship between the alanine dipeptide potential energy surface and calcd. protein φ, χ angles was made and used in optimizing the peptide group torsional parameters. The results demonstrate that use of ab initio structural and energetic data by themselves are not sufficient to obtain an adequate backbone representation for peptides and proteins in soln. and in crystals. Extensive comparisons between mol. dynamics simulation and exptl. data for polypeptides and proteins were performed for both structural and dynamic properties. Calcd. data from energy minimization and dynamics simulations for crystals demonstrate that the latter are needed to obtain meaningful comparisons with exptl. crystal structures. The presented parameters, in combination with the previously published CHARMM all-atom parameters for nucleic acids and lipids, provide a consistent set for condensed-phase simulations of a wide variety of mols. of biol. interest.
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    Kaminski, G. A.; Friesner, R. A.; Tirado-Rives, J.; Jorgensen, W. L. Evaluation and reparametrization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides. J. Phys. Chem. B 2001, 105, 6474– 6487,  DOI: 10.1021/jp003919d
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    Evaluation and Reparametrization of the OPLS-AA Force Field for Proteins via Comparison with Accurate Quantum Chemical Calculations on Peptides
    Kaminski, George A.; Friesner, Richard A.; Tirado-Rives, Julian; Jorgensen, William L.
    Journal of Physical Chemistry B (2001), 105 (28), 6474-6487CODEN: JPCBFK; ISSN:1089-5647. (American Chemical Society)
    We present results of improving the OPLS-AA force field for peptides by means of refitting the key Fourier torsional coeffs. The fitting technique combines using accurate ab initio data as the target, choosing an efficient fitting subspace of the whole potential-energy surface, and detg. wts. for each of the fitting points based on magnitudes of the potential-energy gradient. The av. energy RMS deviation from the LMP2/cc-pVTZ(-f)//HF/6-31G** data is reduced by ∼40% from 0.81 to 0.47 kcal/mol as a result of the fitting for the electrostatically uncharged dipeptides. Transferability of the parameters is demonstrated by using the same alanine dipeptide-fitted backbone torsional parameters for all of the other dipeptides (with the appropriate side-chain refitting) and the alanine tetrapeptide. Parameters of nonbonded interactions have also been refitted for the sulfur-contg. dipeptides (cysteine and methionine), and the validity of the new Coulombic charges and the van der Waals σ's and ε's is proved through reproducing gas-phase energies of complex formation heats of vaporization and densities of pure model liqs. Moreover, a novel approach to fitting torsional parameters for electrostatically charged mol. systems has been presented and successfully tested on five dipeptides with charged side chains.
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    Dasetty, S.; Meza-Morales, P. J.; Getman, R. B.; Sarupria, S. Simulations of interfacial processes: recent advances in force field development. Curr. Opin. Chem. Eng. 2019, 23, 138– 145,  DOI: 10.1016/j.coche.2019.04.003
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    Geada, I. L.; Ramezani-Dakhel, H.; Jamil, T.; Sulpizi, M.; Heinz, H. Insight into induced charges at metal surfaces and biointerfaces using a polarizable Lennard–Jones potential. Nat. Commun. 2018, 9, 716,  DOI: 10.1038/s41467-018-03137-8
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    Insight into induced charges at metal surfaces and biointerfaces using a polarizable Lennard-Jones potential
    Geada Isidro Lorenzo; Sulpizi Marialore; Ramezani-Dakhel Hadi; Heinz Hendrik; Ramezani-Dakhel Hadi; Ramezani-Dakhel Hadi; Jamil Tariq; Heinz Hendrik
    Nature communications (2018), 9 (1), 716 ISSN:.
    Metallic nanostructures have become popular for applications in therapeutics, catalysts, imaging, and gene delivery. Molecular dynamics simulations are gaining influence to predict nanostructure assembly and performance; however, instantaneous polarization effects due to induced charges in the free electron gas are not routinely included. Here we present a simple, compatible, and accurate polarizable potential for gold that consists of a Lennard-Jones potential and a harmonically coupled core-shell charge pair for every metal atom. The model reproduces the classical image potential of adsorbed ions as well as surface, bulk, and aqueous interfacial properties in excellent agreement with experiment. Induced charges affect the adsorption of ions onto gold surfaces in the gas phase at a strength similar to chemical bonds while ions and charged peptides in solution are influenced at a strength similar to intermolecular bonds. The proposed model can be applied to complex gold interfaces, electrode processes, and extended to other metals.
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    Iori, F.; Di Felice, R.; Molinari, E.; Corni, S. GolP: An atomistic force-field to describe the interaction of proteins with Au (111) surfaces in water. J. Comput. Chem. 2009, 30, 1465– 1476,  DOI: 10.1002/jcc.21165
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    GolP: An atomistic force-field to describe the interaction of proteins with Au(111) surfaces in water
    Iori, F.; Di Felice, R.; Molinari, E.; Corni, S.
    Journal of Computational Chemistry (2009), 30 (9), 1465-1476CODEN: JCCHDD; ISSN:0192-8651. (John Wiley & Sons, Inc.)
    A classical atomistic force field to describe the interaction of proteins with gold (111) surfaces in explicit water has been devised. The force field is specifically designed to be easily usable in most common bio-oriented mol. dynamics codes, such as GROMACS and NAMD. Its parametrization is based on quantum mech. (d. functional theory [DFT] and second order Moeller-Plesset perturbation theory [MP2]) calcns. and exptl. data on the adsorption of small mols. on gold. In particular, a systematic DFT survey of the interaction between Au(111) and the natural amino acid side chains has been performed to single out chemisorption effects. Van der Waals parameters have been instead fitted to exptl. desorption energy data of linear alkanes and were also studied via MP2 calcns. Finally, gold polarization (image charge effects) is taken into account by a recently proposed procedure (Iori, F.; Corni, S. J., 2008). Preliminary validation results of GolP on an independent test set of small mols. show the good performances of the force field. © 2008 Wiley Periodicals, Inc. J Comput Chem 2009.
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    Wright, L. B.; Rodger, P. M.; Corni, S.; Walsh, T. R. GolP-CHARMM: first-principles based force fields for the interaction of proteins with Au (111) and Au (100). J. Chem. Theory Comput. 2013, 9, 1616– 1630,  DOI: 10.1021/ct301018m
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    GolP-CHARMM: First-Principles Based Force Fields for the Interaction of Proteins with Au(111) and Au(100)
    Wright, Louise B.; Rodger, P. Mark; Corni, Stefano; Walsh, Tiffany R.
    Journal of Chemical Theory and Computation (2013), 9 (3), 1616-1630CODEN: JCTCCE; ISSN:1549-9618. (American Chemical Society)
    Computational simulation of peptide adsorption at the aq. Au interface is key to advancing the development of many applications based on Au nanoparticles, ranging from nanomedical devices to smart biomimetic materials. Here, the authors present a force field, GolP-CHARMM, designed to capture peptide adsorption at both the aq. Au(111) and Au(100) interfaces. The force field, compatible with the bio-org. force field CHARMM, is parametrized using a combination of exptl. and 1st-principles data. Like its predecessor, GolP (Iori, F.; et al. J. Comput. Chem.2009, 30, 1465), this force field contains terms to describe the dynamic polarization of Au atoms, chemisorbing species, and the interaction between sp2 hybridized C atoms and Au. A systematic study of small mol. adsorption at both surfaces using the vdW-DF functional (Dion, M.; et al. Phys. Rev. Lett.2004, 92, 246401-1. Thonhauser, T.; et al. Phys. Rev. B2007, 76, 125112) is carried out to fit and test force field parameters and also, for the 1st time, gives unique insights into facet selectivity of Au binding in vacuo. Energetic and spatial trends obsd. in DFT calcns. are reproduced by the force field under the same conditions. Finally, the authors use the new force field to calc. adsorption energies, under aq. conditions, for a representative set of amino acids. These data agree with exptl. findings.
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    Iori, F.; Corni, S. Including image charge effects in the molecular dynamics simulations of molecules on metal surfaces. J. Comput. Chem. 2008, 29, 1656– 1666,  DOI: 10.1002/jcc.20928
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    Including image charge effects in the molecular dynamics simulations of molecules on metal surfaces
    Iori, F.; Corni, S.
    Journal of Computational Chemistry (2008), 29 (10), 1656-1666CODEN: JCCHDD; ISSN:0192-8651. (John Wiley & Sons, Inc.)
    Combinatorial bio-techniques have demonstrated that proteins can be good and even selective binders for several inorg. surfaces, including metals. However, the understanding of the basic phys. mechanisms that govern such interactions did not keep up with the success in these expts. The comprehension of such mechanisms would greatly benefit from the computational investigation of the problem. Because of the complexity of the system, classical mol. dynamics simulations based on an atomistic description appear to be the best compromise between reliability and feasibility. For proteins interacting with metal surfaces, however, methodol. improvements with respect to std. Mol. Dynamics (MD) of proteins are needed, since the polarization of the metal induced by the protein (and the surrounding water) is not generally negligible. In this article, the authors present a simple approach to introduce metal polarization effects (often termed image effects) in MD simulations by exploiting std. features of bio-oriented MD codes such as the widely used GROMACS and NAMD. Tests to show the reliability of the proposed methods are presented, and the results for a model application showing the importance of image effects are also discussed.
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  40. 40
    Wright, L. B.; Rodger, P. M.; Walsh, T. R.; Corni, S. First-principles-based force field for the interaction of proteins with Au (100)(5× 1): an extension of GolP-CHARMM. J. Phys. Chem. C 2013, 117, 24292– 24306,  DOI: 10.1021/jp4061329
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    40
    First-Principles-Based Force Field for the Interaction of Proteins with Au(100)(5 × 1): An Extension of GolP-CHARMM
    Wright, Louise B.; Rodger, P. Mark; Walsh, Tiffany R.; Corni, Stefano
    Journal of Physical Chemistry C (2013), 117 (46), 24292-24306CODEN: JPCCCK; ISSN:1932-7447. (American Chemical Society)
    Noncovalent recognition between peptides and inorg. materials is an established phenomenon. Key to exploiting these interactions in a wide range of materials self-assembly applications would be to harness the facet-selective control of peptide binding onto these materials. Fundamental understanding of what drives facet-selectivity in peptide binding is developing, but as yet is not sufficient to enable design of predictable facet-specific sequences. Computational simulation of the aq. peptide-gold interface, commonly used to understand the mechanisms driving adsorption at an at. level, has thus far neglected the role that surface reconstruction might play in facet specificity. Here the polarizable GolP-CHARMM suite of force fields is extended to include the reconstructed Au(100) surface. The force field, compatible with the bio-org. force field CHARMM, is parametrized using first-principles data. Our extended force field is tailored to reproduce the heterogeneity of weak chemisorbing N and S species to specific locations in the Au(100)-(5 × 1) surface identified from the first-principles calcns. We apply our new model to predict and compare the three-dimensional structure of liq. water at Au(111), Au(100)(1 × 1), and Au(100)(5 × 1) interfaces. Using mol. dynamics simulations, we predict an increased likelihood for water-mediated peptide adsorption at the aq.-Au(100)(1 × 1) interface compared with the Au(100)(5 × 1) interface. Therefore, our findings suggest that peptide binding can discriminate between the native and reconstructed Au(100) interfaces and that the role of reconstruction on binding at the Au(100) interface should not be neglected.
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    Wright, L. B.; Rodger, P. M.; Corni, S.; Walsh, T. R. GolP-CHARMM: First-principles based force fields for the interaction of proteins with Au(111) and Au(100). J. Chem. Theory Comput. 2013, 9, 1616– 1630,  DOI: 10.1021/ct301018m
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    41
    GolP-CHARMM: First-Principles Based Force Fields for the Interaction of Proteins with Au(111) and Au(100)
    Wright, Louise B.; Rodger, P. Mark; Corni, Stefano; Walsh, Tiffany R.
    Journal of Chemical Theory and Computation (2013), 9 (3), 1616-1630CODEN: JCTCCE; ISSN:1549-9618. (American Chemical Society)
    Computational simulation of peptide adsorption at the aq. Au interface is key to advancing the development of many applications based on Au nanoparticles, ranging from nanomedical devices to smart biomimetic materials. Here, the authors present a force field, GolP-CHARMM, designed to capture peptide adsorption at both the aq. Au(111) and Au(100) interfaces. The force field, compatible with the bio-org. force field CHARMM, is parametrized using a combination of exptl. and 1st-principles data. Like its predecessor, GolP (Iori, F.; et al. J. Comput. Chem.2009, 30, 1465), this force field contains terms to describe the dynamic polarization of Au atoms, chemisorbing species, and the interaction between sp2 hybridized C atoms and Au. A systematic study of small mol. adsorption at both surfaces using the vdW-DF functional (Dion, M.; et al. Phys. Rev. Lett.2004, 92, 246401-1. Thonhauser, T.; et al. Phys. Rev. B2007, 76, 125112) is carried out to fit and test force field parameters and also, for the 1st time, gives unique insights into facet selectivity of Au binding in vacuo. Energetic and spatial trends obsd. in DFT calcns. are reproduced by the force field under the same conditions. Finally, the authors use the new force field to calc. adsorption energies, under aq. conditions, for a representative set of amino acids. These data agree with exptl. findings.
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    Elechiguerra, J. L.; Reyes-Gasga, J.; Yacaman, M. J. The role of twinning in shape evolution of anisotropic noble metal nanostructures. J. Mater. Chem. 2006, 16, 3906– 3919,  DOI: 10.1039/b607128g
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    The role of twinning in shape evolution of anisotropic noble metal nanostructures
    Elechiguerra, Jose Luis; Reyes-Gasga, Jose; Yacaman, Miguel Jose
    Journal of Materials Chemistry (2006), 16 (40), 3906-3919CODEN: JMACEP; ISSN:0959-9428. (Royal Society of Chemistry)
    Nanotechnol. provides the ability to engineer the properties of materials by controlling their size and shape. Among the most interesting nanostructures are anisotropic noble metal nanocrystals such as nanorods and nanowires. Nevertheless, the prodn. of such crystals in a controlled fashion remains as a challenging task, and many available colloidal techniques produce a mixt. of morphologies. In cases where high yields of a particular anisotropic structure were produced, the growth mechanism was primarily explained in terms of the presence of surfactants or capping agents that regulate the growth of the crystal in a particular direction. However, the growth mechanism should also consider nucleation and kinetics, and not only thermodn. or phys. restrictions imposed by the surface stabilizing agent. In this work, several examples are presented of anisotropic noble metal nanocrystals obtained by different methods. Finally, the important role of twinning in detg. the habit of the final morphol. is discussed.
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    Hjorth Larsen, A.; Jørgen Mortensen, J.; Blomqvist, J.; Castelli, I. E.; Christensen, R.; Dułak, M.; Friis, J.; Groves, M. N.; Hammer, B.; Hargus, C. The atomic simulation environment─a Python library for working with atoms. J. Phys.: Condens. Matter 2017, 29, 273002,  DOI: 10.1088/1361-648x/aa680e
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    The atomic simulation environment-a Python library for working with atoms
    Hjorth Larsen Ask; Jorgen Mortensen Jens; Blomqvist Jakob; Castelli Ivano E; Christensen Rune; Dulak Marcin; Friis Jesper; Groves Michael N; Hammer Bjork; Hargus Cory; Hermes Eric D; Jennings Paul C; Bjerre Jensen Peter; Kermode James; Kitchin John R; Leonhard Kolsbjerg Esben; Kubal Joseph; Kaasbjerg Kristen; Lysgaard Steen; Bergmann Maronsson Jon; Maxson Tristan; Olsen Thomas; Pastewka Lars; Peterson Andrew; Rostgaard Carsten; Schiotz Jakob; Schutt Ole; Strange Mikkel; Thygesen Kristian S; Vegge Tejs; Vilhelmsen Lasse; Walter Michael; Zeng Zhenhua; Jacobsen Karsten W
    Journal of physics. Condensed matter : an Institute of Physics journal (2017), 29 (27), 273002 ISSN:.
    The atomic simulation environment (ASE) is a software package written in the Python programming language with the aim of setting up, steering, and analyzing atomistic simulations. In ASE, tasks are fully scripted in Python. The powerful syntax of Python combined with the NumPy array library make it possible to perform very complex simulation tasks. For example, a sequence of calculations may be performed with the use of a simple 'for-loop' construction. Calculations of energy, forces, stresses and other quantities are performed through interfaces to many external electronic structure codes or force fields using a uniform interface. On top of this calculator interface, ASE provides modules for performing many standard simulation tasks such as structure optimization, molecular dynamics, handling of constraints and performing nudged elastic band calculations.
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    Dodda, L. S.; Cabeza de Vaca, I.; Tirado-Rives, J.; Jorgensen, W. L. LigParGen web server: an automatic OPLS-AA parameter generator for organic ligands. Nucleic Acids Res. 2017, 45, W331– W336,  DOI: 10.1093/nar/gkx312
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    LigParGen web server: an automatic OPLS-AA parameter generator for organic ligands
    Dodda, Leela S.; Cabeza de Vaca, Israel; Tirado-Rives, Julian; Jorgensen, William L.
    Nucleic Acids Research (2017), 45 (W1), W331-W336CODEN: NARHAD; ISSN:1362-4962. (Oxford University Press)
    The accurate calcn. of protein/nucleic acid- ligand interactions or condensed phase properties by force field-based methods require a precise description of the energetics of intermol. interactions. Despite the progress made in force fields, small mol. parameterization remains an open problem due to the magnitude of the chem. space; the most crit. issue is the estn. of a balanced set of at. charges with the ability to reproduce exptl. properties. The LigParGen web server provides an intuitive interface for generating OPLS-AA/1.14*CM1A(-LBCC) force field parameters for org. ligands, in the formats of commonly used mol. dynamics and Monte Carlo simulation packages. This server has high value for researchers interested in studying any phenomena based on intermol. interactions with ligands via mol. mechanics simulations.
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    Vanommeslaeghe, K.; MacKerell, A. D. Automation of the CHARMM General Force Field (CGenFF) I: bond perception and atom typing. J. Chem. Inf. Model. 2012, 52, 3144– 3154,  DOI: 10.1021/ci300363c
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    Automation of the CHARMM General Force Field (CGenFF) I: Bond Perception and Atom Typing
    Vanommeslaeghe, K.; MacKerell, A. D.
    Journal of Chemical Information and Modeling (2012), 52 (12), 3144-3154CODEN: JCISD8; ISSN:1549-9596. (American Chemical Society)
    Mol. mechanics force fields are widely used in computer-aided drug design for the study of drug-like mols. alone or interacting with biol. systems. In simulations involving biol. macromols., the biol. part is typically represented by a specialized biomol. force field, while the drug is represented by a matching general (org.) force field. In order to apply these general force fields to an arbitrary drug-like mol., functionality for assignment of atom types, parameters, and charges is required. In the present article, which is part I of a series of two, we present the algorithms for bond perception and atom typing for the CHARMM General Force Field (CGenFF). The CGenFF atom typer first assocs. attributes to the atoms and bonds in a mol., such as valence, bond order, and ring membership among others. Of note are a no. of features that are specifically required for CGenFF. This information is then used by the atom typing routine to assign CGenFF atom types based on a programmable decision tree. This allows for straight-forward implementation of CGenFF's complicated atom typing rules and for equally straight-forward updating of the atom typing scheme as the force field grows. The presented atom typer was validated by assigning correct atom types on 477 model compds. including in the training set as well as 126 test-set mols. that were constructed to specifically verify its different components. The program may be utilized via an online implementation at https://www.paramchem.org/.
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    Vanommeslaeghe, K.; Raman, E. P.; MacKerell, A. D. Automation of the CHARMM General Force Field (CGenFF) II: assignment of bonded parameters and partial atomic charges. J. Chem. Inf. Model. 2012, 52, 3155– 3168,  DOI: 10.1021/ci3003649
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    Automation of the CHARMM General Force Field (CGenFF) II: Assignment of Bonded Parameters and Partial Atomic Charges
    Vanommeslaeghe, K.; Raman, E. Prabhu; MacKerell, A. D.
    Journal of Chemical Information and Modeling (2012), 52 (12), 3155-3168CODEN: JCISD8; ISSN:1549-9596. (American Chemical Society)
    Mol. mechanics force fields are widely used in computer-aided drug design for the study of drug candidates interacting with biol. systems. In these simulations, the biol. part is typically represented by a specialized biomol. force field, while the drug is represented by a matching general (org.) force field. In order to apply these general force fields to an arbitrary drug-like mol., functionality for assignment of atom types, parameters, and partial at. charges is required. In the present article, algorithms for the assignment of parameters and charges for the CHARMM General Force Field (CGenFF) are presented. These algorithms rely on the existing parameters and charges that were detd. as part of the parametrization of the force field. Bonded parameters are assigned based on the similarity between the atom types that define said parameters, while charges are detd. using an extended bond-charge increment scheme. Charge increments were optimized to reproduce the charges on model compds. that were part of the parametrization of the force field. Case studies are presented to clarify the functioning of the algorithms and the significance of their output data.
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    The missing term in effective pair potentials
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    Journal of Physical Chemistry (1987), 91 (24), 6269-71CODEN: JPCHAX; ISSN:0022-3654.
    Effective pair potentials used for simulations of polar liqs. include the av. effects of polarization. Such potentials are generally adjusted to produce the exptl. heat of vaporization. It has not been recognized before that the self-energy term inherent in any polarizable model should be included in effective pair potentials as well. Inclusion of the self-energy correction with a consequent reparametrization of the simple point charge model of water yields an improvement of the effective pair potential for water, as exemplified by d., radial distribution functions, and diffusion const.
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    Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D.; Impey, R. W.; Klein, M. L. Comparison of simple potential functions for simulating liquid water. J. Chem. Phys. 1983, 79, 926– 935,  DOI: 10.1063/1.445869
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    Comparison of simple potential functions for simulating liquid water
    Jorgensen, William L.; Chandrasekhar, Jayaraman; Madura, Jeffry D.; Impey, Roger W.; Klein, Michael L.
    Journal of Chemical Physics (1983), 79 (2), 926-35CODEN: JCPSA6; ISSN:0021-9606.
    Classical Monte Carlo simulations were carried out for liq. H2O in the NPT ensemble at 25° and 1 atm using 6 of the simpler intermol. potential functions for the dimer. Comparisons were made with exptl. thermodn. and structural data including the neutron diffraction results of Thiessen and Narten (1982). The computed densities and potential energies agree with expt. except for the original Bernal-Fowler model, which yields an 18% overest. of the d. and poor structural results. The discrepancy may be due to the correction terms needed in processing the neutron data or to an effect uniformly neglected in the computations. Comparisons were made for the self-diffusion coeffs. obtained from mol. dynamics simulations.
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    Abraham, M. J.; Murtola, T.; Schulz, R.; Páll, S.; Smith, J. C.; Hess, B.; Lindahl, E. GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX 2015, 1–2, 19– 25,  DOI: 10.1016/j.softx.2015.06.001
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    Molecular Physics (1983), 50 (5), 1055-76CODEN: MOPHAM; ISSN:0026-8976.
    Tech. aspects are discussed of the const. pressure mol. dynamics method proposed by H. C. Andersen (1980) and extended by M. Parrinello and A Rahman (1980) to allow changes in the shape of the mol. dynamics cell. The new mol. dynamics method is extended to treat mol. systems and to include long range charge-charge interactions. Results on the conservation laws, the frequency of oscillation of the mol. dynamics cell, and the equations which constrain the shape of the mol. dynamics cell are also given. An addnl. constraint is introduced to stop the superfluous mol. dynamics cell rotation which would otherwise complicate the anal. of crystal structures. The method is illustrated by examg. the behavior of solid N at high pressure.
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    Hess, B.; Bekker, H.; Berendsen, H. J.; Fraaije, J. G. LINCS: a linear constraint solver for molecular simulations. J. Comput. Chem. 1997, 18, 1463– 1472,  DOI: 10.1002/(SICI)1096-987X(199709)18:12<1463::AID-JCC4>3.0.CO;2-H
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    We present a new LINear Constraint Solver (LINCS) for mol. simulations with bond constraints using the enzyme lysozyme and a 32-residue peptide as test systems. The algorithm is inherently stable, as the constraints themselves are reset instead of derivs. of the constraints, thereby eliminating drift. Although the derivation of the algorithm is presented in terms of matrixes, no matrix matrix multiplications are needed and only the nonzero matrix elements have to be stored, making the method useful for very large mols. At the same accuracy, the LINCS algorithm is 3-4 times faster than the SHAKE algorithm. Parallelization of the algorithm is straightforward.
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    Darden, Tom; York, Darrin; Pedersen, Lee
    Journal of Chemical Physics (1993), 98 (12), 10089-92CODEN: JCPSA6; ISSN:0021-9606.
    An N·log(N) method for evaluating electrostatic energies and forces of large periodic systems is presented. The method is based on interpolation of the reciprocal space Ewald sums and evaluation of the resulting convolution using fast Fourier transforms. Timings and accuracies are presented for three large cryst. ionic systems.
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    Jambeck, J. P.; Lyubartsev, A. P. Exploring the free energy landscape of solutes embedded in lipid bilayers. J. Phys. Chem. Lett. 2013, 4, 1781– 1787,  DOI: 10.1021/jz4007993
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    Exploring the Free Energy Landscape of Solutes Embedded in Lipid Bilayers
    Jambeck Joakim P M; Lyubartsev Alexander P
    The journal of physical chemistry letters (2013), 4 (11), 1781-7 ISSN:1948-7185.
    Free energy calculations are vital for our understanding of biological processes on an atomistic scale and can offer insight to various mechanisms. However, in some cases, degrees of freedom (DOFs) orthogonal to the reaction coordinate have high energy barriers and/or long equilibration times, which prohibit proper sampling. Here we identify these orthogonal DOFs when studying the transfer of a solute from water to a model membrane. Important DOFs are identified in bulk liquids of different dielectric nature with metadynamics simulations and are used as reaction coordinates for the translocation process, resulting in two- and three-dimensional space of reaction coordinates. The results are in good agreement with experiments and elucidate the pitfalls of using one-dimensional reaction coordinates. The calculations performed here offer the most detailed free energy landscape of solutes embedded in lipid bilayers to date and show that free energy calculations can be used to study complex membrane translocation phenomena.
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    Transmembrane helix assembly by window exchange umbrella sampling
    Park, Soohyung; Kim, Taehoon; Im, Wonpil
    Physical Review Letters (2012), 108 (10), 108102/1-108102/4CODEN: PRLTAO; ISSN:0031-9007. (American Physical Society)
    A method of window exchange umbrella sampling mol. dynamics simulation is employed for transmembrane helix assembly. An anal. expression for the av. acceptance probability between neighboring windows is derived and combined with the first passage time optimization method to predetermine a parameter set in an optimal range. With the parameter set, the method provides a substantially more efficient sampling of helix-helix interfaces together with the potential of mean force along the helix-helix distance of a transmembrane helix-dimer model, compared to the umbrella sampling method.
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    Two Dimensional Window Exchange Umbrella Sampling for Transmembrane Helix Assembly
    Park, Soohyung; Im, Wonpil
    Journal of Chemical Theory and Computation (2013), 9 (1), 13-17CODEN: JCTCCE; ISSN:1549-9618. (American Chemical Society)
    The method of window exchange umbrella sampling mol. dynamics (WEUSMD) with a preoptimized parameter set was recently used to obtain the most probable conformations and the energetics of transmembrane (TM) helix assembly of a generic TM sequence. When applied to glycophorin A TM domain (GpA-TM) using the restraint potentials along the helix-helix distance, however, tight interfacial packing of GpA-TM resulted in insufficient conformational sampling at short helix-helix sepn. This sampling issue is addressed by extending the WEUSMD into two dimensions with the restraint potentials along the helix-helix distance and crossing angle. The two-dimensional WEUSMD results demonstrate that the incomplete sampling in the one-dimensional WEUSMD arises from high barriers along the crossing angle between the GpA-TM helixes. Together with the faster convergence in both the assembled conformations and the potential of mean force, the 2D-WEUSMD can be a general and efficient approach in computational studies of TM helix assembly.
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    Jiang, W.; Luo, Y.; Maragliano, L.; Roux, B. Calculation of free energy landscape in multi-dimensions with Hamiltonian-exchange umbrella sampling on petascale supercomputer. J. Chem. Theory Comput. 2012, 8, 4672– 4680,  DOI: 10.1021/ct300468g
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    Calculation of Free Energy Landscape in Multi-Dimensions with Hamiltonian-Exchange Umbrella Sampling on Petascale Supercomputer
    Jiang, Wei; Luo, Yun; Maragliano, Luca; Roux, Benoit
    Journal of Chemical Theory and Computation (2012), 8 (11), 4672-4680CODEN: JCTCCE; ISSN:1549-9618. (American Chemical Society)
    An extremely scalable computational strategy is described for calcns. of the potential of mean force (PMF) in multidimensions on massively distributed supercomputers. The approach involves coupling thousands of umbrella sampling (US) simulation windows distributed to cover the space of order parameters with a Hamiltonian mol. dynamics replica-exchange (H-REMD) algorithm to enhance the sampling of each simulation. In the present application, US/H-REMD is carried out in a two-dimensional (2D) space and exchanges are attempted alternatively along the two axes corresponding to the two order parameters. The US/H-REMD strategy is implemented on the basis of parallel/parallel multiple copy protocol at the MPI level, and therefore can fully exploit computing power of large-scale supercomputers. Here the novel technique is illustrated using the leadership supercomputer IBM Blue Gene/P with an application to a typical biomol. calcn. of general interest, namely the binding of calcium ions to the small protein Calbindin D9k. The free energy landscape assocd. with two order parameters, the distance between the ion and its binding pocket and the root-mean-square deviation (rmsd) of the binding pocket relative the crystal structure, was calcd. using the US/H-REMD method. The results are then used to est. the abs. binding free energy of calcium ion to Calbindin D9k. The tests demonstrate that the 2D US/H-REMD scheme greatly accelerates the configurational sampling of the binding pocket, thereby improving the convergence of the potential of mean force calcn.
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    Hub, J. S.; De Groot, B. L.; van der Spoel, D. g_wham─A Free Weighted Histogram Analysis Implementation Including Robust Error and Autocorrelation Estimates. J. Chem. Theory Comput. 2010, 6, 3713– 3720,  DOI: 10.1021/ct100494z
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    g_wham: A Free Weighted Histogram Analysis Implementation Including Robust Error and Autocorrelation Estimates
    Hub, Jochen S.; de Groot, Bert L.; van der Spoel, David
    Journal of Chemical Theory and Computation (2010), 6 (12), 3713-3720CODEN: JCTCCE; ISSN:1549-9618. (American Chemical Society)
    The Weighted Histogram Anal. Method (WHAM) is a std. technique used to compute potentials of mean force (PMFs) from a set of umbrella sampling simulations. Here, the authors present a new WHAM implementation, termed g_wham, which is distributed freely with the GROMACS mol. simulation suite. G_wham ests. statistical errors using the technique of bootstrap anal. Three bootstrap methods are supported: (i) bootstrapping new trajectories based on the umbrella histograms, (ii) bootstrapping of complete histograms, and (iii) Bayesian bootstrapping of complete histograms, i.e., bootstrapping via the assignment of random wts. to the histograms. Because methods ii and iii consider only complete histograms as independent data points, these methods do not require the accurate calcn. of autocorrelation times. The authors demonstrate that, given sufficient sampling, bootstrapping new trajectories allows for an accurate error est. In the presence of long autocorrelations, however, (Bayesian) bootstrapping of complete histograms yields a more reliable error est., whereas bootstrapping of new trajectories may underestimate the error. In addn., the authors emphasize that the incorporation of autocorrelations into WHAM reduces the bias from limited sampling, in particular, when computing periodic PMFs in inhomogeneous systems such as solvated lipid membranes or protein channels.
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    Johnson, E. R.; Keinan, S.; Mori-Sánchez, P.; Contreras-García, J.; Cohen, A. J.; Yang, W. Revealing noncovalent interactions. J. Am. Chem. Soc. 2010, 132, 6498– 6506,  DOI: 10.1021/ja100936w
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    Revealing Noncovalent Interactions
    Johnson, Erin R.; Keinan, Shahar; Mori-Sanchez, Paula; Contreras-Garcia, Julia; Cohen, Aron J.; Yang, Weitao
    Journal of the American Chemical Society (2010), 132 (18), 6498-6506CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)
    Mol. structure does not easily identify the intricate noncovalent interactions that govern many areas of biol. and chem., including design of new materials and drugs. We develop an approach to detect noncovalent interactions in real space, based on the electron d. and its derivs. Our approach reveals the underlying chem. that compliments the covalent structure. It provides a rich representation of van der Waals interactions, hydrogen bonds, and steric repulsion in small mols., mol. complexes, and solids. Most importantly, the method, requiring only knowledge of the at. coordinates, is efficient and applicable to large systems, such as proteins or DNA. Across these applications, a view of nonbonded interactions emerges as continuous surfaces rather than close contacts between atom pairs, offering rich insight into the design of new and improved ligands.
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  59. 59
    Boto, R. A.; Peccati, F.; Laplaza, R.; Quan, C.; Carbone, A.; Piquemal, J.-P.; Maday, Y.; Contreras-García, J. NCIPLOT4: Fast, robust, and quantitative analysis of noncovalent interactions. J. Chem. Theory Comput. 2020, 16, 4150– 4158,  DOI: 10.1021/acs.jctc.0c00063
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    NCIPLOT4: Fast, Robust, and Quantitative Analysis of Noncovalent Interactions
    Boto, Roberto A.; Peccati, Francesca; Laplaza, Ruben; Quan, Chaoyu; Carbone, Alessandra; Piquemal, Jean-Philip; Maday, Yvon; Contreras-Garcia, Julia
    Journal of Chemical Theory and Computation (2020), 16 (7), 4150-4158CODEN: JCTCCE; ISSN:1549-9618. (American Chemical Society)
    The NonCovalent Interaction index (NCI) enables identification of attractive and repulsive noncovalent interactions from promol. densities in a fast manner. However, the approach remained up to now qual., only providing visual information. We present a new version of NCIPLOT, NCIPLOT4, which allows quantifying the properties of the NCI regions (vol., charge) in small and big systems in a fast manner. Examples are provided of how this new twist enables characterization and retrieval of local information in supramol. chem. and biosystems at the static and dynamic levels.
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    Hoefling, M.; Iori, F.; Corni, S.; Gottschalk, K.-E. Interaction of amino acids with the Au (111) surface: adsorption free energies from molecular dynamics simulations. Langmuir 2010, 26, 8347– 8351,  DOI: 10.1021/la904765u
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    Interaction of Amino Acids with the Au(111) Surface: Adsorption Free Energies from Molecular Dynamics Simulations
    Hoefling, Martin; Iori, Francesco; Corni, Stefano; Gottschalk, Kay-Eberhard
    Langmuir (2010), 26 (11), 8347-8351CODEN: LANGD5; ISSN:0743-7463. (American Chemical Society)
    Interactions of proteins with inorg. surfaces are of great importance in biol. events and in modern biotechnol. applications. Therefore, peptides have been engineered to recognize inorg. surfaces with high specificity. However, the underlying interactions are still not well understood. Here, we investigated the adsorption of amino acids as protein building blocks onto a Au(111) surface. In particular, using mol. dynamics (MD) simulations, we calcd. the potential of mean force between all the 20 amino acids and the gold surface. We found a strong dependence of the binding affinities on the chem. character of the amino acids. Addnl., the interaction free energy is correlated with the propensity of amino acids to form β-sheets, hinting at design principles for gold-binding peptides and induction of β-sheet formation near surfaces.
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    Bellucci, L.; Corni, S. Interaction with a gold surface reshapes the free energy landscape of alanine dipeptide. J. Phys. Chem. C 2014, 118, 11357– 11364,  DOI: 10.1021/jp502494k
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    Interaction with a Gold Surface Reshapes the Free Energy Landscape of Alanine Dipeptide
    Bellucci, Luca; Corni, Stefano
    Journal of Physical Chemistry C (2014), 118 (21), 11357-11364CODEN: JPCCCK; ISSN:1932-7447. (American Chemical Society)
    The adsorption of the alanine dipeptide onto a gold surface in aq. conditions was explored by using mol. dynamics simulations. In particular, using Metadynamics, the authors reconstructed a three-dimensional free energy landscape to study the effect of the metal surface on such landscape. The adsorption process is able to strongly modify the internal free energy surface of the mol., even changing its qual. appearance. The new free energy global min. corresponds to elongated conformations of the biomol., arranged in preferred orientations with respect to the surface. Therefore, the surface-induced changes in the relative stability of the local free energy min. and in the free-energy barriers between them show that the entire conformational ensemble and the interconformer dynamics are also affected by the presence of the surface. The alanine dipeptide is the simplest mol. that exhibits the main features shown by larger peptides. Therefore, these findings provide a basis to rationalize, at the atomistic level, the effects of metal surfaces and nanoparticles on the structure and function of peptides and proteins, which is of paramount importance to engineer new systems for applications in bionanotechnol.
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    Shao, Q.; Hall, C. K. Binding preferences of amino acids for gold nanoparticles: a molecular simulation study. Langmuir 2016, 32, 7888– 7896,  DOI: 10.1021/acs.langmuir.6b01693
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    Binding Preferences of Amino Acids for Gold Nanoparticles: A Molecular Simulation Study
    Shao, Qing; Hall, Carol K.
    Langmuir (2016), 32 (31), 7888-7896CODEN: LANGD5; ISSN:0743-7463. (American Chemical Society)
    A better understanding of the binding preference of amino acids for gold nanoparticles of different diams. could aid in the design of peptides that bind specifically to nanoparticles of a given diam. The authors identify the binding preference of 19 natural amino acids for three gold nanoparticles with diams. of 1.0, 2.0, and 4.0 nm, and investigate the mechanisms that govern these preferences. The authors calc. potentials of mean force between 36 entities (19 amino acids and 17 side chains) and the three gold nanoparticles in explicit water using well-tempered metadynamics simulations. Comparing these potentials of mean force dets. the amino acids' nanoparticle binding preferences and if these preferences are controlled by the backbone, the side chain, or both. Twelve amino acids prefer to bind to the 4.0 nm gold nanoparticle, and seven prefer to bind to the 2.0 nm one. The authors also use atomistic mol. dynamics simulations to investigate how water mols. near the nanoparticle influence the binding of the amino acids. The solvation shells of the larger nanoparticles have higher water densities than those of the smaller nanoparticles while the orientation distributions of the water mols. in the shells of all three nanoparticles are similar. The nanoparticle preferences of the amino acids depend on whether their binding free energy is detd. mainly by their ability to replace or to reorient water mols. in the nanoparticle solvation shell. The amino acids whose binding free energy depends mainly on the replacement of water mols. are likely to prefer to bind to the largest nanoparticle and tend to have relatively simple side chain structures. Those whose binding free energy depends mainly on their ability to reorient water mols. prefer a smaller nanoparticle and tend to have more complex side chain structures.
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    Hughes, Z. E.; Wright, L. B.; Walsh, T. R. Biomolecular adsorption at aqueous silver interfaces: first-principles calculations, polarizable force-field simulations, and comparisons with gold. Langmuir 2013, 29, 13217– 13229,  DOI: 10.1021/la402839q
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    Biomolecular Adsorption at Aqueous Silver Interfaces: First-Principles Calculations, Polarizable Force-Field Simulations, and Comparisons with Gold
    Hughes, Zak E.; Wright, Louise B.; Walsh, Tiffany R.
    Langmuir (2013), 29 (43), 13217-13229CODEN: LANGD5; ISSN:0743-7463. (American Chemical Society)
    The mol. simulation of biomols. adsorbed at noble metal interfaces can assist in the development of bionanotechnol. applications. In line with advances in polarizable force fields for adsorption at aq. gold interfaces, there is scope for developing a similar force field for silver. One way to accomplish this is via the generation of in vacuo adsorption energies calcd. using first-principles approaches for a wide range of different but biol. relevant small mols., including water. The authors present such first-principles data for a comprehensive range of bioorg. mols. obtained from plane-wave d. functional theory calcns. using the vdW-DF functional. The authors have constructed a new force field, AgP-CHARMM, suitable for the simulation of biomols. at the aq. Ag(111) and Ag(100) interfaces. This force field is derived to be consistent with GolP-CHARMM such that adsorption on Ag and Au can be compared on an equal footing. The force fields are used to evaluate the water overlayer stability on both silver and gold, finding good agreement with known behaviors. The authors also calc. and compare the structuring (spatial and orientational) of liq. water adsorbed at both silver and gold. Finally, the authors report the adsorption free energy of a range of amino acids at both the Au(111) and Ag(111) aq. interfaces, calcd. using meta-dynamics. Stronger adsorption on gold was noted in most cases, with the exception being the carboxylate group present in aspartic acid. These findings also indicate differences in the binding free energy profile between silver and gold for some amino acids, notably for His and Arg. The relatively stronger structuring of the first water layer on silver, relative to gold, could give rise to these differences.
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    Rosa, M.; Di Felice, R.; Corni, S. Adsorption mechanisms of nucleobases on the hydrated Au (111) surface. Langmuir 2018, 34, 14749– 14756,  DOI: 10.1021/acs.langmuir.8b00065
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    Adsorption Mechanisms of Nucleobases on the Hydrated Au(111) Surface
    Rosa, Marta; Di Felice, Rosa; Corni, Stefano
    Langmuir (2018), 34 (49), 14749-14756CODEN: LANGD5; ISSN:0743-7463. (American Chemical Society)
    The soln. environment is of fundamental importance in the adsorption of mols. on surfaces, a process that is strongly affected by the capability of the adsorbate to disrupt the hydration layer above the surface. Here we disclose how the presence of interface water influences the adsorption mechanism of DNA nucleobases on a gold surface. By means of metadynamics simulations, we describe the distinctive features of a complex free-energy landscape for each base, which manifests activation barriers for the adsorption process. We characterize the different pathways that allow each nucleobase to overcome the barriers and be adsorbed on the surface, discussing how they influence the kinetics of adsorption of single-stranded DNA oligomers with homogeneous sequences. Our findings offer a rationale as to why exptl. data on the adsorption of single-stranded homo-oligonucleotides do not straightforwardly follow the thermodn. affinity rank.
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    Rapino, S.; Zerbetto, F. Modeling the Stability and the Motion of DNA Nucleobases on the Gold Surface. Langmuir 2005, 21, 2512– 2518,  DOI: 10.1021/la047091o
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    Modeling the Stability and the Motion of DNA Nucleobases on the Gold Surface
    Rapino, Stefania; Zerbetto, Francesco
    Langmuir (2005), 21 (6), 2512-2518CODEN: LANGD5; ISSN:0743-7463. (American Chemical Society)
    We simulate the structure and dynamics of the four DNA bases on the most stable gold surface. The exptl. adsorption energies are reproduced to about 1 kcal mol-1, and the existence of anchor points in the mols. is evidenced. The simulations also show that the bases drift on the gold surface with a degree of mobility that is not inversely proportional to the exptl. (and calcd.) desorption energies. When the same type of calcns. is applied to pairs of bases it is seen that for at least two of them, namely GG and TT, there is a cooperative effect that increases their adsorption energy with respect to those of the single mols. The mol. mobility on the surface is still present when a pair of interacting bases is considered.
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    Feng, J.; Pandey, R. B.; Berry, R. J.; Farmer, B. L.; Naik, R. R.; Heinz, H. Adsorption mechanism of single amino acid and surfactant molecules to Au {111} surfaces in aqueous solution: design rules for metal-binding molecules. Soft Matter 2011, 7, 2113– 2120,  DOI: 10.1039/c0sm01118e
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    Adsorption mechanism of single amino acid and surfactant molecules to Au {111} surfaces in aqueous solution: design rules for metal-binding molecules
    Feng, Jie; Pandey, Ras B.; Berry, Rajiv J.; Farmer, Barry L.; Naik, Rajesh R.; Heinz, Hendrik
    Soft Matter (2011), 7 (5), 2113-2120CODEN: SMOABF; ISSN:1744-683X. (Royal Society of Chemistry)
    The adsorption mechanism of twenty amino acids and four surfactants was examd. on a {111} surface of gold in dil. aq. soln. using mol. dynamics simulation with a broadly applicable intermol. potential CHARMM-METAL. All mols. are attracted to the surface between -3 and -26 kcal mol-1. The adsorption strength correlates with the degree of coordination of polarizable atoms (O, N, C) to multiple epitaxial sites. Therefore, the mol. size and geometry rather than the specific chem. det. the adsorption energy. Large mols. with planar sp2 hybridized groups (Arg, Trp, Gln, Tyr, Asn, and PPh3) adsorb most strongly, followed by mols. with polar sp3 hybridized groups, and short mols. with sp3 hybridized alkyl groups exhibit least attraction. Conformationally flexible, extended mols. such as hexadecyltrimethylammonium bromide (CTAB) also showed significant attraction to the metal surface related to accommodation in epitaxial grooves and coordination with numerous epitaxial sites. Computational results are consistent with combinatorial binding expts., observations in the growth and stabilization of metal nanoparticles, and ab initio data. The mechanism of adsorption conforms to soft epitaxy obsd. for peptides on metal surfaces for binding to a given metal surface. In addn. to soft epitaxy, contributions to adsorption are possible by covalent bonding and induced charges.
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    Dasetty, S.; Barrows, J. K.; Sarupria, S. Adsorption of amino acids on graphene: assessment of current force fields. Soft Matter 2019, 15, 2359– 2372,  DOI: 10.1039/C8SM02621A
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    Adsorption of amino acids on graphene: assessment of current force fields
    Dasetty, Siva; Barrows, John K.; Sarupria, Sapna
    Soft Matter (2019), 15 (11), 2359-2372CODEN: SMOABF; ISSN:1744-6848. (Royal Society of Chemistry)
    We compare the free energies of adsorption (ΔAads) and the structural preferences of amino acids on graphene obtained using the non-polarizable force fields-Amberff99SB-ILDN/TIP3P, CHARMM36/modified-TIP3P, OPLS-AA/M/TIP3P, and Amber03w/TIP4P/2005. The amino acid-graphene interactions are favorable irresp. of the force field. While the magnitudes of ΔAads differ between the force fields, the relative free energy of adsorption across amino acids is similar for the studied force fields. ΔAads pos. correlates with amino acid-graphene and neg. correlates with graphene-water interaction energies. Using a combination of principal component anal. and d.-based clustering technique, we grouped the structures obsd. in the graphene adsorbed state. The resulting population of clusters, and the conformation in each cluster indicate that the structures of the amino acid in the graphene adsorbed state vary across force fields. The differences in the conformations of amino acids are more severe in the graphene adsorbed state compared to the bulk state for all the force fields. Our findings suggest that the force fields studied will give qual. consistent relative strength of adsorption across proteins but different structural preferences in the graphene adsorbed state.
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    Biriukov, D.; Futera, Z. Adsorption of amino acids at the gold/aqueous interface: Effect of an external electric field. J. Phys. Chem. C 2021, 125, 7856– 7867,  DOI: 10.1021/acs.jpcc.0c11248
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    Adsorption of Amino Acids at the Gold/Aqueous Interface: Effect of an External Electric Field
    Biriukov, Denys; Futera, Zdenek
    Journal of Physical Chemistry C (2021), 125 (14), 7856-7867CODEN: JPCCCK; ISSN:1932-7447. (American Chemical Society)
    Gaining accurate mol. descriptions of metal/bio interfaces is a necessary step toward numerous important applications, particularly in electrochem. and bionanotechnol. Here, using atomistic mol. dynamics simulations and free energy calcns. with the GolP-CHARMM force field, we investigate how applied static elec. field disturbs the structure of an aq. Au (111)/amino acid (AA) interface. We show that adsorption of pos. charged AAs (arginine, histidine, and lysine) is more affected by the external elec. field than that of neg. charged (aspartic and glutamic acids) and charge-neutral AAs (alanine, glycine, tryptophan, and asparagine). The adsorption free energies of pos. charged AAs can vary within 55% when static fields of up to 0.5 V/Å are applied, in contrast to considerably weaker responses of neg. charged and charge-neutral AAs (up to 25%). The difference arises from the role of a charged side chain in the adsorption on the gold surface. Pos. charged amines adsorb stronger than neg. charged carboxylates, and this fact together with the trend within pos. charged AAs (arginine > histidine > lysine) is related to the affinity of their side chains for Au (111) surfaces and ability to replace water mols. in the first adsorption layer. The adsorption via a deprotonated carboxyl group is less favorable, indirect, and facilitated by hydrogen bonding with the adsorbed water, while the pos. amines directly interact with surface gold atoms. This eventually leads to relatively weaker adsorption of neg. charged AAs and their smaller response to the external elec. fields due to solvent-induced electrostatic screening. These fundamental results provide a useful insight into the mol. arrangement at the electrified biointerfaces with gold, which can help to interpret electrochem. phenomena and advance bioelectronic applications.
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    Hughes, Z. E.; Tomásio, S. M.; Walsh, T. R. Efficient simulations of the aqueous bio-interface of graphitic nanostructures with a polarisable model. Nanoscale 2014, 6, 5438– 5448,  DOI: 10.1039/C4NR00468J
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    Efficient simulations of the aqueous bio-interface of graphitic nanostructures with a polarisable model
    Hughes, Zak E.; Tomasio, Susana M.; Walsh, Tiffany R.
    Nanoscale (2014), 6 (10), 5438-5448CODEN: NANOHL; ISSN:2040-3372. (Royal Society of Chemistry)
    To fully harness the enormous potential offered by interfaces between graphitic nanostructures and biomols., detailed connections between adsorbed conformations and adsorption behavior are needed. To elucidate these links, a key approach, in partnership with exptl. techniques, is mol. simulation. For this, a force-field (FF) that can appropriately capture the relevant physics and chem. of these complex bio-interfaces, while allowing extensive conformational sampling, and also supporting inter-operability with known biol. FFs, is a pivotal requirement. Here, we present and apply such a force-field, GRAPPA, designed to work with the CHARMM FF. GRAPPA is an efficiently implemented polarisable force-field, informed by extensive plane-wave DFT calcns. using the revPBE-vdW-DF functional. GRAPPA adequately recovers the spatial and orientational structuring of the aq. interface of graphene and carbon nanotubes, compared with more sophisticated approaches. We apply GRAPPA to det. the free energy of adsorption for a range of amino acids, identifying Trp, Tyr and Arg to have the strongest binding affinity and Asp to be a weak binder. The GRAPPA FF can be readily incorporated into mainstream simulation packages, and will enable large-scale polarisable biointerfacial simulations at graphitic interfaces, that will aid the development of biomol.-mediated, soln.-based graphene processing and self-assembly strategies.
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    Rosa, M.; Corni, S.; Di Felice, R. van der Waals effects at molecule-metal interfaces. Phys. Rev. B 2014, 90, 125448,  DOI: 10.1103/PhysRevB.90.125448
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    van der Waals effects at molecule-metal interfaces
    Rosa, Marta; Corni, Stefano; Di Felice, Rosa
    Physical Review B: Condensed Matter and Materials Physics (2014), 90 (12), 125448/1-125448/8, 8 pp.CODEN: PRBMDO; ISSN:1098-0121. (American Physical Society)
    We present the results of plane-wave pseudopotential periodic d. functional theory (DFT) calcns. on the geometries, energetics and electronic structure of small mols. on Au(111). The chosen mols.-benzene, ammonia and cytosine-are representative of different adsorption regimes and interaction strengths. The chosen substrate is a prototype noble-metal surface that is widely employed as a support for org. materials. We assess the relevance of van der Waals effects in the adsorption process and the accuracy of different first-principle d. functionals that have been recently developed to embody such effects. We find that there is no unique functional that is optimal for any system. In particular, our results reveal that functionals designed to reduce the short-term repulsion between the adsorbate and the substrate usually overestimate the adsorption strength and may even predict the wrong adsorption orientation. We show that an accurate description of the substrate does not ensure an accurate evaluation of the adsorption energetics, while the electronic structure is less sensitive to the specific choice. We propose the best choice for DFT calcns. of DNA bases on Au(111) and similar systems in which both short-range and long-range interactions exist.
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    Rosa, M.; Corni, S.; Di Felice, R. A density functional theory study of cytosine on Au (111). J. Phys. Chem. C 2012, 116, 21366– 21373,  DOI: 10.1021/jp305833c
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    A Density Functional Theory Study of Cytosine on Au(111)
    Rosa, Marta; Corni, Stefano; Di Felice, Rosa
    Journal of Physical Chemistry C (2012), 116 (40), 21366-21373CODEN: JPCCCK; ISSN:1932-7447. (American Chemical Society)
    The adsorption of cytosine on Au(111) is investigated using d. functional theory with the nonlocal van der Waals d. functional. Test calcns. performed on the benzene stacked dimer and on a benzene mol. adsorbed on Au(111) allow us to assess the methodol. and reveal the accuracy and predictivity of the van der Waals d. functional relative to exptl. outcome. Our results for cytosine on Au(111) indicate that the inclusion of dispersion interactions is crucial for the treatment of this system. In fact, such terms enhance the value of the adsorption energy and also affect the cytosine bonding geometry: in particular, we find that a tilted geometry is always favorable relative to a parallel geometry, which was not found in std. d. functional theory investigations. The combined new data for energetics and geometry lead to conclusions that contrast the common opinion that the surface-mol. interaction is negligible in the process of monolayer formation.
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    Rosa, M.; Corni, S.; Di Felice, R. Interaction of nucleic acid bases with the Au (111) surface. J. Chem. Theory Comput. 2013, 9, 4552– 4561,  DOI: 10.1021/ct4002416
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    Interaction of Nucleic Acid Bases with the Au(111) Surface
    Rosa, Marta; Corni, Stefano; Di Felice, Rosa
    Journal of Chemical Theory and Computation (2013), 9 (10), 4552-4561CODEN: JCTCCE; ISSN:1549-9618. (American Chemical Society)
    The fate of an individual DNA mol. when it is deposited on a hard inorg. surface in a dry environment is unknown, while it is a crucial determinant for nanotechnol. applications of nucleic acids. In the absence of exptl. approaches that are able to unravel the three-dimensional at. structure of the target system, here we tackle the first step toward a computational soln. of the problem. By using first-principles quantum mech. calcns. of the four nucleobases on the Au(111) surface, we present results for the geometries, energetics, and electronic structure, in view of developing a force field that will enable classical simulations of DNA on Au(111) to investigate the structural modifications of the duplex in these non-native conditions. We fully characterize each system at the individual level. We find that van der Waals interactions are crucial for a correct description of the geometry and energetics. However, the mechanism of adsorption is well beyond pure dispersion interactions. Indeed, we find charge sharing between the substrate and the adsorbate, the formation of hybrid orbitals, and even bonding orbitals. Yet, this mol.-surface assocn. is qual. distinct from the thiol adsorption mechanism; we discuss such differences and also the relation to the adsorption mechanism of pure arom. mols.
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    Rosa, M.; Corni, S.; Di Felice, R. Enthalpy–entropy tuning in the adsorption of nucleobases at the Au (111) surface. J. Chem. Theory Comput. 2014, 10, 1707– 1716,  DOI: 10.1021/ct401117g
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    Enthalpy-Entropy Tuning in the Adsorption of Nucleobases at the Au(111) Surface
    Rosa, Marta; Corni, Stefano; Di Felice, Rosa
    Journal of Chemical Theory and Computation (2014), 10 (4), 1707-1716CODEN: JCTCCE; ISSN:1549-9618. (American Chemical Society)
    The interaction of DNA mols. with hard substrates is of paramount importance both for the study of DNA itself and for the variety of possible technol. applications. Interaction with inorg. surfaces strongly modifies the helical shape of DNA. Hence, an accurate understanding of DNA structure and function at interfaces is a fundamental question with enormous impact in science and society. This work sets the fundamentals for the simulation of entire DNA oligomers on gold surfaces in dry and wet conditions. Thanks to the new GolDNA-AMBER force field, which was derived from first principles and includes dispersion interactions and polarization effects, we simulated self-assembled guanine and adenine monolayers on Au(111) in vacuo and the adsorption of all nucleobases on the same substrate in aq. conditions. The periodic monolayers obtained from classical simulations match very well those from first principle calcns. and expts., assessing the robustness of the force field and motivating the application to more complex systems for which quantum calcns. are not affordable and expts. are elusive. The energetics of nucleobases on Au(111) in soln. reveal fundamental physicochem. effects: we find that the adsorption paradigm shifts from purely enthalpic to dominantly entropic by changing the environment and aggregation phase.
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    Östblom, M.; Liedberg, B.; Demers, L. M.; Mirkin, C. A. On the structure and desorption dynamics of DNA bases adsorbed on gold: A temperature-programmed study. J. Phys. Chem. B 2005, 109, 15150– 15160,  DOI: 10.1021/jp051617b
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    On the structure and desorption dynamics of DNA bases adsorbed on gold: a temperature-programmed study
    Ostblom Mattias; Liedberg Bo; Demers Linette M; Mirkin Chad A
    The journal of physical chemistry. B (2005), 109 (31), 15150-60 ISSN:1520-6106.
    The structure and desorption dynamics of mono- and multilayer samples of adenine, cytosine, guanine, and thymine on polycrystalline gold thin films are studied using temperature-programmed desorption-infrared reflection absorption spectroscopy (TPD-IRAS) and temperature-programmed desorption-mass spectroscopy (TPD-MS). It is shown that the pyrimidines, adenine and guanine, adsorb to gold in a complex manner and that both adhesive (adenine) and cohesive (guanine) interactions contribute the apparent binding energies to the substrate surface. Adenine displays at least two adsorption sites, including a high-energy site (210 degrees C, approximately 136 kJ/mol), wherein the molecule coordinates to the gold substrate via the NH2 group in an sp3-like, strongly perturbed, nonplanar configuration. The purines, cytosine and thymine, display a less complicated adsorption/desorption behavior. The desorption energy for cytosine (160 degrees C, approximately 122 kJ/mol) is similar to those obtained for adenine and guanine, but desorption occurs from a single site of dispersed, nonaggregated cytosine. Thymine desorbs also from a single site but at a significantly lower energy (100 degrees C, approximately 104 kJ/mol). Infrared data reveal that the monolayer architectures discussed herein are structurally very different from those observed for the bases in the bulk crystalline state. It is also evident that both pyrimidines and purines adsorb on gold with the plane of the molecule in a nonparallel orientation with respect to the substrate surface. The results of this work are discussed in the context of improving the understanding of the design of capturing oligonucleotides or DNA strands for bioanalytical applications, in particular, for gold nanoparticle-based assays.
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    Demers, L. M.; Östblom, M.; Zhang, H.; Jang, N.-H.; Liedberg, B.; Mirkin, C. A. Thermal desorption behavior and binding properties of DNA bases and nucleosides on gold. J. Am. Chem. Soc. 2002, 124, 11248– 11249,  DOI: 10.1021/ja0265355
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    Thermal Desorption Behavior and Binding Properties of DNA Bases and Nucleosides on Gold
    Demers, Linette M.; Oestblom, Mattias; Zhang, Hua; Jang, Nak-Han; Liedberg, Bo; Mirkin, Chad A.
    Journal of the American Chemical Society (2002), 124 (38), 11248-11249CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)
    DNA monolayers on gold thin films and electrodes, as well as DNA-protected gold nanoparticles, are the basis for an increasing no. of diagnostic applications that involve the use of surface-enhanced Raman spectroscopy (SERS), surface plasmon resonance spectroscopy (SPRS), and electrochem., scanometric, and colorimetric DNA detection strategies. Thus, the nature and strength of interactions of DNA with gold surfaces for both planar films and charged particles are subjects of great interest to researchers in the disciplines of biotechnol. and nanotechnol. Indeed, a no. of studies aimed at elucidating the binding modes and conformation of DNA and its components (bases and nucleosides) on gold surfaces suggest that the DNA-gold interaction is complex and highly sequence-dependent. Herein, we use temp.-programmed desorption (TPD) and reflection absorption FT IR (RAIR) spectroscopy to directly examine the energetics of the DNA base-gold and DNA nucleoside-gold interactions. To the best of our knowledge this is the first study to quantify and compare the energetics of these important interactions between the fundamental chem. components of DNA and gold.
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    Fleischmann, M.; Hendra, P. J.; McQuillan, A. J. Raman spectra of pyridine adsorbed at a silver electrode. Chem. Phys. Lett. 1974, 26, 163– 166,  DOI: 10.1016/0009-2614(74)85388-1
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    Raman spectra of pyridine adsorbed at a silver electrode
    Fleischmann, M.; Hendra, P. J.; McQuillan, A. J.
    Chemical Physics Letters (1974), 26 (2), 163-6CODEN: CHPLBC; ISSN:0009-2614.
    Raman spectroscopy was employed for the 1st time to study the role of adsorption at electrodes. It was possible to distinguish 2 types of pyridine adsorption at a Ag electrode. The variation in intensity and frequency of some of the bands with potential in the region of the point of zero charge gave further evidence as to the structure of the elec. double layer; the interaction of adsorbed pyridine and water must be taken into account.
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    Albrecht, M. G.; Creighton, J. A. Anomalously intense Raman spectra of pyridine at a silver electrode. J. Am. Chem. Soc. 1977, 99, 5215– 5217,  DOI: 10.1021/ja00457a071
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    Anomalously intense Raman spectra of pyridine at a silver electrode
    Albrecht, M. Grant; Creighton, J. Alan
    Journal of the American Chemical Society (1977), 99 (15), 5215-17CODEN: JACSAT; ISSN:0002-7863.
    Raman bands due to pyridine absorbed at a Ag electrode, which are absent for a freshly cleaned electrode immersed in aq. pyridine/KCl, are anomalously intense after a single electrochem. roughening cycle. The intensity enhancement is estd. to be ∼105-fold, and is possibly due to a resonance Raman effect in pyridine induced by an electronic interaction with the roughened metal surface. The high intensity of Raman bands enables changes in the surface concn. of absorbed pyridine to be readily followed during and after the roughening cycle.
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    Jeanmaire, D. L.; Van Duyne, R. P. Surface Raman spectroelectrochemistry: Part I. Heterocyclic, aromatic, and aliphatic amines adsorbed on the anodized silver electrode. J. Electroanal. Chem. Interfacial Electrochem. 1977, 84, 1– 20,  DOI: 10.1016/S0022-0728(77)80224-6
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    Surface Raman spectroelectrochemistry. Part I. Heterocyclic, aromatic, and aliphatic amines adsorbed on the anodized silver electrode
    Jeanmaire, David L.; Van Duyne, Richard P.
    Journal of Electroanalytical Chemistry and Interfacial Electrochemistry (1977), 84 (1), 1-20CODEN: JEIEBC; ISSN:0022-0728.
    The remarkable sensitivity of Raman spectroscopy was verified for the study of adsorbed pyridine on a Ag surface, and its applicability extended to other N heterocycles and amines. New bands in the scattering spectrum of adsorbed pyridine were characterized, which were not previously reported, as well as the Raman intensity response of all the surface pyridine bands as a function of electrode potential. As a result of these expts., a model is proposed of the adsorbed species for pyridine in which the adsorption is anion induced, leading to an axial end-on attachment to the electrode surface. The ability to obtain resonance Raman spectra with good signal-to-noise ratios with laser powers < 1.0 mW, opens up possibilities of surface Raman studies with relatively inexpensive laser systems. As laser power requirements are relaxed, reliability is improved, and greater tuning ranges can be achieved for wavelength dependent studies. The potential of resonance Raman spectroscopy was previously demonstrated for monitoring soln. kinetic behavior; now it is shown that normal Raman as well as resonance Raman spectroscopy have sufficient sensitivity to extend the studies of kinetic processes to include those occurring at electrode surfaces.
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    Zuo, C.; Jagodzinski, P. W. Surface-Enhanced Raman Scattering of Pyridine Using Different Metals: Differences and Explanation Based on the Selective Formation of α-Pyridyl on Metal Surfaces. J. Phys. Chem. B 2005, 109, 1788– 1793,  DOI: 10.1021/jp0406363
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    Surface-Enhanced Raman Scattering of Pyridine Using Different Metals: Differences and Explanation Based on the Selective Formation of α-Pyridyl on Metal Surfaces
    Zuo, Chen; Jagodzinski, Paul W.
    Journal of Physical Chemistry B (2005), 109 (5), 1788-1793CODEN: JPCBFK; ISSN:1520-6106. (American Chemical Society)
    A simple method has been developed to produce SERS-active metal surfaces. Six metal surfaces (cadmium, nickel, gold, iron, copper, and silver) have been prepd. on an aluminum foil underlayment by chem. redn. and strong surface-enhanced Raman signals have been obsd. for pyridine species on these surfaces. This permits the direct comparison of pyridine spectra on different metal surfaces prepd. by the same chem. clean method. The differences among the SER spectra of the aq. pyridine species using different metals generally follow the trend of silver, cadmium, nickel, iron, gold, and copper, which can be explained by the selective formation of α-pyridyl species and the equil. between end-on adsorbed pyridines and edge-on adsorbed α-pyridyl species on the different metal surfaces.
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    Khaing Oo, M. K.; Guo, Y.; Reddy, K.; Liu, J.; Fan, X. Ultrasensitive vapor detection with surface-enhanced Raman scattering-active gold nanoparticle immobilized flow-through multihole capillaries. Anal. Chem. 2012, 84, 3376– 3381,  DOI: 10.1021/ac300175v
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    Ultrasensitive Vapor Detection with Surface-Enhanced Raman Scattering-Active Gold Nanoparticle Immobilized Flow-Through Multihole Capillaries
    Khaing Oo, Maung Kyaw; Guo, Yunbo; Reddy, Karthik; Liu, Jing; Fan, Xudong
    Analytical Chemistry (Washington, DC, United States) (2012), 84 (7), 3376-3381CODEN: ANCHAM; ISSN:0003-2700. (American Chemical Society)
    The authors developed novel flow-through surface-enhanced Raman scattering (SERS) platforms using gold nanoparticle (Au-NP) immobilized multihole capillaries for rapid and sensitive vapor detection. The multihole capillaries consisting of thousands of micrometer-sized flow-through channels provide many unique characteristics for vapor detection. Most importantly, its three-dimensional SERS-active micro-/nanostructures make available multilayered assembly of Au-NPs, which greatly increase SERS-active surface area within a focal vol. of excitation and collection, thus improving the detection sensitivity. The multihole capillary's inherent longitudinal channels offer rapid and convenient vapor delivery, yet its micrometer-sized holes increase the interaction between vapor mols. and SERS-active substrate. Exptl., rapid pyridine vapor detection (within 1 s of exposure) and ultrasensitive 4-nitrophenol vapor detection (at a sub-ppb level) were successfully achieved in open air at room temp. Such an ultrasensitive SERS platform enabled, for the 1st time, the study of both pyridine and 4-nitrophenol vapor adsorption isotherms at very low concns. Type I and type V behaviors of the International Union of Pure and Applied Chem. isotherm were well obsd., resp.
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    Beljebbar, A.; Sockalingum, G.; Angiboust, J.; Manfait, M. Comparative FT SERS, resonance Raman and SERRS studies of doxorubicin and its complex with DNA. Spectrochim. Acta A Mol. Biomol. Spectrosc. 1995, 51, 2083– 2090,  DOI: 10.1016/0584-8539(95)01515-7
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    Comparative FT SERS, resonance Raman and SERRS studies of doxorubicin and its complex with DNA
    Beljebbar, A.; Sockalingum, G. D.; Angiboust, J. F.; Manfait, M.
    Spectrochimica Acta, Part A: Molecular and Biomolecular Spectroscopy (1995), 51A (12), 2083-90CODEN: SAMCAS; ISSN:0584-8539. (Elsevier)
    Fourier transform surface enhanced Raman scattering (FT SERS) coupled with a microscope has been used as a probe to obtain information on the interaction of a drug and of its complex with DNA. Micro-FT SERS spectra of the antitumor agent doxorubicin (DOX) at 10-5 M and of this complex with DNA have been recorded in aq. silver hydrosol and compared with the corresponding resonance Raman (RR) and SERS (surface enhanced Raman scattering) spectra at concns. of 5 × 10-4 M and 5 × 10-8 M, resp. The interactions between the drug and calf thymus DNA induced identical effects in the RR and visible SERS spectra. The data show that the adsorption of the drug-DNA complex on the silver hydrosol does not induce detectable perturbations of the mol. interactions within the complex. Micro-FT SERS spectra were partially different from those obtained in visible SERS spectra. These differences concern the relative enhancement of some vibrational modes which could hardly be obsd. when resonance excitation was used. The FT SERS approach enables further information to be obtained and addnl. details on the geometry of the drug-DNA interaction to be revealed. An anal. of the FT SERS spectra of the drug and of its complex with DNA not only confirms the model of interaction proposed using RR and SERS data in the visible, but brings about new information, esp. on the vibrations of ring A of the mol., which are usually masked by the vibrations of rings B and C dominant in the visible SERS spectra.
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    Loren, A.; Eliasson, C.; Josefson, M.; Murty, K.; Käll, M.; Abrahamsson, J.; Abrahamsson, K. Feasibility of quantitative determination of doxorubicin with surface-enhanced Raman spectroscopy. J. Raman Spectrosc. 2001, 32, 971– 974,  DOI: 10.1002/jrs.783
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    Feasibility of quantitative determination of doxorubicin with surface-enhanced Raman spectroscopy
    Loren, A.; Eliasson, C.; Josefson, M.; Murty, K. V. G. K.; Kall, M.; Abrahamsson, J.; Abrahamsson, K.
    Journal of Raman Spectroscopy (2001), 32 (11), 971-974CODEN: JRSPAF; ISSN:0377-0486. (John Wiley & Sons Ltd.)
    Surface-enhanced Raman spectroscopy (SERS) was performed using excitation at 488 nm in a blood plasma-doxorubicin-silver colloid system. With a blood plasma content of 1%, a partial least-squares calibration of the doxorubicin was made in the 10-750 nM range. Predictions for a test set generated a root mean square error of prediction of 70 nM. The use of SERS and chemometrics in complex systems made it possible to use the highly informative Raman signals even at low concns. without the need for sample pretreatment such as extn.
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    Lee, K. Y.; Wang, Y.; Nie, S. In vitro study of a pH-sensitive multifunctional doxorubicin–gold nanoparticle system: Therapeutic effect and surface enhanced Raman scattering. RSC Adv. 2015, 5, 65651– 65659,  DOI: 10.1039/C5RA09872F
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    In vitro study of a pH-sensitive multifunctional doxorubicin-gold nanoparticle system: therapeutic effect and surface enhanced Raman scattering
    Lee, Kate Y. J.; Wang, Yiqing; Nie, Shuming
    RSC Advances (2015), 5 (81), 65651-65659CODEN: RSCACL; ISSN:2046-2069. (Royal Society of Chemistry)
    We report the development and characterization of a multifunctional drug delivery system (Au-dox-PEG) for the treatment and SERS spectroscopic detection of tumors. Doxorubicin, a therapeutic agent and a SERS tag, was chem. conjugated to gold nanoparticles via a pH-sensitive hydrazone linker, and then PEG was added to develop Au-dox-PEG. The doxorubicin occupied a max. of 20% of the total surface area of the gold nanoparticles which resulted in colloidal stability. SERS spectra were measured for non-aggregated Au-dox-PEG using near-IR wavelength radiation, and the doxorubicin release was time and pH dependent. Consistency in the release profile and in vitro cell viability results supports the efficacy of the Au-dox-PEG system. Thus, the development of the Au-dox-PEG multifunctional system raises exciting opportunities for the simultaneous spectroscopic detection and therapy of tumors in the future.
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    Smulevich, G.; Feis, A. Surface-enhanced resonance Raman spectra of adriamycin, 11-deoxycarminomycin, their model chromophores, and their complexes with DNA. J. Phys. Chem. 1986, 90, 6388– 6392,  DOI: 10.1021/j100281a064
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    Surface-enhanced resonance Raman spectra of adriamycin, 11-deoxycarminomycin, their model chromophores, and their complexes with DNA
    Smulevich, Giulietta; Feis, Alessandro
    Journal of Physical Chemistry (1986), 90 (23), 6388-92CODEN: JPCHAX; ISSN:0022-3654.
    The surface-enhanced Raman spectra of Ag sols of adriamycin [23214-92-8], 11-deoxycarminomycin [81382-07-2], their model chromophores 1,4- [81-64-1] and 1,8-dihydroxyanthraquinone [117-10-2], and their complexes with DNA were measured. The well-detailed spectra yieled by the combined anal. in terms of symmetry and pseudosymmetry, a nearly complete vibrational assignment of the resonance Raman active modes. The spectra perturbations induced by the adsorption of the compds. onto the Ag particles, by comparison with their resonance Raman spectra in soln., were explained in terms of interaction between one C:O≡O-H group of the chromophore and the Ag surface. The intensity of redn. of some bands assocd. with the HOCCC=O groups obsd. in the drug/DNA complexes was interpreted in terms of changes between the ground and the excited states of the normal coordinates and(or) their equil. positions. The inferred structures of the complexes was consistent with intercalation between daunorubicin and the DNA fragment d(CpGpTpApCpG) previously reported from X-ray measurements.
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    Nonaka, Y.; Tsuboi, M.; Nakamoto, K. Comparative study of aclacinomycin versus adriamycin by means of resonance Raman spectroscopy. J. Raman Spectrosc. 1990, 21, 133– 141,  DOI: 10.1002/jrs.1250210211
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    Comparative study of aclacinomycin versus adriamycin by means of resonance Raman spectroscopy
    Nonaka, Yasuomi; Tsuboi, Masamichi; Nakamoto, Kazuo
    Journal of Raman Spectroscopy (1990), 21 (2), 133-41CODEN: JRSPAF; ISSN:0377-0486.
    Resonance Raman spectra of adriamycin and aclacinomycin A were examd. in their H2O and D2O solns. These spectra appear totally different from each other, but the differences are similar to those between 1,4- and 1,8-dihydroxyanthraquinone, which are considered model chromophores of adriamycin and aclacinomycin, resp. Surface-enhanced resonance Raman spectra of these 2 drugs were compared by the use of Ag sols. The effects of DNA binding on the resonance Raman spectra are different for these 2 drugs. Adriamycin was intercalated in the CpG (or GpC) site of the DNA duplex, but aclacinomycin in the TpA (or ApT) site. Most of the differences in the spectra and sequence specificity are explained in terms of the mol. structures of their chromophores, i.e. in the adriamycin chromophore (1,4-dihydroxyanthraquinone) 2 OH groups are H bonded to different C:O groups, whereas in the aclacinomycin chromophore (1,8-dihydroxyantraquinone) 2 OH groups form H bonds with the same C:O group, leaving the other C:O group free from any intramol. H bonding.
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    Yan, Q.; Priebe, W.; Chaires, J. B.; Czernuszewicz, R. S. Interaction of doxorubicin and its derivatives with DNA: Elucidation by resonance Raman and surface-enhanced resonance Raman spectroscopy. Biospectroscopy 1997, 3, 307– 316,  DOI: 10.1002/(SICI)1520-6343(1997)3:4<307::AID-BSPY6>3.0.CO;2-0
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    Interaction of doxorubicin and its derivatives with DNA: elucidation by resonance Raman and surface-enhanced resonance Raman spectroscopy
    Yan, Qing; Priebe, Waldemar; Chaires, Jonathan B.; Czernuszewicz, Roman S.
    Biospectroscopy (1997), 3 (4), 307-316CODEN: BIOSFS; ISSN:1075-4261. (Wiley)
    The interactions of doxorubicin and its derivs., hydroxyrubicin and adriamycinone, with DNA were studied by resonance Raman (RR) and surface-enhanced resonance Raman scattering (SERRS) spectroscopy. The π-π interaction between the chromophore of the drug and DNA base pairs has been shown to downshift the skeletal stretching mode ∼ 1440 cm-1 by 8,5, and 4 cm-1 for doxorubicin, hydroxyrubicin, and adriamycinone, resp. The addnl. effects of intercalation with DNA on the RR and SERRS spectra for hydroxyrubicin are similar to those for doxorubicin. However, different effects are obsd. for adriamycinone. These results indicate that the sugar moiety is necessary to maintain the max. van der Waals contact between the chromophore and the DNA base pairs and that the amine group in the amino sugar is more favored than the hydroxyl group.
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    Lee, C.-J.; Kang, J.-S.; Kim, M.-S.; Lee, K.-P.; Lee, M.-S. The study of doxorubicin and its complex with DNA by SERS and UV-resonance Raman spectroscopy. Bull. Korean Chem. Soc. 2004, 25, 1211– 1216,  DOI: 10.5012/bkcs.2004.25.8.1211
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    The study of doxorubicin and its complex with DNA by SERS and UV-resonance Raman spectroscopy
    Lee, Chul Jae; Kang, Jae Soo; Kim, Mak Soon; Lee, Kwang Pill; Lee, Mu Sang
    Bulletin of the Korean Chemical Society (2004), 25 (8), 1211-1216CODEN: BKCSDE; ISSN:0253-2964. (Korean Chemical Society)
    The interaction of the antitumor agent doxorubicin with calf thymus DNA is investigated in an aq. soln. at a pH level of 6-7 with molar ratios of 1/10. A UV-resonance Raman spectroscopy and surface enhanced Raman spectroscopy are used to det. the doxorubicin binding sites and the structural variations of doxorubicin-DNA complexes in an aq. soln. Doxorubicin intercalates with adenine and guanine via a hydrogen bond formation between the N7 positions of purine bases and the hydroxyl group of doxorubicin.
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    Olszówka, M.; Russo, R.; Mancini, G.; Cappelli, C. A computational approach to the resonance Raman spectrum of doxorubicin in aqueous solution. Theor. Chem. Acc. 2016, 135, 27,  DOI: 10.1007/s00214-015-1781-9
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    Giovannini, T.; Macchiagodena, M.; Ambrosetti, M.; Puglisi, A.; Lafiosca, P.; Lo Gerfo, G.; Egidi, F.; Cappelli, C. Simulating vertical excitation energies of solvated dyes: From continuum to polarizable discrete modeling. Int. J. Quantum Chem. 2019, 119, e25684  DOI: 10.1002/qua.25684
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    Lafiosca, P.; Gómez, S.; Giovannini, T.; Cappelli, C. Absorption properties of large complex molecular systems: the DFTB/fluctuating charge approach. J. Chem. Theory Comput. 2022, 18, 1765– 1779,  DOI: 10.1021/acs.jctc.1c01066
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    Absorption Properties of Large Complex Molecular Systems: The DFTB/Fluctuating Charge Approach
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    Journal of Chemical Information and Modeling (2023), 63 (4), 1208-1217CODEN: JCISD8; ISSN:1549-9596. (American Chemical Society)
    UV-Resonance Raman (RR) spectroscopy is a valuable tool to study the binding of drugs to biomol. receptors. The extn. of information at the mol. level from exptl. RR spectra is made much easier and more complete thanks to the use of computational approaches, specifically tuned to deal with the complexity of the supramol. system. In this paper, we propose a protocol to simulate RR spectra of complex systems at different levels of sophistication, by exploiting a quantum mechanics/mol. mechanics (QM/MM) approach. The approach is challenged to investigate RR spectra of a widely used chemotherapy drug, doxorubicin (DOX) intercalated into a DNA double strand. The computed results show good agreement with exptl. data, thus confirming the reliability of the computational protocol.
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    Physical Chemistry Chemical Physics (2019), 21 (7), 3877-3893CODEN: PPCPFQ; ISSN:1463-9076. (Royal Society of Chemistry)
    The intercalation process of binding doxorubicin (DOX) in DNA is studied by extensive mol. dynamics (MD) simulations. Many mol. factors that control the binding affinity of DOX to DNA to form a stable complex were inspected and quantified by employing continuum solvation models for estg. the binding free energy. The modified MM-PB(GB)SA methodol. provides a complete energetic profile of ΔGele, ΔGvDW, ΔGpolar, ΔGnon-polar, TΔStotal, ΔGdeform, ΔGcon, and ΔGion. To identify the sequence specificity of DOX, 2 different DNA sequences, d(CGATCG) or DNA1 and d(CGTACG) or DNA2, with one mol. (1:1 complex) or 2 mol. (2:1 complex) configurations of DOX were selected in this study. Our results showed that the DNA deformation energy (ΔGdeform), the energy cost from translational and rotational entropic contributions (TΔStran+rot), the total electrostatic interactions (ΔGpolar-PB/GB + ΔGele) of incorporation, the intramol. electrostatic interactions (ΔGele), and electrostatic polar solvation interactions (ΔGpolar-PB/GB) were all unfavorable to the binding of DOX to DNA. However, they were overcome by at least 5 favorable interactions: the van der Waals interactions (ΔGvDW), the non-polar solvation interaction (ΔGnon-polar), the vibrational entropic contribution (TΔSvib), and the std. concn.-dependent free energies of DOX (ΔGcon) and the ionic soln. (ΔGion). Specifically, the van der Waals interaction appeared to be the major driving force to form a stable DOX-DNA complex. We also predicted that DOX has stronger binding to DNA1 than DNA2. The DNA deformation penalty and entropy cost in the 2:1 complex were less than those in the 1:1 complex; thus, they indicated that the 2:1 complex is more stable than the 1:1 complex. We calcd. the total binding free energy (BFE) (ΔGt-sim) using both MM-PBSA and MM-GBSA methods, which suggested a more stable DOX-DNA complex at lower ionic concn. The calcd. BFE from the modified MM-GBSA method for DOX-DNA1 and DOX-DNA2 in the 1:1 complex was -9.1 and -5.1 kcal/mol, resp. The same quantities from the modified MM-PBSA method were -12.74 and -8.35 kcal/mol, resp. The value of the total BFE ΔGt-sim in the 1:1 complex was in reasonable agreement with the exptl. value of -7.7 ± 0.3 kcal/mol.
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    A review. An in-depth appreciation of how to manipulate the mol.-level recognition between peptides and aq. materials interfaces, including nanoparticles, will advance technologies based on self-organized metamaterials for photonics and plasmonics, biosensing, catalysis, energy generation and harvesting, and nanomedicine. Exploitation of the materials-selective binding of biomols. is pivotal to success in these areas and may be particularly key to producing new hierarchically structured biobased materials. These applications could be accomplished by realizing preferential adsorption of a given biomol. onto one materials compn. over another, one surface facet over another, or one cryst. polymorph over another. Deeper knowledge of the aq. abiotic-biotic interface, to establish clear structure-property relations in these systems, is needed to meet this goal. In particular, a thorough structural characterization of the surface-adsorbed peptides is essential for establishing these relations but can often be challenging to accomplish via exptl. approaches alone. In addn. to myriad existing challenges assocd. with detg. the detailed mol. structure of any mol. adsorbed at an aq. interface, exptl. characterization of materials-binding peptides brings new, complex challenges because many materials-binding peptides are thought to be intrinsically disordered. This means that these peptides are not amenable to exptl. techniques that rely on the presence of well-defined secondary structure in the peptide when in the adsorbed state. To address this challenge, and in partnership with expt., mol. simulations at the atomistic level can bring complementary and crit. insights into the origins of this abiotic/biotic recognition and suggest routes for manipulating this phenomenon to realize new types of hybrid materials. For the reasons outlined above, mol. simulation approaches also face challenges in their successful application to model the biotic-abiotic interface, related to several factors. For instance, simulations require a plausible description of the chem. and the physics of the interface, which comprises two very different states of matter, in the presence of liq. water. Also, it is essential that the conformational ensemble be comprehensively characterized under these conditions; this is esp. challenging because intrinsically disordered peptides do not typically admit one single structure or set of structures. Moreover, a plausible structural model of the substrate is required, which may require a high level of detail, even for single-element materials such as Au surfaces or graphene. Developing and applying strategies to make credible predictions of the conformational ensemble of adsorbed peptides and using these to construct structure-property relations of these interfaces have been the goals of the authors' efforts. The authors have made substantial progress in developing interat. potentials for these interfaces and adapting advanced conformational sampling approaches for these purposes. This Account summarizes the authors' progress in the development and deployment of interfacial force fields and mol. simulation techniques for the purpose of elucidating these insights at biomol.-materials interfaces, using examples from the authors' labs. ranging from noble-metal interfaces to graphitic substrates (including carbon nanotubes and graphene) and oxide materials (such as titania). In addn. to the well-established application areas of plasmonic materials, biosensing, and the prodn. of medical implant materials, the authors outline new directions for this field that have the potential to bring new advances in areas such as energy materials and regenerative medicine.
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    Functionalized gold nanoparticles have crit. applications in biodetection with surface-enhanced Raman spectrum and drug delivery. In this study, reactive force field mol. dynamics simulations were performed to study gold nanoparticles, which are modified with different short-chain peptides consisting of amino acid residues of cysteine and glycine in different grafting densities in the aq. environment. Our study showed slight facet-dependent peptide adsorption on a gold nanoparticle with the 3 nm core diam. Peptide chains prefer to adsorb on the Au(111) facet compared to those on other facets of Au(100) and Au(110). In addn. to the stable thiol interaction with gold nanoparticle surfaces, polarizable oxygen and nitrogen atoms show strong interactions with the gold surface and polarize the gold nanoparticle surfaces with an overall pos. charge. Charges of gold atoms vary according to their contacts with peptide atoms and lattice positions. However, at the outmost peptide layer, the whole functionalized Au nanoparticles exhibit overall neg. electrostatic potential due to the grafted peptides. Moreover, simulations show that thiol groups can be deprotonated and subsequently protons can be transferred to water mols. and carboxyl groups.
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  • Abstract

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    Figure 1

    Figure 1. Structures and atom numberings of the adsorbates studied in this work.

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    Figure 2

    Figure 2. (a) Initial and (b) final configurations of guanine on gold. The system is enclosed in a 3D simulation box (blue lines). Water molecules and ions have been omitted for clarity. In the favorable adsorption geometries, all molecules studied here (see Figure 1) are adsorbed parallel (slightly tilted) to the surface.

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    Figure 3

    Figure 3. Performance of each combination of force fields for the seven studied molecules in estimating minimum distances from the gold surface, dmin (top clustered histogram), and adsorption free energies, ΔEads (bottom clustered histogram), with the corresponding error bars.

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    Figure 4

    Figure 4. (a) Evolution of the time of the minimum distance and (b) free energy profiles along the reaction coordinate for the adsorption of the alanine dipeptide on a gold surface. FF: IFF/OPLS and GolP.

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    Figure 5

    Figure 5. Adsorption free energy profiles of the four nucleobases modeled with OPLS/AA on the left and CHARMM on the right by using GolP FFs.

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    Figure 6

    Figure 6. Analysis of the interactions occurring during the adsorption of guanine on the gold surface (GolP-CHARMM FF). Left: evolution in time of the number of contacts with the surface and water molecules surrounding guanine. Right: NCI plots of guanine in its in-solution state, local minimum, transition state, and global minimum (top and lateral view) configurations. Water molecules within 0.3 nm of guanine are shown. Similar plots using the IFF/CHARMM FF are displayed in Figure S10 in the Supporting Information.

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    Figure 7

    Figure 7. Minimum distance and adsorption free energy plots for PYR (left) and DOX (right) for all of the possible combinations of force fields.

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    4. 4
      Wang, C.; Yu, C. Detection of chemical pollutants in water using gold nanoparticles as sensors: a review. Rev. Anal. Chem. 2013, 32, 1– 14,  DOI: 10.1515/revac-2012-0023
      4
      Detection of chemical pollutants in water using gold nanoparticles as sensors: a review
      Wang, Chao; Yu, Chenxu
      Reviews in Analytical Chemistry (2013), 32 (1), 1-14CODEN: RACYAX; ISSN:0793-0135. (Walter de Gruyter GmbH)
      A review. Rapid and accurate evaluation of pollutant contamination in water is one of the key tasks of environmental monitoring. To make on-site assessment feasible, the anal. tools should be easy to operate, with minimal sample prepn. needs. Gold nanoparticle (AuNP)-based sensors have the potential to detect toxins, heavy metals, and inorg. and org. pollutants in water rapidly with high sensitivity, and they are expected to play an increasingly important role in environmental monitoring. In this article, the synthesis, fabrication and functionalization of AuNPs are discussed, and the recent advances in the development and application of AuNP-based sensors for the detn. of various pollutants contamination in water are reviewed.
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    5. 5
      Kwon, J. A.; Jin, C. M.; Shin, Y.; Kim, H. Y.; Kim, Y.; Kang, T.; Choi, I. Tunable plasmonic cavity for label-free detection of small molecules. ACS Appl. Mater. Interfaces 2018, 10, 13226– 13235,  DOI: 10.1021/acsami.8b01550
      5
      Tunable Plasmonic Cavity for Label-free Detection of Small Molecules
      Kwon, Jung A.; Jin, Chang Min; Shin, Yonghee; Kim, Hye Young; Kim, Yura; Kang, Taewook; Choi, Inhee
      ACS Applied Materials & Interfaces (2018), 10 (15), 13226-13235CODEN: AAMICK; ISSN:1944-8244. (American Chemical Society)
      Owing to its high sensitivity and high selectivity along with rapid response time, plasmonic detection has gained considerable interest in a wide variety of sensing applications. To improve the fieldwork applicability and reliability of plasmonic detection, the integration of plasmonic nanoparticles into optical devices is desirable. Herein, we propose an integrated label-free detection platform comprising a plasmonic cavity that allows sensitive mol. detection via either surface-enhanced Raman scattering (SERS) or plasmon resonance energy transfer (PRET). A small droplet of metal ion soln. spontaneously produces a plasmonic cavity on the surface of uncured poly(dimethylsiloxane) (PDMS), and as PDMS is cured, the metal ions are reduced to form a plasmonic antennae array on the cavity surface. Unique spherical feature and the integrated metallic nanoparticles of the cavity provide excellent optical functions to focus the incident light in the cavity and to rescatter the light absorbed by the nanoparticles. The optical properties of the plasmonic cavity for SERS or PRET are optimized by controlling the compn., size, and d. of the metal nanoparticles. By using the cavity, we accomplish both 1000-fold sensitive detection and real-time monitoring of reactive oxygen species secreted by live cells via PRET. In addn., we achieve sensitive detection of trace amts. of toxic environmental mols. such as 5-chloro-2-methyl-4-isothiazolin-3-one/2-methyl-4-isothiazol-3-one (CMIT/MIT) and bisphenol A, as well as several small biomols. such as glucose, adenine, and tryptophan, via SERS.
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    6. 6
      Chen, Y.; Liu, H.; Jiang, J.; Gu, C.; Zhao, Z.; Jiang, T. Immunoassay of Tumor Markers Based on Graphene Surface-Enhanced Raman Spectroscopy. ACS Appl. Bio Mater. 2020, 3, 8012– 8022,  DOI: 10.1021/acsabm.0c01098
      6
      Immunoassay of Tumor Markers Based on Graphene Surface-Enhanced Raman Spectroscopy
      Chen, Ying; Liu, Hongmei; Jiang, Jiamin; Gu, Chenjie; Zhao, Ziqi; Jiang, Tao
      ACS Applied Bio Materials (2020), 3 (11), 8012-8022CODEN: AABMCB; ISSN:2576-6422. (American Chemical Society)
      With a unique chem. enhancement capability, graphene oxide is exceptionally suitable to serve as an alternative surface-enhanced Raman scattering (SERS) substrate, which is usually defined as GERS. However, such a GERS matrix with both promising uniformity and mol. enrichment ability has not been applied in the quant. detection of tumor markers. Herein, an ultrasensitive and specific immunoassay of carcinoembryonic antigens mediated by the GERS matrix was demonstrated. With the assistance of Au NRs as immunoprobes, a reliable limit of detection as low as 3.01 pg/mL was finally achieved because of the collective effect of chem. and electromagnetic enhancements. Meanwhile, a calibration curve with a high R2 value of 0.996 was obtained in the range from 1μg/mL to 10 pg/mL. These results exhibit that the GERS matrix has a great promise for participating in immunoassay, which may pave a potential avenue for the real utilization of the SERS technique in clin. biomedicine.
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    7. 7
      Long, L.; Ju, W.; Yang, H.-Y.; Li, Z. Dimensional design for surface-enhanced raman spectroscopy. ACS Mater. Au 2022, 2, 552– 575,  DOI: 10.1021/acsmaterialsau.2c00005
      7
      Dimensional Design for Surface-Enhanced Raman Spectroscopy
      Long, Li; Ju, Wenbo; Yang, Hai-Yao; Li, Zhiyuan
      ACS Materials Au (2022), 2 (5), 552-575CODEN: AMACGU; ISSN:2694-2461. (American Chemical Society)
      A review. Surface-enhanced Raman spectroscopy (SERS) is a vibrational spectroscopy technique that enables specific identification of target analytes with sensitivity down to the singlemol. level by harnessing metal nanoparticles and nanostructures. Excitation of localized surface plasmon resonance of a nanostructured surface and the assocd. huge local elec. field enhancement lie at the heart of SERS, and things will become better if strong chem. enhancement is also available simultaneously. Thus, the precise control of surface characteristics of enhancing substrates plays a key role in broadening the scope of SERS for scientific purposes and developing SERS into a routine anal. tool. In this review, the development of SERS substrates is outlined with some milestones in the nearly half-century history of SERS. In particular, these substrates are classified into zero-dimensional, one-dimensional, two-dimensional, and threedimensional substrates according to their geometric dimension. We show that, in each category of SERS substrates, design upon the geometric and composite configuration can be made to achieve an optimized enhancement factor for the Raman signal. We also show that the temporal dimension can be incorporated into SERS by applying femtosecond pulse laser technol., so that the SERS technique can be used not only to identify the chem. structure of mols. but also to uncover the ultrafast dynamics of mol. structural changes. By adopting SERS substrates with the power of four-dimensional spatiotemporal control and design, the ultimate goal of probing the single-mol. chem. structural changes in the femtosecond time scale, watching the chem. reactions in four dimensions, and visualizing the elementary reaction steps in chem. might be realized in the near future.
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    8. 8
      Paria, D.; Kwok, K. S.; Raj, P.; Zheng, P.; Gracias, D. H.; Barman, I. Label-free spectroscopic SARS-CoV-2 detection on versatile nanoimprinted substrates. Nano Lett. 2022, 22, 3620– 3627,  DOI: 10.1021/acs.nanolett.1c04722
      8
      Label-free spectroscopic SARS-CoV-2 detection on versatile nanoimprinted substrates
      Paria, Debadrita; Kwok, Kam Sang; Raj, Piyush; Zheng, Peng; Gracias, David H.; Barman, Ishan
      Nano Letters (2022), 22 (9), 3620-3627CODEN: NALEFD; ISSN:1530-6984. (American Chemical Society)
      Widespread testing and isolation of infected patients is a cornerstone of viral outbreak management, as underscored during the ongoing COVID-19 pandemic. Here, we report a large-area and label-free testing platform that combines surface-enhanced Raman spectroscopy and machine learning for the rapid and accurate detection of SARS-CoV-2. Spectroscopic signatures acquired from virus samples on metal-insulator-metal nanostructures, fabricated using nanoimprint lithog. and transfer printing, can provide test results within 25 min. Not only can our technique accurately distinguish between different respiratory and nonrespiratory viruses, but it can also detect virus signatures in physiol. relevant matrixes such as human saliva without any addnl. sample prepn. Furthermore, our large area nanopatterning approach allows sensors to be fabricated on flexible surfaces allowing them to be mounted on any surface or used as wearables. We envision that our versatile and portable label-free spectroscopic platform will offer an important tool for virus detection and future outbreak preparedness.
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    9. 9
      Premachandran, S.; Haldavnekar, R.; Das, S.; Venkatakrishnan, K.; Tan, B. DEEP Surveillance of Brain Cancer Using Self-Functionalized 3D Nanoprobes for Noninvasive Liquid Biopsy. ACS Nano 2022, 16, 17948– 17964,  DOI: 10.1021/acsnano.2c04187
      9
      DEEP Surveillance of Brain Cancer Using Self-Functionalized 3D Nanoprobes for Noninvasive Liquid Biopsy
      Premachandran, Srilakshmi; Haldavnekar, Rupa; Das, Sunit; Venkatakrishnan, Krishnan; Tan, Bo
      ACS Nano (2022), 16 (11), 17948-17964CODEN: ANCAC3; ISSN:1936-0851. (American Chemical Society)
      Brain cancers, one of the most fatal malignancies, require accurate diagnosis for guided therapeutic intervention. However, conventional methods for brain cancer prognosis (imaging and tissue biopsy) face challenges due to the complex nature and inaccessible anatomy of the brain. Therefore, deep anal. of brain cancer is necessary to (i) detect the presence of a malignant tumor, (ii) identify primary or secondary origin, and (iii) find where the tumor is housed. In order to provide a diagnostic technique with such exhaustive information here, we attempted a liq. biopsy-based deep surveillance of brain cancer using a very minimal amt. of blood serum (5μL) in real time. We hypothesize that holistic anal. of serum can act as a reliable source for deep brain cancer surveillance. To identify minute amts. of tumor-derived material in circulation, we synthesized an ultrasensitive 3D nanosensor, adopted SERS as a diagnostic methodol., and undertook a DEEP neural network-based brain cancer surveillance. Detection of primary and secondary tumor achieved 100% accuracy. Prediction of intracranial tumor location achieved 96% accuracy. This modality of using patient sera for deep surveillance is a promising noninvasive liq. biopsy tool with the potential to complement current brain cancer diagnostic methodologies.
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    10. 10
      Curry, D.; Cameron, A.; MacDonald, B.; Nganou, C.; Scheller, H.; Marsh, J.; Beale, S.; Lu, M.; Shan, Z.; Kaliaperumal, R. Adsorption of doxorubicin on citrate-capped gold nanoparticles: insights into engineering potent chemotherapeutic delivery systems. Nanoscale 2015, 7, 19611– 19619,  DOI: 10.1039/c5nr05826k
      10
      Adsorption of doxorubicin on citrate-capped gold nanoparticles: insights into engineering potent chemotherapeutic delivery systems
      Curry, Dennis; Cameron, Amanda; MacDonald, Bruce; Nganou, Collins; Scheller, Hope; Marsh, James; Beale, Stefanie; Lu, Mingsheng; Shan, Zhi; Kaliaperumal, Rajendran; Xu, Heping; Servos, Mark; Bennett, Craig; MacQuarrie, Stephanie; Oakes, Ken D.; Mkandawire, Martin; Zhang, Xu
      Nanoscale (2015), 7 (46), 19611-19619CODEN: NANOHL; ISSN:2040-3372. (Royal Society of Chemistry)
      Gold nanomaterials have received great interest for their use in cancer theranostic applications over the past two decades. Many gold nanoparticle-based drug delivery system designs rely on adsorbed ligands such as DNA or cleavable linkers to load therapeutic cargo. The heightened research interest was recently demonstrated in the simple design of nanoparticle-drug conjugates wherein drug mols. are directly adsorbed onto the as-synthesized nanoparticle surface. The potent chemotherapeutic, doxorubicin often serves as a model drug for gold nanoparticle-based delivery platforms; however, the specific interaction facilitating adsorption in this system remains understudied. Here, for the first time, we propose empirical and theor. evidence suggestive of the main adsorption process where (1) hydrophobic forces drive doxorubicin towards the gold nanoparticle surface before (2) cation-π interactions and gold-carbonyl coordination between the drug mol. and the cations on AuNP surface facilitate DOX adsorption. In addn., biol. relevant compds., such as serum albumin and glutathione, were shown to enhance desorption of loaded drug mols. from AuNP at physiol. relevant concns., providing insight into the drug release and in vivo stability of such drug conjugates.
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    11. 11
      Brancolini, G.; Corazza, A.; Vuano, M.; Fogolari, F.; Mimmi, M. C.; Bellotti, V.; Stoppini, M.; Corni, S.; Esposito, G. Probing the influence of citrate-capped gold nanoparticles on an amyloidogenic protein. ACS Nano 2015, 9, 2600– 2613,  DOI: 10.1021/nn506161j
      11
      Probing the Influence of Citrate-Capped Gold Nanoparticles on an Amyloidogenic Protein
      Brancolini, Giorgia; Corazza, Alessandra; Vuano, Marco; Fogolari, Federico; Mimmi, Maria Chiara; Bellotti, Vittorio; Stoppini, Monica; Corni, Stefano; Esposito, Gennaro
      ACS Nano (2015), 9 (3), 2600-2613CODEN: ANCAC3; ISSN:1936-0851. (American Chemical Society)
      Nanoparticles (NPs) are known to exhibit distinct phys. and chem. properties compared with the same materials in bulk form. NPs have been repeatedly reported to interact with proteins, and this interaction can be exploited to affect processes undergone by proteins, such as fibrillogenesis. Fibrillation is common to many proteins, and in living organisms, it causes tissue-specific or systemic amyloid diseases. The nature of NPs and their surface chem. is crucial in assessing their affinity for proteins and their effects on them. Here the authors present the first detailed structural characterization and mol. mechanics model of the interaction between a fibrillogenic protein, β2-microglobulin, and a NP, 5 nm hydrophilic citrate-capped gold nanoparticles. NMR measurements and simulations at multiple levels (enhanced sampling mol. dynamics, Brownian dynamics, and Poisson-Boltzmann electrostatics) explain the origin of the obsd. protein perturbations mostly localized at the amino-terminal region. The protein-NP interaction is weak in the physiol.-like, conditions and do not induce protein fibrillation. Simulations reproduce these findings and reveal instead the role of the citrate in destabilizing the lower pH protonated form of β2-microglobulin. The results offer possible strategies for controlling the desired effect of NPs on the conformational changes of the proteins, which have significant roles in the fibrillation process.
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    12. 12
      Tang, Z.; Palafox-Hernandez, J. P.; Law, W.-C.; Hughes, Z. E.; Swihart, M. T.; Prasad, P. N.; Knecht, M. R.; Walsh, T. R. Biomolecular recognition principles for bionanocombinatorics: an integrated approach to elucidate enthalpic and entropic factors. ACS Nano 2013, 7, 9632– 9646,  DOI: 10.1021/nn404427y
      12
      Biomolecular Recognition Principles for Bionanocombinatorics: An Integrated Approach To Elucidate Enthalpic and Entropic Factors
      Tang, Zhenghua; Palafox-Hernandez, J. Pablo; Law, Wing-Cheung; E. Hughes, Zak; Swihart, Mark T.; Prasad, Paras N.; Knecht, Marc R.; Walsh, Tiffany R.
      ACS Nano (2013), 7 (11), 9632-9646CODEN: ANCAC3; ISSN:1936-0851. (American Chemical Society)
      Bionanocombinatorics is an emerging field that aims to use combinations of positionally encoded biomols. and nanostructures to create materials and devices with unique properties or functions. The full potential of this new paradigm could be accessed by exploiting specific noncovalent interactions between diverse palettes of biomols. and inorg. nanostructures. Advancement of this paradigm requires peptide sequences with desired binding characteristics that can be rationally designed, based upon fundamental, mol.-level understanding of biomol.-inorg. nanoparticle interactions. Here, the authors introduce an integrated method for building this understanding using exptl. measurements and advanced mol. simulation of the binding of peptide sequences to gold surfaces. From this integrated approach, the importance of entropically driven binding is quant. demonstrated, and the first design rules for creating both enthalpically and entropically driven nanomaterial-binding peptide sequences are developed. The approach presented here for gold is now being expanded in the authors' labs. to a range of inorg. nanomaterials and represents a key step toward establishing a bionanocombinatorics assembly paradigm based on noncovalent peptide-materials recognition.
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    13. 13
      Corni, S.; Hnilova, M.; Tamerler, C.; Sarikaya, M. Conformational Behavior of Genetically-Engineered Dodecapeptides as a Determinant of Binding Affinity for Gold. J. Phys. Chem. C 2013, 117, 16990– 17003,  DOI: 10.1021/jp404057h
      13
      Conformational Behavior of Genetically-Engineered Dodecapeptides as a Determinant of Binding Affinity for Gold.
      Corni, Stefano; Hnilova, Marketa; Tamerler, Candan; Sarikaya, Mehmet
      Journal of Physical Chemistry C (2013), 117 (33), 16990-17003CODEN: JPCCCK; ISSN:1932-7447. (American Chemical Society)
      Genetically engineered solid binding peptides, because of their unique affinity and specificity for solid materials, represent a promising mol. toolbox for nanoscience and nanotechnol. Despite their potential, the physicochem. determinants of their high affinity for surfaces remain, in most cases, poorly understood. Here the authors present exptl. data and classical atomistic mol. dynamics simulations for two gold binding dodecapeptides (AuBP1 and AuBP2) and a control peptide that does not bind to gold, to unravel the key microscopic differences among them. In particular, by extensive sampling via replica exchange simulations, the authors show here that the conformational ensemble of the three peptides in soln. and on the gold surface can be examd., and that the role played by their different conformational flexibility can be analyzed. The authors found, specifically, that AuBP1 and AuBP2 are much more flexible than the control peptide, which allows all the potential Au-binding amino acids present in these AuBPs to concurrently bind to the gold surface. On the contrary, the potential Au-binding amino acids in the rigid control peptide cannot contact the surface all at the same time, hampering the overall binding. The role of conformational flexibility has been also analyzed in terms of the configurational entropy of the free and adsorbed peptides. Such anal. suggests a possible route to improve upon current flexible gold binding peptides.
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    14. 14
      Hughes, Z. E.; Wei, G.; Drew, K. L.; Colombi Ciacchi, L.; Walsh, T. R. Adsorption of DNA fragments at aqueous graphite and Au (111) via integration of experiment and simulation. Langmuir 2017, 33, 10193– 10204,  DOI: 10.1021/acs.langmuir.7b02480
      14
      Adsorption of DNA Fragments at Aqueous Graphite and Au(111) via Integration of Experiment and Simulation
      Hughes, Zak E.; Wei, Gang; Drew, Kurt L. M.; Colombi Ciacchi, Lucio; Walsh, Tiffany R.
      Langmuir (2017), 33 (39), 10193-10204CODEN: LANGD5; ISSN:0743-7463. (American Chemical Society)
      The authors combine single mol. force spectroscopy measurements with all-atom metadynamics simulations to study the cross-materials binding strength trends of DNA fragments adsorbed at the aq. graphite C(0001) and Au(111) interfaces. The authors' simulations predict this adsorption at the level of the nucleobase, nucleoside, and nucleotide. Despite challenges in making clear, careful connections between the exptl. and simulation data, reasonable consistency between the binding trends between the two approaches and two substrates was evident. On C(0001), the authors' simulations predict a binding trend of dG > dA ≈ dT > dC, which broadly aligns with the exptl. trend. On Au(111), the simulation-based binding strength trends reveal stronger adsorption for the purines relative to the pyrimidines, with dG ≈ dA > dT ≈ dC. Moreover, the authors' simulations provide structural insights into the origins of the similarities and differences in adsorption of the nucleic acid fragments at the two interfaces. In particular, the authors' simulation data offer an explanation for the differences obsd. in the relative binding trend between adenosine and guanine on the two substrates.
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    15. 15
      Cohavi, O.; Corni, S.; De Rienzo, F.; Di Felice, R.; Gottschalk, K. E.; Hoefling, M.; Kokh, D.; Molinari, E.; Schreiber, G.; Vaskevich, A. Protein–surface interactions: challenging experiments and computations. J. Mol. Recognit. 2010, 23, 259– 262,  DOI: 10.1002/jmr.993
      15
      Protein-surface interactions: challenging experiments and computations
      Cohavi, Ori; Corni, Stefano; De Rienzo, Francesca; Di Felice, Rosa; Gottschalk, Kay E.; Hoefling, Martin; Kokh, Daria; Molinari, Elisa; Schreiber, Gideon; Vaskevich, Alexander; Wade, Rebecca C.
      Journal of Molecular Recognition (2010), 23 (3), 259-262CODEN: JMORE4; ISSN:0952-3499. (John Wiley & Sons Ltd.)
      Protein-surface interactions are fundamental in natural processes, and have great potential for applications ranging from nanotechnol. to medicine. A recent workshop highlighted the current achievements and the main challenges in the field. Copyright © 2009 John Wiley & Sons, Ltd.
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    16. 16
      Brancolini, G.; Kokh, D. B.; Calzolai, L.; Wade, R. C.; Corni, S. Docking of ubiquitin to gold nanoparticles. ACS Nano 2012, 6, 9863– 9878,  DOI: 10.1021/nn303444b
      16
      Docking of Ubiquitin to Gold Nanoparticles
      Brancolini, Giorgia; Kokh, Daria B.; Calzolai, Luigi; Wade, Rebecca C.; Corni, Stefano
      ACS Nano (2012), 6 (11), 9863-9878CODEN: ANCAC3; ISSN:1936-0851. (American Chemical Society)
      Protein-nanoparticle assocns. have important applications in nanoscience and nanotechnol. such as targeted drug delivery and theranostics. However, the mechanisms by which proteins recognize nanoparticles and the determinants of specificity are still poorly understood at the microscopic level. Gold is a promising material in nanoparticles for nanobiotechnol. applications because of the ease of its functionalization and its tunable optical properties. Ubiquitin is a small, cysteine-free protein (ubiquitous in eukaryotes) whose binding to gold nanoparticles has been characterized recently by NMR (NMR). To reveal the mol. basis of these protein-nanoparticle interactions, we performed simulations at multiple levels (ab initio quantum mechanics, classical mol. dynamics and Brownian dynamics) and compared the results with exptl. data (CD and NMR). The results provide a model of the ensemble of structures constituting the ubiquitin-gold surface complex, and insights into the driving forces for the binding of ubiquitin to gold nanoparticles, the role of nanoparticle surfactants (citrate) in the assocn. process, and the origin of the perturbations in the NMR chem. shifts.
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    17. 17
      Charchar, P.; Christofferson, A. J.; Todorova, N.; Yarovsky, I. Understanding and designing the gold–bio interface: Insights from simulations. Small 2016, 12, 2395– 2418,  DOI: 10.1002/smll.201503585
      17
      Understanding and Designing the Gold-Bio Interface: Insights from Simulations
      Charchar, Patrick; Christofferson, Andrew J.; Todorova, Nevena; Yarovsky, Irene
      Small (2016), 12 (18), 2395-2418CODEN: SMALBC; ISSN:1613-6810. (Wiley-VCH Verlag GmbH & Co. KGaA)
      A review. Gold nanoparticles (AuNPs) are an integral part of many exciting and novel biomedical applications, sparking the urgent need for a thorough understanding of the physicochem. interactions occurring between these inorg. materials, their functional layers, and the biol. species they interact with. Computational approaches are instrumental in providing the necessary mol. insight into the structural and dynamic behavior of the Au-bio interface with spatial and temporal resolns. not yet achievable in the lab., and are able to facilitate a rational approach to AuNP design for specific applications. A perspective of the current successes and challenges assocd. with the multiscale computational treatment of Au-bio interfacial systems, from electronic structure calcns. to force field methods, is provided to illustrate the links between different approaches and their relation to expt. and applications.
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    18. 18
      Brancolini, G.; Bellucci, L.; Maschio, M. C.; Di Felice, R.; Corni, S. The interaction of peptides and proteins with nanostructures surfaces: a challenge for nanoscience. Curr. Opin. Colloid Interface Sci. 2019, 41, 86– 94,  DOI: 10.1016/j.cocis.2018.12.003
      18
      The interaction of peptides and proteins with nanostructures surfaces: a challenge for nanoscience
      Brancolini, Giorgia; Bellucci, Luca; Maschio, Maria Celeste; Di Felice, Rosa; Corni, Stefano
      Current Opinion in Colloid & Interface Science (2019), 41 (), 86-94CODEN: COCSFL; ISSN:1359-0294. (Elsevier Ltd.)
      A review. The impact of nanotechnologies in biomedicine and biotechnol. is becoming more and more evident. It imposes practical challenges, for instance, raising specific issues on the biocompatibility of nanostructures. Nanoparticles are characterized by a high surface-to-vol. ratio, which makes them reactive to foreign species. Thus, when proteins or peptides approach an inorg. nanoparticle, as well as a flat surface, they are likely to interact with the substrate to some extent. This interaction is crucial for applications in drug delivery, imaging, diagnostics, implants, and other medical devices. Specifically, gold nanoparticles are highly versatile and particularly appealing. It is widely accepted that the surfaces of nanoparticles adsorb proteins either transiently in the soft corona layer or permanently in the hard corona layer. As a consequence, the protein structure and/or function may undergo profound adjustments or remain conserved. Detailing the interaction of different inorg. substrates with proteins and peptides at the at. level, and designing ways to control the interaction, is the key for biomedical applications of nanoparticles, both from a fundamental viewpoint and for practical implementations. In the last decade, we have addressed protein-nanoparticle interactions, focusing on interfaces of gold surfaces and nanoparticles with amyloidogenic peptides and protein models. We have developed classical force fields, performed advanced mol. dynamics simulations, and compared computational outcomes with data from NMR expts. Protein-gold complexes with differently coated gold nanoparticles have been modeled to explore the effects of charge and size on the protein structure. Our work unravels that a complex interplay between surface properties and characteristics of the biol. adsorbate dets. whether peptide conformation is influenced and whether protein aggregation is accelerated or inhibited by the presence of the substrate. General guidelines to cope with amyloidogenic proteins could be inferred: these can be essentially summarized with the necessity of balancing the hydrophobic and electrostatic interactions that the amyloidogenic proteins establish with the coating moieties.
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    19. 19
      Martin, L.; Bilek, M. M.; Weiss, A. S.; Kuyucak, S. Force fields for simulating the interaction of surfaces with biological molecules. Interface Focus 2016, 6, 20150045,  DOI: 10.1098/rsfs.2015.0045
      19
      Force fields for simulating the interaction of surfaces with biological molecules
      Martin Lewis; Bilek Marcela M; Kuyucak Serdar; Weiss Anthony S
      Interface focus (2016), 6 (1), 20150045 ISSN:2042-8898.
      The interaction of biomolecules with solid interfaces is of fundamental importance to several emerging biotechnologies such as medical implants, anti-fouling coatings and novel diagnostic devices. Many of these technologies rely on the binding of peptides to a solid surface, but a full understanding of the mechanism of binding, as well as the effect on the conformation of adsorbed peptides, is beyond the resolution of current experimental techniques. Nanoscale simulations using molecular mechanics offer potential insights into these processes. However, most models at this scale have been developed for aqueous peptide and protein simulation, and there are no proven models for describing biointerfaces. In this review, we detail the current research towards developing a non-polarizable molecular model for peptide-surface interactions, with a particular focus on fitting the model parameters as well as validation by choice of appropriate experimental data.
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    20. 20
      Latour, R. A. Molecular simulation of protein-surface interactions: Benefits, problems, solutions, and future directions (Review). Biointerphases 2008, 3, FC2– FC12,  DOI: 10.1116/1.2965132
      20
      Molecular simulation of protein-surface interactions: benefits, problems, solutions, and future directions (review)
      Latour, Robert A.
      Biointerphases (2008), 3 (3), FC2-FC12CODEN: BJIOBN; ISSN:1559-4106. (AVS-Science and Technology of Materials, Interfaces and Processing)
      A review. While the importance of protein adsorption to materials surfaces is widely recognized, little is understood at this time regarding how to design surfaces to control protein adsorption behavior. All-atom empirical force field mol. simulation methods have enormous potential to address this problem by providing an approach to directly investigate the adsorption behavior of peptides and proteins at the at. level. As with any type of technol., however, these methods must be appropriately developed and applied if they are to provide realistic and useful results. Three issues that are particularly important for the accurate simulation of protein adsorption behavior are the selection of a valid force field to represent the at.-level interactions involved, the accurate representation of solvation effects, and system sampling. In this article, each of these areas is addressed and future directions for continued development are presented.
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    21. 21
      Ozboyaci, M.; Kokh, D. B.; Corni, S.; Wade, R. C. Modeling and simulation of protein-surface interactions: Achievements and challenges. Q. Rev. Biophys. 2016, 49, e4  DOI: 10.1017/s0033583515000256
      21
      Modeling and simulation of protein-surface interactions: achievements and challenges
      Ozboyaci, Musa; Kokh, Daria B.; Corni, Stefano; Wade, Rebecca C.
      Quarterly Reviews of Biophysics (2016), 49 (), e4/1-e4/87CODEN: QURBAW; ISSN:0033-5835. (Cambridge University Press)
      Understanding protein-inorg. surface interactions is central to the rational design of new tools in biomaterial sciences, nanobiotechnol. and nanomedicine. Although a significant amt. of exptl. research on protein adsorption onto solid substrates has been reported, many aspects of the recognition and interaction mechanisms of biomols. and inorg. surfaces are still unclear. Theor. modeling and simulations provide complementary approaches for exptl. studies, and they have been applied for exploring protein-surface binding mechanisms, the determinants of binding specificity towards different surfaces, as well as the thermodn. and kinetics of adsorption. Although the general computational approaches employed to study the dynamics of proteins and materials are similar, the models and force-fields (FFs) used for describing the phys. properties and interactions of material surfaces and biol. mols. differ. In particular, FF and water models designed for use in biomol. simulations are often not directly transferable to surface simulations and vice versa. The adsorption events span a wide range of time- and length-scales that vary from nanoseconds to days, and from nanometers to micrometers, resp., rendering the use of multi-scale approaches unavoidable. Further, changes in the at. structure of material surfaces that can lead to surface reconstruction, and in the structure of proteins that can result in complete denaturation of the adsorbed mols., can create many intermediate structural and energetic states that complicate sampling. In this review, we address the challenges posed to theor. and computational methods in achieving accurate descriptions of the phys., chem. and mech. properties of protein-surface systems. In this context, we discuss the applicability of different modeling and simulation techniques ranging from quantum mechanics through all-atom mol. mechanics to coarse-grained approaches. We examine uses of different sampling methods, as well as free energy calcns. Furthermore, we review computational studies of protein-surface interactions and discuss the successes and limitations of current approaches.
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      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC28XitVSrsbk%253D&md5=a99ab8677ef801d85ff7e2e0fa222528
    22. 22
      Aliaga, A. E.; Ahumada, H.; Sepúlveda, K.; Gomez-Jeria, J. S.; Garrido, C.; Weiss-López, B. E.; Campos-Vallette, M. M. SERS, molecular dynamics and molecular orbital studies of the MRKDV peptide on silver and membrane surfaces. J. Phys. Chem. C 2011, 115, 3982– 3989,  DOI: 10.1021/jp1107153
      22
      SERS, Molecular Dynamics and Molecular Orbital Studies of the MRKDV Peptide on Silver and Membrane Surfaces
      Aliaga, Alvaro E.; Ahumada, Hernan; Sepulveda, Karen; Gomez-Jeria, Juan S.; Garrido, Carlos; Weiss-Lopez, Boris E.; Campos-Vallette, Marcelo M.
      Journal of Physical Chemistry C (2011), 115 (10), 3982-3989CODEN: JPCCCK; ISSN:1932-7447. (American Chemical Society)
      The MRKDV peptide, structurally assocd. with an immunomodulatory protein, was studied using surface enhanced Raman scattering (SERS), mol. dynamics (MD) simulations, and quantum chem. calcns. The SERS spectrum of the MRKDV peptide adsorbed on the silver surface is dominated by signals coming from the guanidinium moiety of the arginine amino acid (R). Guanidinium is the intrinsic probe that drives the orientation of the peptide onto the silver surface. Mol. mechanics and extended Hueckel calcns. of a model of MRKDV interacting with a silver surface support the exptl. results. MD calcns. representing the evolution of the peptide toward a model membrane were also performed. The guanidinium moiety interacts with the phospholipid membrane surface. A hydrophobic C-terminal modification favors the peptide membrane affinity.
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    23. 23
      Thimes, R. L.; Santos, A. V. B.; Chen, R.; Kaur, G.; Jensen, L.; Jenkins, D. M.; Camden, J. P. Using Surface-Enhanced Raman Spectroscopy to Unravel the Wingtip-Dependent Orientation of N-Heterocyclic Carbenes on Gold Nanoparticles. J. Phys. Chem. Lett. 2023, 14, 4219– 4224,  DOI: 10.1021/acs.jpclett.3c00588
      23
      Using Surface-Enhanced Raman Spectroscopy to Unravel the Wingtip-Dependent Orientation of N-Heterocyclic Carbenes on Gold Nanoparticles
      Thimes, Rebekah L.; Santos, Alyssa V. B.; Chen, Ran; Kaur, Gurkiran; Jensen, Lasse; Jenkins, David M.; Camden, Jon P.
      Journal of Physical Chemistry Letters (2023), 14 (18), 4219-4224CODEN: JPCLCD; ISSN:1948-7185. (American Chemical Society)
      N-Heterocyclic carbenes (NHCs) are an attractive alternative to thiol ligands when forming self-assembled monolayers on noble-metal surfaces; however, relative to the well-studied thiol monolayers, comparatively little is known about the binding, orientation, and packing of NHC monolayers. Herein, we combine surface-enhanced Raman spectroscopy (SERS) and first-principles theory to investigate how the alkyl "wingtip" groups, i.e., those attached to the nitrogens of N-heterocyclic carbenes, affect the NHC orientation on gold nanoparticles. Consistent with previous literature, smaller wingtip groups lead to stable flat configurations; surprisingly, bulkier wingtips also have stable flat configurations likely due to the presence of an adatom. Comparison of exptl. SERS results with the theor. calcd. spectra for flat and vertical configurations shows that we are simultaneously detecting both NHC configurations. In addn. to providing information on the adsorbate geometry, this study highlights the extreme SERS enhancement of vibrational modes perpendicular to the surface.
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    24. 24
      Dutta, S.; Corni, S.; Brancolini, G. Atomistic simulations of functionalized nano-materials for biosensors applications. Int. J. Mol. Sci. 2022, 23, 1484,  DOI: 10.3390/ijms23031484
      24
      Atomistic Simulations of Functionalized Nano-Materials for Biosensors Applications
      Dutta, Sutapa; Corni, Stefano; Brancolini, Giorgia
      International Journal of Molecular Sciences (2022), 23 (3), 1484CODEN: IJMCFK; ISSN:1422-0067. (MDPI AG)
      A review. Nanoscale biosensors, a highly promising technique in clin. anal., can provide sensitive yet label-free detection of biomols. The spatial and chem. specificity of the surface coverage, the proper immobilization of the bioreceptor as well as the underlying interfacial phenomena are crucial elements for optimizing the performance of a biosensor. Due to exptl. limitations at the microscopic level, integrated cross-disciplinary approaches that combine in silico design with exptl. measurements have the potential to present a powerful new paradigm that tackles the issue of developing novel biosensors. In some cases, computational studies can be seen as alternative approaches to assess the microscopic working mechanisms of biosensors. Nonetheless, the complex architecture of a biosensor, assocd. with the collective contribution from "substrate-receptor-analyte" conjugate in a solvent, often requires extensive atomistic simulations and systems of prohibitive size which need to be addressed. In silico studies of functionalized surfaces also require ad hoc force field parameterization, as existing force fields for biomols. are usually unable to correctly describe the biomol./surface interface. Thus, the computational studies in this field are limited to date. In this review, we aim to introduce fundamental principles that govern the absorption of biomols. onto functionalized nanomaterials and to report state-of-the-art computational strategies to rationally design nanoscale biosensors. A detailed account of available in silico strategies used to drive and/or optimize the synthesis of functionalized nanomaterials for biosensing will be presented. The insights will not only stimulate the field to rationally design functionalized nanomaterials with improved biosensing performance but also foster research on the required functionalization to improve biomol.-surface complex formation as a whole.
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    25. 25
      Kästner, J. Umbrella sampling. Wiley Interdiscip. Rev. Comput. Mol. Sci. 2011, 1, 932– 942,  DOI: 10.1002/wcms.66
      There is no corresponding record for this reference.
    26. 26
      Baştuğ, T.; Chen, P.-C.; Patra, S. M.; Kuyucak, S. Potential of mean force calculations of ligand binding to ion channels from Jarzynski’s equality and umbrella sampling. J. Chem. Phys. 2008, 128, 04B614,  DOI: 10.1063/1.2904461
      There is no corresponding record for this reference.
    27. 27
      Bochicchio, D.; Panizon, E.; Ferrando, R.; Monticelli, L.; Rossi, G. Calculating the free energy of transfer of small solutes into a model lipid membrane: Comparison between metadynamics and umbrella sampling. J. Chem. Phys. 2015, 143, 10B612_1,  DOI: 10.1063/1.4932159
      There is no corresponding record for this reference.
    28. 28
      Noh, S. Y.; Notman, R. Comparison of umbrella sampling and steered molecular dynamics methods for computing free energy profiles of aromatic substrates through phospholipid bilayers. J. Chem. Phys. 2020, 153, 034115,  DOI: 10.1063/5.0016114
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      Comparison of umbrella sampling and steered molecular dynamics methods for computing free energy profiles of aromatic substrates through phospholipid bilayers
      Noh, Sang Young; Notman, Rebecca
      Journal of Chemical Physics (2020), 153 (3), 034115CODEN: JCPSA6; ISSN:0021-9606. (American Institute of Physics)
      Understanding the permeation of mols. through lipid membranes is fundamental for predicting the cellular uptake of solutes and drug delivery mechanisms. In mol. simulations, the usual approach is to compute the free energy (FE) profile of a mol. across a model lipid bilayer, which can then be used to est. the permeability of the mol. Umbrella Sampling (US), which involves carrying out a series of biased simulations along a defined reaction coordinate (usually the bilayer normal direction), is a popular method for the computation of such FE profiles. However, US can be challenging to implement because the results are dependent on the strength of the biasing potential and the spacing of windows along the reaction coordinate, which, in practice, are usually optimized by an inefficient trial and error approach. The Steered Mol. Dynamics implementation of the Jarzynski Equality (JE-SMD) has been identified as an alternative to equil. sampling methods for measuring the FE change across a reaction coordinate. In the JE-SMD approach, equil. FE values are evaluated from the av. of rapid non-equil. trajectories, thus avoiding the practical issues that come with US. Here, the authors use three different corrections of the JE-SMD method to calc. the FE change for the translocation of two arom. substrates, phenylalanine and toluene, across a lipid bilayer and compare the accuracy and computational efficiency of these approaches to the results obtained using US. The authors show evidence that when computing the free energy profile, the JE-SMD approach suffers from insufficient sampling convergence of the bilayer environment and is dependent on the characteristic of the arom. substrate itself. Despite its drawbacks, US remains the more viable approach of the two for computing the FE profile. (c) 2020 American Institute of Physics.
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    29. 29
      Wei, Q.; Zhao, W.; Yang, Y.; Cui, B.; Xu, Z.; Yang, X. Method evaluations for adsorption free energy calculations at the solid/water interface through metadynamics, umbrella sampling, and jarzynski’s equality. ChemPhysChem 2018, 19, 690– 702,  DOI: 10.1002/cphc.201701241
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      Method Evaluations for Adsorption Free Energy Calculations at the Solid/Water Interface through Metadynamics, Umbrella Sampling, and Jarzynski's Equality
      Wei, Qichao; Zhao, Weilong; Yang, Yang; Cui, Beiliang; Xu, Zhijun; Yang, Xiaoning
      ChemPhysChem (2018), 19 (6), 690-702CODEN: CPCHFT; ISSN:1439-4235. (Wiley-VCH Verlag GmbH & Co. KGaA)
      Considerable interest in characterizing protein/peptide-surface interactions has prompted extensive computational studies on calcns. of adsorption free energy. However, in many cases, each individual study has focused on the application of free energy calcns. to a specific system; therefore, it is difficult to combine the results into a general picture for choosing an appropriate strategy for the system of interest. Herein, three well-established computational algorithms are systemically compared and evaluated to compute the adsorption free energy of small mols. on two representative surfaces. The results clearly demonstrate that the characteristics of studied interfacial systems have crucial effects on the accuracy and efficiency of the adsorption free energy calcns. For the hydrophobic surface, steered mol. dynamics exhibits the highest efficiency, which appears to be a favorable method of choice for enhanced sampling simulations. However, for the charged surface, only the umbrella sampling method has the ability to accurately explore the adsorption free energy surface. The affinity of the water layer to the surface significantly affects the performance of free energy calcn. methods, esp. at the region close to the surface. Therefore, a general principle of how to discriminate between methodol. and sampling issues based on the interfacial characteristics of the system under investigation is proposed.
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    30. 30
      Heinz, H.; Vaia, R. A.; Farmer, B. L.; Naik, R. R. Accurate simulation of surfaces and interfaces of face-centered cubic metals using 12–6 and 9–6 Lennard-Jones potentials. J. Phys. Chem. C 2008, 112, 17281– 17290,  DOI: 10.1021/jp801931d
      30
      Accurate Simulation of Surfaces and Interfaces of Face-Centered Cubic Metals Using 12-6 and 9-6 Lennard-Jones Potentials
      Heinz, Hendrik; Vaia, R. A.; Farmer, B. L.; Naik, R. R.
      Journal of Physical Chemistry C (2008), 112 (44), 17281-17290CODEN: JPCCCK; ISSN:1932-7447. (American Chemical Society)
      Mol. dynamics and Monte Carlo simulations often rely on Lennard-Jones (LJ) potentials for nonbond interactions. The authors present 12-6 and 9-6 LJ parameters for several fcc. metals (Ag, Al, Au, Cu, Ni, Pb, Pd, Pt) which reproduce densities, surface tensions, interface properties with H2O and (bio)org. mols., as well as mech. properties in quant. (<0.1%) to good qual. (25%) agreement with expt. under ambient conditions. Deviations assocd. with earlier LJ models were reduced by 1 order of magnitude due to the precise fit of the new models to densities and surface tensions under std. conditions, which also leads to significantly improved results for surface energy anisotropies, interface tensions, and mech. properties. The performance is comparable to tight-binding and embedded atom models at up to a million times lower computational cost. The models extend classical simulation methods to metals and a variety of interfaces with biopolymers, surfactants, and other nanostructured materials through compatibility with widely used force fields, including AMBER, CHARMM, COMPASS, CVFF, OPLS-AA, and PCFF. Limitations include the neglect of electronic structure effects and the restriction to noncovalent interactions with the metals.
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    31. 31
      Heinz, H.; Lin, T.-J.; Kishore Mishra, R.; Emami, F. S. Thermodynamically consistent force fields for the assembly of inorganic, organic, and biological nanostructures: the INTERFACE force field. Langmuir 2013, 29, 1754– 1765,  DOI: 10.1021/la3038846
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      Thermodynamically Consistent Force Fields for the Assembly of Inorganic, Organic, and Biological Nanostructures: The INTERFACE Force Field
      Heinz, Hendrik; Lin, Tzu-Jen; Kishore Mishra, Ratan; Emami, Fateme S.
      Langmuir (2013), 29 (6), 1754-1765CODEN: LANGD5; ISSN:0743-7463. (American Chemical Society)
      A review. The complexity of the mol. recognition and assembly of biotic-abiotic interfaces on a scale of 1 to 1000 nm can be understood more effectively using simulation tools along with lab. instrumentation. We discuss the current capabilities and limitations of atomistic force fields and explain a strategy to obtain dependable parameters for inorg. compds. that has been developed and tested over the past decade. Parameter developments include several silicates, aluminates, metals, oxides, sulfates, and apatites that are summarized in what we call the INTERFACE force field. The INTERFACE force field operates as an extension of common harmonic force fields (PCFF, COMPASS, CHARMM, AMBER, GROMACS, and OPLS-AA) by employing the same functional form and combination rules to enable simulations of inorg.-org. and inorg.-biomol. interfaces. The parametrization builds on an in-depth understanding of phys.-chem. properties on the at. scale to assign each parameter, esp. at. charges and van der Waals consts., as well as on the validation of macroscale phys.-chem. properties for each compd. in comparison to measurements. The approach eliminates large discrepancies between computed and measured bulk and surface properties of up to 2 orders of magnitude using other parametrization protocols and increases the transferability of the parameters by introducing thermodn. consistency. As a result, a wide range of properties can be computed in quant. agreement with expt., including densities, surface energies, solid-water interface tensions, anisotropies of interfacial energies of different crystal facets, adsorption energies of biomols., and thermal and mech. properties. Applications include insight into the assembly of inorg.-org. multiphase materials, the recognition of inorg. facets by biomols., growth and shape preferences of nanocrystals and nanoparticles, as well as thermal transitions and nanomechanics. Limitations and opportunities for further development are also described.
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    32. 32
      Cornell, W. D.; Cieplak, P.; Bayly, C. I.; Gould, I. R.; Merz, K. M.; Ferguson, D. M.; Spellmeyer, D. C.; Fox, T.; Caldwell, J. W.; Kollman, P. A. A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. J. Am. Chem. Soc. 1995, 117, 5179– 5197,  DOI: 10.1021/ja00124a002
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      A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules
      Cornell, Wendy D.; Cieplak, Piotr; Bayly, Christopher I.; Gould, Ian R.; Merz, Kenneth M., Jr.; Ferguson, David M.; Spellmeyer, David C.; Fox, Thomas; Caldwell, James W.; Kollman, Peter A.
      Journal of the American Chemical Society (1995), 117 (19), 5179-97CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)
      The authors present the derivation of a new mol. mech. force field for simulating the structures, conformational energies, and interaction energies of proteins, nucleic acids, and many related org. mols. in condensed phases. This effective two-body force field is the successor to the Weiner et al. force field and was developed with some of the same philosophies, such as the use of a simple diagonal potential function and electrostatic potential fit atom centered charges. The need for a 10-12 function for representing hydrogen bonds is no longer necessary due to the improved performance of the new charge model and new van der Waals parameters. These new charges are detd. using a 6-31G* basis set and restrained electrostatic potential (RESP) fitting and have been shown to reproduce interaction energies, free energies of solvation, and conformational energies of simple small mols. to a good degree of accuracy. Furthermore, the new RESP charges exhibit less variability as a function of the mol. conformation used in the charge detn. The new van der Waals parameters have been derived from liq. simulations and include hydrogen parameters which take into account the effects of any geminal electroneg. atoms. The bonded parameters developed by Weiner et al. were modified as necessary to reproduce exptl. vibrational frequencies and structures. Most of the simple dihedral parameters have been retained from Weiner et al., but a complex set of .vphi. and ψ parameters which do a good job of reproducing the energies of the low-energy conformations of glycyl and alanyl dipeptides was developed for the peptide backbone.
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    33. 33
      MacKerell, A. D.; Bashford, D.; Bellott, M.; Dunbrack, R. L.; Evanseck, J. D.; Field, M. J.; Fischer, S.; Gao, J.; Guo, H.; Ha, S. All-atom empirical potential for molecular modeling and dynamics studies of proteins. J. Phys. Chem. B 1998, 102, 3586– 3616,  DOI: 10.1021/jp973084f
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      All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins
      MacKerell, A. D., Jr.; Bashford, D.; Bellott, M.; Dunbrack, R. L.; Evanseck, J. D.; Field, M. J.; Fischer, S.; Gao, J.; Guo, H.; Ha, S.; Joseph-McCarthy, D.; Kuchnir, L.; Kuczera, K.; Lau, F. T. K.; Mattos, C.; Michnick, S.; Ngo, T.; Nguyen, D. T.; Prodhom, B.; Reiher, W. E., III; Roux, B.; Schlenkrich, M.; Smith, J. C.; Stote, R.; Straub, J.; Watanabe, M.; Wiorkiewicz-Kuczera, J.; Yin, D.; Karplus, M.
      Journal of Physical Chemistry B (1998), 102 (18), 3586-3616CODEN: JPCBFK; ISSN:1089-5647. (American Chemical Society)
      New protein parameters are reported for the all-atom empirical energy function in the CHARMM program. The parameter evaluation was based on a self-consistent approach designed to achieve a balance between the internal (bonding) and interaction (nonbonding) terms of the force field and among the solvent-solvent, solvent-solute, and solute-solute interactions. Optimization of the internal parameters used exptl. gas-phase geometries, vibrational spectra, and torsional energy surfaces supplemented with ab initio results. The peptide backbone bonding parameters were optimized with respect to data for N-methylacetamide and the alanine dipeptide. The interaction parameters, particularly the at. charges, were detd. by fitting ab initio interaction energies and geometries of complexes between water and model compds. that represented the backbone and the various side chains. In addn., dipole moments, exptl. heats and free energies of vaporization, solvation and sublimation, mol. vols., and crystal pressures and structures were used in the optimization. The resulting protein parameters were tested by applying them to noncyclic tripeptide crystals, cyclic peptide crystals, and the proteins crambin, bovine pancreatic trypsin inhibitor, and carbonmonoxy myoglobin in vacuo and in a crystal. A detailed anal. of the relationship between the alanine dipeptide potential energy surface and calcd. protein φ, χ angles was made and used in optimizing the peptide group torsional parameters. The results demonstrate that use of ab initio structural and energetic data by themselves are not sufficient to obtain an adequate backbone representation for peptides and proteins in soln. and in crystals. Extensive comparisons between mol. dynamics simulation and exptl. data for polypeptides and proteins were performed for both structural and dynamic properties. Calcd. data from energy minimization and dynamics simulations for crystals demonstrate that the latter are needed to obtain meaningful comparisons with exptl. crystal structures. The presented parameters, in combination with the previously published CHARMM all-atom parameters for nucleic acids and lipids, provide a consistent set for condensed-phase simulations of a wide variety of mols. of biol. interest.
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    34. 34
      Kaminski, G. A.; Friesner, R. A.; Tirado-Rives, J.; Jorgensen, W. L. Evaluation and reparametrization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides. J. Phys. Chem. B 2001, 105, 6474– 6487,  DOI: 10.1021/jp003919d
      34
      Evaluation and Reparametrization of the OPLS-AA Force Field for Proteins via Comparison with Accurate Quantum Chemical Calculations on Peptides
      Kaminski, George A.; Friesner, Richard A.; Tirado-Rives, Julian; Jorgensen, William L.
      Journal of Physical Chemistry B (2001), 105 (28), 6474-6487CODEN: JPCBFK; ISSN:1089-5647. (American Chemical Society)
      We present results of improving the OPLS-AA force field for peptides by means of refitting the key Fourier torsional coeffs. The fitting technique combines using accurate ab initio data as the target, choosing an efficient fitting subspace of the whole potential-energy surface, and detg. wts. for each of the fitting points based on magnitudes of the potential-energy gradient. The av. energy RMS deviation from the LMP2/cc-pVTZ(-f)//HF/6-31G** data is reduced by ∼40% from 0.81 to 0.47 kcal/mol as a result of the fitting for the electrostatically uncharged dipeptides. Transferability of the parameters is demonstrated by using the same alanine dipeptide-fitted backbone torsional parameters for all of the other dipeptides (with the appropriate side-chain refitting) and the alanine tetrapeptide. Parameters of nonbonded interactions have also been refitted for the sulfur-contg. dipeptides (cysteine and methionine), and the validity of the new Coulombic charges and the van der Waals σ's and ε's is proved through reproducing gas-phase energies of complex formation heats of vaporization and densities of pure model liqs. Moreover, a novel approach to fitting torsional parameters for electrostatically charged mol. systems has been presented and successfully tested on five dipeptides with charged side chains.
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    35. 35
      Dasetty, S.; Meza-Morales, P. J.; Getman, R. B.; Sarupria, S. Simulations of interfacial processes: recent advances in force field development. Curr. Opin. Chem. Eng. 2019, 23, 138– 145,  DOI: 10.1016/j.coche.2019.04.003
      There is no corresponding record for this reference.
    36. 36
      Geada, I. L.; Ramezani-Dakhel, H.; Jamil, T.; Sulpizi, M.; Heinz, H. Insight into induced charges at metal surfaces and biointerfaces using a polarizable Lennard–Jones potential. Nat. Commun. 2018, 9, 716,  DOI: 10.1038/s41467-018-03137-8
      36
      Insight into induced charges at metal surfaces and biointerfaces using a polarizable Lennard-Jones potential
      Geada Isidro Lorenzo; Sulpizi Marialore; Ramezani-Dakhel Hadi; Heinz Hendrik; Ramezani-Dakhel Hadi; Ramezani-Dakhel Hadi; Jamil Tariq; Heinz Hendrik
      Nature communications (2018), 9 (1), 716 ISSN:.
      Metallic nanostructures have become popular for applications in therapeutics, catalysts, imaging, and gene delivery. Molecular dynamics simulations are gaining influence to predict nanostructure assembly and performance; however, instantaneous polarization effects due to induced charges in the free electron gas are not routinely included. Here we present a simple, compatible, and accurate polarizable potential for gold that consists of a Lennard-Jones potential and a harmonically coupled core-shell charge pair for every metal atom. The model reproduces the classical image potential of adsorbed ions as well as surface, bulk, and aqueous interfacial properties in excellent agreement with experiment. Induced charges affect the adsorption of ions onto gold surfaces in the gas phase at a strength similar to chemical bonds while ions and charged peptides in solution are influenced at a strength similar to intermolecular bonds. The proposed model can be applied to complex gold interfaces, electrode processes, and extended to other metals.
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    37. 37
      Iori, F.; Di Felice, R.; Molinari, E.; Corni, S. GolP: An atomistic force-field to describe the interaction of proteins with Au (111) surfaces in water. J. Comput. Chem. 2009, 30, 1465– 1476,  DOI: 10.1002/jcc.21165
      37
      GolP: An atomistic force-field to describe the interaction of proteins with Au(111) surfaces in water
      Iori, F.; Di Felice, R.; Molinari, E.; Corni, S.
      Journal of Computational Chemistry (2009), 30 (9), 1465-1476CODEN: JCCHDD; ISSN:0192-8651. (John Wiley & Sons, Inc.)
      A classical atomistic force field to describe the interaction of proteins with gold (111) surfaces in explicit water has been devised. The force field is specifically designed to be easily usable in most common bio-oriented mol. dynamics codes, such as GROMACS and NAMD. Its parametrization is based on quantum mech. (d. functional theory [DFT] and second order Moeller-Plesset perturbation theory [MP2]) calcns. and exptl. data on the adsorption of small mols. on gold. In particular, a systematic DFT survey of the interaction between Au(111) and the natural amino acid side chains has been performed to single out chemisorption effects. Van der Waals parameters have been instead fitted to exptl. desorption energy data of linear alkanes and were also studied via MP2 calcns. Finally, gold polarization (image charge effects) is taken into account by a recently proposed procedure (Iori, F.; Corni, S. J., 2008). Preliminary validation results of GolP on an independent test set of small mols. show the good performances of the force field. © 2008 Wiley Periodicals, Inc. J Comput Chem 2009.
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    38. 38
      Wright, L. B.; Rodger, P. M.; Corni, S.; Walsh, T. R. GolP-CHARMM: first-principles based force fields for the interaction of proteins with Au (111) and Au (100). J. Chem. Theory Comput. 2013, 9, 1616– 1630,  DOI: 10.1021/ct301018m
      38
      GolP-CHARMM: First-Principles Based Force Fields for the Interaction of Proteins with Au(111) and Au(100)
      Wright, Louise B.; Rodger, P. Mark; Corni, Stefano; Walsh, Tiffany R.
      Journal of Chemical Theory and Computation (2013), 9 (3), 1616-1630CODEN: JCTCCE; ISSN:1549-9618. (American Chemical Society)
      Computational simulation of peptide adsorption at the aq. Au interface is key to advancing the development of many applications based on Au nanoparticles, ranging from nanomedical devices to smart biomimetic materials. Here, the authors present a force field, GolP-CHARMM, designed to capture peptide adsorption at both the aq. Au(111) and Au(100) interfaces. The force field, compatible with the bio-org. force field CHARMM, is parametrized using a combination of exptl. and 1st-principles data. Like its predecessor, GolP (Iori, F.; et al. J. Comput. Chem.2009, 30, 1465), this force field contains terms to describe the dynamic polarization of Au atoms, chemisorbing species, and the interaction between sp2 hybridized C atoms and Au. A systematic study of small mol. adsorption at both surfaces using the vdW-DF functional (Dion, M.; et al. Phys. Rev. Lett.2004, 92, 246401-1. Thonhauser, T.; et al. Phys. Rev. B2007, 76, 125112) is carried out to fit and test force field parameters and also, for the 1st time, gives unique insights into facet selectivity of Au binding in vacuo. Energetic and spatial trends obsd. in DFT calcns. are reproduced by the force field under the same conditions. Finally, the authors use the new force field to calc. adsorption energies, under aq. conditions, for a representative set of amino acids. These data agree with exptl. findings.
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    39. 39
      Iori, F.; Corni, S. Including image charge effects in the molecular dynamics simulations of molecules on metal surfaces. J. Comput. Chem. 2008, 29, 1656– 1666,  DOI: 10.1002/jcc.20928
      39
      Including image charge effects in the molecular dynamics simulations of molecules on metal surfaces
      Iori, F.; Corni, S.
      Journal of Computational Chemistry (2008), 29 (10), 1656-1666CODEN: JCCHDD; ISSN:0192-8651. (John Wiley & Sons, Inc.)
      Combinatorial bio-techniques have demonstrated that proteins can be good and even selective binders for several inorg. surfaces, including metals. However, the understanding of the basic phys. mechanisms that govern such interactions did not keep up with the success in these expts. The comprehension of such mechanisms would greatly benefit from the computational investigation of the problem. Because of the complexity of the system, classical mol. dynamics simulations based on an atomistic description appear to be the best compromise between reliability and feasibility. For proteins interacting with metal surfaces, however, methodol. improvements with respect to std. Mol. Dynamics (MD) of proteins are needed, since the polarization of the metal induced by the protein (and the surrounding water) is not generally negligible. In this article, the authors present a simple approach to introduce metal polarization effects (often termed image effects) in MD simulations by exploiting std. features of bio-oriented MD codes such as the widely used GROMACS and NAMD. Tests to show the reliability of the proposed methods are presented, and the results for a model application showing the importance of image effects are also discussed.
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    40. 40
      Wright, L. B.; Rodger, P. M.; Walsh, T. R.; Corni, S. First-principles-based force field for the interaction of proteins with Au (100)(5× 1): an extension of GolP-CHARMM. J. Phys. Chem. C 2013, 117, 24292– 24306,  DOI: 10.1021/jp4061329
      40
      First-Principles-Based Force Field for the Interaction of Proteins with Au(100)(5 × 1): An Extension of GolP-CHARMM
      Wright, Louise B.; Rodger, P. Mark; Walsh, Tiffany R.; Corni, Stefano
      Journal of Physical Chemistry C (2013), 117 (46), 24292-24306CODEN: JPCCCK; ISSN:1932-7447. (American Chemical Society)
      Noncovalent recognition between peptides and inorg. materials is an established phenomenon. Key to exploiting these interactions in a wide range of materials self-assembly applications would be to harness the facet-selective control of peptide binding onto these materials. Fundamental understanding of what drives facet-selectivity in peptide binding is developing, but as yet is not sufficient to enable design of predictable facet-specific sequences. Computational simulation of the aq. peptide-gold interface, commonly used to understand the mechanisms driving adsorption at an at. level, has thus far neglected the role that surface reconstruction might play in facet specificity. Here the polarizable GolP-CHARMM suite of force fields is extended to include the reconstructed Au(100) surface. The force field, compatible with the bio-org. force field CHARMM, is parametrized using first-principles data. Our extended force field is tailored to reproduce the heterogeneity of weak chemisorbing N and S species to specific locations in the Au(100)-(5 × 1) surface identified from the first-principles calcns. We apply our new model to predict and compare the three-dimensional structure of liq. water at Au(111), Au(100)(1 × 1), and Au(100)(5 × 1) interfaces. Using mol. dynamics simulations, we predict an increased likelihood for water-mediated peptide adsorption at the aq.-Au(100)(1 × 1) interface compared with the Au(100)(5 × 1) interface. Therefore, our findings suggest that peptide binding can discriminate between the native and reconstructed Au(100) interfaces and that the role of reconstruction on binding at the Au(100) interface should not be neglected.
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    41. 41
      Wright, L. B.; Rodger, P. M.; Corni, S.; Walsh, T. R. GolP-CHARMM: First-principles based force fields for the interaction of proteins with Au(111) and Au(100). J. Chem. Theory Comput. 2013, 9, 1616– 1630,  DOI: 10.1021/ct301018m
      41
      GolP-CHARMM: First-Principles Based Force Fields for the Interaction of Proteins with Au(111) and Au(100)
      Wright, Louise B.; Rodger, P. Mark; Corni, Stefano; Walsh, Tiffany R.
      Journal of Chemical Theory and Computation (2013), 9 (3), 1616-1630CODEN: JCTCCE; ISSN:1549-9618. (American Chemical Society)
      Computational simulation of peptide adsorption at the aq. Au interface is key to advancing the development of many applications based on Au nanoparticles, ranging from nanomedical devices to smart biomimetic materials. Here, the authors present a force field, GolP-CHARMM, designed to capture peptide adsorption at both the aq. Au(111) and Au(100) interfaces. The force field, compatible with the bio-org. force field CHARMM, is parametrized using a combination of exptl. and 1st-principles data. Like its predecessor, GolP (Iori, F.; et al. J. Comput. Chem.2009, 30, 1465), this force field contains terms to describe the dynamic polarization of Au atoms, chemisorbing species, and the interaction between sp2 hybridized C atoms and Au. A systematic study of small mol. adsorption at both surfaces using the vdW-DF functional (Dion, M.; et al. Phys. Rev. Lett.2004, 92, 246401-1. Thonhauser, T.; et al. Phys. Rev. B2007, 76, 125112) is carried out to fit and test force field parameters and also, for the 1st time, gives unique insights into facet selectivity of Au binding in vacuo. Energetic and spatial trends obsd. in DFT calcns. are reproduced by the force field under the same conditions. Finally, the authors use the new force field to calc. adsorption energies, under aq. conditions, for a representative set of amino acids. These data agree with exptl. findings.
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      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3sXhsFGrt7k%253D&md5=e5b7f6c2b8187e506e07e640c9cc2e8d
    42. 42
      Elechiguerra, J. L.; Reyes-Gasga, J.; Yacaman, M. J. The role of twinning in shape evolution of anisotropic noble metal nanostructures. J. Mater. Chem. 2006, 16, 3906– 3919,  DOI: 10.1039/b607128g
      42
      The role of twinning in shape evolution of anisotropic noble metal nanostructures
      Elechiguerra, Jose Luis; Reyes-Gasga, Jose; Yacaman, Miguel Jose
      Journal of Materials Chemistry (2006), 16 (40), 3906-3919CODEN: JMACEP; ISSN:0959-9428. (Royal Society of Chemistry)
      Nanotechnol. provides the ability to engineer the properties of materials by controlling their size and shape. Among the most interesting nanostructures are anisotropic noble metal nanocrystals such as nanorods and nanowires. Nevertheless, the prodn. of such crystals in a controlled fashion remains as a challenging task, and many available colloidal techniques produce a mixt. of morphologies. In cases where high yields of a particular anisotropic structure were produced, the growth mechanism was primarily explained in terms of the presence of surfactants or capping agents that regulate the growth of the crystal in a particular direction. However, the growth mechanism should also consider nucleation and kinetics, and not only thermodn. or phys. restrictions imposed by the surface stabilizing agent. In this work, several examples are presented of anisotropic noble metal nanocrystals obtained by different methods. Finally, the important role of twinning in detg. the habit of the final morphol. is discussed.
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    43. 43
      Hjorth Larsen, A.; Jørgen Mortensen, J.; Blomqvist, J.; Castelli, I. E.; Christensen, R.; Dułak, M.; Friis, J.; Groves, M. N.; Hammer, B.; Hargus, C. The atomic simulation environment─a Python library for working with atoms. J. Phys.: Condens. Matter 2017, 29, 273002,  DOI: 10.1088/1361-648x/aa680e
      43
      The atomic simulation environment-a Python library for working with atoms
      Hjorth Larsen Ask; Jorgen Mortensen Jens; Blomqvist Jakob; Castelli Ivano E; Christensen Rune; Dulak Marcin; Friis Jesper; Groves Michael N; Hammer Bjork; Hargus Cory; Hermes Eric D; Jennings Paul C; Bjerre Jensen Peter; Kermode James; Kitchin John R; Leonhard Kolsbjerg Esben; Kubal Joseph; Kaasbjerg Kristen; Lysgaard Steen; Bergmann Maronsson Jon; Maxson Tristan; Olsen Thomas; Pastewka Lars; Peterson Andrew; Rostgaard Carsten; Schiotz Jakob; Schutt Ole; Strange Mikkel; Thygesen Kristian S; Vegge Tejs; Vilhelmsen Lasse; Walter Michael; Zeng Zhenhua; Jacobsen Karsten W
      Journal of physics. Condensed matter : an Institute of Physics journal (2017), 29 (27), 273002 ISSN:.
      The atomic simulation environment (ASE) is a software package written in the Python programming language with the aim of setting up, steering, and analyzing atomistic simulations. In ASE, tasks are fully scripted in Python. The powerful syntax of Python combined with the NumPy array library make it possible to perform very complex simulation tasks. For example, a sequence of calculations may be performed with the use of a simple 'for-loop' construction. Calculations of energy, forces, stresses and other quantities are performed through interfaces to many external electronic structure codes or force fields using a uniform interface. On top of this calculator interface, ASE provides modules for performing many standard simulation tasks such as structure optimization, molecular dynamics, handling of constraints and performing nudged elastic band calculations.
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    44. 44
      Dodda, L. S.; Cabeza de Vaca, I.; Tirado-Rives, J.; Jorgensen, W. L. LigParGen web server: an automatic OPLS-AA parameter generator for organic ligands. Nucleic Acids Res. 2017, 45, W331– W336,  DOI: 10.1093/nar/gkx312
      44
      LigParGen web server: an automatic OPLS-AA parameter generator for organic ligands
      Dodda, Leela S.; Cabeza de Vaca, Israel; Tirado-Rives, Julian; Jorgensen, William L.
      Nucleic Acids Research (2017), 45 (W1), W331-W336CODEN: NARHAD; ISSN:1362-4962. (Oxford University Press)
      The accurate calcn. of protein/nucleic acid- ligand interactions or condensed phase properties by force field-based methods require a precise description of the energetics of intermol. interactions. Despite the progress made in force fields, small mol. parameterization remains an open problem due to the magnitude of the chem. space; the most crit. issue is the estn. of a balanced set of at. charges with the ability to reproduce exptl. properties. The LigParGen web server provides an intuitive interface for generating OPLS-AA/1.14*CM1A(-LBCC) force field parameters for org. ligands, in the formats of commonly used mol. dynamics and Monte Carlo simulation packages. This server has high value for researchers interested in studying any phenomena based on intermol. interactions with ligands via mol. mechanics simulations.
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    45. 45
      Vanommeslaeghe, K.; MacKerell, A. D. Automation of the CHARMM General Force Field (CGenFF) I: bond perception and atom typing. J. Chem. Inf. Model. 2012, 52, 3144– 3154,  DOI: 10.1021/ci300363c
      45
      Automation of the CHARMM General Force Field (CGenFF) I: Bond Perception and Atom Typing
      Vanommeslaeghe, K.; MacKerell, A. D.
      Journal of Chemical Information and Modeling (2012), 52 (12), 3144-3154CODEN: JCISD8; ISSN:1549-9596. (American Chemical Society)
      Mol. mechanics force fields are widely used in computer-aided drug design for the study of drug-like mols. alone or interacting with biol. systems. In simulations involving biol. macromols., the biol. part is typically represented by a specialized biomol. force field, while the drug is represented by a matching general (org.) force field. In order to apply these general force fields to an arbitrary drug-like mol., functionality for assignment of atom types, parameters, and charges is required. In the present article, which is part I of a series of two, we present the algorithms for bond perception and atom typing for the CHARMM General Force Field (CGenFF). The CGenFF atom typer first assocs. attributes to the atoms and bonds in a mol., such as valence, bond order, and ring membership among others. Of note are a no. of features that are specifically required for CGenFF. This information is then used by the atom typing routine to assign CGenFF atom types based on a programmable decision tree. This allows for straight-forward implementation of CGenFF's complicated atom typing rules and for equally straight-forward updating of the atom typing scheme as the force field grows. The presented atom typer was validated by assigning correct atom types on 477 model compds. including in the training set as well as 126 test-set mols. that were constructed to specifically verify its different components. The program may be utilized via an online implementation at https://www.paramchem.org/.
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    46. 46
      Vanommeslaeghe, K.; Raman, E. P.; MacKerell, A. D. Automation of the CHARMM General Force Field (CGenFF) II: assignment of bonded parameters and partial atomic charges. J. Chem. Inf. Model. 2012, 52, 3155– 3168,  DOI: 10.1021/ci3003649
      46
      Automation of the CHARMM General Force Field (CGenFF) II: Assignment of Bonded Parameters and Partial Atomic Charges
      Vanommeslaeghe, K.; Raman, E. Prabhu; MacKerell, A. D.
      Journal of Chemical Information and Modeling (2012), 52 (12), 3155-3168CODEN: JCISD8; ISSN:1549-9596. (American Chemical Society)
      Mol. mechanics force fields are widely used in computer-aided drug design for the study of drug candidates interacting with biol. systems. In these simulations, the biol. part is typically represented by a specialized biomol. force field, while the drug is represented by a matching general (org.) force field. In order to apply these general force fields to an arbitrary drug-like mol., functionality for assignment of atom types, parameters, and partial at. charges is required. In the present article, algorithms for the assignment of parameters and charges for the CHARMM General Force Field (CGenFF) are presented. These algorithms rely on the existing parameters and charges that were detd. as part of the parametrization of the force field. Bonded parameters are assigned based on the similarity between the atom types that define said parameters, while charges are detd. using an extended bond-charge increment scheme. Charge increments were optimized to reproduce the charges on model compds. that were part of the parametrization of the force field. Case studies are presented to clarify the functioning of the algorithms and the significance of their output data.
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    47. 47
      Berendsen, H.; Grigera, J.; Straatsma, T. The missing term in effective pair potentials. J. Phys. Chem. 1987, 91, 6269– 6271,  DOI: 10.1021/j100308a038
      47
      The missing term in effective pair potentials
      Berendsen, H. J. C.; Grigera, J. R.; Straatsma, T. P.
      Journal of Physical Chemistry (1987), 91 (24), 6269-71CODEN: JPCHAX; ISSN:0022-3654.
      Effective pair potentials used for simulations of polar liqs. include the av. effects of polarization. Such potentials are generally adjusted to produce the exptl. heat of vaporization. It has not been recognized before that the self-energy term inherent in any polarizable model should be included in effective pair potentials as well. Inclusion of the self-energy correction with a consequent reparametrization of the simple point charge model of water yields an improvement of the effective pair potential for water, as exemplified by d., radial distribution functions, and diffusion const.
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      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaL2sXmt1els7w%253D&md5=6668667f6252092fc001ae8d422ebb94
    48. 48
      Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D.; Impey, R. W.; Klein, M. L. Comparison of simple potential functions for simulating liquid water. J. Chem. Phys. 1983, 79, 926– 935,  DOI: 10.1063/1.445869
      48
      Comparison of simple potential functions for simulating liquid water
      Jorgensen, William L.; Chandrasekhar, Jayaraman; Madura, Jeffry D.; Impey, Roger W.; Klein, Michael L.
      Journal of Chemical Physics (1983), 79 (2), 926-35CODEN: JCPSA6; ISSN:0021-9606.
      Classical Monte Carlo simulations were carried out for liq. H2O in the NPT ensemble at 25° and 1 atm using 6 of the simpler intermol. potential functions for the dimer. Comparisons were made with exptl. thermodn. and structural data including the neutron diffraction results of Thiessen and Narten (1982). The computed densities and potential energies agree with expt. except for the original Bernal-Fowler model, which yields an 18% overest. of the d. and poor structural results. The discrepancy may be due to the correction terms needed in processing the neutron data or to an effect uniformly neglected in the computations. Comparisons were made for the self-diffusion coeffs. obtained from mol. dynamics simulations.
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    49. 49
      Abraham, M. J.; Murtola, T.; Schulz, R.; Páll, S.; Smith, J. C.; Hess, B.; Lindahl, E. GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX 2015, 1–2, 19– 25,  DOI: 10.1016/j.softx.2015.06.001
      There is no corresponding record for this reference.
    50. 50
      Nosé, S.; Klein, M. Constant pressure molecular dynamics for molecular systems. Mol. Phys. 1983, 50, 1055– 1076,  DOI: 10.1080/00268978300102851
      50
      Constant pressure molecular dynamics for molecular systems
      Nose, Shuichi; Klein, M. L.
      Molecular Physics (1983), 50 (5), 1055-76CODEN: MOPHAM; ISSN:0026-8976.
      Tech. aspects are discussed of the const. pressure mol. dynamics method proposed by H. C. Andersen (1980) and extended by M. Parrinello and A Rahman (1980) to allow changes in the shape of the mol. dynamics cell. The new mol. dynamics method is extended to treat mol. systems and to include long range charge-charge interactions. Results on the conservation laws, the frequency of oscillation of the mol. dynamics cell, and the equations which constrain the shape of the mol. dynamics cell are also given. An addnl. constraint is introduced to stop the superfluous mol. dynamics cell rotation which would otherwise complicate the anal. of crystal structures. The method is illustrated by examg. the behavior of solid N at high pressure.
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      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaL2cXhvVSgtrc%253D&md5=c598220a548834e0237637246735a3b9
    51. 51
      Hess, B.; Bekker, H.; Berendsen, H. J.; Fraaije, J. G. LINCS: a linear constraint solver for molecular simulations. J. Comput. Chem. 1997, 18, 1463– 1472,  DOI: 10.1002/(SICI)1096-987X(199709)18:12<1463::AID-JCC4>3.0.CO;2-H
      51
      LINCS: a linear constraint solver for molecular simulations
      Hess, Berk; Bekker, Henk; Berendsen, Herman J. C.; Fraaije, Johannes G. E. M.
      Journal of Computational Chemistry (1997), 18 (12), 1463-1472CODEN: JCCHDD; ISSN:0192-8651. (Wiley)
      We present a new LINear Constraint Solver (LINCS) for mol. simulations with bond constraints using the enzyme lysozyme and a 32-residue peptide as test systems. The algorithm is inherently stable, as the constraints themselves are reset instead of derivs. of the constraints, thereby eliminating drift. Although the derivation of the algorithm is presented in terms of matrixes, no matrix matrix multiplications are needed and only the nonzero matrix elements have to be stored, making the method useful for very large mols. At the same accuracy, the LINCS algorithm is 3-4 times faster than the SHAKE algorithm. Parallelization of the algorithm is straightforward.
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    52. 52
      Darden, T.; York, D.; Pedersen, L. Particle mesh Ewald: An N log (N) method for Ewald sums in large systems. J. Chem. Phys. 1993, 98, 10089– 10092,  DOI: 10.1063/1.464397
      52
      Particle mesh Ewald: an N·log(N) method for Ewald sums in large systems
      Darden, Tom; York, Darrin; Pedersen, Lee
      Journal of Chemical Physics (1993), 98 (12), 10089-92CODEN: JCPSA6; ISSN:0021-9606.
      An N·log(N) method for evaluating electrostatic energies and forces of large periodic systems is presented. The method is based on interpolation of the reciprocal space Ewald sums and evaluation of the resulting convolution using fast Fourier transforms. Timings and accuracies are presented for three large cryst. ionic systems.
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      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaK3sXks1Ohsr0%253D&md5=3c9f230bd01b7b714fd096d4d2e755f6
    53. 53
      Jambeck, J. P.; Lyubartsev, A. P. Exploring the free energy landscape of solutes embedded in lipid bilayers. J. Phys. Chem. Lett. 2013, 4, 1781– 1787,  DOI: 10.1021/jz4007993
      53
      Exploring the Free Energy Landscape of Solutes Embedded in Lipid Bilayers
      Jambeck Joakim P M; Lyubartsev Alexander P
      The journal of physical chemistry letters (2013), 4 (11), 1781-7 ISSN:1948-7185.
      Free energy calculations are vital for our understanding of biological processes on an atomistic scale and can offer insight to various mechanisms. However, in some cases, degrees of freedom (DOFs) orthogonal to the reaction coordinate have high energy barriers and/or long equilibration times, which prohibit proper sampling. Here we identify these orthogonal DOFs when studying the transfer of a solute from water to a model membrane. Important DOFs are identified in bulk liquids of different dielectric nature with metadynamics simulations and are used as reaction coordinates for the translocation process, resulting in two- and three-dimensional space of reaction coordinates. The results are in good agreement with experiments and elucidate the pitfalls of using one-dimensional reaction coordinates. The calculations performed here offer the most detailed free energy landscape of solutes embedded in lipid bilayers to date and show that free energy calculations can be used to study complex membrane translocation phenomena.
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    54. 54
      Park, S.; Kim, T.; Im, W. Transmembrane helix assembly by window exchange umbrella sampling. Phys. Rev. Lett. 2012, 108, 108102,  DOI: 10.1103/PhysRevLett.108.108102
      54
      Transmembrane helix assembly by window exchange umbrella sampling
      Park, Soohyung; Kim, Taehoon; Im, Wonpil
      Physical Review Letters (2012), 108 (10), 108102/1-108102/4CODEN: PRLTAO; ISSN:0031-9007. (American Physical Society)
      A method of window exchange umbrella sampling mol. dynamics simulation is employed for transmembrane helix assembly. An anal. expression for the av. acceptance probability between neighboring windows is derived and combined with the first passage time optimization method to predetermine a parameter set in an optimal range. With the parameter set, the method provides a substantially more efficient sampling of helix-helix interfaces together with the potential of mean force along the helix-helix distance of a transmembrane helix-dimer model, compared to the umbrella sampling method.
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    55. 55
      Park, S.; Im, W. Two dimensional window exchange umbrella sampling for transmembrane helix assembly. J. Chem. Theory Comput. 2013, 9, 13– 17,  DOI: 10.1021/ct3008556
      55
      Two Dimensional Window Exchange Umbrella Sampling for Transmembrane Helix Assembly
      Park, Soohyung; Im, Wonpil
      Journal of Chemical Theory and Computation (2013), 9 (1), 13-17CODEN: JCTCCE; ISSN:1549-9618. (American Chemical Society)
      The method of window exchange umbrella sampling mol. dynamics (WEUSMD) with a preoptimized parameter set was recently used to obtain the most probable conformations and the energetics of transmembrane (TM) helix assembly of a generic TM sequence. When applied to glycophorin A TM domain (GpA-TM) using the restraint potentials along the helix-helix distance, however, tight interfacial packing of GpA-TM resulted in insufficient conformational sampling at short helix-helix sepn. This sampling issue is addressed by extending the WEUSMD into two dimensions with the restraint potentials along the helix-helix distance and crossing angle. The two-dimensional WEUSMD results demonstrate that the incomplete sampling in the one-dimensional WEUSMD arises from high barriers along the crossing angle between the GpA-TM helixes. Together with the faster convergence in both the assembled conformations and the potential of mean force, the 2D-WEUSMD can be a general and efficient approach in computational studies of TM helix assembly.
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    56. 56
      Jiang, W.; Luo, Y.; Maragliano, L.; Roux, B. Calculation of free energy landscape in multi-dimensions with Hamiltonian-exchange umbrella sampling on petascale supercomputer. J. Chem. Theory Comput. 2012, 8, 4672– 4680,  DOI: 10.1021/ct300468g
      56
      Calculation of Free Energy Landscape in Multi-Dimensions with Hamiltonian-Exchange Umbrella Sampling on Petascale Supercomputer
      Jiang, Wei; Luo, Yun; Maragliano, Luca; Roux, Benoit
      Journal of Chemical Theory and Computation (2012), 8 (11), 4672-4680CODEN: JCTCCE; ISSN:1549-9618. (American Chemical Society)
      An extremely scalable computational strategy is described for calcns. of the potential of mean force (PMF) in multidimensions on massively distributed supercomputers. The approach involves coupling thousands of umbrella sampling (US) simulation windows distributed to cover the space of order parameters with a Hamiltonian mol. dynamics replica-exchange (H-REMD) algorithm to enhance the sampling of each simulation. In the present application, US/H-REMD is carried out in a two-dimensional (2D) space and exchanges are attempted alternatively along the two axes corresponding to the two order parameters. The US/H-REMD strategy is implemented on the basis of parallel/parallel multiple copy protocol at the MPI level, and therefore can fully exploit computing power of large-scale supercomputers. Here the novel technique is illustrated using the leadership supercomputer IBM Blue Gene/P with an application to a typical biomol. calcn. of general interest, namely the binding of calcium ions to the small protein Calbindin D9k. The free energy landscape assocd. with two order parameters, the distance between the ion and its binding pocket and the root-mean-square deviation (rmsd) of the binding pocket relative the crystal structure, was calcd. using the US/H-REMD method. The results are then used to est. the abs. binding free energy of calcium ion to Calbindin D9k. The tests demonstrate that the 2D US/H-REMD scheme greatly accelerates the configurational sampling of the binding pocket, thereby improving the convergence of the potential of mean force calcn.
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    57. 57
      Hub, J. S.; De Groot, B. L.; van der Spoel, D. g_wham─A Free Weighted Histogram Analysis Implementation Including Robust Error and Autocorrelation Estimates. J. Chem. Theory Comput. 2010, 6, 3713– 3720,  DOI: 10.1021/ct100494z
      57
      g_wham: A Free Weighted Histogram Analysis Implementation Including Robust Error and Autocorrelation Estimates
      Hub, Jochen S.; de Groot, Bert L.; van der Spoel, David
      Journal of Chemical Theory and Computation (2010), 6 (12), 3713-3720CODEN: JCTCCE; ISSN:1549-9618. (American Chemical Society)
      The Weighted Histogram Anal. Method (WHAM) is a std. technique used to compute potentials of mean force (PMFs) from a set of umbrella sampling simulations. Here, the authors present a new WHAM implementation, termed g_wham, which is distributed freely with the GROMACS mol. simulation suite. G_wham ests. statistical errors using the technique of bootstrap anal. Three bootstrap methods are supported: (i) bootstrapping new trajectories based on the umbrella histograms, (ii) bootstrapping of complete histograms, and (iii) Bayesian bootstrapping of complete histograms, i.e., bootstrapping via the assignment of random wts. to the histograms. Because methods ii and iii consider only complete histograms as independent data points, these methods do not require the accurate calcn. of autocorrelation times. The authors demonstrate that, given sufficient sampling, bootstrapping new trajectories allows for an accurate error est. In the presence of long autocorrelations, however, (Bayesian) bootstrapping of complete histograms yields a more reliable error est., whereas bootstrapping of new trajectories may underestimate the error. In addn., the authors emphasize that the incorporation of autocorrelations into WHAM reduces the bias from limited sampling, in particular, when computing periodic PMFs in inhomogeneous systems such as solvated lipid membranes or protein channels.
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    58. 58
      Johnson, E. R.; Keinan, S.; Mori-Sánchez, P.; Contreras-García, J.; Cohen, A. J.; Yang, W. Revealing noncovalent interactions. J. Am. Chem. Soc. 2010, 132, 6498– 6506,  DOI: 10.1021/ja100936w
      58
      Revealing Noncovalent Interactions
      Johnson, Erin R.; Keinan, Shahar; Mori-Sanchez, Paula; Contreras-Garcia, Julia; Cohen, Aron J.; Yang, Weitao
      Journal of the American Chemical Society (2010), 132 (18), 6498-6506CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)
      Mol. structure does not easily identify the intricate noncovalent interactions that govern many areas of biol. and chem., including design of new materials and drugs. We develop an approach to detect noncovalent interactions in real space, based on the electron d. and its derivs. Our approach reveals the underlying chem. that compliments the covalent structure. It provides a rich representation of van der Waals interactions, hydrogen bonds, and steric repulsion in small mols., mol. complexes, and solids. Most importantly, the method, requiring only knowledge of the at. coordinates, is efficient and applicable to large systems, such as proteins or DNA. Across these applications, a view of nonbonded interactions emerges as continuous surfaces rather than close contacts between atom pairs, offering rich insight into the design of new and improved ligands.
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    59. 59
      Boto, R. A.; Peccati, F.; Laplaza, R.; Quan, C.; Carbone, A.; Piquemal, J.-P.; Maday, Y.; Contreras-García, J. NCIPLOT4: Fast, robust, and quantitative analysis of noncovalent interactions. J. Chem. Theory Comput. 2020, 16, 4150– 4158,  DOI: 10.1021/acs.jctc.0c00063
      59
      NCIPLOT4: Fast, Robust, and Quantitative Analysis of Noncovalent Interactions
      Boto, Roberto A.; Peccati, Francesca; Laplaza, Ruben; Quan, Chaoyu; Carbone, Alessandra; Piquemal, Jean-Philip; Maday, Yvon; Contreras-Garcia, Julia
      Journal of Chemical Theory and Computation (2020), 16 (7), 4150-4158CODEN: JCTCCE; ISSN:1549-9618. (American Chemical Society)
      The NonCovalent Interaction index (NCI) enables identification of attractive and repulsive noncovalent interactions from promol. densities in a fast manner. However, the approach remained up to now qual., only providing visual information. We present a new version of NCIPLOT, NCIPLOT4, which allows quantifying the properties of the NCI regions (vol., charge) in small and big systems in a fast manner. Examples are provided of how this new twist enables characterization and retrieval of local information in supramol. chem. and biosystems at the static and dynamic levels.
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    60. 60
      Hoefling, M.; Iori, F.; Corni, S.; Gottschalk, K.-E. Interaction of amino acids with the Au (111) surface: adsorption free energies from molecular dynamics simulations. Langmuir 2010, 26, 8347– 8351,  DOI: 10.1021/la904765u
      60
      Interaction of Amino Acids with the Au(111) Surface: Adsorption Free Energies from Molecular Dynamics Simulations
      Hoefling, Martin; Iori, Francesco; Corni, Stefano; Gottschalk, Kay-Eberhard
      Langmuir (2010), 26 (11), 8347-8351CODEN: LANGD5; ISSN:0743-7463. (American Chemical Society)
      Interactions of proteins with inorg. surfaces are of great importance in biol. events and in modern biotechnol. applications. Therefore, peptides have been engineered to recognize inorg. surfaces with high specificity. However, the underlying interactions are still not well understood. Here, we investigated the adsorption of amino acids as protein building blocks onto a Au(111) surface. In particular, using mol. dynamics (MD) simulations, we calcd. the potential of mean force between all the 20 amino acids and the gold surface. We found a strong dependence of the binding affinities on the chem. character of the amino acids. Addnl., the interaction free energy is correlated with the propensity of amino acids to form β-sheets, hinting at design principles for gold-binding peptides and induction of β-sheet formation near surfaces.
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    61. 61
      Bellucci, L.; Corni, S. Interaction with a gold surface reshapes the free energy landscape of alanine dipeptide. J. Phys. Chem. C 2014, 118, 11357– 11364,  DOI: 10.1021/jp502494k
      61
      Interaction with a Gold Surface Reshapes the Free Energy Landscape of Alanine Dipeptide
      Bellucci, Luca; Corni, Stefano
      Journal of Physical Chemistry C (2014), 118 (21), 11357-11364CODEN: JPCCCK; ISSN:1932-7447. (American Chemical Society)
      The adsorption of the alanine dipeptide onto a gold surface in aq. conditions was explored by using mol. dynamics simulations. In particular, using Metadynamics, the authors reconstructed a three-dimensional free energy landscape to study the effect of the metal surface on such landscape. The adsorption process is able to strongly modify the internal free energy surface of the mol., even changing its qual. appearance. The new free energy global min. corresponds to elongated conformations of the biomol., arranged in preferred orientations with respect to the surface. Therefore, the surface-induced changes in the relative stability of the local free energy min. and in the free-energy barriers between them show that the entire conformational ensemble and the interconformer dynamics are also affected by the presence of the surface. The alanine dipeptide is the simplest mol. that exhibits the main features shown by larger peptides. Therefore, these findings provide a basis to rationalize, at the atomistic level, the effects of metal surfaces and nanoparticles on the structure and function of peptides and proteins, which is of paramount importance to engineer new systems for applications in bionanotechnol.
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    62. 62
      Shao, Q.; Hall, C. K. Binding preferences of amino acids for gold nanoparticles: a molecular simulation study. Langmuir 2016, 32, 7888– 7896,  DOI: 10.1021/acs.langmuir.6b01693
      62
      Binding Preferences of Amino Acids for Gold Nanoparticles: A Molecular Simulation Study
      Shao, Qing; Hall, Carol K.
      Langmuir (2016), 32 (31), 7888-7896CODEN: LANGD5; ISSN:0743-7463. (American Chemical Society)
      A better understanding of the binding preference of amino acids for gold nanoparticles of different diams. could aid in the design of peptides that bind specifically to nanoparticles of a given diam. The authors identify the binding preference of 19 natural amino acids for three gold nanoparticles with diams. of 1.0, 2.0, and 4.0 nm, and investigate the mechanisms that govern these preferences. The authors calc. potentials of mean force between 36 entities (19 amino acids and 17 side chains) and the three gold nanoparticles in explicit water using well-tempered metadynamics simulations. Comparing these potentials of mean force dets. the amino acids' nanoparticle binding preferences and if these preferences are controlled by the backbone, the side chain, or both. Twelve amino acids prefer to bind to the 4.0 nm gold nanoparticle, and seven prefer to bind to the 2.0 nm one. The authors also use atomistic mol. dynamics simulations to investigate how water mols. near the nanoparticle influence the binding of the amino acids. The solvation shells of the larger nanoparticles have higher water densities than those of the smaller nanoparticles while the orientation distributions of the water mols. in the shells of all three nanoparticles are similar. The nanoparticle preferences of the amino acids depend on whether their binding free energy is detd. mainly by their ability to replace or to reorient water mols. in the nanoparticle solvation shell. The amino acids whose binding free energy depends mainly on the replacement of water mols. are likely to prefer to bind to the largest nanoparticle and tend to have relatively simple side chain structures. Those whose binding free energy depends mainly on their ability to reorient water mols. prefer a smaller nanoparticle and tend to have more complex side chain structures.
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    63. 63
      Hughes, Z. E.; Wright, L. B.; Walsh, T. R. Biomolecular adsorption at aqueous silver interfaces: first-principles calculations, polarizable force-field simulations, and comparisons with gold. Langmuir 2013, 29, 13217– 13229,  DOI: 10.1021/la402839q
      63
      Biomolecular Adsorption at Aqueous Silver Interfaces: First-Principles Calculations, Polarizable Force-Field Simulations, and Comparisons with Gold
      Hughes, Zak E.; Wright, Louise B.; Walsh, Tiffany R.
      Langmuir (2013), 29 (43), 13217-13229CODEN: LANGD5; ISSN:0743-7463. (American Chemical Society)
      The mol. simulation of biomols. adsorbed at noble metal interfaces can assist in the development of bionanotechnol. applications. In line with advances in polarizable force fields for adsorption at aq. gold interfaces, there is scope for developing a similar force field for silver. One way to accomplish this is via the generation of in vacuo adsorption energies calcd. using first-principles approaches for a wide range of different but biol. relevant small mols., including water. The authors present such first-principles data for a comprehensive range of bioorg. mols. obtained from plane-wave d. functional theory calcns. using the vdW-DF functional. The authors have constructed a new force field, AgP-CHARMM, suitable for the simulation of biomols. at the aq. Ag(111) and Ag(100) interfaces. This force field is derived to be consistent with GolP-CHARMM such that adsorption on Ag and Au can be compared on an equal footing. The force fields are used to evaluate the water overlayer stability on both silver and gold, finding good agreement with known behaviors. The authors also calc. and compare the structuring (spatial and orientational) of liq. water adsorbed at both silver and gold. Finally, the authors report the adsorption free energy of a range of amino acids at both the Au(111) and Ag(111) aq. interfaces, calcd. using meta-dynamics. Stronger adsorption on gold was noted in most cases, with the exception being the carboxylate group present in aspartic acid. These findings also indicate differences in the binding free energy profile between silver and gold for some amino acids, notably for His and Arg. The relatively stronger structuring of the first water layer on silver, relative to gold, could give rise to these differences.
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    64. 64
      Rosa, M.; Di Felice, R.; Corni, S. Adsorption mechanisms of nucleobases on the hydrated Au (111) surface. Langmuir 2018, 34, 14749– 14756,  DOI: 10.1021/acs.langmuir.8b00065
      64
      Adsorption Mechanisms of Nucleobases on the Hydrated Au(111) Surface
      Rosa, Marta; Di Felice, Rosa; Corni, Stefano
      Langmuir (2018), 34 (49), 14749-14756CODEN: LANGD5; ISSN:0743-7463. (American Chemical Society)
      The soln. environment is of fundamental importance in the adsorption of mols. on surfaces, a process that is strongly affected by the capability of the adsorbate to disrupt the hydration layer above the surface. Here we disclose how the presence of interface water influences the adsorption mechanism of DNA nucleobases on a gold surface. By means of metadynamics simulations, we describe the distinctive features of a complex free-energy landscape for each base, which manifests activation barriers for the adsorption process. We characterize the different pathways that allow each nucleobase to overcome the barriers and be adsorbed on the surface, discussing how they influence the kinetics of adsorption of single-stranded DNA oligomers with homogeneous sequences. Our findings offer a rationale as to why exptl. data on the adsorption of single-stranded homo-oligonucleotides do not straightforwardly follow the thermodn. affinity rank.
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    65. 65
      Rapino, S.; Zerbetto, F. Modeling the Stability and the Motion of DNA Nucleobases on the Gold Surface. Langmuir 2005, 21, 2512– 2518,  DOI: 10.1021/la047091o
      65
      Modeling the Stability and the Motion of DNA Nucleobases on the Gold Surface
      Rapino, Stefania; Zerbetto, Francesco
      Langmuir (2005), 21 (6), 2512-2518CODEN: LANGD5; ISSN:0743-7463. (American Chemical Society)
      We simulate the structure and dynamics of the four DNA bases on the most stable gold surface. The exptl. adsorption energies are reproduced to about 1 kcal mol-1, and the existence of anchor points in the mols. is evidenced. The simulations also show that the bases drift on the gold surface with a degree of mobility that is not inversely proportional to the exptl. (and calcd.) desorption energies. When the same type of calcns. is applied to pairs of bases it is seen that for at least two of them, namely GG and TT, there is a cooperative effect that increases their adsorption energy with respect to those of the single mols. The mol. mobility on the surface is still present when a pair of interacting bases is considered.
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    66. 66
      Feng, J.; Pandey, R. B.; Berry, R. J.; Farmer, B. L.; Naik, R. R.; Heinz, H. Adsorption mechanism of single amino acid and surfactant molecules to Au {111} surfaces in aqueous solution: design rules for metal-binding molecules. Soft Matter 2011, 7, 2113– 2120,  DOI: 10.1039/c0sm01118e
      66
      Adsorption mechanism of single amino acid and surfactant molecules to Au {111} surfaces in aqueous solution: design rules for metal-binding molecules
      Feng, Jie; Pandey, Ras B.; Berry, Rajiv J.; Farmer, Barry L.; Naik, Rajesh R.; Heinz, Hendrik
      Soft Matter (2011), 7 (5), 2113-2120CODEN: SMOABF; ISSN:1744-683X. (Royal Society of Chemistry)
      The adsorption mechanism of twenty amino acids and four surfactants was examd. on a {111} surface of gold in dil. aq. soln. using mol. dynamics simulation with a broadly applicable intermol. potential CHARMM-METAL. All mols. are attracted to the surface between -3 and -26 kcal mol-1. The adsorption strength correlates with the degree of coordination of polarizable atoms (O, N, C) to multiple epitaxial sites. Therefore, the mol. size and geometry rather than the specific chem. det. the adsorption energy. Large mols. with planar sp2 hybridized groups (Arg, Trp, Gln, Tyr, Asn, and PPh3) adsorb most strongly, followed by mols. with polar sp3 hybridized groups, and short mols. with sp3 hybridized alkyl groups exhibit least attraction. Conformationally flexible, extended mols. such as hexadecyltrimethylammonium bromide (CTAB) also showed significant attraction to the metal surface related to accommodation in epitaxial grooves and coordination with numerous epitaxial sites. Computational results are consistent with combinatorial binding expts., observations in the growth and stabilization of metal nanoparticles, and ab initio data. The mechanism of adsorption conforms to soft epitaxy obsd. for peptides on metal surfaces for binding to a given metal surface. In addn. to soft epitaxy, contributions to adsorption are possible by covalent bonding and induced charges.
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    67. 67
      Dasetty, S.; Barrows, J. K.; Sarupria, S. Adsorption of amino acids on graphene: assessment of current force fields. Soft Matter 2019, 15, 2359– 2372,  DOI: 10.1039/C8SM02621A
      67
      Adsorption of amino acids on graphene: assessment of current force fields
      Dasetty, Siva; Barrows, John K.; Sarupria, Sapna
      Soft Matter (2019), 15 (11), 2359-2372CODEN: SMOABF; ISSN:1744-6848. (Royal Society of Chemistry)
      We compare the free energies of adsorption (ΔAads) and the structural preferences of amino acids on graphene obtained using the non-polarizable force fields-Amberff99SB-ILDN/TIP3P, CHARMM36/modified-TIP3P, OPLS-AA/M/TIP3P, and Amber03w/TIP4P/2005. The amino acid-graphene interactions are favorable irresp. of the force field. While the magnitudes of ΔAads differ between the force fields, the relative free energy of adsorption across amino acids is similar for the studied force fields. ΔAads pos. correlates with amino acid-graphene and neg. correlates with graphene-water interaction energies. Using a combination of principal component anal. and d.-based clustering technique, we grouped the structures obsd. in the graphene adsorbed state. The resulting population of clusters, and the conformation in each cluster indicate that the structures of the amino acid in the graphene adsorbed state vary across force fields. The differences in the conformations of amino acids are more severe in the graphene adsorbed state compared to the bulk state for all the force fields. Our findings suggest that the force fields studied will give qual. consistent relative strength of adsorption across proteins but different structural preferences in the graphene adsorbed state.
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    68. 68
      Biriukov, D.; Futera, Z. Adsorption of amino acids at the gold/aqueous interface: Effect of an external electric field. J. Phys. Chem. C 2021, 125, 7856– 7867,  DOI: 10.1021/acs.jpcc.0c11248
      68
      Adsorption of Amino Acids at the Gold/Aqueous Interface: Effect of an External Electric Field
      Biriukov, Denys; Futera, Zdenek
      Journal of Physical Chemistry C (2021), 125 (14), 7856-7867CODEN: JPCCCK; ISSN:1932-7447. (American Chemical Society)
      Gaining accurate mol. descriptions of metal/bio interfaces is a necessary step toward numerous important applications, particularly in electrochem. and bionanotechnol. Here, using atomistic mol. dynamics simulations and free energy calcns. with the GolP-CHARMM force field, we investigate how applied static elec. field disturbs the structure of an aq. Au (111)/amino acid (AA) interface. We show that adsorption of pos. charged AAs (arginine, histidine, and lysine) is more affected by the external elec. field than that of neg. charged (aspartic and glutamic acids) and charge-neutral AAs (alanine, glycine, tryptophan, and asparagine). The adsorption free energies of pos. charged AAs can vary within 55% when static fields of up to 0.5 V/Å are applied, in contrast to considerably weaker responses of neg. charged and charge-neutral AAs (up to 25%). The difference arises from the role of a charged side chain in the adsorption on the gold surface. Pos. charged amines adsorb stronger than neg. charged carboxylates, and this fact together with the trend within pos. charged AAs (arginine > histidine > lysine) is related to the affinity of their side chains for Au (111) surfaces and ability to replace water mols. in the first adsorption layer. The adsorption via a deprotonated carboxyl group is less favorable, indirect, and facilitated by hydrogen bonding with the adsorbed water, while the pos. amines directly interact with surface gold atoms. This eventually leads to relatively weaker adsorption of neg. charged AAs and their smaller response to the external elec. fields due to solvent-induced electrostatic screening. These fundamental results provide a useful insight into the mol. arrangement at the electrified biointerfaces with gold, which can help to interpret electrochem. phenomena and advance bioelectronic applications.
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    69. 69
      Hughes, Z. E.; Tomásio, S. M.; Walsh, T. R. Efficient simulations of the aqueous bio-interface of graphitic nanostructures with a polarisable model. Nanoscale 2014, 6, 5438– 5448,  DOI: 10.1039/C4NR00468J
      69
      Efficient simulations of the aqueous bio-interface of graphitic nanostructures with a polarisable model
      Hughes, Zak E.; Tomasio, Susana M.; Walsh, Tiffany R.
      Nanoscale (2014), 6 (10), 5438-5448CODEN: NANOHL; ISSN:2040-3372. (Royal Society of Chemistry)
      To fully harness the enormous potential offered by interfaces between graphitic nanostructures and biomols., detailed connections between adsorbed conformations and adsorption behavior are needed. To elucidate these links, a key approach, in partnership with exptl. techniques, is mol. simulation. For this, a force-field (FF) that can appropriately capture the relevant physics and chem. of these complex bio-interfaces, while allowing extensive conformational sampling, and also supporting inter-operability with known biol. FFs, is a pivotal requirement. Here, we present and apply such a force-field, GRAPPA, designed to work with the CHARMM FF. GRAPPA is an efficiently implemented polarisable force-field, informed by extensive plane-wave DFT calcns. using the revPBE-vdW-DF functional. GRAPPA adequately recovers the spatial and orientational structuring of the aq. interface of graphene and carbon nanotubes, compared with more sophisticated approaches. We apply GRAPPA to det. the free energy of adsorption for a range of amino acids, identifying Trp, Tyr and Arg to have the strongest binding affinity and Asp to be a weak binder. The GRAPPA FF can be readily incorporated into mainstream simulation packages, and will enable large-scale polarisable biointerfacial simulations at graphitic interfaces, that will aid the development of biomol.-mediated, soln.-based graphene processing and self-assembly strategies.
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    70. 70
      Rosa, M.; Corni, S.; Di Felice, R. van der Waals effects at molecule-metal interfaces. Phys. Rev. B 2014, 90, 125448,  DOI: 10.1103/PhysRevB.90.125448
      70
      van der Waals effects at molecule-metal interfaces
      Rosa, Marta; Corni, Stefano; Di Felice, Rosa
      Physical Review B: Condensed Matter and Materials Physics (2014), 90 (12), 125448/1-125448/8, 8 pp.CODEN: PRBMDO; ISSN:1098-0121. (American Physical Society)
      We present the results of plane-wave pseudopotential periodic d. functional theory (DFT) calcns. on the geometries, energetics and electronic structure of small mols. on Au(111). The chosen mols.-benzene, ammonia and cytosine-are representative of different adsorption regimes and interaction strengths. The chosen substrate is a prototype noble-metal surface that is widely employed as a support for org. materials. We assess the relevance of van der Waals effects in the adsorption process and the accuracy of different first-principle d. functionals that have been recently developed to embody such effects. We find that there is no unique functional that is optimal for any system. In particular, our results reveal that functionals designed to reduce the short-term repulsion between the adsorbate and the substrate usually overestimate the adsorption strength and may even predict the wrong adsorption orientation. We show that an accurate description of the substrate does not ensure an accurate evaluation of the adsorption energetics, while the electronic structure is less sensitive to the specific choice. We propose the best choice for DFT calcns. of DNA bases on Au(111) and similar systems in which both short-range and long-range interactions exist.
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    71. 71
      Rosa, M.; Corni, S.; Di Felice, R. A density functional theory study of cytosine on Au (111). J. Phys. Chem. C 2012, 116, 21366– 21373,  DOI: 10.1021/jp305833c
      71
      A Density Functional Theory Study of Cytosine on Au(111)
      Rosa, Marta; Corni, Stefano; Di Felice, Rosa
      Journal of Physical Chemistry C (2012), 116 (40), 21366-21373CODEN: JPCCCK; ISSN:1932-7447. (American Chemical Society)
      The adsorption of cytosine on Au(111) is investigated using d. functional theory with the nonlocal van der Waals d. functional. Test calcns. performed on the benzene stacked dimer and on a benzene mol. adsorbed on Au(111) allow us to assess the methodol. and reveal the accuracy and predictivity of the van der Waals d. functional relative to exptl. outcome. Our results for cytosine on Au(111) indicate that the inclusion of dispersion interactions is crucial for the treatment of this system. In fact, such terms enhance the value of the adsorption energy and also affect the cytosine bonding geometry: in particular, we find that a tilted geometry is always favorable relative to a parallel geometry, which was not found in std. d. functional theory investigations. The combined new data for energetics and geometry lead to conclusions that contrast the common opinion that the surface-mol. interaction is negligible in the process of monolayer formation.
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    72. 72
      Rosa, M.; Corni, S.; Di Felice, R. Interaction of nucleic acid bases with the Au (111) surface. J. Chem. Theory Comput. 2013, 9, 4552– 4561,  DOI: 10.1021/ct4002416
      72
      Interaction of Nucleic Acid Bases with the Au(111) Surface
      Rosa, Marta; Corni, Stefano; Di Felice, Rosa
      Journal of Chemical Theory and Computation (2013), 9 (10), 4552-4561CODEN: JCTCCE; ISSN:1549-9618. (American Chemical Society)
      The fate of an individual DNA mol. when it is deposited on a hard inorg. surface in a dry environment is unknown, while it is a crucial determinant for nanotechnol. applications of nucleic acids. In the absence of exptl. approaches that are able to unravel the three-dimensional at. structure of the target system, here we tackle the first step toward a computational soln. of the problem. By using first-principles quantum mech. calcns. of the four nucleobases on the Au(111) surface, we present results for the geometries, energetics, and electronic structure, in view of developing a force field that will enable classical simulations of DNA on Au(111) to investigate the structural modifications of the duplex in these non-native conditions. We fully characterize each system at the individual level. We find that van der Waals interactions are crucial for a correct description of the geometry and energetics. However, the mechanism of adsorption is well beyond pure dispersion interactions. Indeed, we find charge sharing between the substrate and the adsorbate, the formation of hybrid orbitals, and even bonding orbitals. Yet, this mol.-surface assocn. is qual. distinct from the thiol adsorption mechanism; we discuss such differences and also the relation to the adsorption mechanism of pure arom. mols.
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    73. 73
      Rosa, M.; Corni, S.; Di Felice, R. Enthalpy–entropy tuning in the adsorption of nucleobases at the Au (111) surface. J. Chem. Theory Comput. 2014, 10, 1707– 1716,  DOI: 10.1021/ct401117g
      73
      Enthalpy-Entropy Tuning in the Adsorption of Nucleobases at the Au(111) Surface
      Rosa, Marta; Corni, Stefano; Di Felice, Rosa
      Journal of Chemical Theory and Computation (2014), 10 (4), 1707-1716CODEN: JCTCCE; ISSN:1549-9618. (American Chemical Society)
      The interaction of DNA mols. with hard substrates is of paramount importance both for the study of DNA itself and for the variety of possible technol. applications. Interaction with inorg. surfaces strongly modifies the helical shape of DNA. Hence, an accurate understanding of DNA structure and function at interfaces is a fundamental question with enormous impact in science and society. This work sets the fundamentals for the simulation of entire DNA oligomers on gold surfaces in dry and wet conditions. Thanks to the new GolDNA-AMBER force field, which was derived from first principles and includes dispersion interactions and polarization effects, we simulated self-assembled guanine and adenine monolayers on Au(111) in vacuo and the adsorption of all nucleobases on the same substrate in aq. conditions. The periodic monolayers obtained from classical simulations match very well those from first principle calcns. and expts., assessing the robustness of the force field and motivating the application to more complex systems for which quantum calcns. are not affordable and expts. are elusive. The energetics of nucleobases on Au(111) in soln. reveal fundamental physicochem. effects: we find that the adsorption paradigm shifts from purely enthalpic to dominantly entropic by changing the environment and aggregation phase.
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    74. 74
      Östblom, M.; Liedberg, B.; Demers, L. M.; Mirkin, C. A. On the structure and desorption dynamics of DNA bases adsorbed on gold: A temperature-programmed study. J. Phys. Chem. B 2005, 109, 15150– 15160,  DOI: 10.1021/jp051617b
      74
      On the structure and desorption dynamics of DNA bases adsorbed on gold: a temperature-programmed study
      Ostblom Mattias; Liedberg Bo; Demers Linette M; Mirkin Chad A
      The journal of physical chemistry. B (2005), 109 (31), 15150-60 ISSN:1520-6106.
      The structure and desorption dynamics of mono- and multilayer samples of adenine, cytosine, guanine, and thymine on polycrystalline gold thin films are studied using temperature-programmed desorption-infrared reflection absorption spectroscopy (TPD-IRAS) and temperature-programmed desorption-mass spectroscopy (TPD-MS). It is shown that the pyrimidines, adenine and guanine, adsorb to gold in a complex manner and that both adhesive (adenine) and cohesive (guanine) interactions contribute the apparent binding energies to the substrate surface. Adenine displays at least two adsorption sites, including a high-energy site (210 degrees C, approximately 136 kJ/mol), wherein the molecule coordinates to the gold substrate via the NH2 group in an sp3-like, strongly perturbed, nonplanar configuration. The purines, cytosine and thymine, display a less complicated adsorption/desorption behavior. The desorption energy for cytosine (160 degrees C, approximately 122 kJ/mol) is similar to those obtained for adenine and guanine, but desorption occurs from a single site of dispersed, nonaggregated cytosine. Thymine desorbs also from a single site but at a significantly lower energy (100 degrees C, approximately 104 kJ/mol). Infrared data reveal that the monolayer architectures discussed herein are structurally very different from those observed for the bases in the bulk crystalline state. It is also evident that both pyrimidines and purines adsorb on gold with the plane of the molecule in a nonparallel orientation with respect to the substrate surface. The results of this work are discussed in the context of improving the understanding of the design of capturing oligonucleotides or DNA strands for bioanalytical applications, in particular, for gold nanoparticle-based assays.
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    75. 75
      Demers, L. M.; Östblom, M.; Zhang, H.; Jang, N.-H.; Liedberg, B.; Mirkin, C. A. Thermal desorption behavior and binding properties of DNA bases and nucleosides on gold. J. Am. Chem. Soc. 2002, 124, 11248– 11249,  DOI: 10.1021/ja0265355
      75
      Thermal Desorption Behavior and Binding Properties of DNA Bases and Nucleosides on Gold
      Demers, Linette M.; Oestblom, Mattias; Zhang, Hua; Jang, Nak-Han; Liedberg, Bo; Mirkin, Chad A.
      Journal of the American Chemical Society (2002), 124 (38), 11248-11249CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)
      DNA monolayers on gold thin films and electrodes, as well as DNA-protected gold nanoparticles, are the basis for an increasing no. of diagnostic applications that involve the use of surface-enhanced Raman spectroscopy (SERS), surface plasmon resonance spectroscopy (SPRS), and electrochem., scanometric, and colorimetric DNA detection strategies. Thus, the nature and strength of interactions of DNA with gold surfaces for both planar films and charged particles are subjects of great interest to researchers in the disciplines of biotechnol. and nanotechnol. Indeed, a no. of studies aimed at elucidating the binding modes and conformation of DNA and its components (bases and nucleosides) on gold surfaces suggest that the DNA-gold interaction is complex and highly sequence-dependent. Herein, we use temp.-programmed desorption (TPD) and reflection absorption FT IR (RAIR) spectroscopy to directly examine the energetics of the DNA base-gold and DNA nucleoside-gold interactions. To the best of our knowledge this is the first study to quantify and compare the energetics of these important interactions between the fundamental chem. components of DNA and gold.
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    76. 76
      Fleischmann, M.; Hendra, P. J.; McQuillan, A. J. Raman spectra of pyridine adsorbed at a silver electrode. Chem. Phys. Lett. 1974, 26, 163– 166,  DOI: 10.1016/0009-2614(74)85388-1
      76
      Raman spectra of pyridine adsorbed at a silver electrode
      Fleischmann, M.; Hendra, P. J.; McQuillan, A. J.
      Chemical Physics Letters (1974), 26 (2), 163-6CODEN: CHPLBC; ISSN:0009-2614.
      Raman spectroscopy was employed for the 1st time to study the role of adsorption at electrodes. It was possible to distinguish 2 types of pyridine adsorption at a Ag electrode. The variation in intensity and frequency of some of the bands with potential in the region of the point of zero charge gave further evidence as to the structure of the elec. double layer; the interaction of adsorbed pyridine and water must be taken into account.
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    77. 77
      Albrecht, M. G.; Creighton, J. A. Anomalously intense Raman spectra of pyridine at a silver electrode. J. Am. Chem. Soc. 1977, 99, 5215– 5217,  DOI: 10.1021/ja00457a071
      77
      Anomalously intense Raman spectra of pyridine at a silver electrode
      Albrecht, M. Grant; Creighton, J. Alan
      Journal of the American Chemical Society (1977), 99 (15), 5215-17CODEN: JACSAT; ISSN:0002-7863.
      Raman bands due to pyridine absorbed at a Ag electrode, which are absent for a freshly cleaned electrode immersed in aq. pyridine/KCl, are anomalously intense after a single electrochem. roughening cycle. The intensity enhancement is estd. to be ∼105-fold, and is possibly due to a resonance Raman effect in pyridine induced by an electronic interaction with the roughened metal surface. The high intensity of Raman bands enables changes in the surface concn. of absorbed pyridine to be readily followed during and after the roughening cycle.
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    78. 78
      Jeanmaire, D. L.; Van Duyne, R. P. Surface Raman spectroelectrochemistry: Part I. Heterocyclic, aromatic, and aliphatic amines adsorbed on the anodized silver electrode. J. Electroanal. Chem. Interfacial Electrochem. 1977, 84, 1– 20,  DOI: 10.1016/S0022-0728(77)80224-6
      78
      Surface Raman spectroelectrochemistry. Part I. Heterocyclic, aromatic, and aliphatic amines adsorbed on the anodized silver electrode
      Jeanmaire, David L.; Van Duyne, Richard P.
      Journal of Electroanalytical Chemistry and Interfacial Electrochemistry (1977), 84 (1), 1-20CODEN: JEIEBC; ISSN:0022-0728.
      The remarkable sensitivity of Raman spectroscopy was verified for the study of adsorbed pyridine on a Ag surface, and its applicability extended to other N heterocycles and amines. New bands in the scattering spectrum of adsorbed pyridine were characterized, which were not previously reported, as well as the Raman intensity response of all the surface pyridine bands as a function of electrode potential. As a result of these expts., a model is proposed of the adsorbed species for pyridine in which the adsorption is anion induced, leading to an axial end-on attachment to the electrode surface. The ability to obtain resonance Raman spectra with good signal-to-noise ratios with laser powers < 1.0 mW, opens up possibilities of surface Raman studies with relatively inexpensive laser systems. As laser power requirements are relaxed, reliability is improved, and greater tuning ranges can be achieved for wavelength dependent studies. The potential of resonance Raman spectroscopy was previously demonstrated for monitoring soln. kinetic behavior; now it is shown that normal Raman as well as resonance Raman spectroscopy have sufficient sensitivity to extend the studies of kinetic processes to include those occurring at electrode surfaces.
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    79. 79
      Zuo, C.; Jagodzinski, P. W. Surface-Enhanced Raman Scattering of Pyridine Using Different Metals: Differences and Explanation Based on the Selective Formation of α-Pyridyl on Metal Surfaces. J. Phys. Chem. B 2005, 109, 1788– 1793,  DOI: 10.1021/jp0406363
      79
      Surface-Enhanced Raman Scattering of Pyridine Using Different Metals: Differences and Explanation Based on the Selective Formation of α-Pyridyl on Metal Surfaces
      Zuo, Chen; Jagodzinski, Paul W.
      Journal of Physical Chemistry B (2005), 109 (5), 1788-1793CODEN: JPCBFK; ISSN:1520-6106. (American Chemical Society)
      A simple method has been developed to produce SERS-active metal surfaces. Six metal surfaces (cadmium, nickel, gold, iron, copper, and silver) have been prepd. on an aluminum foil underlayment by chem. redn. and strong surface-enhanced Raman signals have been obsd. for pyridine species on these surfaces. This permits the direct comparison of pyridine spectra on different metal surfaces prepd. by the same chem. clean method. The differences among the SER spectra of the aq. pyridine species using different metals generally follow the trend of silver, cadmium, nickel, iron, gold, and copper, which can be explained by the selective formation of α-pyridyl species and the equil. between end-on adsorbed pyridines and edge-on adsorbed α-pyridyl species on the different metal surfaces.
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    80. 80
      Khaing Oo, M. K.; Guo, Y.; Reddy, K.; Liu, J.; Fan, X. Ultrasensitive vapor detection with surface-enhanced Raman scattering-active gold nanoparticle immobilized flow-through multihole capillaries. Anal. Chem. 2012, 84, 3376– 3381,  DOI: 10.1021/ac300175v
      80
      Ultrasensitive Vapor Detection with Surface-Enhanced Raman Scattering-Active Gold Nanoparticle Immobilized Flow-Through Multihole Capillaries
      Khaing Oo, Maung Kyaw; Guo, Yunbo; Reddy, Karthik; Liu, Jing; Fan, Xudong
      Analytical Chemistry (Washington, DC, United States) (2012), 84 (7), 3376-3381CODEN: ANCHAM; ISSN:0003-2700. (American Chemical Society)
      The authors developed novel flow-through surface-enhanced Raman scattering (SERS) platforms using gold nanoparticle (Au-NP) immobilized multihole capillaries for rapid and sensitive vapor detection. The multihole capillaries consisting of thousands of micrometer-sized flow-through channels provide many unique characteristics for vapor detection. Most importantly, its three-dimensional SERS-active micro-/nanostructures make available multilayered assembly of Au-NPs, which greatly increase SERS-active surface area within a focal vol. of excitation and collection, thus improving the detection sensitivity. The multihole capillary's inherent longitudinal channels offer rapid and convenient vapor delivery, yet its micrometer-sized holes increase the interaction between vapor mols. and SERS-active substrate. Exptl., rapid pyridine vapor detection (within 1 s of exposure) and ultrasensitive 4-nitrophenol vapor detection (at a sub-ppb level) were successfully achieved in open air at room temp. Such an ultrasensitive SERS platform enabled, for the 1st time, the study of both pyridine and 4-nitrophenol vapor adsorption isotherms at very low concns. Type I and type V behaviors of the International Union of Pure and Applied Chem. isotherm were well obsd., resp.
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    81. 81
      Beljebbar, A.; Sockalingum, G.; Angiboust, J.; Manfait, M. Comparative FT SERS, resonance Raman and SERRS studies of doxorubicin and its complex with DNA. Spectrochim. Acta A Mol. Biomol. Spectrosc. 1995, 51, 2083– 2090,  DOI: 10.1016/0584-8539(95)01515-7
      81
      Comparative FT SERS, resonance Raman and SERRS studies of doxorubicin and its complex with DNA
      Beljebbar, A.; Sockalingum, G. D.; Angiboust, J. F.; Manfait, M.
      Spectrochimica Acta, Part A: Molecular and Biomolecular Spectroscopy (1995), 51A (12), 2083-90CODEN: SAMCAS; ISSN:0584-8539. (Elsevier)
      Fourier transform surface enhanced Raman scattering (FT SERS) coupled with a microscope has been used as a probe to obtain information on the interaction of a drug and of its complex with DNA. Micro-FT SERS spectra of the antitumor agent doxorubicin (DOX) at 10-5 M and of this complex with DNA have been recorded in aq. silver hydrosol and compared with the corresponding resonance Raman (RR) and SERS (surface enhanced Raman scattering) spectra at concns. of 5 × 10-4 M and 5 × 10-8 M, resp. The interactions between the drug and calf thymus DNA induced identical effects in the RR and visible SERS spectra. The data show that the adsorption of the drug-DNA complex on the silver hydrosol does not induce detectable perturbations of the mol. interactions within the complex. Micro-FT SERS spectra were partially different from those obtained in visible SERS spectra. These differences concern the relative enhancement of some vibrational modes which could hardly be obsd. when resonance excitation was used. The FT SERS approach enables further information to be obtained and addnl. details on the geometry of the drug-DNA interaction to be revealed. An anal. of the FT SERS spectra of the drug and of its complex with DNA not only confirms the model of interaction proposed using RR and SERS data in the visible, but brings about new information, esp. on the vibrations of ring A of the mol., which are usually masked by the vibrations of rings B and C dominant in the visible SERS spectra.
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    82. 82
      Loren, A.; Eliasson, C.; Josefson, M.; Murty, K.; Käll, M.; Abrahamsson, J.; Abrahamsson, K. Feasibility of quantitative determination of doxorubicin with surface-enhanced Raman spectroscopy. J. Raman Spectrosc. 2001, 32, 971– 974,  DOI: 10.1002/jrs.783
      82
      Feasibility of quantitative determination of doxorubicin with surface-enhanced Raman spectroscopy
      Loren, A.; Eliasson, C.; Josefson, M.; Murty, K. V. G. K.; Kall, M.; Abrahamsson, J.; Abrahamsson, K.
      Journal of Raman Spectroscopy (2001), 32 (11), 971-974CODEN: JRSPAF; ISSN:0377-0486. (John Wiley & Sons Ltd.)
      Surface-enhanced Raman spectroscopy (SERS) was performed using excitation at 488 nm in a blood plasma-doxorubicin-silver colloid system. With a blood plasma content of 1%, a partial least-squares calibration of the doxorubicin was made in the 10-750 nM range. Predictions for a test set generated a root mean square error of prediction of 70 nM. The use of SERS and chemometrics in complex systems made it possible to use the highly informative Raman signals even at low concns. without the need for sample pretreatment such as extn.
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    83. 83
      Lee, K. Y.; Wang, Y.; Nie, S. In vitro study of a pH-sensitive multifunctional doxorubicin–gold nanoparticle system: Therapeutic effect and surface enhanced Raman scattering. RSC Adv. 2015, 5, 65651– 65659,  DOI: 10.1039/C5RA09872F
      83
      In vitro study of a pH-sensitive multifunctional doxorubicin-gold nanoparticle system: therapeutic effect and surface enhanced Raman scattering
      Lee, Kate Y. J.; Wang, Yiqing; Nie, Shuming
      RSC Advances (2015), 5 (81), 65651-65659CODEN: RSCACL; ISSN:2046-2069. (Royal Society of Chemistry)
      We report the development and characterization of a multifunctional drug delivery system (Au-dox-PEG) for the treatment and SERS spectroscopic detection of tumors. Doxorubicin, a therapeutic agent and a SERS tag, was chem. conjugated to gold nanoparticles via a pH-sensitive hydrazone linker, and then PEG was added to develop Au-dox-PEG. The doxorubicin occupied a max. of 20% of the total surface area of the gold nanoparticles which resulted in colloidal stability. SERS spectra were measured for non-aggregated Au-dox-PEG using near-IR wavelength radiation, and the doxorubicin release was time and pH dependent. Consistency in the release profile and in vitro cell viability results supports the efficacy of the Au-dox-PEG system. Thus, the development of the Au-dox-PEG multifunctional system raises exciting opportunities for the simultaneous spectroscopic detection and therapy of tumors in the future.
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    84. 84
      Smulevich, G.; Feis, A. Surface-enhanced resonance Raman spectra of adriamycin, 11-deoxycarminomycin, their model chromophores, and their complexes with DNA. J. Phys. Chem. 1986, 90, 6388– 6392,  DOI: 10.1021/j100281a064
      84
      Surface-enhanced resonance Raman spectra of adriamycin, 11-deoxycarminomycin, their model chromophores, and their complexes with DNA
      Smulevich, Giulietta; Feis, Alessandro
      Journal of Physical Chemistry (1986), 90 (23), 6388-92CODEN: JPCHAX; ISSN:0022-3654.
      The surface-enhanced Raman spectra of Ag sols of adriamycin [23214-92-8], 11-deoxycarminomycin [81382-07-2], their model chromophores 1,4- [81-64-1] and 1,8-dihydroxyanthraquinone [117-10-2], and their complexes with DNA were measured. The well-detailed spectra yieled by the combined anal. in terms of symmetry and pseudosymmetry, a nearly complete vibrational assignment of the resonance Raman active modes. The spectra perturbations induced by the adsorption of the compds. onto the Ag particles, by comparison with their resonance Raman spectra in soln., were explained in terms of interaction between one C:O≡O-H group of the chromophore and the Ag surface. The intensity of redn. of some bands assocd. with the HOCCC=O groups obsd. in the drug/DNA complexes was interpreted in terms of changes between the ground and the excited states of the normal coordinates and(or) their equil. positions. The inferred structures of the complexes was consistent with intercalation between daunorubicin and the DNA fragment d(CpGpTpApCpG) previously reported from X-ray measurements.
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    85. 85
      Nonaka, Y.; Tsuboi, M.; Nakamoto, K. Comparative study of aclacinomycin versus adriamycin by means of resonance Raman spectroscopy. J. Raman Spectrosc. 1990, 21, 133– 141,  DOI: 10.1002/jrs.1250210211
      85
      Comparative study of aclacinomycin versus adriamycin by means of resonance Raman spectroscopy
      Nonaka, Yasuomi; Tsuboi, Masamichi; Nakamoto, Kazuo
      Journal of Raman Spectroscopy (1990), 21 (2), 133-41CODEN: JRSPAF; ISSN:0377-0486.
      Resonance Raman spectra of adriamycin and aclacinomycin A were examd. in their H2O and D2O solns. These spectra appear totally different from each other, but the differences are similar to those between 1,4- and 1,8-dihydroxyanthraquinone, which are considered model chromophores of adriamycin and aclacinomycin, resp. Surface-enhanced resonance Raman spectra of these 2 drugs were compared by the use of Ag sols. The effects of DNA binding on the resonance Raman spectra are different for these 2 drugs. Adriamycin was intercalated in the CpG (or GpC) site of the DNA duplex, but aclacinomycin in the TpA (or ApT) site. Most of the differences in the spectra and sequence specificity are explained in terms of the mol. structures of their chromophores, i.e. in the adriamycin chromophore (1,4-dihydroxyanthraquinone) 2 OH groups are H bonded to different C:O groups, whereas in the aclacinomycin chromophore (1,8-dihydroxyantraquinone) 2 OH groups form H bonds with the same C:O group, leaving the other C:O group free from any intramol. H bonding.
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    86. 86
      Yan, Q.; Priebe, W.; Chaires, J. B.; Czernuszewicz, R. S. Interaction of doxorubicin and its derivatives with DNA: Elucidation by resonance Raman and surface-enhanced resonance Raman spectroscopy. Biospectroscopy 1997, 3, 307– 316,  DOI: 10.1002/(SICI)1520-6343(1997)3:4<307::AID-BSPY6>3.0.CO;2-0
      86
      Interaction of doxorubicin and its derivatives with DNA: elucidation by resonance Raman and surface-enhanced resonance Raman spectroscopy
      Yan, Qing; Priebe, Waldemar; Chaires, Jonathan B.; Czernuszewicz, Roman S.
      Biospectroscopy (1997), 3 (4), 307-316CODEN: BIOSFS; ISSN:1075-4261. (Wiley)
      The interactions of doxorubicin and its derivs., hydroxyrubicin and adriamycinone, with DNA were studied by resonance Raman (RR) and surface-enhanced resonance Raman scattering (SERRS) spectroscopy. The π-π interaction between the chromophore of the drug and DNA base pairs has been shown to downshift the skeletal stretching mode ∼ 1440 cm-1 by 8,5, and 4 cm-1 for doxorubicin, hydroxyrubicin, and adriamycinone, resp. The addnl. effects of intercalation with DNA on the RR and SERRS spectra for hydroxyrubicin are similar to those for doxorubicin. However, different effects are obsd. for adriamycinone. These results indicate that the sugar moiety is necessary to maintain the max. van der Waals contact between the chromophore and the DNA base pairs and that the amine group in the amino sugar is more favored than the hydroxyl group.
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    87. 87
      Lee, C.-J.; Kang, J.-S.; Kim, M.-S.; Lee, K.-P.; Lee, M.-S. The study of doxorubicin and its complex with DNA by SERS and UV-resonance Raman spectroscopy. Bull. Korean Chem. Soc. 2004, 25, 1211– 1216,  DOI: 10.5012/bkcs.2004.25.8.1211
      87
      The study of doxorubicin and its complex with DNA by SERS and UV-resonance Raman spectroscopy
      Lee, Chul Jae; Kang, Jae Soo; Kim, Mak Soon; Lee, Kwang Pill; Lee, Mu Sang
      Bulletin of the Korean Chemical Society (2004), 25 (8), 1211-1216CODEN: BKCSDE; ISSN:0253-2964. (Korean Chemical Society)
      The interaction of the antitumor agent doxorubicin with calf thymus DNA is investigated in an aq. soln. at a pH level of 6-7 with molar ratios of 1/10. A UV-resonance Raman spectroscopy and surface enhanced Raman spectroscopy are used to det. the doxorubicin binding sites and the structural variations of doxorubicin-DNA complexes in an aq. soln. Doxorubicin intercalates with adenine and guanine via a hydrogen bond formation between the N7 positions of purine bases and the hydroxyl group of doxorubicin.
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    88. 88
      Olszówka, M.; Russo, R.; Mancini, G.; Cappelli, C. A computational approach to the resonance Raman spectrum of doxorubicin in aqueous solution. Theor. Chem. Acc. 2016, 135, 27,  DOI: 10.1007/s00214-015-1781-9
      There is no corresponding record for this reference.
    89. 89
      Giovannini, T.; Macchiagodena, M.; Ambrosetti, M.; Puglisi, A.; Lafiosca, P.; Lo Gerfo, G.; Egidi, F.; Cappelli, C. Simulating vertical excitation energies of solvated dyes: From continuum to polarizable discrete modeling. Int. J. Quantum Chem. 2019, 119, e25684  DOI: 10.1002/qua.25684
      There is no corresponding record for this reference.
    90. 90
      Lafiosca, P.; Gómez, S.; Giovannini, T.; Cappelli, C. Absorption properties of large complex molecular systems: the DFTB/fluctuating charge approach. J. Chem. Theory Comput. 2022, 18, 1765– 1779,  DOI: 10.1021/acs.jctc.1c01066
      90
      Absorption Properties of Large Complex Molecular Systems: The DFTB/Fluctuating Charge Approach
      Lafiosca, Piero; Gomez, Sara; Giovannini, Tommaso; Cappelli, Chiara
      Journal of Chemical Theory and Computation (2022), 18 (3), 1765-1779CODEN: JCTCCE; ISSN:1549-9618. (American Chemical Society)
      We report on the first formulation of a novel polarizable QM/MM approach, where the D. Functional Tight Binding (DFTB) is coupled with the Fluctuating Charge (FQ) force field. The resulting method (DFTB/FQ) is then extended to linear response within the TD-DFTB framework and challenged to study absorption spectra of large condensed-phase systems.
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    91. 91
      Gómez, S.; Lafiosca, P.; Egidi, F.; Giovannini, T.; Cappelli, C. UV-Resonance Raman Spectra of Systems in Complex Environments: A Multiscale Modeling Applied to Doxorubicin Intercalated into DNA. J. Chem. Inf. Model. 2023, 63, 1208– 1217,  DOI: 10.1021/acs.jcim.2c01495
      91
      UV-Resonance Raman Spectra of Systems in Complex Environments: A Multiscale Modeling Applied to Doxorubicin Intercalated into DNA
      Gomez, Sara; Lafiosca, Piero; Egidi, Franco; Giovannini, Tommaso; Cappelli, Chiara
      Journal of Chemical Information and Modeling (2023), 63 (4), 1208-1217CODEN: JCISD8; ISSN:1549-9596. (American Chemical Society)
      UV-Resonance Raman (RR) spectroscopy is a valuable tool to study the binding of drugs to biomol. receptors. The extn. of information at the mol. level from exptl. RR spectra is made much easier and more complete thanks to the use of computational approaches, specifically tuned to deal with the complexity of the supramol. system. In this paper, we propose a protocol to simulate RR spectra of complex systems at different levels of sophistication, by exploiting a quantum mechanics/mol. mechanics (QM/MM) approach. The approach is challenged to investigate RR spectra of a widely used chemotherapy drug, doxorubicin (DOX) intercalated into a DNA double strand. The computed results show good agreement with exptl. data, thus confirming the reliability of the computational protocol.
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    92. 92
      Jawad, B.; Poudel, L.; Podgornik, R.; Steinmetz, N. F.; Ching, W.-Y. Molecular mechanism and binding free energy of doxorubicin intercalation in DNA. Phys. Chem. Chem. Phys. 2019, 21, 3877– 3893,  DOI: 10.1039/C8CP06776G
      92
      Molecular mechanism and binding free energy of doxorubicin intercalation in DNA
      Jawad, Bahaa; Poudel, Lokendra; Podgornik, Rudolf; Steinmetz, Nicole F.; Ching, Wai-Yim
      Physical Chemistry Chemical Physics (2019), 21 (7), 3877-3893CODEN: PPCPFQ; ISSN:1463-9076. (Royal Society of Chemistry)
      The intercalation process of binding doxorubicin (DOX) in DNA is studied by extensive mol. dynamics (MD) simulations. Many mol. factors that control the binding affinity of DOX to DNA to form a stable complex were inspected and quantified by employing continuum solvation models for estg. the binding free energy. The modified MM-PB(GB)SA methodol. provides a complete energetic profile of ΔGele, ΔGvDW, ΔGpolar, ΔGnon-polar, TΔStotal, ΔGdeform, ΔGcon, and ΔGion. To identify the sequence specificity of DOX, 2 different DNA sequences, d(CGATCG) or DNA1 and d(CGTACG) or DNA2, with one mol. (1:1 complex) or 2 mol. (2:1 complex) configurations of DOX were selected in this study. Our results showed that the DNA deformation energy (ΔGdeform), the energy cost from translational and rotational entropic contributions (TΔStran+rot), the total electrostatic interactions (ΔGpolar-PB/GB + ΔGele) of incorporation, the intramol. electrostatic interactions (ΔGele), and electrostatic polar solvation interactions (ΔGpolar-PB/GB) were all unfavorable to the binding of DOX to DNA. However, they were overcome by at least 5 favorable interactions: the van der Waals interactions (ΔGvDW), the non-polar solvation interaction (ΔGnon-polar), the vibrational entropic contribution (TΔSvib), and the std. concn.-dependent free energies of DOX (ΔGcon) and the ionic soln. (ΔGion). Specifically, the van der Waals interaction appeared to be the major driving force to form a stable DOX-DNA complex. We also predicted that DOX has stronger binding to DNA1 than DNA2. The DNA deformation penalty and entropy cost in the 2:1 complex were less than those in the 1:1 complex; thus, they indicated that the 2:1 complex is more stable than the 1:1 complex. We calcd. the total binding free energy (BFE) (ΔGt-sim) using both MM-PBSA and MM-GBSA methods, which suggested a more stable DOX-DNA complex at lower ionic concn. The calcd. BFE from the modified MM-GBSA method for DOX-DNA1 and DOX-DNA2 in the 1:1 complex was -9.1 and -5.1 kcal/mol, resp. The same quantities from the modified MM-PBSA method were -12.74 and -8.35 kcal/mol, resp. The value of the total BFE ΔGt-sim in the 1:1 complex was in reasonable agreement with the exptl. value of -7.7 ± 0.3 kcal/mol.
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    93. 93
      Jawad, B.; Poudel, L.; Podgornik, R.; Ching, W.-Y. Thermodynamic Dissection of the Intercalation Binding Process of Doxorubicin to dsDNA with Implications of Ionic and Solvent Effects. J. Phys. Chem. B 2020, 124, 7803– 7818,  DOI: 10.1021/acs.jpcb.0c05840
      93
      Thermodynamic dissection of the intercalation binding process of doxorubicin to dsDNA with implications of ionic and solvent effects
      Jawad, Bahaa; Poudel, Lokendra; Podgornik, Rudolf; Ching, Wai-Yim
      Journal of Physical Chemistry B (2020), 124 (36), 7803-7818CODEN: JPCBFK; ISSN:1520-5207. (American Chemical Society)
      Doxorubicin (DOX) is a cancer drug that binds to dsDNA through intercalation. A comprehensive microsecond timescale mol. dynamics study is performed for DOX with 16 tetradecamer dsDNA sequences in explicit aq. solvent, in order to investigate the intercalation process at both binding stages (conformational change and insertion binding stages). The mol. mechanics generalized Born surface area (MM-GBSA) method is adapted to quantify and break down the binding free energy (BFE) into its thermodn. components, for a variety of different soln. conditions as well as different DNA sequences. Our results show that the van der Waals interaction provides the largest contribution to the BFE at each stage of binding. The sequence selectivity depends mainly on the base pairs located downstream from the DOX intercalation site, with a preference for (AT)2 or (TA)2 driven by the favorable electrostatic and/or van der Waals interactions. Invoking the quartet sequence model proved to be most successful to predict the sequence selectivity. Our findings also indicate that the aq. bathing soln. (i.e., water and ions) opposes the formation of the DOX-DNA complex at every binding stage, thus implying that the complexation process preferably occurs at low ionic strength and is crucially dependent on solvent effects.
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    94. 94
      Latour, R. A. Perspectives on the simulation of protein–surface interactions using empirical force field methods. Colloids Surf., B 2014, 124, 25– 37,  DOI: 10.1016/j.colsurfb.2014.06.050
      94
      Perspectives on the simulation of protein-surface interactions using empirical force field methods
      Latour, Robert A.
      Colloids and Surfaces, B: Biointerfaces (2014), 124 (), 25-37CODEN: CSBBEQ; ISSN:0927-7765. (Elsevier B.V.)
      A review. Protein-surface interactions are of fundamental importance for a broad range of applications in the fields of biomaterials and biotechnol. Present exptl. methods are limited in their ability to provide a comprehensive depiction of these interactions at the atomistic level. In contrast, empirical force field based simulation methods inherently provide the ability to predict and visualize protein-surface interactions with full atomistic detail. These methods, however, must be carefully developed, validated, and properly applied before confidence can be placed in results from the simulations. In this perspectives paper, I provide an overview of the crit. aspects that I consider being of greatest importance for the development of these methods, with a focus on the research that my combined exptl. and mol. simulation groups have conducted over the past decade to address these issues. These crit. issues include the tuning of interfacial force field parameters to accurately represent the thermodn. of interfacial behavior, adequate sampling of these types of complex mol. systems to generate results that can be comparable with exptl. data, and the generation of exptl. data that can be used for simulation results evaluation and validation.
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    95. 95
      Walsh, T. R. Pathways to structure–property relationships of peptide–materials interfaces: Challenges in predicting molecular structures. Acc. Chem. Res. 2017, 50, 1617– 1624,  DOI: 10.1021/acs.accounts.7b00065
      95
      Pathways to Structure-Property Relationships of Peptide-Materials Interfaces: Challenges in Predicting Molecular Structures
      Walsh, Tiffany R.
      Accounts of Chemical Research (2017), 50 (7), 1617-1624CODEN: ACHRE4; ISSN:0001-4842. (American Chemical Society)
      A review. An in-depth appreciation of how to manipulate the mol.-level recognition between peptides and aq. materials interfaces, including nanoparticles, will advance technologies based on self-organized metamaterials for photonics and plasmonics, biosensing, catalysis, energy generation and harvesting, and nanomedicine. Exploitation of the materials-selective binding of biomols. is pivotal to success in these areas and may be particularly key to producing new hierarchically structured biobased materials. These applications could be accomplished by realizing preferential adsorption of a given biomol. onto one materials compn. over another, one surface facet over another, or one cryst. polymorph over another. Deeper knowledge of the aq. abiotic-biotic interface, to establish clear structure-property relations in these systems, is needed to meet this goal. In particular, a thorough structural characterization of the surface-adsorbed peptides is essential for establishing these relations but can often be challenging to accomplish via exptl. approaches alone. In addn. to myriad existing challenges assocd. with detg. the detailed mol. structure of any mol. adsorbed at an aq. interface, exptl. characterization of materials-binding peptides brings new, complex challenges because many materials-binding peptides are thought to be intrinsically disordered. This means that these peptides are not amenable to exptl. techniques that rely on the presence of well-defined secondary structure in the peptide when in the adsorbed state. To address this challenge, and in partnership with expt., mol. simulations at the atomistic level can bring complementary and crit. insights into the origins of this abiotic/biotic recognition and suggest routes for manipulating this phenomenon to realize new types of hybrid materials. For the reasons outlined above, mol. simulation approaches also face challenges in their successful application to model the biotic-abiotic interface, related to several factors. For instance, simulations require a plausible description of the chem. and the physics of the interface, which comprises two very different states of matter, in the presence of liq. water. Also, it is essential that the conformational ensemble be comprehensively characterized under these conditions; this is esp. challenging because intrinsically disordered peptides do not typically admit one single structure or set of structures. Moreover, a plausible structural model of the substrate is required, which may require a high level of detail, even for single-element materials such as Au surfaces or graphene. Developing and applying strategies to make credible predictions of the conformational ensemble of adsorbed peptides and using these to construct structure-property relations of these interfaces have been the goals of the authors' efforts. The authors have made substantial progress in developing interat. potentials for these interfaces and adapting advanced conformational sampling approaches for these purposes. This Account summarizes the authors' progress in the development and deployment of interfacial force fields and mol. simulation techniques for the purpose of elucidating these insights at biomol.-materials interfaces, using examples from the authors' labs. ranging from noble-metal interfaces to graphitic substrates (including carbon nanotubes and graphene) and oxide materials (such as titania). In addn. to the well-established application areas of plasmonic materials, biosensing, and the prodn. of medical implant materials, the authors outline new directions for this field that have the potential to bring new advances in areas such as energy materials and regenerative medicine.
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    96. 96
      Van Duin, A. C.; Dasgupta, S.; Lorant, F.; Goddard, W. A. ReaxFF: a reactive force field for hydrocarbons. J. Phys. Chem. A 2001, 105, 9396– 9409,  DOI: 10.1021/jp004368u
      96
      ReaxFF: A Reactive Force Field for Hydrocarbons
      van Duin, Adri C. T.; Dasgupta, Siddharth; Lorant, Francois; Goddard, William A., III
      Journal of Physical Chemistry A (2001), 105 (41), 9396-9409CODEN: JPCAFH; ISSN:1089-5639. (American Chemical Society)
      To make practical the mol. dynamics simulation of large scale reactive chem. systems (1000 s of atoms), the authors developed ReaxFF, a force field for reactive systems. ReaxFF uses a general relation between bond distance and bond order on one hand and between bond order and bond energy however, that leads to proper dissocn. of bonds to sepd. atoms. Other valence terms present in the force field (angle and torsion) are defined in terms of the same bond orders so that all these terms go to zero smoothly as bonds break. In addn., ReaxFF has Coulomb and Morse (van der Waals) potentials to describe nonbond interactions between all atoms (no exclusions). These nonbond interactions are shielded at short range so that the Coulomb and van der Waals interactions become const. as Rij → 0. The authors report here the ReaxFF for hydrocarbons. The parameters were derived from quantum chem. calcns. on bond dissocn. and reactions of small mols. plus heat of formation and geometry data for a no. of stable hydrocarbon compds. The ReaxFF provides a good description of these data. Generally, the results are of an accuracy similar or better than PM3, while ReaxFF is ∼100 times faster. In turn, the PM3 is ∼100 times faster than the QC calcns. Thus, with ReaxFF the authors hope to be able to study complex reactions in hydrocarbons.
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    97. 97
      Senftle, T. The ReaxFF reactive force-field: development, applications and future directions. Npj Comput. Mater. 2016, 2, 15011,  DOI: 10.1038/npjcompumats.2015.11
      97
      The ReaxFF reactive force-field: development, applications and future directions
      Senftle, Thomas P.; Hong, Sungwook; Islam, Md. Mahbubul; Kylasa, Sudhir B.; Zheng, Yuanxia; Shin, Yun Kyung; Junkermeier, Chad; Engel-Herbert, Roman; Janik, Michael J.; Aktulga, Hasan Metin; Verstraelen, Toon; Grama, Ananth; van Duin, Adri C. T.
      npj Computational Materials (2016), 2 (), 15011CODEN: NCMPCS; ISSN:2057-3960. (Nature Publishing Group)
      The reactive force-field (ReaxFF) interat. potential is a powerful computational tool for exploring, developing and optimizing material properties. Methods based on the principles of quantum mechanics (QM), while offering valuable theor. guidance at the electronic level, are often too computationally intense for simulations that consider the full dynamic evolution of a system. Alternatively, empirical interat. potentials that are based on classical principles require significantly fewer computational resources, which enables simulations to better describe dynamic processes over longer timeframes and on larger scales. Such methods, however, typically require a predefined connectivity between atoms, precluding simulations that involve reactive events. The ReaxFF method was developed to help bridge this gap. Approaching the gap from the classical side, ReaxFF casts the empirical interat. potential within a bond-order formalism, thus implicitly describing chem. bonding without expensive QM calcns. This article provides an overview of the development, application, and future directions of the ReaxFF method.
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    98. 98
      Monti, S.; Carravetta, V.; Ågren, H. Decoration of gold nanoparticles with cysteine in solution: reactive molecular dynamics simulations. Nanoscale 2016, 8, 12929– 12938,  DOI: 10.1039/C6NR03181A
      98
      Decoration of gold nanoparticles with cysteine in solution: reactive molecular dynamics simulations
      Monti, Susanna; Carravetta, Vincenzo; Agren, Hans
      Nanoscale (2016), 8 (26), 12929-12938CODEN: NANOHL; ISSN:2040-3372. (Royal Society of Chemistry)
      The dynamics of gold nanoparticle functionalization by means of adsorption of cysteine mols. in water soln.is simulated through classical reactive mol. dynamics simulations based on an accurately parametrized force field. The adsorption modes of the mols. are characterized in detail disclosing the nature of the cysteine-gold interactions and the stability of the final material. The simulation results agree satisfactorily with recent exptl. and theor.data and confirm previous findings for a similar system. The covalent attachments of the mols. to the gold support are all slow physisorptions followed by fast chemisorptions. However, a great variety of binding arrangements can be obsd. Interactions with the adsorbate caused surface modulations in terms of adatoms and dislocations which contributed to strengthen the cysteine adsorption.
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    99. 99
      Samieegohar, M.; Sha, F.; Clayborne, A. Z.; Wei, T. ReaxFF MD simulations of peptide-grafted gold nanoparticles. Langmuir 2019, 35, 5029– 5036,  DOI: 10.1021/acs.langmuir.8b03951
      99
      ReaxFF MD Simulations of Peptide-Grafted Gold Nanoparticles
      Samieegohar, Mohammadreza; Sha, Feng; Clayborne, Andre Z.; Wei, Tao
      Langmuir (2019), 35 (14), 5029-5036CODEN: LANGD5; ISSN:0743-7463. (American Chemical Society)
      Functionalized gold nanoparticles have crit. applications in biodetection with surface-enhanced Raman spectrum and drug delivery. In this study, reactive force field mol. dynamics simulations were performed to study gold nanoparticles, which are modified with different short-chain peptides consisting of amino acid residues of cysteine and glycine in different grafting densities in the aq. environment. Our study showed slight facet-dependent peptide adsorption on a gold nanoparticle with the 3 nm core diam. Peptide chains prefer to adsorb on the Au(111) facet compared to those on other facets of Au(100) and Au(110). In addn. to the stable thiol interaction with gold nanoparticle surfaces, polarizable oxygen and nitrogen atoms show strong interactions with the gold surface and polarize the gold nanoparticle surfaces with an overall pos. charge. Charges of gold atoms vary according to their contacts with peptide atoms and lattice positions. However, at the outmost peptide layer, the whole functionalized Au nanoparticles exhibit overall neg. electrostatic potential due to the grafted peptides. Moreover, simulations show that thiol groups can be deprotonated and subsequently protons can be transferred to water mols. and carboxyl groups.
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  • Supporting Information

    Supporting Information

    The Supporting Information is available free of charge at https://pubs.acs.org/doi/10.1021/acs.jpca.3c05560.

    • Adsorption free energies and minimum distances of the seven studied molecules with IFF/CHARMM and GolP-CHARMM; plots of minimum distances and adsorption free energy profiles for alanine dipeptide and the four nucleobases; NCI analyses; and clustered structures of doxorubicin (PDF)


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