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Polyethylene Glycol 20k. Does It Fluoresce?
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Polyethylene Glycol 20k. Does It Fluoresce?
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  • Bethany F. Laatsch
    Bethany F. Laatsch
    Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, Eau Claire, Wisconsin 54701, United States
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  • Michael Brandt
    Michael Brandt
    Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, Eau Claire, Wisconsin 54701, United States
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    Brianna Finke
    Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, Eau Claire, Wisconsin 54701, United States
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    Carl J. Fossum
    Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, Eau Claire, Wisconsin 54701, United States
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    Miles J. Wackett
    Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, Eau Claire, Wisconsin 54701, United States
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    Harrison R. Lowater
    Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, Eau Claire, Wisconsin 54701, United States
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    Alex Narkiewicz-Jodko
    Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, Eau Claire, Wisconsin 54701, United States
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    Christine N. Le
    Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, Eau Claire, Wisconsin 54701, United States
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    Thao Yang
    Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, Eau Claire, Wisconsin 54701, United States
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    Elizabeth M. Glogowski
    Department of Materials Science and Biomedical Engineering, University of Wisconsin-Eau Claire, Eau Claire, Wisconsin, 54701, United States
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    Scott C. Bailey-Hartsel
    Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, Eau Claire, Wisconsin 54701, United States
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  • Sudeep Bhattacharyya*
    Sudeep Bhattacharyya
    Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, Eau Claire, Wisconsin 54701, United States
    *Email: [email protected]. Phone: 715-836-2278. Fax: 715-836-4979.
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    Orcidhttps://orcid.org/0000-0002-3960-1239
  • Sanchita Hati*
    Sanchita Hati
    Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, Eau Claire, Wisconsin 54701, United States
    *Email: [email protected]. Phone: 715-836-3850. Fax: 715-836-4979.
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ACS Omega

Cite this: ACS Omega 2023, 8, 15, 14208–14218
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https://doi.org/10.1021/acsomega.3c01124
Published April 6, 2023

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Abstract

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Polyethylene glycol (PEG) is a polyether compound commonly used in biological research and medicine because it is biologically inert. This simple polymer exists in variable chain lengths (and molecular weights). As they are devoid of any contiguous π-system, PEGs are expected to lack fluorescence properties. However, recent studies suggested the occurrence of fluorescence properties in non-traditional fluorophores like PEGs. Herein, a thorough investigation has been conducted to explore if PEG 20k fluoresces. Results of this combined experimental and computational study suggested that although PEG 20k could exhibit “through-space” delocalization of lone pairs of electrons in aggregates/clusters, formed via intermolecular and intramolecular interactions, the actual contributor of fluorescence between 300 and 400 nm is the stabilizer molecule, i.e., 3-tert-butyl-4-hydroxyanisole present in the commercially available PEG 20k. Therefore, the reported fluorescence properties of PEG should be taken with a grain of salt, warranting further investigation.

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Introduction

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Polyethylene glycol (PEG) is a flexible, non-toxic polymer. (1,2) Due to its repeating ether groups, low-molecular-weight PEGs are hydrophilic and high-molecular-weight PEGs are amphiphilic in nature. (3,4) PEG is considered biologically inert and has numerous applications in medicine and industry. One common application of PEG is as an osmotic laxative. (5) Also, PEG is often attached to drug molecules in a process called PEGylation to enhance their stability and solubility, decrease the immune response, and increase circulation time throughout the body. (6) Recently, PEGylated lipids have been included as an ingredient in the vaccines for COVID-19, and PEG allergies in patients are suspected to be the likely cause of the rare anaphylactic response to the vaccine. (3) Additionally, PEG is used to coat surfaces to serve as a lubricant or a preservative. (7,8) Moreover, PEG molecules of variable sizes are commonly used for studying the effects of molecular crowding and confinement on the conformation and function of proteins and nucleic acids. (9,10) While probing the conformational change of a protein in crowded “intracellular-like” environments using intrinsic fluorescence spectroscopy, it was observed that the solution crowded with PEG of 20 kDa molecular weight (PEG 20k) fluoresced even in the absence of the protein under investigation; the fluorescence intensity of an aqueous solution containing phosphate buffer, PEG 20k, and sodium chloride was abnormally high. Unlike traditional fluorophores, which possess conjugated π-systems, PEG does not have such structural characteristics but interestingly fluoresced regardless.
Based on recent studies, it was revealed that PEG can be classified as a nontraditional intrinsic luminophore, and the resulting luminescent properties are due to the phenomenon referred to as aggregation-induced emission (AIE). (4,11−14) When in an aggregated state, heteroatoms are brought into proximity so that their lone pairs of electrons are easily delocalized. Additionally, the aggregation creates a more rigid structure, thereby reducing non-radiative relaxation. (15) In a recent study, the PEG of molecular weights from 2k to 12k were found to be emissive. (14) Moreover, it was reported that PEG 8k has the maximum emission among PEG 2k to 12k at 340 nm when excited at 280 nm. The fluorescence property of PEG 20k, however, remained unexplored. Various experimental studies revealed aggregate formation that might induce intrinsic fluorescence properties to PEG molecules via “through-space” delocalization. (14) However, the exact mechanism of the fluorescence has remained elusive. In the present study, we report a comprehensive investigation of the molecular basis of the fluorescent properties of PEG 20k molecules using combined experimental and computational methods. Fluorescence measurements of PEG 20k were conducted in aqueous solutions as well as in the presence of metal ions. Also, atomic force microscopy (AFM), dynamic light scattering (DLS), fluorescence anisotropy, and proton nuclear magnetic resonance (1H NMR) were used to analyze PEG 20k aggregates, assess their sizes, and investigate the presence of delocalization. Atomistic molecular dynamics (MD) simulations were performed to explore the structural properties of PEG 20k. Quantum chemical calculations were performed at the level of density functional theory with improved functionals (16−18) to probe if the “through-space” delocalization of the PEG 20k aggregates gives rise to the fluorescence properties.

Methods

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Experimental Section

Fluorescence Spectroscopy

Steady-state fluorescence experiments were performed using an Agilent Cary Eclipse fluorescence spectrophotometer. Samples of various concentrations of PEG 20k and other variable-sized PEG molecules were prepared by dissolving the required quantity of PEG in water or water along with 100 mM NaCl and 30 mM phosphate buffer of pH 7.4 to mimic biological conditions. Solutions of 100 mg/mL PEG 20k in the presence of six different metal ions were prepared using 10 mM NaCl, MgCl2, CoCl2, FeCl3, CrCl3, and K2CrO4. Blank samples containing only water and the corresponding metal salt were prepared for each of the six ionic compounds. PEG 600, PEG 2k, and PEG 8k were purchased from Thermo Fisher Scientific and were used as received without further purification. PEG 20k was obtained from Thermo Fisher Scientific and MilliporeSigma. Fluorescence of PEG 20k was recorded before and after purification with diethyl ether. Samples were excited within a range of 210–300 nm, and the emission spectra were recorded from 300 to 400 nm with 5 mm spectral slits. All experiments were performed using a quartz cuvette with a 1 cm optical path length and were done in triplicate.

Gas Chromatography–Mass Spectrometry

13 mL of 400 mg/mL PEG 20k sample (purified before and after washing with diethyl ether 6 and 12 times) was pipetted from the original sample into a 40 mL brown septum vial with a lid, and a Monotrap monolithic disc coated with octadecyl silane activated carbon (Monotrap DCC18, GL Sciences) was floated on top. Samples were then incubated in a water bath at 37 °C for 1 h. Following removal from the water bath, the Monotrap disk was removed from the vial, patted dry with a Kimwipe, and gently placed into a 3.0 mL microreaction vial with a lid. 2.0 mL of mass spectrometry (MS)-grade dichloromethane (DCM) was added, and the lid was tightly shut. The samples were put into the sonication bath for 10 min. All the remaining DCM was then extracted from the microreaction vial and placed into 1.5 mL Agilent screw cap vials and labeled. The compounds were separated and detected using an Agilent Technologies gas chromatography system (model: 7820 A GC System) with a quadrupole mass spectrometer. The instrument used a J&W DB624 GC column, 60 m, 0.32 mm, 1.80 μm, 7 inches. The oven temperature was set to 40 °C for 3 min and then increased to 320 °C at a rate of 9 °C/min. The front inlet temperature was 250 °C. The injection was in the split mode with a 1:1 ratio and 1 μL of injection volume at 7.14 psi. The detector temperature was 230 °C. The detection and data acquisition were performed in the scan mode at 35 scans/s, from 35 to 450 Da. Peaks were identified by comparison with the National Institute for Standards and Technology (NIST) database. All samples were done in duplicate, and a deionized H2O control was run alongside the PEG 20k duplicates.

Atomic Force Microscopy

Samples were prepared by applying 100 μg/mL, 20 mg/mL, 200 mg/mL, and 300 mg/mL PEG 20k solutions to freshly cleaved pieces of highly oriented pyrolytic graphite (HOPG) as to cover the whole surface of the HOPG. Samples on HOPG were incubated for 30 min. After 30 min, excess PEG 20k solution was removed from the HOPG substrate with a dry Kimwipe by capillary action. The sample was then dried in vacuo for 30 min and scanned using the MFP-3D Origin atomic force microscope from Asylum Research. Scans were conducted in a 5 μm area using the uniqprobe qp-BioAC probe and a force constant of 0.15–0.55 N/m. The scan rate was maintained at 0.4 Hz, and the scans were done with 512 scan points and lines. All samples were run in duplicate.

Dynamic Light Scattering

To examine if there is a formation of vesicles of PEG 20k in water and assess the distribution of the hydrodynamic radius of those vesicles, the DLS experiment was conducted using a Wyatt Mobius in the DLS-only mode with disposable cuvettes at 20 °C. Standard correlation cutoffs were used with auto-attenuation on and normal laser mode with a laser wavelength of 532.0 nm and a detector angle of 163.5°. An acquisition time of 2 s was used, and 10 runs were averaged per sample set. Each sample was duplicated 5 times to determine the statistical consistency of the data. The built-in Wyatt-developed regularization fit was used to determine the average hydrodynamic radius assuming multiple peaks in solution with data plotted in radius and percent intensity with a random coil model. Samples of 100, 200, and 300 mg/mL PEG 20k were each prepared with 100 mM NaCl and 10 mM phosphate buffer, pH 7.4, and filtered using VWR brand PES membrane 0.2 μm syringe filters.

Fluorescence Anisotropy

Anisotropy can reveal information about the size, shape, and rigidity of a sample in solution. Samples of 100, 200, and 300 mg/mL PEG 20k were each prepared in 100 mM NaCl and 10 mM phosphate buffer, pH 7.4. The anisotropy measurements were conducted with the automated polarizer accessory of the Agilent Cary Eclipse fluorescence spectrophotometer. Samples were excited at 288 nm because it was found to give the highest emission intensity recorded from 320 to 340 nm at temperatures of 25 and 50 °C.

1D-1H NMR

The NMR experiment was conducted to analyze the chemical shift of the ethylene group of PEG 20k in D2O at different concentrations. Solid PEG 20k was dissolved in D2O to prepare 20 and 200 mg/mL solution. 1D-1H NMR spectra were recorded using the Bruker Avance II 400 MHz NMR spectrometer.

UV–Vis Spectroscopy

The samples (30 and 300 mg/mL of PEG 20k) were prepared by dissolving the required amount of solid PEG 20k in deionized water. The spectra were recorded from 190 to 900 nm using the Varian Cary 50 UV–Vis spectrophotometer.

Computational

Software and Hardware

Visualization and molecular editing were carried out using the visual MD (VMD) program suite. (19) All MD simulations were performed using GPU-enabled nanoscale MD (NAMD). (20,21) Calculations were performed on the hybrid GPU–CPU BOSE supercomputer with 61 nodes and 3904 cores of the Blugold Center for High-Performance Computing, University of Wisconsin-Eau Claire. Each node of the cluster contains two CPUs, equipped with 2.3 GHz/32-core AMD EPYC 7452, and is connected through Hewlett Packard Slingshot internode connection. Additionally, GPU nodes have NVIDIA Tesla V100S 32GB GPU cards that enable NAMD to have hardware acceleration using GPU or CPU vectorization.
The CHARMM36 force field (22,23) was employed for molecular mechanical calculations. Non-bonding interactions were modeled using a switching function with a “switchdist” of 10 Å, a cutoff of 14 Å, and a “pairlistdist” of 16 Å. Furthermore, electrostatic interactions were treated with the particle mesh Ewald method. (24) The leapfrog Verlet algorithm (25) with a time step of 2 fs was used to compute atomic velocities and displacements. A modified Nosé-Hoover method (26,27) was employed for conformational sampling, where fluctuations in the barostat were controlled using Langevin dynamics. (28,29) For all solvated calculations, a periodic boundary condition, which controls the pressure by dynamically adjusting the unit cell volume and rescaling atomic coordinates, was used.
Electronic structure calculations were carried out using density functional theory. (30,31) Gas- and solvation-phase calculations were performed on Gaussian16 with the M06-2X density functional (16) using the 6-31+G(d,p) basis set. (32) Implicit solvation calculations were performed using the continuum solvation model, SMD. (33) Time-dependent density functional theory (TD-DFT) (34) was used to compute the excited state and model the electronic absorption of the PEG clusters as well as the monomeric EG. In these calculations, ground-state geometrically optimized structures were used to compute the excited-state potential energies using the Coulomb-attenuating method Becke 3-parameter, Lee–Yang–Parr (CAM-B3LYP) functional (34−37) along with the 6-311++g(d,p) basis set. (32)

Building a PEG 20k Monomer

A PEG 20k molecule was constructed with the CHARMM program (22) suite using homemade scripts. At first, ethylene glycol (EG) and its dimer were built. A major axis along the dimeric EG unit was defined, and that unit was copied and translated along the axis several times. These units were patched together using a homemade script to build a large chain. The final PEG 20k molecule had a molecular weight of 19,963 Da. The linear construct of the PEG chain was subjected to 100 ns MD simulation. A compact structure of PEG 20k was formed, which was solvated, and the resultant system was minimized for 50 ps. This minimized system was subjected to MD simulation for an additional 100 ns.

Building a PEG 20k Heptamer

The linear PEG 20k structure was duplicated 6 times to form a heptamer. The heptamer was first minimized, and then, a 200 ns MD simulation was performed in the gas phase. Upon gas-phase equilibration, the heptameric system was solvated at neutral pH. This resultant system was simulated for an additional 200 ns.

Determining the Ground- and Excited-State Structures of PEG 20k Clusters

To examine the structure, electron delocalization, and bonding of the PEG 20k interior, a quantum chemical study was conducted at the level of density functional theory. (30,31) Briefly, spherical regions of 5, 7.5, and 10 Å radii were extracted from the classical mechanically equilibrated structures and stored in the MD simulation trajectory of the PEG 20K monomer. Hydrogen atoms were added to complete the valences of the carbon and oxygen atoms. The smaller clusters were geometry-optimized using the smaller basis set 6-31+g(d,p). Excited states were computed from these optimized ground-state geometries using the expanded basis set of 6-311++g(d,p). The excited states for the cluster of 10 Å radius could not be determined because of the lack of convergence. A separate calculation of atomic charges was carried out on the ground states using natural bond orbital population analysis, which computes the localized electron density from the optimized electronic wavefunctions. (38)

Results and Discussion

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Fluorescence Measurements

Excitation Wavelength Variation Study of PEG 20k

The wavelength of maximum emission was examined by measuring the fluorescence of PEG 20k for a range of excitation wavelengths (λex) (Figure 1). The aqueous solution of unpurified PEG 20k was found to fluoresce at all wavelengths within the range, but the emission intensity was the highest at λex ∼ 290 nm for the intervals chosen. In the present study, we decided to use a λex of 295 nm due to its significance in protein studies. It should be noted that a comparison of PEG 20k (100 mg/mL) dissolved in buffer (100 mM NaCl and 10 mM phosphate buffer, pH 7.4) versus dissolved in water alone did not display a significant difference in emission intensity. Also, PEG 20k from Thermo Fisher Scientific and MilliporeSigma exhibited similar fluorescence behavior (Figure S1).

Figure 1

Figure 1. 100 mg/mL PEG 20k was excited at wavelengths of 280–300 nm in increments of 5 nm to determine the maximum emissions. Each fluorescence spectrum represents an average of three trials.

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Fluorescence Behavior of Different Molecular Weights of PEG

The fluorescent properties of PEG of various molecular weights were compared by exciting the PEG samples at 295 nm. Only PEG 20k displayed a significant fluorescence under the experimental condition, i.e., 100 mg/mL PEG in the presence of 100 mM NaCl and 10 mM phosphate buffer, pH 7.4, and λex = 295 nm (Figure 2). This was a deviation from the existing literature where PEG 2k to PEG 12k were reported to fluoresce at varying degrees. (4,14) The earlier work by Sun et al. (14) revealed an absence of a linear trend between the molecular weight and the extent of emission; PEG 8k exhibited the highest emission intensity when excited at 280 nm, whereas PEG 2k and PEG 12k exhibited very low emission intensity. As a significantly higher fluorescence intensity was observed for PEG 20k and almost no emission was observed from the lower molecular weight PEGs (Figures 2 and S2), it led us to investigate if any chemicals were present as impurities in the commercially available PEG 20k.

Figure 2

Figure 2. Solutions containing 100 mg/mL PEG, 100 mM NaCl, and 30 mM phosphate buffer of pH 7.4 were excited at 295 nm for molecular weights of PEG 600, PEG 2k, PEG 8k, and PEG 20k. Each fluorescence spectrum represents an average of three trials. No significant fluorescence was observed for any other PEG molecules except for PEG 20k.

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Detection of Impurity Using GC–MS

GC–MS experiment to investigate the presence of any impurities in PEG 20k

To examine the presence of impurities in PEG 20k samples, gas chromatography (GC)–MS experiments were carried out. For the unpurified PEG 20k, a single peak was observed at approximately 18 min in the GC–MS chromatogram (Figure 3). After a comparison of the spectra to the NIST database, a 96% match to the spectra for 3-tert-butyl-4-hydroxyanisole (3-BHA) was observed (Figure 3a). A value of 533898 was seen for the total ion current for this trial (Figure 3b,c). The second trial also showed a peak at the same 18 min mark and similar high spectral match values for 3-BHA in the NIST database. The GC–MS chromatograms of PEG 20k after washing with diethyl ether 6 and 12 times were also recorded. Washing with diethyl ether was done by adding an excess of diethyl ether to the powdered PEG 20k and incubating it for 30 min in a closed container. The dissolved 3-BHA in diethyl ether was then extracted. This process was repeated several times. The GC–MS chromatograms of purified PEG 20k demonstrated a significant decrease in peak height compared to the unpurified sample, 81.4% after 6 washes and 95.7% after 12 washes (Figure 3b,c and Table 1). The analysis of the area under the peak for GC–MS spectra revealed a ∼93% decrease in the concentration of 3-BHA after 12 washes with diethyl ether (Table 1). These results suggested that the thorough washing of solid PEG 20k with diethyl ether failed to remove completely the impurities in the form of 3-BHA, and possibly, remaining 3-BHA molecules were encapsulated by the PEG 20k polymer. The fluorescence spectra of PEG 20k (100 mg/mL) revealed a ∼50% decrease in fluorescence intensity after 6 washes and another 10% decrease (a total of 62% decrease) after 12 washes with diethyl ether compared to the unwashed sample (Figure 3d and Table 1). This demonstrates that the percent decrease in the area under fluorescence peaks between 6 and 12 washes is roughly proportional to the decrease in the area under GC–MS peak height between 6 and 12 washes. This correlation and the reduction in fluorescence intensity after treating the solid PEG 20k with diethyl ether suggested that the main contributor to the fluorescence between 300 and 400 nm is 3-BHA. Further investigation revealed that stabilizers like 3-BHA are used for higher molecular weight PEG (Sigma-Aldrich, CAS-No: 25322-68-3).

Figure 3

Figure 3. (a) GC–MS spectrum of 3-tert-butyl-4-hydroxyanisole (3-BHA), which is a 96% match to the spectrum of 3-BHA from the NIST Chemistry Webbook. (b) Chromatogram of the 3-BHA peak under three different washing conditions of 400 mg/mL PEG 20k. A full 30 min GC–MS analysis was run, and the 3-BHA peak is seen at approximately 18 min. Chromatogram only shows 15–20 min for clarity. (c) Peak intensity for the three trials of PEG 20k with different levels of purity. Data were taken at the apex of each 3-BHA peak, all within 0.02 s of each other and showing a match to 3-BHA in the NIST database. (d) Fluorescence spectra of 100 mg/mL PEG 20k before and after washing with diethyl ether.

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Although the GC–MS method employed here is qualitative in nature, ∼30 to 40% residual fluorescence intensity does not completely eliminate the possibility of PEG 20k having fluorescent properties. Particularly, previous studies reported the fluorescent properties of various PEG molecules. (4,14) Therefore, further studies were conducted to examine the possibility of PEG 20k to fluoresce, especially focusing on the aggregate formation and the “through-space” delocalization of lone pairs of electrons on oxygen atoms, resulting in AIE. An attempt was made to examine if PEG 20K forms clusters in an aqueous solution using AFM and DLS.

Aggregate Formation of PEG 20k

AFM Imaging-Identified Small Clusters

Aqueous solutions of PEG 20k of variable concentrations were applied to freshly cleaved pieces of HOPG (free HOPG substrate is shown in Figure S3). The topography of PEG 20k, deposited on the HOPG surface, was investigated by tapping-mode AFM. AFM images exhibited irregular-shaped aggregates (Figure 4). PEG 20k tends to form clusters at all concentrations, but their specific aggregation behavior changes depending on the concentration. At higher concentrations, PEG 20K appeared to aggregate in sheets as observed in the 200 and 300 mg/mL samples. At lower concentrations, PEG clusters formed, but the clusters were separated and smaller in size, as seen in the 20 mg/mL sample. This aggregation behavior was observed even at a lower concentration (100 μg/mL); however, the clusters were tiny.

Figure 4

Figure 4. AFM images of the PEG 20 k on the HOPG substrate. (a) Height-retraced and (b) amplitude-retraced images of PEG 20k on the HOPG substrate. Each AFM image size is 5 μm × 5 μm. The key in each image indicates a length of 1 μm. The image of the free HOPG substrate is shown in Figure S3.

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DLS Confirmed the Presence of Small Clusters of PEG 20k

To investigate the average hydrodynamic radius and size distribution of PEG species in solution, DLS analyses were conducted for PEG 20k solutions as a function of polymer concentration. Samples were filtered using PES membrane 0.2 μm syringe filters to ensure no dust or other large contaminants. The autocorrelation data (Figure 5a) showed a plateau that began at approximately 50 μs. This plateau was consistent for all PEG 20k polymer samples and increased in intensity with increasing polymer concentration, which indicated that this was a feature of the sample and not an anomalous result due to low concentration. The regularization fit of the data using a random coil model (Figure 5b) indicated that two species were present. The first peak is centered at 2.5 nm hydrodynamic radius, which corresponds to individual PEG chains. The second peak is centered at 600 nm hydrodynamic radius, which corresponds to clusters of polymer chains. This size range between 10 and 20%, similar to the dispersity for the individual polymer chain’s peak, indicates clearly defined clusters. The clusters are larger than previously reported polymer clusters, (14) which is consistent with the higher molecular weight PEG being used in this study.
Table 1. Comparative Analysis of the Decrease in Fluorescence and GC–MS Peak Areasa
 Number of Washes% Decrease After a Certain Number of Washes
 0612612
GC–MS peak height533898993192293981.495.7
the area under the GC–MS peak integrated from 17.95 to 18.25 min174733630125079.292.8
the area under the fluorescence peak integrated from 300 to 450 nm37121182031419651.061.8
a

The comparison was made by computing the peak areas for both measurement types. The GC–MS and fluorescence results were obtained after washing PEG 20k with diethyl ether.

Figure 5

Figure 5. (a) DLS autocorrelation functions of PEG 20k of 100, 200, and 300 mg/mL dissolved in 100 mM NaCl and 30 mM phosphate buffer of pH 7.4. (b) Regularization fit for 100 mg/mL PEG 20k dissolved in 100 mM NaCl and 30 mM phosphate buffer of pH 7.4.

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Fluorescence Anisotropy Measurement to Assess the Cluster Size

Both AFM and DLS experiments suggested the formation of aggregates in an aqueous solution. To examine the size, shape, and rigidity of the PEG 20k in an aqueous solution, fluorescence anisotropy was measured at various concentrations and at different temperatures. A fluorophore with low mobility and slow rotation relative to its fluorescent excitation lifetime will have a larger value of vertically polarized emissions than horizontal and so the anisotropy will be large. A fluorophore with high mobility will tumble rapidly through the solution relative to its fluorescent excitation lifetime and will have similar values of vertically and horizontally polarized emissions, making the anisotropy value small. The samples of 100, 200, and 300 mg/mL PEG 20k were excited at 288 nm, the wavelength at which emission was maximum for PEG 20k, and emissions were read at 320–340 nm at 25 and 50 °C (Figure 6). The anisotropy is higher at 25 °C than at 50 °C for all concentrations of PEG 20k, which is expected as the PEG 20k solution will be more mobile as the temperature and energy of the system increase.

Figure 6

Figure 6. Fluorescence anisotropy of PEG 20k of 100, 200, and 300 mg/mL dissolved in 100 mM NaCl and 30 mM phosphate buffer of pH 7.4. Samples were excited at 288 nm, and emissions were read from 320 to 340 nm. (a) Anisotropy at 25 °C and (b) anisotropy at 50 °C.

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Even at 25 °C, all concentrations of PEG 20k have relatively low anisotropy values. However, the data show a trend that as the concentration increases, so does the anisotropy value (Figure 6a). This suggests that there is less mobility of the PEG 20k aggregates at higher concentrations.
Perhaps this is because, at lower concentrations, there are smaller aggregates of PEG 20k that can easily tumble through the solution, whereas, at higher concentrations, there are larger aggregates that are not as mobile. The expected trends emerged, such as higher anisotropy values at higher concentrations, indicating the presence of some larger aggregates that continue to fluoresce but with a larger hydrodynamic radius. On the other hand, higher temperatures induced lower anisotropy values, indicating that aggregates have dissociated, and fluorescent species are similar in fluorescence properties and likely of similar sizes. Similar anisotropies for a low and high concentration of PEG 20k at a higher temperature (Figure 6b) also implicated the presence of a core structure with a generally low anisotropy value. However, it should be noted that all anisotropy values were relatively low, and there was more depolarization than expected for this relatively large polymer at all temperatures. These low anisotropy values indicated that the observed fluorescence from an aqueous solution of PEG 20k could simply be originating from the small fluorescent impurity, i.e., 3-BHA instead.

Melting and Cooling Experiments to Ascertain the Cluster Formation

In order to understand more about the characteristics of the PEG 20k clusters, a thermal variation experiment was performed in which the fluorescence intensity of the 100 mg/mL PEG 20k solution was measured with increasing temperature. It was found that the fluorescence intensity decreased linearly with increasing temperature (Figure 7). To examine whether the fluorophore could regain its emission intensity and therefore presumably attain its native clustered/aggregated form after cooling, the temperature was subsequently decreased in identical increments. It was found that the melting and cooling processes were reversible. However, no cooperativity in the melting or folding process was observed. This observation indicates two possibilities─(i) the fluorescence intensity decreases at higher temperature due to the disruption in the self-assembled clusters of PEG 20k, which prevented the “through-space” delocalization of lone pairs of electrons on oxygen atoms, and (ii) this decrease in fluorescence intensity is resulting from the dynamic quenching of the 3-BHA, trapped within the PEG 20k matrix, which increases at a higher temperature.

Figure 7

Figure 7. Solution containing 100 mg/mL PEG 20k, 100 mM NaCl, and 30 mM phosphate buffer of pH 7.4 was excited at 295 nm. The emission was recorded at 320 nm. The temperature was increased at 5° increments from 25 to 75 °C (marked with X). Similarly, cooling was done at 5° increments from 75 to 25 °C (marked with filled circles).

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Fluorescence Quenching due to Metal Ions

Impact of Metal ions on PEG 20k Emission Properties

Metal ions are known to act as fluorescence quenchers by employing different mechanisms such as ground-state complex formation, heavy atom quenching, the paramagnetic effect, resonance energy transfer, etc. (39) For a specific fluorophore, the quenching mechanism would be unique, and therefore, if the fluorescence properties of PEG 20k are a result of trapped 3-BHA, we would be able to see a pattern of fluorescence quenching, comparable to the free 3-BHA. To test this hypothesis, the fluorescence of PEG 20k was measured in the presence of various metal ions at a ratio of two metal ions for one PEG molecule and was excited at 295 nm. Co2+ and Cr3+ were observed to quench the fluorescence of PEG 20k to some extent, but Fe3+ and Cr6+ quenched the fluorescence completely (Figure 8). Na+ and Mg2+ had no effect on the fluorescence. These results were similar to what was reported by Paik et al. (4) and Sun et al. (14) and increased the possibility that metal ions interact with the lone pairs of oxygen (40) and thereby disrupt the delocalized electron cloud formed due to the clustering of PEG molecules.

Figure 8

Figure 8. Solutions of 100 mg/mL PEG 20k in the presence of metal ions of 10 mM concentration were excited at 295 nm. Each fluorescence spectrum represents an average of three trials. Na+, Mg2+, and Co2+ had no effect on the fluorescence of PEG 20k. Cr3+ displayed minimal quenching, whereas Fe3+ and Cr6+ quenched the fluorescence of PEG 20k completely.

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Controlled quenching experiments on 5 nM 3-BHA in water–ethanol (1:1 volume ratio) exhibited loss of fluorescent intensity across all metal ions (Table S1). While the partial quenching occurred at various degrees for Na+, Mg2+ Co2+, and Cr3+, a complete quenching was observed for Cr6+ and Fe3+ for 3-BHA (Table S1). The partial quenching of 3-BHA was significantly more than what was observed for PEG 20k. These results, although not completely confirmatory, indicate that the origin of fluorescence could very well be the 3-BHA fluorophore trapped in the network of PEG clusters. However, the absence of any effect by Na+ and Mg2+ and a minor impact due to Co2+ and Cr3+ on the fluorescence intensity in PEG 20k increases the possibility of emission due to aggregation of the PEG matrix, which might involve delocalized electrons interacting “through space” within the PEG 20k aggregates.

Through-Space Delocalization in PEG 20k

1D-1H NMR to Confirm Electron Delocalization

To further investigate the effect of through-space delocalization, 1H NMR of PEG 20k in D2O was recorded. 1H NMR analysis of PEG 20k in D2O at different concentrations revealed a chemical shift at 3.599 ppm for the ethylene (−CH2CH2−) protons for 20 mg/mL PEG 20k solution. The NMR peak for the methylene protons shifted toward the low field with the increase in the PEG 20k concentration; the peak for methylene protons appeared at 3.622 ppm for PEG 20k at a concentration of 200 mg/mL (Figure 9). This notable shift (∼0.023 ppm) toward the low field supports the fact that the electron density around the −CH2– protons was decreasing with increased PEG 20k concentration. The effect of electron-withdrawing groups, i.e., the ether O atoms, on the chemical shift of −CH2– protons is due to the cluster formation at higher concentrations. The cluster formation resulted in “through-space” delocalization. A similar observation was reported earlier for PEG 8k. (14)

Figure 9

Figure 9. 1H NMR spectra of PEG 20k in D2O at different concentrations.

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Although most of the experimental techniques used indicated the presence of PEG 20k clusters in an aqueous solution, which could lead to AIE, none of them confirmed that PEG 20k fluoresces around 300–400 nm. Hence, atomistic simulations and quantum calculations of molecular models were carried out to explore the structure of PEG 20k and examine the possibilities of AIE due to “through-space” delocalization.

Molecular Models of PEG

MD Simulation of PEG 20k Aggregates

At first, atomistic MD simulations were performed to investigate the structure of PEG 20k in an aqueous environment. Three types of MD simulations were conducted: a single-folded PEG 20k molecule in the aqueous phase, a partially folded single PEG 20k molecule with water in a spherical boundary, and a heptamer of PEG 20k in the gas phase and aqueous phase. At first, the PEG 20k polymer was built and the structure was minimized, which was then immersed into a water sphere. The initial ball-shaped conformation of the PEG 20k, obtained from the gaseous simulation, began to organize into hexagonal columns when solvated to mimic experimental conditions and simulated for 100 ns (Figure 10a,b). It is also important to note that the interior of the folded structure after 100 ns simulation did not contain any water molecules (Figure 10c). In contrast, when a single PEG 20k chain was allowed to fold in water, it formed clusters at the two ends of the chain, which then floated over the spherical water (Figure 11). This clustering phenomenon suggested that the hydrophobic interactions between the methylene groups of PEG 20k are stronger than the hydrophilic interactions with water molecules. Moreover, hydrophobic clustering also favors the delocalization of the lone pairs of electrons on oxygen atoms. (41)

Figure 10

Figure 10. Folded structure of PEG 20k, which was obtained after the gas-phase folded structure was immersed in water and then simulated for 100 ns. The following structures, displayed through VMD, represent planes of the folded PEG 20k─(a) the side view, (b) the top view, and (c) the zoomed-in top view of the planes.

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Figure 11

Figure 11. Simulated partially folded PEG 20k molecule in the water sphere.

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The initial gaseous PEG 20k heptamer simulation was used to examine interactions between PEG 20k molecules (intermolecular interactions) and those within a molecule (intramolecular interactions). After 200 ns simulation, each of the seven PEG 20k chains exhibited interactions, not only intramolecular but also between the PEG 20k molecules. Additionally, the structure became much more compact (Figure 12a). To investigate the potential impacts of water on the interactions between PEG 20k molecules, the final structure of the gaseous simulation was solvated at a neutral pH and then simulated for another 200 ns. An extension of the MD simulation time yielded a more compact and organized structure (Figure 12b) than previously seen in the first 200 ns. Similar to a single PEG 20k simulation, the large clusters of the PEG 20k heptamer did not contain any water molecules at the core of the organized cluster, which possessed both inter- and intramolecular interactions.

Figure 12

Figure 12. Organized structures of heptameric PEG 20k after 200 ns of gaseous simulation (a) followed by 200 ns of an aqueous simulation (b). These structures are displayed and rendered through VMD. The varying colors represent individual PEG 20k molecules.

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Electronic Structure Calculations of PEG 20k

The quantum chemical nature of the intramolecular interactions within the interior region of the folded PEG 20k was further investigated in small clusters of radii 5, 7.5, and 10 Å, with 70, 223, and 499 number of atoms, respectively (Table 2). In addition, a monomer and a dimer of EG were also used.
Table 2. HOMO–LUMO Energy Gap (in kcal/mol) in EG and PEG Clusters of Varied Sizes
moleculenumber of atomsHOMO–LUMO energy gap (kcal/mol)
EG (monomer)10230.4
EG (dimer)19221.6
5 Å sphere70201.8
7.5 Å sphere223194.1
10 Å sphere499188.2
The M06-2X functional was chosen for all calculations as this functional is parametrized to model the dispersion interactions that arise due to the electron correlational effect. (42) Furthermore, previous studies demonstrated that the M06-2X functional provides a reliable measure of energetics and geometry with a delocalized electron system. (17,18)
The electronic structure calculations revealed ordered arrangements of atoms with average interatomic distances of C–C, O–O, and C–O ranging from 3.4 to 4.0 Å between the adjacent columns. As the size of the clusters increased, these interatomic distances remained invariant. However, as the size increased, the highest occupied molecular orbital (HOMO) of these clusters appear to spread over a larger block of atoms, demonstrating increased delocalization (Figure 13). An increase in delocalization with the increase in the cluster size is further established by the decrease in the HOMO–LUMO energy gap (Table 2). A subsequent computation of the electronic transition using TD-DFT confirmed the ground-state calculation results, as described above. The excited-state calculation showed a single peak at 155 nm for the monomeric EG. As discussed in the work of Ueno et al., this peak arises due to the n-to-Rydberg orbital transition. (40) Our computation showed that as the size increased, the peak was red-shifted to 175 nm; this demonstrated more delocalization of the electron density (Figure 14) upon an increase in cluster size. The computed models did not exhibit any absorbance beyond 200 nm, and hence, the study conclusively demonstrated that the core of the PEG 20k aggregate has no absorbance in the 280–300 nm range.

Figure 13

Figure 13. Delocalization of the electron cloud as observed through electronic structure calculation of clusters of variable sizes, extracted from a folded PEG 20k polymer. The HOMO in each cluster is shown; the purple and green colors represent the positive and negative amplitudes, respectively, of the molecular orbital’s wavefunction. Hydrogen atoms are omitted for clarity.

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Figure 14

Figure 14. Simulated electronic spectra of EG (monomer) and PEG 20k clusters computed using time-dependent density functional theory.

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Analysis of Partial Charges of Oxygen

The analysis of partial charges of oxygen atoms with the increasing size of PEG 20k clusters portrayed a picture supporting the delocalization. As evident from the data provided in Table 3, there appears to be a discrete change in the partial charges as clusters formed, regardless of their size. The geometry-optimized structures of the EG monomer and its dimer (side-by-side) produced partial charges of ∼−0.8 for oxygen atoms.
Table 3. Partial Charge Distribution of Oxygen in EG and PEG Clusters of Varied Sizesa
moleculepercentage of atoms carrying an average partial charge of −0.85 or higherpercentage of atoms carrying an average partial charge of −0.65 or higher
EG (monomer/dimer)1000
5 Å sphere4456
7.5 Å sphere1486
10 Å sphere1783
a

The larger delocalization resulted in the reduced negative charge on oxygen atoms.

In contrast, for all clusters, a maximum partial charge for oxygen atoms of approximately −0.6 occurred (Table 3). As the cluster size increased, the percentage of oxygen atoms carrying diminished negative partial charges increased too, indicating increased delocalization.

Conclusions

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A detailed study, which involved experiments and computations, was conducted to investigate the origin of fluorescence in PEG 20k. Within the range of 280–300 nm excitation wavelength, the emission intensity of PEG 20k is maximum at ∼325 nm for λex ∼ 290 nm. Also, PEG 20k emission intensity increased with the increase in concentrations. In the aqueous state, the fluorescence intensity was maximum for PEG 20k compared to other PEG molecules when excited at 295 nm. The lack of fluorescence from lower molecular weight PEG molecules under the present experimental condition, which were earlier reported to exhibit fluorescence properties, prompted us to thoroughly investigate the origin of fluorescence in PEG 20k. We first checked the presence of any fluorescent molecules as impurities in the PEG 20k samples. The GC–MS experiments revealed the presence of 3-BHA in the commercially available PEG 20k. Removal of 3-BHA from PEG 20k using diethyl ether resulted in a significant decrease in the fluorescence intensity compared to the fluorescence intensity of the unpurified PEG 20k. This observation suggested that the emission observed between 300 and 400 nm from the aqueous solution of unpurified PEG 20K is mainly due to 3-BHA. Although the 3-BHA was not completely removed from the PEG 20k sample (there was ∼5% residual 3-BHA present), the fluorescence experiment does not exclude the possibility of PEG 20k behaving as a non-traditional fluorophore.
Various experimental studies suggested that the PEG 20k could form clusters in aqueous solution via intermolecular and intramolecular interactions within and between PEG 20k chains. The formation of clusters, which favors electron delocalization, was observed by AFM imaging and size measurements through DLS. Also, the fluorescent anisotropy measurement revealed the existence of clusters of PEG 20k at higher concentrations at 25 °C; PEG 20k clusters dissociate at a higher temperature (50 °C). This cluster formation could favor the “through-space” delocalization of lone pairs of electrons and could make this non-traditional fluorophore fluoresce via “aggregation-induced emission”. However, the melting temperature experiment and effects of metal ions were inconclusive regarding AIE. Nonetheless, NMR analyses of 20 and 200 mg/mL demonstrated a chemical shift of the ethylene protons (−CH2CH2−) toward the low field, from 3.599 to 3.622 ppm, suggesting the “through-space” delocalization due to cluster formation.
MD simulations of the PEG 20k monomer and heptamer in the gas phase and the aqueous phase also showed the existence of well-organized hexagonal columns in the folded polymers. These folded polymers were devoid of water molecules at the core, and the folding was favored due to hydrophobic interactions, intra- and intermolecular, between the methylene carbons. The hydrophobic clustering enabled electron delocalization among the organized oxygen atoms with lone pairs and is expected to induce the fluorescent property in PEG 20k. The electronic structure calculations of variable sizes of clusters, extracted from the core of a folded PEG 20k polymer, revealed ordered arrangements of hexagonal columns, where interatomic distances, i.e., C–C, O–O, and C–O, remained independent of cluster size. As the cluster size increased, electron clouds spread over a larger region, and the degree of delocalization increased. The electronic structure calculations provided a clear picture of the lone pairs of electron delocalization and the extended through-space delocalization. The computation of electronic transitions using TD-DFT revealed a single peak due to n-to-Rydberg orbital transition, which was red-shifted from 155 to 175 nm with increasing cluster size (Figure 14). However, the UV–Vis spectra of commercially available PEG 20k in water revealed the absorption maxima at ∼220 and ∼290 nm (Figure S4), which matched the reported UV–vis spectra of 3-BHA. (43) This observation suggested that although PEG 20k forms clusters at higher concentrations, which favors “through-space” delocalization of lone pairs of electrons, there is no evidence that it absorbs in the 280–300 nm range. In contrast, 3-BHA is the main chromophore that absorbs at 290 nm and emits between 300 and 400 nm. Taken together, the observed absence of fluorescent properties of the smaller PEG molecules and the lack of absorption of the quantum chemically simulated PEG 20k core at the excitation wavelength used in earlier studies (4,14) ─despite “through-space” delocalization ─ strongly suggested that PEG molecules do not fluoresce between 300–400 nm . Furthermore, the presence of the fluorogenic 3-BHA in the commercially available PEG 20k could be deceptive regarding the fluorescence observed for PEG molecules, irrespective of their sizes. Therefore, the reported fluorescent properties (4,14) of variable-sized PEG molecules should be re-examined.

Supporting Information

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The Supporting Information is available free of charge at https://pubs.acs.org/doi/10.1021/acsomega.3c01124.

  • Comparative decrease in fluorescence due to metal ions for PEG 20k vs 3-BHA, emission spectra of PEG 20k and PEG of different molecular weights, AFM images, and UV–vis spectrum of PEG 20k (PDF)

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Author Information

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  • Corresponding Authors
    • Sudeep Bhattacharyya - Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, Eau Claire, Wisconsin 54701, United States;  Orcidhttps://orcid.org/0000-0002-3960-1239;  Email: [email protected]
    • Sanchita Hati - Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, Eau Claire, Wisconsin 54701, United States;  Email: [email protected]
  • Authors
    • Bethany F. Laatsch - Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, Eau Claire, Wisconsin 54701, United States
    • Michael Brandt - Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, Eau Claire, Wisconsin 54701, United States
    • Brianna Finke - Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, Eau Claire, Wisconsin 54701, United States
    • Carl J. Fossum - Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, Eau Claire, Wisconsin 54701, United States;  Present Address: Department of Chemistry, Virginia Tech, Blacksburg, VA 24061
    • Miles J. Wackett - Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, Eau Claire, Wisconsin 54701, United States
    • Harrison R. Lowater - Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, Eau Claire, Wisconsin 54701, United States
    • Alex Narkiewicz-Jodko - Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, Eau Claire, Wisconsin 54701, United States
    • Christine N. Le - Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, Eau Claire, Wisconsin 54701, United States
    • Thao Yang - Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, Eau Claire, Wisconsin 54701, United States
    • Elizabeth M. Glogowski - Department of Materials Science and Biomedical Engineering, University of Wisconsin-Eau Claire, Eau Claire, Wisconsin, 54701, United States
    • Scott C. Bailey-Hartsel - Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, Eau Claire, Wisconsin 54701, United States
  • Funding

    This work was supported in part by the National Institute of Health [grant no R15 GM117510-02 (S.H. and S.B.). The computational resources of the study were provided by the Blugold Center for High-Performance Computing under NSF grant CNS 1920220.

  • Notes
    The authors declare no competing financial interest.

Acknowledgments

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We are grateful to the three anonymous reviewers for their constructive suggestions. We also thank the Learning and Technology Services at UW-Eau Claire for their support in using supercomputing clusters.

Abbreviations

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AFM

atomic force microscopy

AIE

aggregation-induced emission

DLS

dynamic light scattering

EG

ethylene glycol

HOPG

highly oriented pyrolytic graphite

PEG 20k

polyethylene glycol 20,000

MD

molecular dynamics

1H NMR

proton nuclear magnetic resonance

References

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    Tribological characteristics of polyethylene glycol (PEG) as a lubricant for wear resistance of ultra-high-molecular-weight polyethylene (UHMWPE ) in artificial knee join
    Kobayashi, Masanori; Koide, Takayuki; Hyon, Suong-Hyu
    Journal of the Mechanical Behavior of Biomedical Materials (2014), 38 (), 33-38CODEN: JMBBCP; ISSN:1878-0180. (Elsevier Ltd.)
    For the longevity of total knee joint prostheses, we have developed an artificial lubricant using polyethylene glycol (PEG) for the prevention of wear of ultra-high-mol.-wt. polyethylene (UHMWPE). In the present study, the lubricative function of this PEG lubricant was evaluated by a wear test using Co-Cr alloy and UHMWPE counter surface samples. As a result, human synovial fluid including the PEG lubricant showed good result regarding the wear vol. and a worn surface of UHMWPE. Considering its lubrication mechanism, it is suspected that interaction between the PEG mols. and the proteins in synovial fluid was involved. Since PE mols. are also org. compds. having a hydroxyl group at one or both ends, the albumin and PEG mol. complex would have bound more strongly to the metal oxide surface and UHMWPE surfaces might enhance and stabilize the lubricating film between the contact surfaces under the boundary lubrication. This study suggests that PEG lubricant as an intra-articular viscous supplement has the potential to prevent wear of UHMWPE by mixing with synovial fluid and to contribute to the longevity of knee joint prostheses.
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  8. 8
    Salaita, G. N.; Ma, F. M. S.; Parker, T. C.; Hoflund, G. B. Weathering Properties of Treated Southern Yellow Pine Wood Examined by X-Ray Photoelectron Spectroscopy, Scanning Electron Microscopy and Physical Characterization. Appl. Surf. Sci. 2008, 254, 3925– 3934,  DOI: 10.1016/j.apsusc.2007.12.017
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    Weathering properties of treated southern yellow pine wood examined by X-ray photoelectron spectroscopy, scanning electron microscopy and physical characterization
    Salaita, Ghaleb N.; Ma, Frank M. S.; Parker, Trudy C.; Hoflund, Gar B.
    Applied Surface Science (2008), 254 (13), 3925-3934CODEN: ASUSEE; ISSN:0169-4332. (Elsevier B.V.)
    In this study the weathering behavior of southern yellow pine (SYP) wood samples pretreated in different solns. was examd. using XPS, SEM and various types of phys. characterization regarding material loss and discoloration. The treatment solns. include water as a control, a com. available water repellent (WR) wood treating additive and polyethylene glycol (PEG) products including PEG PLUS, PEG 8000 solns. and Compd. 20M in varying concns. All contained the wood preservative chromated copper arsenate (CCA). One sample was treated with a CCA soln. only. The treatments were carried out at 20 °C and 150 psig for 1/2 h after exposure to vacuum (28 mmHg) for 15 min. Simulated weathering was achieved in an Atlas 65-W Weather-Ometer for 2000 h with both light and dark periods and rain. The temp. ranged from 23 °C during the dark cycle to 35 °C during the light cycle. With weathering the XPS O/C ratios increase due to oxidn. of the surface. Exposure to UV light results in bond breakage and reaction with oxygen in the presence of air to form org. functional groups such as C-O-C-O, cyclic C2O, C=O and/or O-C-O. These oxidized products can protect the underlying wood from deterioration if they are insol. in water and remain on the surface as a protective coating. If sol., rain washes the compds. away and assists in the degrdn. Correlated changes are obsd. in the XPS O/C ratios, the high-resoln. XPS C 1s spectra, the SEM micrographs and phys. measurements including thickness alteration, wt. loss, and discoloration by yellowing or whitening of the weathered wood. The PEG treatments are effective in protecting wood with the 2% PEG PLUS treatment providing the best weathering behavior similar to that of the CCA treatment. The WR and water treatments yield the poorest weathering properties.
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  9. 9
    Kuznetsova, I. M.; Turoverov, K. K.; Uversky, V. N. What Macromolecular Crowding Can Do to a Protein. Int. J. Mol. Sci. 2014, 15, 23090– 23140,  DOI: 10.3390/ijms151223090
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    What macromolecular crowding can do to a protein
    Kuznetsova, Irina M.; Turoverov, Konstantin K.; Uversky, Vladimir N.
    International Journal of Molecular Sciences (2014), 15 (12), 23090-23140, 51 pp.CODEN: IJMCFK; ISSN:1422-0067. (MDPI AG)
    A review. The intracellular environment represents an extremely crowded milieu, with a limited amt. of free water and an almost complete lack of unoccupied space. Obviously, slightly salted aq. solns. contg. low concns. of a biomol. of interest are too simplistic to mimic the "real life" situation, where the biomol. of interest scrambles and wades through the tightly packed crowd. In lab. practice, such macromol. crowding is typically mimicked by concd. solns. of various polymers that serve as model "crowding agents". Studies under these conditions revealed that macromol. crowding might affect protein structure, folding, shape, conformational stability, binding of small mols., enzymic activity, protein-protein interactions, protein-nucleic acid interactions, and pathol. aggregation. The goal of this review is to systematically analyze currently available exptl. data on the variety of effects of macromol. crowding on a protein mol. The review covers more than 320 papers and therefore represents one of the most comprehensive compendia of the current knowledge in this exciting area.
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  10. 10
    Adams, L. M. M.; Andrews, R. J. J.; Hu, Q. H. H.; Schmit, H. L. L.; Hati, S.; Bhattacharyya, S. Crowder-Induced Conformational Ensemble Shift in Escherichia Coli Prolyl-TRNA Synthetase. Biophys. J. 2019, 117, 1269– 1284,  DOI: 10.1016/j.bpj.2019.08.033
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    10
    Crowder-Induced Conformational Ensemble Shift in Escherichia coli Prolyl-tRNA Synthetase
    Adams, Lauren M.; Andrews, Ryan J.; Hu, Quin H.; Schmit, Heidi L.; Hati, Sanchita; Bhattacharyya, Sudeep
    Biophysical Journal (2019), 117 (7), 1269-1284CODEN: BIOJAU; ISSN:0006-3495. (Cell Press)
    The effect of mol. crowding on the structure and function of Escherichia coli prolyl-tRNA synthetase (Ec ProRS), a member of the aminoacyl-tRNA synthetase family, has been investigated using a combined exptl. and theor. method. Ec ProRS is a multidomain enzyme; coupled-domain dynamics are essential for efficient catalysis. To gain insight into the mechanistic detail of the crowding effect, kinetic studies were conducted with varying concns. and sizes of crowders. In parallel, spectroscopic and quantum chem. studies were employed to probe the "soft interactions" between crowders and protein side chains. Finally, the dynamics of the dimeric protein was examd. in the presence of crowders using a long-duration (70 ns) classical mol. dynamic simulations. The results of the simulations revealed a shift in the conformational ensemble, which is consistent with the preferential exclusion of cosolutes. The "soft interactions" model of the crowding effect also explained the alteration in kinetic parameters. In summary, the study found that the effects of mol. crowding on both conformational dynamics and catalytic function are correlated in the multidomain Ec ProRS, an enzyme that is central to protein synthesis in all living cells. This study affirmed that large and small cosolutes have considerable impacts on the structure, dynamics, and function of modular proteins and therefore must be considered for stabilizing protein-based pharmaceuticals and industrial enzymes.
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    Wang, Y.; Zhao, Z.; Yuan, W. Z. Intrinsic Luminescence from Nonaromatic Biomolecules. ChemPlusChem 2020, 85, 1065– 1080,  DOI: 10.1002/cplu.202000021
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    Intrinsic Luminescence from Nonaromatic Biomolecules
    Wang, Yunzhong; Zhao, Zihao; Yuan, Wang Zhang
    ChemPlusChem (2020), 85 (5), 1065-1080CODEN: CHEMM5; ISSN:2192-6506. (Wiley-VCH Verlag GmbH & Co. KGaA)
    A review. Novel emitters that do not contain traditional chromophores but only electron-rich moieties (e. g. amine, C=O, -OH, ether, and imide), which are classified as nonconventional luminophores, have been more frequently reported. Although more and more examples have been demonstrated, their emission mechanism remains unclear. The clustering-triggered emission (CTE) mechanism has previously been proposed to rationalize the luminescence of unconventional chromophores. Moreover, great attention has been paid to the distinctive inherent luminescence from nonarom. biomols. such as cellulose, starch, sugars, and nonarom. amino acids and proteins. In this Review, we summarize these unconventional biomol. luminophores and apply the CTE mechanism to rationalize such a phenomenon. This Review may shed new light on the understanding of intrinsic emission of nonarom. biomols. and decipher the intrinsic fluorescence from cells and tissues.
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  12. 12
    Li, Q.; Tang, Y.; Hu, W.; Li, Z. Fluorescence of Nonaromatic Organic Systems and Room Temperature Phosphorescence of Organic Luminogens: The Intrinsic Principle and Recent Progress. Small 2018, 14, 1801560,  DOI: 10.1002/smll.201801560
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    Zhang Yuan, W.; Zhang, Y. Nonconventional Macromolecular Luminogens with Aggregation-Induced Emission Characteristics. J. Polym. Sci., Part A: Polym. Chem. 2017, 55, 560– 574,  DOI: 10.1002/pola.28420
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    Sun, C.; Jiang, X.; Li, B.; Li, S.; Kong, X. Z. Fluorescence Behavior and Mechanisms of Poly(Ethylene Glycol) and Their Applications in Fe3+ and Cr6+ Detections, Data Encryption, and Cell Imaging. ACS Sustain. Chem. Eng. 2021, 9, 5166– 5178,  DOI: 10.1021/acssuschemeng.1c00250
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    Chatterjee, D. P.; Pakhira, M.; Nandi, A. K. Fluorescence in “Nonfluorescent” Polymers. ACS Omega 2020, 5, 30747– 30766,  DOI: 10.1021/acsomega.0c04700
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    Fluorescence in "Nonfluorescent" Polymers
    Chatterjee, Dhruba P.; Pakhira, Mahuya; Nandi, Arun K.
    ACS Omega (2020), 5 (48), 30747-30766CODEN: ACSODF; ISSN:2470-1343. (American Chemical Society)
    A review. Recently, a great deal of research has been started on generating fairly strong photoluminescence from org. mols. without having any conjugated π-system or fluorophore. Discrete chromophores or auxochromophores termed as "subfluorophores" may undergo "space conjugation" via cooperative intramol. conformation followed by intermol. aggregation to generate fluorescence or sometimes phosphorescence emission. Polymeric materials are important in this regard as nonconjugated polymers self-assemble/aggregate in a moderately concd. soln. and also in the solid state, producing membranes, films, and so forth with good phys. and mech. properties. Therefore, promoting fluorescence in these commodity polymers is very much useful for sensing, org. light emitting diodes (OLED), and biol. applications. In this perspective, we have discussed the aggregation-induced emission from four different types of architectures, for example, (1) dendrimers or hyperbranched polymers, (2) entrapped polymeric micellar self-assembly, (3) cluster formation, and (4) stretching-induced aggregation, begining with the genesis of fluorescence from aggregation of propeller-shaped small org. mols. The mechanism of induced fluorescence of polymers with subfluorophoric groups is also discussed from the theor. calcns. of the energy bands in the aggregated state. Also, an attempt has been made to highlight some useful applications in the sensing of surfactants, bacteria, cell imaging, drug delivery, gene delivery, OLED, and so forth.
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    Zhao, Y.; Truhlar, D. G. The M06 Suite of Density Functionals for Main Group Thermochemistry, Thermochemical Kinetics, Noncovalent Interactions, Excited States, and Transition Elements: Two New Functionals and Systematic Testing of Four M06-Class Functionals and 12 Other Functionals. Theor. Chem. Acc. 2008, 120, 215– 241,  DOI: 10.1007/s00214-007-0310-x
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    The M06 suite of density functionals for main group thermochemistry, thermochemical kinetics, noncovalent interactions, excited states, and transition elements: two new functionals and systematic testing of four M06-class functionals and 12 other functionals
    Zhao, Yan; Truhlar, Donald G.
    Theoretical Chemistry Accounts (2008), 120 (1-3), 215-241CODEN: TCACFW; ISSN:1432-881X. (Springer GmbH)
    We present two new hybrid meta exchange-correlation functionals, called M06 and M06-2X. The M06 functional is parametrized including both transition metals and nonmetals, whereas the M06-2X functional is a high-nonlocality functional with double the amt. of nonlocal exchange (2X), and it is parametrized only for nonmetals. The functionals, along with the previously published M06-L local functional and the M06-HF full-Hartree-Fock functionals, constitute the M06 suite of complementary functionals. We assess these four functionals by comparing their performance to that of 12 other functionals and Hartree-Fock theory for 403 energetic data in 29 diverse databases, including ten databases for thermochem., four databases for kinetics, eight databases for noncovalent interactions, three databases for transition metal bonding, one database for metal atom excitation energies, and three databases for mol. excitation energies. We also illustrate the performance of these 17 methods for three databases contg. 40 bond lengths and for databases contg. 38 vibrational frequencies and 15 vibrational zero point energies. We recommend the M06-2X functional for applications involving main-group thermochem., kinetics, noncovalent interactions, and electronic excitation energies to valence and Rydberg states. We recommend the M06 functional for application in organometallic and inorganometallic chem. and for noncovalent interactions.
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    North, M. A.; Bhattacharyya, S.; Truhlar, D. G. Improved Density Functional Description of the Electrochemistry and Structure-Property Descriptors of Substituted Flavins. J. Phys. Chem. B 2010, 114, 14907– 14915,  DOI: 10.1021/jp108024b
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    Improved Density Functional Description of the Electrochemistry and Structure-Property Descriptors of Substituted Flavins
    North, Michael A.; Bhattacharyya, Sudeep; Truhlar, Donald G.
    Journal of Physical Chemistry B (2010), 114 (46), 14907-14915CODEN: JPCBFK; ISSN:1520-6106. (American Chemical Society)
    The energetics of electrochem. changes have been investigated for several substituted flavins with the M06-L d. functional. The redn. potentials for one- and two-electron redns. of these mols. have been detd. and the results are consistent with exptl. findings with a mean unsigned error of only 42 mV. It is esp. noteworthy that the M06-L d. functional makes a significant difference in the computed free energy of the first redn. of lumiflavin, which produces a neutral semiquinone. We also investigate the effects of flavin ring substituents on the geometries, charge distributions, redn. potentials, pKa's, ionization potentials, electron affinities, hardnesses, softnesses, electrophilic powers, and nucleophilicities.
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  18. 18
    Bresnahan, C. G.; Reinhardt, C. R.; Bartholow, T. G.; Rumpel, J. P.; North, M.; Bhattacharyya, S. Effect of Stacking Interactions on the Thermodynamics and Kinetics of Lumiflavin: A Study with Improved Density Functionals and Density Functional Tight-Binding Protocol. J. Phys. Chem. A 2015, 119, 172– 182,  DOI: 10.1021/jp510020v
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    Effect of Stacking Interactions on the Thermodynamics and Kinetics of Lumiflavin: A Study with Improved Density Functionals and Density Functional Tight-Binding Protocol
    Bresnahan, Caitlin G.; Reinhardt, Clorice R.; Bartholow, Thomas G.; Rumpel, John P.; North, Michael; Bhattacharyya, Sudeep
    Journal of Physical Chemistry A (2015), 119 (1), 172-182CODEN: JPCAFH; ISSN:1089-5639. (American Chemical Society)
    The π-π stacking interaction between lumiflavin and a no. of π-electron-rich mols. has been studied by d. functional theory using several new-generation d. functionals. Six known lumiflavin-arom. adducts were used and the models were evaluated by comparing the geometry and energetics with exptl. results. The study found that dispersion-cor. and hybrid functionals with larger (>50%) Hartree-Fock exchanges produced superior results in modeling thermodn. characteristics of these complexes. The functional producing the best energetics for these model systems was used to study the stacking interactions of lumiflavin with biol. relevant arom. groups. Addnl., the redn. of flavin-in the presence of both a hydride donor and a nondonor π-electronic system was also studied. Weak interactions were obsd. in the stacked lumiflavin complexes of benzene, phenol, and indole, mimicking Ph alanine, tryptophan, and tyrosine side chains, resp., of an enzyme. The stacked complex of naphthalene and flavin showed little change in flavin's redox potential indicating insignificant effect on the thermodn. of the hydride transfer reaction. In contrast, the hydride transfer reaction with the hydride donor N-Me nicotinamide tells a different story, as the transition state was found to be strongly impacted by the stacking interactions. A comparison of performance between the d. functional theory (DFT) and the computationally less expensive dispersion-cor. self-consistent d. functional tight-binding (SCC-DFTB-D) theory revealed that the latter produces consistent energetics for this hydride transfer reaction and addnl. DFT-computed perturbative corrections could significantly improve these results.
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    Humphrey, W.; Dalke, A.; Schulten, K. VMD: Visual Molecular Dynamics. J. Mol. Graph. 1996, 14, 33– 38,  DOI: 10.1016/0263-7855(96)00018-5
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    VDM: visual molecular dynamics
    Humphrey, William; Dalke, Andrew; Schulten, Klaus
    Journal of Molecular Graphics (1996), 14 (1), 33-8, plates, 27-28CODEN: JMGRDV; ISSN:0263-7855. (Elsevier)
    VMD is a mol. graphics program designed for the display and anal. of mol. assemblies, in particular, biopolymers such as proteins and nucleic acids. VMD can simultaneously display any no. of structures using a wide variety of rendering styles and coloring methods. Mols. are displayed as one or more "representations," in which each representation embodies a particular rendering method and coloring scheme for a selected subset of atoms. The atoms displayed in each representation are chosen using an extensive atom selection syntax, which includes Boolean operators and regular expressions. VMD provides a complete graphical user interface for program control, as well as a text interface using the Tcl embeddable parser to allow for complex scripts with variable substitution, control loops, and function calls. Full session logging is supported, which produces a VMD command script for later playback. High-resoln. raster images of displayed mols. may be produced by generating input scripts for use by a no. of photorealistic image-rendering applications. VMD has also been expressly designed with the ability to animate mol. dynamics (MD) simulation trajectories, imported either from files or from a direct connection to a running MD simulation. VMD is the visualization component of MDScope, a set of tools for interactive problem solving in structural biol., which also includes the parallel MD program NAMD, and the MDCOMM software used to connect the visualization and simulation programs, VMD is written in C++, using an object-oriented design; the program, including source code and extensive documentation, is freely available via anonymous ftp and through the World Wide Web.
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    Phillips, J. C.; Braun, R.; Wang, W.; Gumbart, J.; Tajkhorshid, E.; Villa, E.; Chipot, C.; Skeel, R. D.; Kalé, L.; Schulten, K. Scalable Molecular Dynamics with NAMD. J. Comput. Chem. 2005, 26, 1781– 1802,  DOI: 10.1002/jcc.20289
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    Scalable molecular dynamics with NAMD
    Phillips, James C.; Braun, Rosemary; Wang, Wei; Gumbart, James; Tajkhorshid, Emad; Villa, Elizabeth; Chipot, Christophe; Skeel, Robert D.; Kale, Laxmikant; Schulten, Klaus
    Journal of Computational Chemistry (2005), 26 (16), 1781-1802CODEN: JCCHDD; ISSN:0192-8651. (John Wiley & Sons, Inc.)
    NAMD is a parallel mol. dynamics code designed for high-performance simulation of large biomol. systems. NAMD scales to hundreds of processors on high-end parallel platforms, as well as tens of processors on low-cost commodity clusters, and also runs on individual desktop and laptop computers. NAMD works with AMBER and CHARMM potential functions, parameters, and file formats. This article, directed to novices as well as experts, first introduces concepts and methods used in the NAMD program, describing the classical mol. dynamics force field, equations of motion, and integration methods along with the efficient electrostatics evaluation algorithms employed and temp. and pressure controls used. Features for steering the simulation across barriers and for calcg. both alchem. and conformational free energy differences are presented. The motivations for and a roadmap to the internal design of NAMD, implemented in C++ and based on Charm++ parallel objects, are outlined. The factors affecting the serial and parallel performance of a simulation are discussed. Finally, typical NAMD use is illustrated with representative applications to a small, a medium, and a large biomol. system, highlighting particular features of NAMD, for example, the Tcl scripting language. The article also provides a list of the key features of NAMD and discusses the benefits of combining NAMD with the mol. graphics/sequence anal. software VMD and the grid computing/collab. software BioCoRE. NAMD is distributed free of charge with source code at www.ks.uiuc.edu.
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    Phillips, J. C.; Hardy, D. J.; Maia, J. D. C. C.; Stone, J. E.; Ribeiro, J. v.; Bernardi, R. C.; Buch, R.; Fiorin, G.; Hénin, J.; Jiang, W.; McGreevy, R.; Melo, M. C. R. R.; Radak, B. K.; Skeel, R. D.; Singharoy, A.; Wang, Y.; Roux, B.; Aksimentiev, A.; Luthey-Schulten, Z.; Kalé, L. v.; Schulten, K.; Chipot, C.; Tajkhorshid, E. Scalable Molecular Dynamics on CPU and GPU Architectures with NAMD. J. Chem. Phys. 2020, 153, 044130,  DOI: 10.1063/5.0014475
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    Scalable molecular dynamics on CPU and GPU architectures with NAMD
    Phillips, James C.; Hardy, David J.; Maia, Julio D. C.; Stone, John E.; Ribeiro, Joao V.; Bernardi, Rafael C.; Buch, Ronak; Fiorin, Giacomo; Henin, Jerome; Jiang, Wei; McGreevy, Ryan; Melo, Marcelo C. R.; Radak, Brian K.; Skeel, Robert D.; Singharoy, Abhishek; Wang, Yi; Roux, Benoit; Aksimentiev, Aleksei; Luthey-Schulten, Zaida; Kale, Laxmikant V.; Schulten, Klaus; Chipot, Christophe; Tajkhorshid, Emad
    Journal of Chemical Physics (2020), 153 (4), 044130CODEN: JCPSA6; ISSN:0021-9606. (American Institute of Physics)
    A review. NAMD is a mol. dynamics program designed for high-performance simulations of very large biol. objects on CPU- and GPU-based architectures. NAMD offers scalable performance on petascale parallel supercomputers consisting of hundreds of thousands of cores, as well as on inexpensive commodity clusters commonly found in academic environments. It is written in C++ and leans on Charm++ parallel objects for optimal performance on low-latency architectures. NAMD is a versatile, multipurpose code that gathers state-of-the-art algorithms to carry out simulations in apt thermodn. ensembles, using the widely popular CHARMM, AMBER, OPLS, and GROMOS biomol. force fields. Here, the authors review the main features of NAMD that allow both equil. and enhanced-sampling mol. dynamics simulations with numerical efficiency. The authors describe the underlying concepts used by NAMD and their implementation, most notably for handling long-range electrostatics; controlling the temp., pressure, and pH; applying external potentials on tailored grids; leveraging massively parallel resources in multiple-copy simulations; and hybrid quantum-mech./mol.-mech. descriptions. The authors detail the variety of options offered by NAMD for enhanced-sampling simulations aimed at detg. free-energy differences of either alchem. or geometrical transformations and outline their applicability to specific problems. Last, the roadmap for the development of NAMD and the authors' current efforts toward achieving optimal performance on GPU-based architectures, for pushing back the limitations that have prevented biol. realistic billion-atom objects to be fruitfully simulated, and for making large-scale simulations less expensive and easier to set up, run, and analyze are discussed. NAMD is distributed free of charge with its source code at www.ks.uiuc.edu. (c) 2020 American Institute of Physics.
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    Brooks, B. R.; Bruccoleri, R. E.; Olafson, B. D.; States, D. J.; Swaminathan, S. J.; Karplus, M. CHARMM: A Program for Macromolecular Energy, Minimization, and Dynamics Calculations. J. Comput. Chem. 1983, 4, 187– 217,  DOI: 10.1002/jcc.540040211
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    CHARMM: a program for macromolecular energy, minimization, and dynamics calculations
    Brooks, Bernard R.; Bruccoleri, Robert E.; Olafson, Barry D.; States, David J.; Swaminathan, S.; Karplus, Martin
    Journal of Computational Chemistry (1983), 4 (2), 187-217CODEN: JCCHDD; ISSN:0192-8651.
    CHARMM (Chem. at HARvard Macromol. Mechanics) is a highly flexible computer program which uses empirical energy functions to model macromol. systems. The program can read or model build structures, energy minimize them by first- or second-deriv. techniques, perform a normal mode or mol. dynamics simulation, and analyze the structural, equil., and dynamic properties detd. in these calcns. The operations that CHARMM can perform are described, and some implementation details are given. A set of parameters for the empirical energy function and a sample run are included.
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    Brooks, B. R.; Brooks, C. L.; Mackerell, A. D.; Nilsson, L.; Petrella, R. J.; Roux, B.; Won, Y.; Archontis, G.; Bartels, C.; Boresch, S.; Caflisch, A.; Caves, L.; Cui, Q.; Dinner, A. R.; Feig, M.; Fischer, S.; Gao, J.; Hodoscek, M.; Im, W.; Kuczera, K.; Lazaridis, T.; Ma, J.; Ovchinnikov, V.; Paci, E.; Pastor, R. W.; Post, C. B.; Pu, J. Z.; Schaefer, M.; Tidor, B.; Venable, R. M.; Woodcock, H. L.; Wu, X.; Yang, W.; York, D. M.; Karplus, M. CHARMM: The Biomolecular Simulation Program. J. Comput. Chem. 2009, 30, 1545– 1614,  DOI: 10.1002/jcc.21287
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    Journal of Computational Chemistry (2009), 30 (10), 1545-1614CODEN: JCCHDD; ISSN:0192-8651. (John Wiley & Sons, Inc.)
    A review. CHARMM (Chem. at HARvard Mol. Mechanics) is a highly versatile and widely used mol. simulation program. It has been developed over the last three decades with a primary focus on mols. of biol. interest, including proteins, peptides, lipids, nucleic acids, carbohydrates, and small mol. ligands, as they occur in soln., crystals, and membrane environments. For the study of such systems, the program provides a large suite of computational tools that include numerous conformational and path sampling methods, free energy estimators, mol. minimization, dynamics, and anal. techniques, and model-building capabilities. The CHARMM program is applicable to problems involving a much broader class of many-particle systems. Calcns. with CHARMM can be performed using a no. of different energy functions and models, from mixed quantum mech.-mol. mech. force fields, to all-atom classical potential energy functions with explicit solvent and various boundary conditions, to implicit solvent and membrane models. The program has been ported to numerous platforms in both serial and parallel architectures. This article provides an overview of the program as it exists today with an emphasis on developments since the publication of the original CHARMM article in 1983. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2009.
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    The previously developed particle mesh Ewald method is reformulated in terms of efficient B-spline interpolation of the structure factors. This reformulation allows a natural extension of the method to potentials of the form 1/rp with p ≥ 1. Furthermore, efficient calcn. of the virial tensor follows. Use of B-splines in the place of Lagrange interpolation leads to analytic gradients as well as a significant improvement in the accuracy. The authors demonstrate that arbitrary accuracy can be achieved, independent of system size N, at a cost that scales as N log(N). For biomol. systems with many thousands of atoms and this method permits the use of Ewald summation at a computational cost comparable to that of a simple truncation method of 10 Å or less.
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    The equation of motion of a system of 864 particles interacting through a Lennard-Jones potential was integrated for various values of the temp. and d., relative, generally, to a fluid state. The equil. properties agree with the corresponding properties of Ar. The equil. state of Ar can be described through a 2-body potential.
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    Three recently proposed const. temp. mol. dynamics methods [N., (1984) (1); W. G. Hoover et al., (1982) (2); D. J. Evans and G. P. Morris, (1983) (2); and J. M. Haile and S. Gupta, 1983) (3)] are examd. anal. via calcg. the equil. distribution functions and comparing them with that of the canonical ensemble. Except for effects due to momentum and angular momentum conservation, method (1) yields the rigorous canonical distribution in both momentum and coordinate space. Method (2) can be made rigorous in coordinate space, and can be derived from method (1) by imposing a specific constraint. Method (3) is not rigorous and gives a deviation of order N-1/2 from the canonical distribution (N the no. of particles). The results for the const. temp.-const. pressure ensemble are similar to the canonical ensemble case.
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    Hoover, W. G. Canonical Dynamics: Equilibrium Phase-Space Distributions. Phys. Rev. A: At., Mol., Opt. Phys. 1985, 31, 1695– 1697,  DOI: 10.1103/physreva.31.1695
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    There is no expanded citation for this reference.
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    A new method for performing mol. dynamics simulations under const. pressure is presented. In the method, which is based on the extended system formalism introduced by Andersen, the deterministic equations of motion for the piston degree of freedom are replaced by a Langevin equation; a suitable choice of collision frequency then eliminates the unphys. "ringing" of the vol. assocd. with the piston mass. In this way it is similar to the "weak coupling algorithm" developed by Berendsen and co-workers to perform mol. dynamics simulation without piston mass effects. It is shown, however, that the weak coupling algorithm induces artifacts into the simulation which can be quite severe for inhomogeneous systems such as aq. biopolymers or liq./liq. interfaces.
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    Modularly invariant equations of motion are derived that generate the isothermal-isobaric ensemble as their phase space avs. Isotropic vol. fluctuations and fully flexible simulation cells as well as a hybrid scheme that naturally combines the two motions are considered. The resulting methods are tested on two problems, a particle in a one-dimensional periodic potential and a spherical model of C60 in the solid/fluid phase.
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    Kohn, W.; Becke, A. D.; Parr, R. G. Density Functional Theory of Electronic Structure. J. Phys. Chem. 1996, 100, 12974– 12980,  DOI: 10.1021/jp960669l
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    Journal of Physical Chemistry (1996), 100 (31), 12974-12980CODEN: JPCHAX; ISSN:0022-3654. (American Chemical Society)
    A review with 74 refs. D. functional theory (DFT) is a (in principle exact) theory of electronic structure, based on the electron d. distribution n(r), instead of the many-electron wave function Ψ(r1,r2,r3,...). Having been widely used for over 30 yr by physicists working on the electronic structure of solids, surfaces, defects, etc., it has more recently also become popular with theor. and computational chemists. The present article is directed at the chem. community. It aims to convey the basic concepts and breadth of applications: the current status and trends of approxn. methods (local d. and generalized gradient approxns., hybrid methods) and the new light which DFT has been shedding on important concepts like electronegativity, hardness, and chem. reactivity index.
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    Hariharan, P. C.; Pople, J. A. The Influence of Polarization Functions on Molecular Orbital Hydrogenation Energies. Theor. Chim. Acta 1973, 28, 213– 222,  DOI: 10.1007/bf00533485
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    Influence of polarization functions on MO hydrogenation energies
    Hariharan, P. C.; Pople, J. A.
    Theoretica Chimica Acta (1973), 28 (3), 213-22CODEN: TCHAAM; ISSN:0040-5744.
    The hydrogenation energies of mols. involving H, C, O, N, and F with 2 non-H atoms were calcd. by a basis including polarization functions. The mean abs. deviation between theory and expt. for heats of hydrogenation of the closed shell species is 4 kcal/mole for the basis set with full polarization. Ests. of hydrogenation energy errors at the Hartree-Fock limit are reported.
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    Bernales, V. S.; Marenich, A. v.; Contreras, R.; Cramer, C. J.; Truhlar, D. G. Quantum Mechanical Continuum Solvation Models for Ionic Liquids. J. Phys. Chem. B 2012, 116, 9122– 9129,  DOI: 10.1021/jp304365v
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    Quantum Mechanical Continuum Solvation Models for Ionic Liquids
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    Journal of Physical Chemistry B (2012), 116 (30), 9122-9129CODEN: JPCBFK; ISSN:1520-5207. (American Chemical Society)
    The quantum mech. SMD continuum universal solvation model can be applied to predict the free energy of solvation of any solute in any solvent following specification of various macroscopic solvent parameters. For three ionic liqs. where these descriptors are readily available, the SMD solvation model exhibits a mean unsigned error of 0.48 kcal/mol for 93 solvation free energies of neutral solutes and a mean unsigned error of 1.10 kcal/mol for 148 water-to-IL transfer free energies. Because the necessary solvent parameters are not always available for a given ionic liq., we det. av. values for a set of ionic liqs. over which measurements have been made in order to define a generic ionic liq. solvation model, SMD-GIL. Considering 11 different ionic liqs., the SMD-GIL solvation model exhibits a mean unsigned error of 0.43 kcal/mol for 344 solvation free energies of neutral solutes and a mean unsigned error of 0.61 kcal/mol for 431 water-to-IL transfer free energies. As these errors are similar in magnitude to those typically obsd. when applying continuum solvation models to ordinary liqs., we conclude that the SMD universal solvation model may be applied to ionic liqs. as well as ordinary liqs.
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    Runge, E.; Gross, E. K. U. Density-Functional Theory for Time-Dependent Systems. Phys. Rev. Lett. 1984, 52, 997– 1000,  DOI: 10.1103/physrevlett.52.997
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    Density-functional theory for time-dependent systems
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    Physical Review Letters (1984), 52 (12), 997-1000CODEN: PRLTAO; ISSN:0031-9007.
    A d. functional formalism comparable to the Hohenberg-Kohn-Sham theory of the ground state is developed for arbitrary time-dependent systems. The single-particle potential v(.vector.rt) leading to a given v-representable d. n(.vector.rt) is uniquely detd. so that the corresponding map v → n is invertible. On the basis of this theorem, three schemes are derived to calc. the d.: a set of hydrodynamical equations, a stationary action principle, and an effective single-particle Schroedinger equation.
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    Becke, A. D. Density-Functional Thermochemistry. III. The Role of Exact Exchange. J. Chem. Phys. 1993, 98, 5648– 5652,  DOI: 10.1063/1.464913
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    Density-functional thermochemistry. III. The role of exact exchange
    Becke, Axel D.
    Journal of Chemical Physics (1993), 98 (7), 5648-52CODEN: JCPSA6; ISSN:0021-9606.
    Despite the remarkable thermochem. accuracy of Kohn-Sham d.-functional theories with gradient corrections for exchange-correlation, the author believes that further improvements are unlikely unless exact-exchange information is considered. Arguments to support this view are presented, and a semiempirical exchange-correlation functional (contg. local-spin-d., gradient, and exact-exchange terms) is tested for 56 atomization energies, 42 ionization potentials, 8 proton affinities, and 10 total at. energies of first- and second-row systems. This functional performs better than previous functionals with gradient corrections only, and fits expt. atomization energies with an impressively small av. abs. deviation of 2.4 kcal/mol.
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    Lee, C.; Yang, W.; Parr, R. G. Development of the Colle-Salvetti Correlation-Energy Formula into a Functional of the Electron Density. Phys. Rev. B 1988, 37, 785– 789,  DOI: 10.1103/physrevb.37.785
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    Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density
    Lee, Chengteh; Yang, Weitao; Parr, Robert G.
    Physical Review B: Condensed Matter and Materials Physics (1988), 37 (2), 785-9CODEN: PRBMDO; ISSN:0163-1829.
    A correlation-energy formula due to R. Colle and D. Salvetti (1975), in which the correlation energy d. is expressed in terms of the electron d. and a Laplacian of the 2nd-order Hartree-Fock d. matrix, is restated as a formula involving the d. and local kinetic-energy d. On insertion of gradient expansions for the local kinetic-energy d., d.-functional formulas for the correlation energy and correlation potential are then obtained. Through numerical calcns. on a no. of atoms, pos. ions, and mols., of both open- and closed-shell type, it is demonstrated that these formulas, like the original Colle-Salvetti formulas, give correlation energies within a few percent.
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    Stephens, P. J.; Devlin, F. J.; Chabalowski, C. F.; Frisch, M. J. Ab Initio Calculation of Vibrational Absorption and Circular Dichroism Spectra Using Density Functional Force Fields. J. Phys. Chem. 1994, 98, 11623– 11627,  DOI: 10.1021/j100096a001
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    Ab Initio Calculation of Vibrational Absorption and Circular Dichroism Spectra Using Density Functional Force Fields
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    Journal of Physical Chemistry (1994), 98 (45), 11623-7CODEN: JPCHAX; ISSN:0022-3654.
    The unpolarized absorption and CD spectra of the fundamental vibrational transitions of the chiral mol. 4-methyl-2-oxetanone are calcd. ab initio. Harmonic force fields are obtained using d. functional theory (DFT), MP2 and SCF methodologies, and a [5s4p2d/3s2p] (TZ2P) basis set. DFT calcns. use the LSDA, BLYP, and Becke3LYP (B3LYP) d. functionals. Mid-IR spectra predicted using LSDA, BLYP, and B3LYP force fields are of significantly different quality, the B3LYP force field yielding spectra in clearly superior, and overall excellent, agreement with expt. The MP2 force field yields spectra in slightly worse agreement with expt. than the B3LYP force field. The SCF force field yields spectra in poor agreement with expt. The basis set dependence of B3LYP force fields is also explored: the 6-31G* and TZ2P basis sets give very similar results while the 3-21G basis set yields spectra in substantially worse agreement with expt.
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    Glendening, E. D.; Landis, C. R.; Weinhold, F. Natural Bond Orbital Methods. Wiley Interdiscip. Rev. Comput. Mol. Sci. 2012, 2, 1– 42,  DOI: 10.1002/wcms.51
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    Natural bond orbital methods
    Glendening, Eric D.; Landis, Clark R.; Weinhold, Frank
    Wiley Interdisciplinary Reviews: Computational Molecular Science (2012), 2 (1), 1-43CODEN: WIRCAH; ISSN:1759-0884. (Wiley-Blackwell)
    A review. Natural bond orbital (NBO) methods encompass a suite of algorithms that enable fundamental bonding concepts to be extd. from Hartree-Fock (HF), D. Functional Theory (DFT), and post-HF computations. NBO terminol. and general math. formulations for atoms and polyat. species are presented. NBO analyses of selected mols. that span the periodic table illustrate the deciphering of the mol. wavefunction in terms commonly understood by chemists: Lewis structures, charge, bond order, bond type, hybridization, resonance, donor-acceptor interactions, etc. Upcoming features in the NBO program address ongoing advances in ab initio computing technol. and burgeoning demands of its user community by introducing major new methods, keywords, and electronic structure system/NBO communication enhancements.
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    Hariharan, C.; Vijaysree, V.; Mishra, A. K. Quenching of 2,5-Diphenyloxazole (PPO) Fluorescence by Metal Ions. J. Lumin. 1997, 75, 205– 211,  DOI: 10.1016/s0022-2313(97)00126-9
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    Quenching of 2,5-diphenyloxazole (PPO) fluorescence by metal ions
    Hariharan, Chithra; Vijaysree, V.; Mishra, A. K.
    Journal of Luminescence (1997), 75 (3), 205-211CODEN: JLUMA8; ISSN:0022-2313. (Elsevier)
    The quenching of 2, 5-diphenyloxazole (PPO) fluorescence by transition metal ions (Mn2+, Fe2+, Co2+, Ni2+, Cu2+, Zn2+, Cd2+, Hg2+, Pb2+) were studied. From a reasonably linear fit of the logarithm of the bimol. quenching const. (log kq) with the half-wave redn. potential (E1/2 in V vs. SCE) of the various metal ions, the quenching probably proceeds via the formation of a non-emissive exciplex with charge transfer taking place from the excited fluorophore (PPO) to the metal ions. Ions like Fe2+, Hg2+ and Pb2+ are extremely efficient quenchers, Cu2+ and Ni2+ are moderate quenchers and Co2+, Zn2+, Cd2+ and Mn2+ are very poor quenchers of PPO fluorescence. Various other probable mechanisms like ground-state complex formation, heavy atom quenching, paramagnetic effect, resonance energy transfer, etc., do not appear to be important in the fluorescence quenching of (PPO) though their presence cannot be completely excluded.
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    Ueno, N.; Wakabayashi, T.; Sato, H.; Morisawa, Y. Changes in the Electronic Transitions of Polyethylene Glycol upon the Formation of a Coordinate Bond with Li+, Studied by ATR Far-Ultraviolet Spectroscopy. J. Phys. Chem. A 2019, 123, 10746– 10756,  DOI: 10.1021/acs.jpca.9b09274
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    Changes in the Electronic Transitions of Polyethylene Glycol upon the Formation of a Coordinate Bond with Li+, Studied by ATR Far-Ultraviolet Spectroscopy
    Ueno, Nami; Wakabayashi, Tomonari; Sato, Harumi; Morisawa, Yusuke
    Journal of Physical Chemistry A (2019), 123 (50), 10746-10756CODEN: JPCAFH; ISSN:1089-5639. (American Chemical Society)
    This study investigates the electronic transitions of complexes of lithium with polyethylene glycol (PEG) by the absorption bands of solvent mols. via attenuated total reflectance spectroscopy in the far-UV region (ATR-FUV). Alkali-metal complexes are interesting materials because of their functional characteristics such as good ionic cond. These complexes are used as polymer electrolytes for Li batteries and as one of the new types of room-temp. ionic liqs., termed solvation ionic liqs. Considering these applications, alkali-metal complexes have been studied mainly for their electrochem. characteristics; there is no fundamental study providing a clear understanding of electronic states in terms of electronic structures for the ground and excitation states near the HOMO-lowest occupied MO transitions. This study explores the electronic transitions of ligand mols. in alkali-metal complexes. In the ATR-FUV spectra of the Li-PEG complex, a decrease in intensity and a large blue shift (over 4 nm) were obsd. to result from an increase in the concn. of Li salts. This observation suggests the formation of a complex, with coordinate bonding between Li+ and the O atoms in PEG. Comparison of the exptl. spectrum with a simulated spectrum of the Li-PEG complex calcd. by time-dependent d. functional theory indicated that changes in the intensities and peak positions of bands at approx. 155 and 177 nm (pure PEG shows bands at 155, 163, and 177 nm) are due to the formation of coordinate bonding between Li+ and the O atoms in the ether mol. The intensity of the 177 nm band depends on the no. of residual free O atoms in the ether, and the peak wavelength at approx. 177 nm changes with the expansion of the electron clouds of PEG. We assign a band in the 145-155 nm region to the alkali-metal complex because we obsd. a new band at approx. 150 nm in the ATR-FUV spectra of very highly concd. binary mixts.
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    Ensing, B.; Tiwari, A.; Tros, M.; Hunger, J.; Domingos, S. R.; Pérez, C.; Smits, G.; Bonn, M.; Bonn, D.; Woutersen, S. On the Origin of the Extremely Different Solubilities of Polyethers in Water. Nat. Commun. 2019, 10, 2893,  DOI: 10.1038/s41467-019-10783-z
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    On the origin of the extremely different solubilities of polyethers in water
    Ensing Bernd; Tiwari Ambuj; Tros Martijn; Woutersen Sander; Hunger Johannes; Bonn Mischa; Domingos Sergio R; Perez Cristobal; Smits Gertien; Bonn Daniel
    Nature communications (2019), 10 (1), 2893 ISSN:.
    The solubilities of polyethers are surprisingly counter-intuitive. The best-known example is the difference between polyethylene glycol ([-CH2-CH2-O-]n) which is infinitely soluble, and polyoxymethylene ([-CH2-O-]n) which is completely insoluble in water, exactly the opposite of what one expects from the C/O ratios of these molecules. Similar anomalies exist for oligomeric and cyclic polyethers. To solve this apparent mystery, we use femtosecond vibrational and GHz dielectric spectroscopy with complementary ab initio calculations and molecular dynamics simulations. We find that the dynamics of water molecules solvating polyethers is fundamentally different depending on their C/O composition. The ab initio calculations and simulations show that this is not because of steric effects (as is commonly believed), but because the partial charge on the O atoms depends on the number of C atoms by which they are separated. Our results thus show that inductive effects can have a major impact on aqueous solubilities.
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    Walker, M.; Harvey, A. J. A.; Sen, A.; Dessent, C. E. H. Performance of M06, M06-2X, and M06-HF Density Functionals for Conformationally Flexible Anionic Clusters: M06 Functionals Perform Better than B3LYP for a Model System with Dispersion and Ionic Hydrogen-Bonding Interactions. J. Phys. Chem. A 2013, 117, 12590– 12600,  DOI: 10.1021/jp408166m
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    Performance of M06, M06-2X, and M06-HF Density Functionals for Conformationally Flexible Anionic Clusters: M06 Functionals Perform Better than B3LYP for a Model System with Dispersion and Ionic Hydrogen-Bonding Interactions
    Walker, Martin; Harvey, Andrew J. A.; Sen, Ananya; Dessent, Caroline E. H.
    Journal of Physical Chemistry A (2013), 117 (47), 12590-12600CODEN: JPCAFH; ISSN:1089-5639. (American Chemical Society)
    We present a comparative assessment of the performance of the M06 suite of d. functionals (M06, M06-2X, and M06-HF) against an MP2 benchmark for calcg. the relative energies and geometric structures of the Cl-·arginine and Br-·arginine halide ion-amino acid clusters. Addnl. results are presented for the popular B3LYP d. functional. The Cl-·arginine and Br-·arginine complexes are important prototypes for the phenomenon of anion-induced zwitterion formation. Results are presented for the canonical (noncharge sepd.) and zwitterionic (charge sepd.) tautomers of the clusters, as well as the numerous conformational isomers of the clusters. We find that all of the M06 functions perform well in terms of predicting the general trends in the conformer relative energies and identifying the global min. conformer. This is in contrast to the B3LYP functional, which performed significantly less well for the canonical tautomers of the clusters where dispersion interactions contribute more significantly to the conformer energetics. We find that the M06 functional gave the lowest mean unsigned error for the relative energies of the canonical conformers (2.10 and 2.36 kJ/mol for Br-·arginine and Cl-·arginine), while M06-2X gave the lowest mean unsigned error for the zwitterionic conformers (0.85 and 1.23 kJ/mol for Br-·arginine and Cl-·arginine), thus providing insight into the types of phys. systems where each of these functionals should perform best.
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  1. Jessica Liebau, Bethany F. Laatsch, Joshua Rusnak, Keegan Gunderson, Brianna Finke, Kassandra Bargender, Alex Narkiewicz-Jodko, Katelyn Weeks, Murphi T. Williams, Irina Shulgina, Karin Musier-Forsyth, Sudeep Bhattacharyya, Sanchita Hati. Polyethylene Glycol Impacts Conformation and Dynamics of Escherichia coli Prolyl-tRNA Synthetase Via Crowding and Confinement Effects. Biochemistry 2024, 63 (13) , 1621-1635. https://doi.org/10.1021/acs.biochem.3c00719
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  • Abstract

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    Figure 1

    Figure 1. 100 mg/mL PEG 20k was excited at wavelengths of 280–300 nm in increments of 5 nm to determine the maximum emissions. Each fluorescence spectrum represents an average of three trials.

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    Figure 2

    Figure 2. Solutions containing 100 mg/mL PEG, 100 mM NaCl, and 30 mM phosphate buffer of pH 7.4 were excited at 295 nm for molecular weights of PEG 600, PEG 2k, PEG 8k, and PEG 20k. Each fluorescence spectrum represents an average of three trials. No significant fluorescence was observed for any other PEG molecules except for PEG 20k.

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    Figure 3

    Figure 3. (a) GC–MS spectrum of 3-tert-butyl-4-hydroxyanisole (3-BHA), which is a 96% match to the spectrum of 3-BHA from the NIST Chemistry Webbook. (b) Chromatogram of the 3-BHA peak under three different washing conditions of 400 mg/mL PEG 20k. A full 30 min GC–MS analysis was run, and the 3-BHA peak is seen at approximately 18 min. Chromatogram only shows 15–20 min for clarity. (c) Peak intensity for the three trials of PEG 20k with different levels of purity. Data were taken at the apex of each 3-BHA peak, all within 0.02 s of each other and showing a match to 3-BHA in the NIST database. (d) Fluorescence spectra of 100 mg/mL PEG 20k before and after washing with diethyl ether.

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    Figure 4

    Figure 4. AFM images of the PEG 20 k on the HOPG substrate. (a) Height-retraced and (b) amplitude-retraced images of PEG 20k on the HOPG substrate. Each AFM image size is 5 μm × 5 μm. The key in each image indicates a length of 1 μm. The image of the free HOPG substrate is shown in Figure S3.

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    Figure 5

    Figure 5. (a) DLS autocorrelation functions of PEG 20k of 100, 200, and 300 mg/mL dissolved in 100 mM NaCl and 30 mM phosphate buffer of pH 7.4. (b) Regularization fit for 100 mg/mL PEG 20k dissolved in 100 mM NaCl and 30 mM phosphate buffer of pH 7.4.

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    Figure 6

    Figure 6. Fluorescence anisotropy of PEG 20k of 100, 200, and 300 mg/mL dissolved in 100 mM NaCl and 30 mM phosphate buffer of pH 7.4. Samples were excited at 288 nm, and emissions were read from 320 to 340 nm. (a) Anisotropy at 25 °C and (b) anisotropy at 50 °C.

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    Figure 7

    Figure 7. Solution containing 100 mg/mL PEG 20k, 100 mM NaCl, and 30 mM phosphate buffer of pH 7.4 was excited at 295 nm. The emission was recorded at 320 nm. The temperature was increased at 5° increments from 25 to 75 °C (marked with X). Similarly, cooling was done at 5° increments from 75 to 25 °C (marked with filled circles).

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    Figure 8

    Figure 8. Solutions of 100 mg/mL PEG 20k in the presence of metal ions of 10 mM concentration were excited at 295 nm. Each fluorescence spectrum represents an average of three trials. Na+, Mg2+, and Co2+ had no effect on the fluorescence of PEG 20k. Cr3+ displayed minimal quenching, whereas Fe3+ and Cr6+ quenched the fluorescence of PEG 20k completely.

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    Figure 9

    Figure 9. 1H NMR spectra of PEG 20k in D2O at different concentrations.

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    Figure 10

    Figure 10. Folded structure of PEG 20k, which was obtained after the gas-phase folded structure was immersed in water and then simulated for 100 ns. The following structures, displayed through VMD, represent planes of the folded PEG 20k─(a) the side view, (b) the top view, and (c) the zoomed-in top view of the planes.

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    Figure 11

    Figure 11. Simulated partially folded PEG 20k molecule in the water sphere.

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    Figure 12

    Figure 12. Organized structures of heptameric PEG 20k after 200 ns of gaseous simulation (a) followed by 200 ns of an aqueous simulation (b). These structures are displayed and rendered through VMD. The varying colors represent individual PEG 20k molecules.

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    Figure 13

    Figure 13. Delocalization of the electron cloud as observed through electronic structure calculation of clusters of variable sizes, extracted from a folded PEG 20k polymer. The HOMO in each cluster is shown; the purple and green colors represent the positive and negative amplitudes, respectively, of the molecular orbital’s wavefunction. Hydrogen atoms are omitted for clarity.

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    Figure 14

    Figure 14. Simulated electronic spectra of EG (monomer) and PEG 20k clusters computed using time-dependent density functional theory.

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  • References

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      Clinical manifestations and impact on daily life of allergy to polyethylene glycol (PEG) in ten patients
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      Clinical & Experimental Allergy (2021), 51 (3), 463-470CODEN: CLEAEN; ISSN:0954-7894. (John Wiley & Sons Ltd.)
      Polyethylene glycols (PEGs) are widely used as excipients in drugs, cosmetics and household products. Immediate-type allergy to PEGs including anaphylaxis is rare. The recent introduction of the mRNA-based COVID-19 vaccines has led to an increased focus on PEG as a possible culprit of allergic reactions to the vaccines. A low awareness of the allergenic potential of PEG among consumers, manufacturers and doctors leads to under-diagnosis and under-reporting of allergy to PEGs, putting patients at risk of repeated severe reactions. To investigate clin. manifestations, time to diagnosis and impact of a PEG allergy diagnosis on the daily life of patients diagnosed with allergy to PEG from 2010 to 2019. Ten patients diagnosed with allergy to PEG were included. Detailed clin. history was obtained, and allergy investigations had been performed at the time of diagnosis. All patients were contacted and asked to retrospectively complete a questionnaire about causes and impact on daily life of an allergy to PEG, scored on a likert scale (0-10) before and after diagnosis. Eight patients had experienced at least one anaphylactic reaction requiring adrenaline treatment. Anaphylaxis was primarily caused by antibiotic/analgesic tablets, depot-steroids, antacids and laxatives. Seven patients reported repeated reactions before diagnosis (median 3, range 2-6). Median time from first reaction to diagnosis was 20 mo (range 2-120). None of the patients experienced severe allergic reactions after the diagnosis. Median likert score of the impact on daily life before diagnosis was 7 compared with 4 after diagnosis. Conclusion and clin. relevance : The clin. manifestations of PEG allergy are often dramatic. Improved awareness about the clin. presentation and common culprits, clear product labeling and a standardized nomenclature is needed to ensure the timely diagnosis of PEG allergy to prevent repeated anaphylactic reactions with severe impact on patients' lives.
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      Vaccines against COVID-19 (and its emerging variants) are an essential global intervention to control the current pandemic situation. Vaccines often cause adverse events; however, the vast majority of adverse events following immunization (AEFI) are a consequence of the vaccine stimulating a protective immune response, and not allergic in etiol. Anaphylaxis as an AEFI is uncommon, occurring at a rate of less than 1 per million doses for most vaccines. However, within the first days of initiating mass vaccination with the Pfizer-BioNTech COVID-19 vaccine BNT162b2, there were reports of anaphylaxis from the United Kingdom and United States. More recent data imply an incidence of anaphylaxis closer to 1:200,000 doses with respect to the Pfizer-BioNTech vaccine. In this position paper, we discuss the background to reactions to the current COVID-19 vaccines and relevant steps to mitigate against the risk of anaphylaxis as an AEFI. We propose a global surveillance strategy led by allergists in order to understand the potential risk and generate data to inform evidence-based guidance, and thus provide reassurance to public health bodies and members of the public.
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      Allergenic components of the mRNA-1273 vaccine for COVID-19: Possible involvement of polyethylene glycol and IgG-mediated complement activation
      Klimek, Ludger; Novak, Natalija; Cabanillas, Beatriz; Jutel, Marek; Bousquet, Jean; Akdis, Cezmi A.
      Allergy (Oxford, United Kingdom) (2021), 76 (11), 3307-3313CODEN: LLRGDY; ISSN:0105-4538. (Wiley-Blackwell)
      A review. Following the emergency use authorization of the mRNA-1273 vaccine on the 18th of Dec. 2020, two mRNA vaccines are in current use for the prevention of coronavirus disease 2019 (COVID-19). For both mRNA vaccines, the phase III pivotal trials excluded individuals with a history of allergy to vaccine components. Immediately after the initiation of vaccination in the United Kingdom, Canada, and the United States, anaphylactic reactions were reported. While the culprit trigger requires investigation, initial reports suggested the excipient polyethylene glycol 2000 (PEG-2000)-contained in both vaccines as the PEG-micellar carrier system-as the potential culprit. Surface PEG chains form a hydrate shell to increase stability and prevent opsonization. Allergic reactions to such PEGylated lipids can be IgE-mediated, but may also result from complement activation-related pseudoallergy (CARPA) that has been described in similar liposomes. In addn., mRNA-1273 also contains tromethamine (trometamol), which has been reported to cause anaphylaxis to substances such as gadolinium-based contrast media. Skin prick, intradermal and epicutaneous tests, in vitro sIgE assessment, evaluation of sIgG/IgM, and basophil activation tests are being used to demonstrate allergic reactions to various components of the vaccines.
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      Poly(ethylene glycol) Vesicles: Self-Assembled Site for Luminescence Generation
      Paik, Sankar Prasad; Ghatak, Sumanta Kumar; Dey, Debarati; Sen, Kamalika
      Analytical Chemistry (Washington, DC, United States) (2012), 84 (17), 7555-7561CODEN: ANCHAM; ISSN:0003-2700. (American Chemical Society)
      Fluorescence in poly(ethylene glycol) (PEGs 400-12000) solns. is reported here for the first time. PEG solns. form a vesicular organization with the hydrophilic groups attached at both ends which arrange themselves beyond a particular concn. and offer electron-dense regions at the center of the vesicle. These vesicles provide an inherent site for fluorescence generation in PEG solns. Fluorescence emission was obsd. at ∼380 nm with an excitation wavelength of 300 nm. PEG of mol. wt. 6000 was found to show max. emission intensity at a particular concn. The formation of PEG vesicles (∼1 nm size) was confirmed by dynamic light scattering (DLS) and confocal laser microscopy. On addn. of metal ions the polymeric vesicle breaks up to monomeric PEG, and hence, the fluorescence intensity decreases with a red shift. Fluorescence lifetime measurements indicate the nature of complexation of the metals with PEG. Since PEGs are used as one of the phases in aq. biphasic systems (ABS) of liq.-liq. extns., the nature of the fluorescence emission spectrum of the PEG phase after extn. was studied. Metal extn. in the PEG-rich phase of an ABS leads to quenching of fluorescence in PEG.
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      Alper, A.; Pashankar, D. S. Polyethylene Glycol: A Game-Changer Laxative for Children. J. Pediatr. Gastroenterol. Nutr. 2013, 57, 134– 140,  DOI: 10.1097/mpg.0b013e318296404a
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      Polyethylene Glycol: A Game-Changer Laxative for Children
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      A review. Constipation is a common problem in children worldwide. It can also be a chronic problem persisting for many months to years. Successful treatment of constipation requires long-term use of laxatives. Commonly used laxatives in children include milk of magnesia, lactulose, mineral oil, and polyethylene glycol. Compared with other laxatives, polyethylene glycol (with and without electrolytes) is a relatively new laxative used during the last decade. Recent studies report excellent efficacy and safety of polyethylene glycol for the long-term treatment of constipation in children. Because of excellent patient acceptance, polyethylene glycol has become a preferred choice of laxative for many practitioners. This article reviews the recently published pediatric literature on biochem., efficacy, safety, patient acceptance, and pharmacoeconomics of polyethylene glycol.
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      Advances in PEGylation of important biotech molecules: delivery aspects
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      A review. Although various injected peptide and protein therapeutics have been developed successfully over the past 25 years, several pharmacokinetic and immunol. challenges are still encountered that can limit the efficacy of both novel and established biotech mols. PEGylation is a popular technique to address such properties. PEGylated drugs exhibit prolonged half-life, higher stability, water soly., lower immunogenicity and antigenicity, as well as potential for specific cell targeting. Although PEGylated drug conjugates have been on the market for many years, the technol. has steadily developed in respect of site-specific chem., chain length, mol. wts. and purity of conjugate. These developments have occurred in parallel to improvements in physicochem. methods of characterization. This review will discuss recent achievements in PEGylation processes with an emphasis on novel PEG-drugs constructs, the unrealized potential of PEGylation for non-injected routes of delivery, and also on PEGylated versions of polymeric nanoparticles, including dendrimers and liposomes.
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      Kobayashi, M.; Koide, T.; Hyon, S. H. Tribological Characteristics of Polyethylene Glycol (PEG) as a Lubricant for Wear Resistance of Ultra-High-Molecular-Weight Polyethylene (UHMWPE) in Artificial Knee Joint. J. Mech. Behav. Biomed. Mater. 2014, 38, 33– 38,  DOI: 10.1016/j.jmbbm.2014.06.003
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      Tribological characteristics of polyethylene glycol (PEG) as a lubricant for wear resistance of ultra-high-molecular-weight polyethylene (UHMWPE ) in artificial knee join
      Kobayashi, Masanori; Koide, Takayuki; Hyon, Suong-Hyu
      Journal of the Mechanical Behavior of Biomedical Materials (2014), 38 (), 33-38CODEN: JMBBCP; ISSN:1878-0180. (Elsevier Ltd.)
      For the longevity of total knee joint prostheses, we have developed an artificial lubricant using polyethylene glycol (PEG) for the prevention of wear of ultra-high-mol.-wt. polyethylene (UHMWPE). In the present study, the lubricative function of this PEG lubricant was evaluated by a wear test using Co-Cr alloy and UHMWPE counter surface samples. As a result, human synovial fluid including the PEG lubricant showed good result regarding the wear vol. and a worn surface of UHMWPE. Considering its lubrication mechanism, it is suspected that interaction between the PEG mols. and the proteins in synovial fluid was involved. Since PE mols. are also org. compds. having a hydroxyl group at one or both ends, the albumin and PEG mol. complex would have bound more strongly to the metal oxide surface and UHMWPE surfaces might enhance and stabilize the lubricating film between the contact surfaces under the boundary lubrication. This study suggests that PEG lubricant as an intra-articular viscous supplement has the potential to prevent wear of UHMWPE by mixing with synovial fluid and to contribute to the longevity of knee joint prostheses.
      >> More from SciFinder ®
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      Salaita, G. N.; Ma, F. M. S.; Parker, T. C.; Hoflund, G. B. Weathering Properties of Treated Southern Yellow Pine Wood Examined by X-Ray Photoelectron Spectroscopy, Scanning Electron Microscopy and Physical Characterization. Appl. Surf. Sci. 2008, 254, 3925– 3934,  DOI: 10.1016/j.apsusc.2007.12.017
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      Weathering properties of treated southern yellow pine wood examined by X-ray photoelectron spectroscopy, scanning electron microscopy and physical characterization
      Salaita, Ghaleb N.; Ma, Frank M. S.; Parker, Trudy C.; Hoflund, Gar B.
      Applied Surface Science (2008), 254 (13), 3925-3934CODEN: ASUSEE; ISSN:0169-4332. (Elsevier B.V.)
      In this study the weathering behavior of southern yellow pine (SYP) wood samples pretreated in different solns. was examd. using XPS, SEM and various types of phys. characterization regarding material loss and discoloration. The treatment solns. include water as a control, a com. available water repellent (WR) wood treating additive and polyethylene glycol (PEG) products including PEG PLUS, PEG 8000 solns. and Compd. 20M in varying concns. All contained the wood preservative chromated copper arsenate (CCA). One sample was treated with a CCA soln. only. The treatments were carried out at 20 °C and 150 psig for 1/2 h after exposure to vacuum (28 mmHg) for 15 min. Simulated weathering was achieved in an Atlas 65-W Weather-Ometer for 2000 h with both light and dark periods and rain. The temp. ranged from 23 °C during the dark cycle to 35 °C during the light cycle. With weathering the XPS O/C ratios increase due to oxidn. of the surface. Exposure to UV light results in bond breakage and reaction with oxygen in the presence of air to form org. functional groups such as C-O-C-O, cyclic C2O, C=O and/or O-C-O. These oxidized products can protect the underlying wood from deterioration if they are insol. in water and remain on the surface as a protective coating. If sol., rain washes the compds. away and assists in the degrdn. Correlated changes are obsd. in the XPS O/C ratios, the high-resoln. XPS C 1s spectra, the SEM micrographs and phys. measurements including thickness alteration, wt. loss, and discoloration by yellowing or whitening of the weathered wood. The PEG treatments are effective in protecting wood with the 2% PEG PLUS treatment providing the best weathering behavior similar to that of the CCA treatment. The WR and water treatments yield the poorest weathering properties.
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      Kuznetsova, I. M.; Turoverov, K. K.; Uversky, V. N. What Macromolecular Crowding Can Do to a Protein. Int. J. Mol. Sci. 2014, 15, 23090– 23140,  DOI: 10.3390/ijms151223090
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      What macromolecular crowding can do to a protein
      Kuznetsova, Irina M.; Turoverov, Konstantin K.; Uversky, Vladimir N.
      International Journal of Molecular Sciences (2014), 15 (12), 23090-23140, 51 pp.CODEN: IJMCFK; ISSN:1422-0067. (MDPI AG)
      A review. The intracellular environment represents an extremely crowded milieu, with a limited amt. of free water and an almost complete lack of unoccupied space. Obviously, slightly salted aq. solns. contg. low concns. of a biomol. of interest are too simplistic to mimic the "real life" situation, where the biomol. of interest scrambles and wades through the tightly packed crowd. In lab. practice, such macromol. crowding is typically mimicked by concd. solns. of various polymers that serve as model "crowding agents". Studies under these conditions revealed that macromol. crowding might affect protein structure, folding, shape, conformational stability, binding of small mols., enzymic activity, protein-protein interactions, protein-nucleic acid interactions, and pathol. aggregation. The goal of this review is to systematically analyze currently available exptl. data on the variety of effects of macromol. crowding on a protein mol. The review covers more than 320 papers and therefore represents one of the most comprehensive compendia of the current knowledge in this exciting area.
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      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2MXlsl2nsg%253D%253D&md5=b412b7a7101548b140433175b8fe0ea5
    10. 10
      Adams, L. M. M.; Andrews, R. J. J.; Hu, Q. H. H.; Schmit, H. L. L.; Hati, S.; Bhattacharyya, S. Crowder-Induced Conformational Ensemble Shift in Escherichia Coli Prolyl-TRNA Synthetase. Biophys. J. 2019, 117, 1269– 1284,  DOI: 10.1016/j.bpj.2019.08.033
      10
      Crowder-Induced Conformational Ensemble Shift in Escherichia coli Prolyl-tRNA Synthetase
      Adams, Lauren M.; Andrews, Ryan J.; Hu, Quin H.; Schmit, Heidi L.; Hati, Sanchita; Bhattacharyya, Sudeep
      Biophysical Journal (2019), 117 (7), 1269-1284CODEN: BIOJAU; ISSN:0006-3495. (Cell Press)
      The effect of mol. crowding on the structure and function of Escherichia coli prolyl-tRNA synthetase (Ec ProRS), a member of the aminoacyl-tRNA synthetase family, has been investigated using a combined exptl. and theor. method. Ec ProRS is a multidomain enzyme; coupled-domain dynamics are essential for efficient catalysis. To gain insight into the mechanistic detail of the crowding effect, kinetic studies were conducted with varying concns. and sizes of crowders. In parallel, spectroscopic and quantum chem. studies were employed to probe the "soft interactions" between crowders and protein side chains. Finally, the dynamics of the dimeric protein was examd. in the presence of crowders using a long-duration (70 ns) classical mol. dynamic simulations. The results of the simulations revealed a shift in the conformational ensemble, which is consistent with the preferential exclusion of cosolutes. The "soft interactions" model of the crowding effect also explained the alteration in kinetic parameters. In summary, the study found that the effects of mol. crowding on both conformational dynamics and catalytic function are correlated in the multidomain Ec ProRS, an enzyme that is central to protein synthesis in all living cells. This study affirmed that large and small cosolutes have considerable impacts on the structure, dynamics, and function of modular proteins and therefore must be considered for stabilizing protein-based pharmaceuticals and industrial enzymes.
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    11. 11
      Wang, Y.; Zhao, Z.; Yuan, W. Z. Intrinsic Luminescence from Nonaromatic Biomolecules. ChemPlusChem 2020, 85, 1065– 1080,  DOI: 10.1002/cplu.202000021
      11
      Intrinsic Luminescence from Nonaromatic Biomolecules
      Wang, Yunzhong; Zhao, Zihao; Yuan, Wang Zhang
      ChemPlusChem (2020), 85 (5), 1065-1080CODEN: CHEMM5; ISSN:2192-6506. (Wiley-VCH Verlag GmbH & Co. KGaA)
      A review. Novel emitters that do not contain traditional chromophores but only electron-rich moieties (e. g. amine, C=O, -OH, ether, and imide), which are classified as nonconventional luminophores, have been more frequently reported. Although more and more examples have been demonstrated, their emission mechanism remains unclear. The clustering-triggered emission (CTE) mechanism has previously been proposed to rationalize the luminescence of unconventional chromophores. Moreover, great attention has been paid to the distinctive inherent luminescence from nonarom. biomols. such as cellulose, starch, sugars, and nonarom. amino acids and proteins. In this Review, we summarize these unconventional biomol. luminophores and apply the CTE mechanism to rationalize such a phenomenon. This Review may shed new light on the understanding of intrinsic emission of nonarom. biomols. and decipher the intrinsic fluorescence from cells and tissues.
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    12. 12
      Li, Q.; Tang, Y.; Hu, W.; Li, Z. Fluorescence of Nonaromatic Organic Systems and Room Temperature Phosphorescence of Organic Luminogens: The Intrinsic Principle and Recent Progress. Small 2018, 14, 1801560,  DOI: 10.1002/smll.201801560
      There is no corresponding record for this reference.
    13. 13
      Zhang Yuan, W.; Zhang, Y. Nonconventional Macromolecular Luminogens with Aggregation-Induced Emission Characteristics. J. Polym. Sci., Part A: Polym. Chem. 2017, 55, 560– 574,  DOI: 10.1002/pola.28420
      There is no corresponding record for this reference.
    14. 14
      Sun, C.; Jiang, X.; Li, B.; Li, S.; Kong, X. Z. Fluorescence Behavior and Mechanisms of Poly(Ethylene Glycol) and Their Applications in Fe3+ and Cr6+ Detections, Data Encryption, and Cell Imaging. ACS Sustain. Chem. Eng. 2021, 9, 5166– 5178,  DOI: 10.1021/acssuschemeng.1c00250
      There is no corresponding record for this reference.
    15. 15
      Chatterjee, D. P.; Pakhira, M.; Nandi, A. K. Fluorescence in “Nonfluorescent” Polymers. ACS Omega 2020, 5, 30747– 30766,  DOI: 10.1021/acsomega.0c04700
      15
      Fluorescence in "Nonfluorescent" Polymers
      Chatterjee, Dhruba P.; Pakhira, Mahuya; Nandi, Arun K.
      ACS Omega (2020), 5 (48), 30747-30766CODEN: ACSODF; ISSN:2470-1343. (American Chemical Society)
      A review. Recently, a great deal of research has been started on generating fairly strong photoluminescence from org. mols. without having any conjugated π-system or fluorophore. Discrete chromophores or auxochromophores termed as "subfluorophores" may undergo "space conjugation" via cooperative intramol. conformation followed by intermol. aggregation to generate fluorescence or sometimes phosphorescence emission. Polymeric materials are important in this regard as nonconjugated polymers self-assemble/aggregate in a moderately concd. soln. and also in the solid state, producing membranes, films, and so forth with good phys. and mech. properties. Therefore, promoting fluorescence in these commodity polymers is very much useful for sensing, org. light emitting diodes (OLED), and biol. applications. In this perspective, we have discussed the aggregation-induced emission from four different types of architectures, for example, (1) dendrimers or hyperbranched polymers, (2) entrapped polymeric micellar self-assembly, (3) cluster formation, and (4) stretching-induced aggregation, begining with the genesis of fluorescence from aggregation of propeller-shaped small org. mols. The mechanism of induced fluorescence of polymers with subfluorophoric groups is also discussed from the theor. calcns. of the energy bands in the aggregated state. Also, an attempt has been made to highlight some useful applications in the sensing of surfactants, bacteria, cell imaging, drug delivery, gene delivery, OLED, and so forth.
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    16. 16
      Zhao, Y.; Truhlar, D. G. The M06 Suite of Density Functionals for Main Group Thermochemistry, Thermochemical Kinetics, Noncovalent Interactions, Excited States, and Transition Elements: Two New Functionals and Systematic Testing of Four M06-Class Functionals and 12 Other Functionals. Theor. Chem. Acc. 2008, 120, 215– 241,  DOI: 10.1007/s00214-007-0310-x
      16
      The M06 suite of density functionals for main group thermochemistry, thermochemical kinetics, noncovalent interactions, excited states, and transition elements: two new functionals and systematic testing of four M06-class functionals and 12 other functionals
      Zhao, Yan; Truhlar, Donald G.
      Theoretical Chemistry Accounts (2008), 120 (1-3), 215-241CODEN: TCACFW; ISSN:1432-881X. (Springer GmbH)
      We present two new hybrid meta exchange-correlation functionals, called M06 and M06-2X. The M06 functional is parametrized including both transition metals and nonmetals, whereas the M06-2X functional is a high-nonlocality functional with double the amt. of nonlocal exchange (2X), and it is parametrized only for nonmetals. The functionals, along with the previously published M06-L local functional and the M06-HF full-Hartree-Fock functionals, constitute the M06 suite of complementary functionals. We assess these four functionals by comparing their performance to that of 12 other functionals and Hartree-Fock theory for 403 energetic data in 29 diverse databases, including ten databases for thermochem., four databases for kinetics, eight databases for noncovalent interactions, three databases for transition metal bonding, one database for metal atom excitation energies, and three databases for mol. excitation energies. We also illustrate the performance of these 17 methods for three databases contg. 40 bond lengths and for databases contg. 38 vibrational frequencies and 15 vibrational zero point energies. We recommend the M06-2X functional for applications involving main-group thermochem., kinetics, noncovalent interactions, and electronic excitation energies to valence and Rydberg states. We recommend the M06 functional for application in organometallic and inorganometallic chem. and for noncovalent interactions.
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    17. 17
      North, M. A.; Bhattacharyya, S.; Truhlar, D. G. Improved Density Functional Description of the Electrochemistry and Structure-Property Descriptors of Substituted Flavins. J. Phys. Chem. B 2010, 114, 14907– 14915,  DOI: 10.1021/jp108024b
      17
      Improved Density Functional Description of the Electrochemistry and Structure-Property Descriptors of Substituted Flavins
      North, Michael A.; Bhattacharyya, Sudeep; Truhlar, Donald G.
      Journal of Physical Chemistry B (2010), 114 (46), 14907-14915CODEN: JPCBFK; ISSN:1520-6106. (American Chemical Society)
      The energetics of electrochem. changes have been investigated for several substituted flavins with the M06-L d. functional. The redn. potentials for one- and two-electron redns. of these mols. have been detd. and the results are consistent with exptl. findings with a mean unsigned error of only 42 mV. It is esp. noteworthy that the M06-L d. functional makes a significant difference in the computed free energy of the first redn. of lumiflavin, which produces a neutral semiquinone. We also investigate the effects of flavin ring substituents on the geometries, charge distributions, redn. potentials, pKa's, ionization potentials, electron affinities, hardnesses, softnesses, electrophilic powers, and nucleophilicities.
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    18. 18
      Bresnahan, C. G.; Reinhardt, C. R.; Bartholow, T. G.; Rumpel, J. P.; North, M.; Bhattacharyya, S. Effect of Stacking Interactions on the Thermodynamics and Kinetics of Lumiflavin: A Study with Improved Density Functionals and Density Functional Tight-Binding Protocol. J. Phys. Chem. A 2015, 119, 172– 182,  DOI: 10.1021/jp510020v
      18
      Effect of Stacking Interactions on the Thermodynamics and Kinetics of Lumiflavin: A Study with Improved Density Functionals and Density Functional Tight-Binding Protocol
      Bresnahan, Caitlin G.; Reinhardt, Clorice R.; Bartholow, Thomas G.; Rumpel, John P.; North, Michael; Bhattacharyya, Sudeep
      Journal of Physical Chemistry A (2015), 119 (1), 172-182CODEN: JPCAFH; ISSN:1089-5639. (American Chemical Society)
      The π-π stacking interaction between lumiflavin and a no. of π-electron-rich mols. has been studied by d. functional theory using several new-generation d. functionals. Six known lumiflavin-arom. adducts were used and the models were evaluated by comparing the geometry and energetics with exptl. results. The study found that dispersion-cor. and hybrid functionals with larger (>50%) Hartree-Fock exchanges produced superior results in modeling thermodn. characteristics of these complexes. The functional producing the best energetics for these model systems was used to study the stacking interactions of lumiflavin with biol. relevant arom. groups. Addnl., the redn. of flavin-in the presence of both a hydride donor and a nondonor π-electronic system was also studied. Weak interactions were obsd. in the stacked lumiflavin complexes of benzene, phenol, and indole, mimicking Ph alanine, tryptophan, and tyrosine side chains, resp., of an enzyme. The stacked complex of naphthalene and flavin showed little change in flavin's redox potential indicating insignificant effect on the thermodn. of the hydride transfer reaction. In contrast, the hydride transfer reaction with the hydride donor N-Me nicotinamide tells a different story, as the transition state was found to be strongly impacted by the stacking interactions. A comparison of performance between the d. functional theory (DFT) and the computationally less expensive dispersion-cor. self-consistent d. functional tight-binding (SCC-DFTB-D) theory revealed that the latter produces consistent energetics for this hydride transfer reaction and addnl. DFT-computed perturbative corrections could significantly improve these results.
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    19. 19
      Humphrey, W.; Dalke, A.; Schulten, K. VMD: Visual Molecular Dynamics. J. Mol. Graph. 1996, 14, 33– 38,  DOI: 10.1016/0263-7855(96)00018-5
      19
      VDM: visual molecular dynamics
      Humphrey, William; Dalke, Andrew; Schulten, Klaus
      Journal of Molecular Graphics (1996), 14 (1), 33-8, plates, 27-28CODEN: JMGRDV; ISSN:0263-7855. (Elsevier)
      VMD is a mol. graphics program designed for the display and anal. of mol. assemblies, in particular, biopolymers such as proteins and nucleic acids. VMD can simultaneously display any no. of structures using a wide variety of rendering styles and coloring methods. Mols. are displayed as one or more "representations," in which each representation embodies a particular rendering method and coloring scheme for a selected subset of atoms. The atoms displayed in each representation are chosen using an extensive atom selection syntax, which includes Boolean operators and regular expressions. VMD provides a complete graphical user interface for program control, as well as a text interface using the Tcl embeddable parser to allow for complex scripts with variable substitution, control loops, and function calls. Full session logging is supported, which produces a VMD command script for later playback. High-resoln. raster images of displayed mols. may be produced by generating input scripts for use by a no. of photorealistic image-rendering applications. VMD has also been expressly designed with the ability to animate mol. dynamics (MD) simulation trajectories, imported either from files or from a direct connection to a running MD simulation. VMD is the visualization component of MDScope, a set of tools for interactive problem solving in structural biol., which also includes the parallel MD program NAMD, and the MDCOMM software used to connect the visualization and simulation programs, VMD is written in C++, using an object-oriented design; the program, including source code and extensive documentation, is freely available via anonymous ftp and through the World Wide Web.
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    20. 20
      Phillips, J. C.; Braun, R.; Wang, W.; Gumbart, J.; Tajkhorshid, E.; Villa, E.; Chipot, C.; Skeel, R. D.; Kalé, L.; Schulten, K. Scalable Molecular Dynamics with NAMD. J. Comput. Chem. 2005, 26, 1781– 1802,  DOI: 10.1002/jcc.20289
      20
      Scalable molecular dynamics with NAMD
      Phillips, James C.; Braun, Rosemary; Wang, Wei; Gumbart, James; Tajkhorshid, Emad; Villa, Elizabeth; Chipot, Christophe; Skeel, Robert D.; Kale, Laxmikant; Schulten, Klaus
      Journal of Computational Chemistry (2005), 26 (16), 1781-1802CODEN: JCCHDD; ISSN:0192-8651. (John Wiley & Sons, Inc.)
      NAMD is a parallel mol. dynamics code designed for high-performance simulation of large biomol. systems. NAMD scales to hundreds of processors on high-end parallel platforms, as well as tens of processors on low-cost commodity clusters, and also runs on individual desktop and laptop computers. NAMD works with AMBER and CHARMM potential functions, parameters, and file formats. This article, directed to novices as well as experts, first introduces concepts and methods used in the NAMD program, describing the classical mol. dynamics force field, equations of motion, and integration methods along with the efficient electrostatics evaluation algorithms employed and temp. and pressure controls used. Features for steering the simulation across barriers and for calcg. both alchem. and conformational free energy differences are presented. The motivations for and a roadmap to the internal design of NAMD, implemented in C++ and based on Charm++ parallel objects, are outlined. The factors affecting the serial and parallel performance of a simulation are discussed. Finally, typical NAMD use is illustrated with representative applications to a small, a medium, and a large biomol. system, highlighting particular features of NAMD, for example, the Tcl scripting language. The article also provides a list of the key features of NAMD and discusses the benefits of combining NAMD with the mol. graphics/sequence anal. software VMD and the grid computing/collab. software BioCoRE. NAMD is distributed free of charge with source code at www.ks.uiuc.edu.
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    21. 21
      Phillips, J. C.; Hardy, D. J.; Maia, J. D. C. C.; Stone, J. E.; Ribeiro, J. v.; Bernardi, R. C.; Buch, R.; Fiorin, G.; Hénin, J.; Jiang, W.; McGreevy, R.; Melo, M. C. R. R.; Radak, B. K.; Skeel, R. D.; Singharoy, A.; Wang, Y.; Roux, B.; Aksimentiev, A.; Luthey-Schulten, Z.; Kalé, L. v.; Schulten, K.; Chipot, C.; Tajkhorshid, E. Scalable Molecular Dynamics on CPU and GPU Architectures with NAMD. J. Chem. Phys. 2020, 153, 044130,  DOI: 10.1063/5.0014475
      21
      Scalable molecular dynamics on CPU and GPU architectures with NAMD
      Phillips, James C.; Hardy, David J.; Maia, Julio D. C.; Stone, John E.; Ribeiro, Joao V.; Bernardi, Rafael C.; Buch, Ronak; Fiorin, Giacomo; Henin, Jerome; Jiang, Wei; McGreevy, Ryan; Melo, Marcelo C. R.; Radak, Brian K.; Skeel, Robert D.; Singharoy, Abhishek; Wang, Yi; Roux, Benoit; Aksimentiev, Aleksei; Luthey-Schulten, Zaida; Kale, Laxmikant V.; Schulten, Klaus; Chipot, Christophe; Tajkhorshid, Emad
      Journal of Chemical Physics (2020), 153 (4), 044130CODEN: JCPSA6; ISSN:0021-9606. (American Institute of Physics)
      A review. NAMD is a mol. dynamics program designed for high-performance simulations of very large biol. objects on CPU- and GPU-based architectures. NAMD offers scalable performance on petascale parallel supercomputers consisting of hundreds of thousands of cores, as well as on inexpensive commodity clusters commonly found in academic environments. It is written in C++ and leans on Charm++ parallel objects for optimal performance on low-latency architectures. NAMD is a versatile, multipurpose code that gathers state-of-the-art algorithms to carry out simulations in apt thermodn. ensembles, using the widely popular CHARMM, AMBER, OPLS, and GROMOS biomol. force fields. Here, the authors review the main features of NAMD that allow both equil. and enhanced-sampling mol. dynamics simulations with numerical efficiency. The authors describe the underlying concepts used by NAMD and their implementation, most notably for handling long-range electrostatics; controlling the temp., pressure, and pH; applying external potentials on tailored grids; leveraging massively parallel resources in multiple-copy simulations; and hybrid quantum-mech./mol.-mech. descriptions. The authors detail the variety of options offered by NAMD for enhanced-sampling simulations aimed at detg. free-energy differences of either alchem. or geometrical transformations and outline their applicability to specific problems. Last, the roadmap for the development of NAMD and the authors' current efforts toward achieving optimal performance on GPU-based architectures, for pushing back the limitations that have prevented biol. realistic billion-atom objects to be fruitfully simulated, and for making large-scale simulations less expensive and easier to set up, run, and analyze are discussed. NAMD is distributed free of charge with its source code at www.ks.uiuc.edu. (c) 2020 American Institute of Physics.
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    22. 22
      Brooks, B. R.; Bruccoleri, R. E.; Olafson, B. D.; States, D. J.; Swaminathan, S. J.; Karplus, M. CHARMM: A Program for Macromolecular Energy, Minimization, and Dynamics Calculations. J. Comput. Chem. 1983, 4, 187– 217,  DOI: 10.1002/jcc.540040211
      22
      CHARMM: a program for macromolecular energy, minimization, and dynamics calculations
      Brooks, Bernard R.; Bruccoleri, Robert E.; Olafson, Barry D.; States, David J.; Swaminathan, S.; Karplus, Martin
      Journal of Computational Chemistry (1983), 4 (2), 187-217CODEN: JCCHDD; ISSN:0192-8651.
      CHARMM (Chem. at HARvard Macromol. Mechanics) is a highly flexible computer program which uses empirical energy functions to model macromol. systems. The program can read or model build structures, energy minimize them by first- or second-deriv. techniques, perform a normal mode or mol. dynamics simulation, and analyze the structural, equil., and dynamic properties detd. in these calcns. The operations that CHARMM can perform are described, and some implementation details are given. A set of parameters for the empirical energy function and a sample run are included.
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    23. 23
      Brooks, B. R.; Brooks, C. L.; Mackerell, A. D.; Nilsson, L.; Petrella, R. J.; Roux, B.; Won, Y.; Archontis, G.; Bartels, C.; Boresch, S.; Caflisch, A.; Caves, L.; Cui, Q.; Dinner, A. R.; Feig, M.; Fischer, S.; Gao, J.; Hodoscek, M.; Im, W.; Kuczera, K.; Lazaridis, T.; Ma, J.; Ovchinnikov, V.; Paci, E.; Pastor, R. W.; Post, C. B.; Pu, J. Z.; Schaefer, M.; Tidor, B.; Venable, R. M.; Woodcock, H. L.; Wu, X.; Yang, W.; York, D. M.; Karplus, M. CHARMM: The Biomolecular Simulation Program. J. Comput. Chem. 2009, 30, 1545– 1614,  DOI: 10.1002/jcc.21287
      23
      CHARMM: The biomolecular simulation program
      Brooks, B. R.; Brooks, C. L., III; Mackerell, A. D., Jr.; Nilsson, L.; Petrella, R. J.; Roux, B.; Won, Y.; Archontis, G.; Bartels, C.; Boresch, S.; Caflisch, A.; Caves, L.; Cui, Q.; Dinner, A. R.; Feig, M.; Fischer, S.; Gao, J.; Hodoscek, M.; Im, W.; Kuczera, K.; Lazaridis, T.; Ma, J.; Ovchinnikov, V.; Paci, E.; Pastor, R. W.; Post, C. B.; Pu, J. Z.; Schaefer, M.; Tidor, B.; Venable, R. M.; Woodcock, H. L.; Wu, X.; Yang, W.; York, D. M.; Karplus, M.
      Journal of Computational Chemistry (2009), 30 (10), 1545-1614CODEN: JCCHDD; ISSN:0192-8651. (John Wiley & Sons, Inc.)
      A review. CHARMM (Chem. at HARvard Mol. Mechanics) is a highly versatile and widely used mol. simulation program. It has been developed over the last three decades with a primary focus on mols. of biol. interest, including proteins, peptides, lipids, nucleic acids, carbohydrates, and small mol. ligands, as they occur in soln., crystals, and membrane environments. For the study of such systems, the program provides a large suite of computational tools that include numerous conformational and path sampling methods, free energy estimators, mol. minimization, dynamics, and anal. techniques, and model-building capabilities. The CHARMM program is applicable to problems involving a much broader class of many-particle systems. Calcns. with CHARMM can be performed using a no. of different energy functions and models, from mixed quantum mech.-mol. mech. force fields, to all-atom classical potential energy functions with explicit solvent and various boundary conditions, to implicit solvent and membrane models. The program has been ported to numerous platforms in both serial and parallel architectures. This article provides an overview of the program as it exists today with an emphasis on developments since the publication of the original CHARMM article in 1983. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2009.
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    24. 24
      Essmann, U.; Perera, L.; Berkowitz, M. L.; Darden, T.; Lee, H.; Pedersen, L. G. A Smooth Particle Mesh Ewald Method. J. Chem. Phys. 1995, 103, 8577– 8593,  DOI: 10.1063/1.470117
      24
      A smooth particle mesh Ewald method
      Essmann, Ulrich; Perera, Lalith; Berkowitz, Max L.; Darden, Tom; Lee, Hsing; Pedersen, Lee G.
      Journal of Chemical Physics (1995), 103 (19), 8577-93CODEN: JCPSA6; ISSN:0021-9606. (American Institute of Physics)
      The previously developed particle mesh Ewald method is reformulated in terms of efficient B-spline interpolation of the structure factors. This reformulation allows a natural extension of the method to potentials of the form 1/rp with p ≥ 1. Furthermore, efficient calcn. of the virial tensor follows. Use of B-splines in the place of Lagrange interpolation leads to analytic gradients as well as a significant improvement in the accuracy. The authors demonstrate that arbitrary accuracy can be achieved, independent of system size N, at a cost that scales as N log(N). For biomol. systems with many thousands of atoms and this method permits the use of Ewald summation at a computational cost comparable to that of a simple truncation method of 10 Å or less.
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    25. 25
      Verlet, L. Computer “Experiments” on Classical Fluids. I. Thermodynamical Properties of Lennard-Jones Molecules. Phys. Rev. 1967, 159, 98– 103,  DOI: 10.1103/physrev.159.98
      25
      Computer "experiments" on classical fluids. I. Thermodynamical properties of Lennard-Jones molecules
      Verlet, Loup
      Physical Review (1967), 159 (1), 98-103CODEN: PHRVAO; ISSN:0031-899X.
      The equation of motion of a system of 864 particles interacting through a Lennard-Jones potential was integrated for various values of the temp. and d., relative, generally, to a fluid state. The equil. properties agree with the corresponding properties of Ar. The equil. state of Ar can be described through a 2-body potential.
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    26. 26
      Nosé, S. A Unified Formulation of the Constant Temperature Molecular Dynamics Methods. J. Chem. Phys. 1984, 81, 511– 519,  DOI: 10.1063/1.447334
      26
      A unified formulation of the constant-temperature molecular-dynamics methods
      Nose, Shuichi
      Journal of Chemical Physics (1984), 81 (1), 511-19CODEN: JCPSA6; ISSN:0021-9606.
      Three recently proposed const. temp. mol. dynamics methods [N., (1984) (1); W. G. Hoover et al., (1982) (2); D. J. Evans and G. P. Morris, (1983) (2); and J. M. Haile and S. Gupta, 1983) (3)] are examd. anal. via calcg. the equil. distribution functions and comparing them with that of the canonical ensemble. Except for effects due to momentum and angular momentum conservation, method (1) yields the rigorous canonical distribution in both momentum and coordinate space. Method (2) can be made rigorous in coordinate space, and can be derived from method (1) by imposing a specific constraint. Method (3) is not rigorous and gives a deviation of order N-1/2 from the canonical distribution (N the no. of particles). The results for the const. temp.-const. pressure ensemble are similar to the canonical ensemble case.
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    27. 27
      Hoover, W. G. Canonical Dynamics: Equilibrium Phase-Space Distributions. Phys. Rev. A: At., Mol., Opt. Phys. 1985, 31, 1695– 1697,  DOI: 10.1103/physreva.31.1695
      27
      Canonical dynamics: Equilibrium phase-space distributions
      Hoover
      Physical review. A, General physics (1985), 31 (3), 1695-1697 ISSN:0556-2791.
      There is no expanded citation for this reference.
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    28. 28
      Feller, S. E.; Zhang, Y.; Pastor, R. W.; Brooks, B. R. Constant Pressure Molecular Dynamics Simulation: The Langevin Piston Method. J. Chem. Phys. 1995, 103, 4613– 4621,  DOI: 10.1063/1.470648
      28
      Constant pressure molecular dynamics simulation: the Langevin piston method
      Feller, Scott E.; Zhang, Yuhong; Pastor, Richard W.; Brooks, Bernard R.
      Journal of Chemical Physics (1995), 103 (11), 4613-21CODEN: JCPSA6; ISSN:0021-9606. (American Institute of Physics)
      A new method for performing mol. dynamics simulations under const. pressure is presented. In the method, which is based on the extended system formalism introduced by Andersen, the deterministic equations of motion for the piston degree of freedom are replaced by a Langevin equation; a suitable choice of collision frequency then eliminates the unphys. "ringing" of the vol. assocd. with the piston mass. In this way it is similar to the "weak coupling algorithm" developed by Berendsen and co-workers to perform mol. dynamics simulation without piston mass effects. It is shown, however, that the weak coupling algorithm induces artifacts into the simulation which can be quite severe for inhomogeneous systems such as aq. biopolymers or liq./liq. interfaces.
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    29. 29
      Martyna, G. J.; Tobias, D. J.; Klein, M. L. Constant Pressure Molecular Dynamics Algorithms. J. Chem. Phys. 1994, 101, 4177– 4189,  DOI: 10.1063/1.467468
      29
      Constant pressure molecular dynamics algorithms
      Martyna, Glenn J.; Tobias, Douglas J.; Klein, Michael L.
      Journal of Chemical Physics (1994), 101 (5), 4177-89CODEN: JCPSA6; ISSN:0021-9606.
      Modularly invariant equations of motion are derived that generate the isothermal-isobaric ensemble as their phase space avs. Isotropic vol. fluctuations and fully flexible simulation cells as well as a hybrid scheme that naturally combines the two motions are considered. The resulting methods are tested on two problems, a particle in a one-dimensional periodic potential and a spherical model of C60 in the solid/fluid phase.
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    30. 30
      Kohn, W.; Sham, L. J. Self-Consistent Equations Including Exchange and Correlation Effects. Phys. Rev. 1965, 140, 1133– 1138,  DOI: 10.1103/physrev.140.a1133
      There is no corresponding record for this reference.
    31. 31
      Kohn, W.; Becke, A. D.; Parr, R. G. Density Functional Theory of Electronic Structure. J. Phys. Chem. 1996, 100, 12974– 12980,  DOI: 10.1021/jp960669l
      31
      Density Functional Theory of Electronic Structure
      Kohn, W.; Becke, A. D.; Parr, R. G.
      Journal of Physical Chemistry (1996), 100 (31), 12974-12980CODEN: JPCHAX; ISSN:0022-3654. (American Chemical Society)
      A review with 74 refs. D. functional theory (DFT) is a (in principle exact) theory of electronic structure, based on the electron d. distribution n(r), instead of the many-electron wave function Ψ(r1,r2,r3,...). Having been widely used for over 30 yr by physicists working on the electronic structure of solids, surfaces, defects, etc., it has more recently also become popular with theor. and computational chemists. The present article is directed at the chem. community. It aims to convey the basic concepts and breadth of applications: the current status and trends of approxn. methods (local d. and generalized gradient approxns., hybrid methods) and the new light which DFT has been shedding on important concepts like electronegativity, hardness, and chem. reactivity index.
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    32. 32
      Hariharan, P. C.; Pople, J. A. The Influence of Polarization Functions on Molecular Orbital Hydrogenation Energies. Theor. Chim. Acta 1973, 28, 213– 222,  DOI: 10.1007/bf00533485
      32
      Influence of polarization functions on MO hydrogenation energies
      Hariharan, P. C.; Pople, J. A.
      Theoretica Chimica Acta (1973), 28 (3), 213-22CODEN: TCHAAM; ISSN:0040-5744.
      The hydrogenation energies of mols. involving H, C, O, N, and F with 2 non-H atoms were calcd. by a basis including polarization functions. The mean abs. deviation between theory and expt. for heats of hydrogenation of the closed shell species is 4 kcal/mole for the basis set with full polarization. Ests. of hydrogenation energy errors at the Hartree-Fock limit are reported.
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    33. 33
      Bernales, V. S.; Marenich, A. v.; Contreras, R.; Cramer, C. J.; Truhlar, D. G. Quantum Mechanical Continuum Solvation Models for Ionic Liquids. J. Phys. Chem. B 2012, 116, 9122– 9129,  DOI: 10.1021/jp304365v
      33
      Quantum Mechanical Continuum Solvation Models for Ionic Liquids
      Bernales, Varinia S.; Marenich, Aleksandr V.; Contreras, Renato; Cramer, Christopher J.; Truhlar, Donald G.
      Journal of Physical Chemistry B (2012), 116 (30), 9122-9129CODEN: JPCBFK; ISSN:1520-5207. (American Chemical Society)
      The quantum mech. SMD continuum universal solvation model can be applied to predict the free energy of solvation of any solute in any solvent following specification of various macroscopic solvent parameters. For three ionic liqs. where these descriptors are readily available, the SMD solvation model exhibits a mean unsigned error of 0.48 kcal/mol for 93 solvation free energies of neutral solutes and a mean unsigned error of 1.10 kcal/mol for 148 water-to-IL transfer free energies. Because the necessary solvent parameters are not always available for a given ionic liq., we det. av. values for a set of ionic liqs. over which measurements have been made in order to define a generic ionic liq. solvation model, SMD-GIL. Considering 11 different ionic liqs., the SMD-GIL solvation model exhibits a mean unsigned error of 0.43 kcal/mol for 344 solvation free energies of neutral solutes and a mean unsigned error of 0.61 kcal/mol for 431 water-to-IL transfer free energies. As these errors are similar in magnitude to those typically obsd. when applying continuum solvation models to ordinary liqs., we conclude that the SMD universal solvation model may be applied to ionic liqs. as well as ordinary liqs.
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    34. 34
      Runge, E.; Gross, E. K. U. Density-Functional Theory for Time-Dependent Systems. Phys. Rev. Lett. 1984, 52, 997– 1000,  DOI: 10.1103/physrevlett.52.997
      34
      Density-functional theory for time-dependent systems
      Runge, Erich; Gross, E. K. U.
      Physical Review Letters (1984), 52 (12), 997-1000CODEN: PRLTAO; ISSN:0031-9007.
      A d. functional formalism comparable to the Hohenberg-Kohn-Sham theory of the ground state is developed for arbitrary time-dependent systems. The single-particle potential v(.vector.rt) leading to a given v-representable d. n(.vector.rt) is uniquely detd. so that the corresponding map v → n is invertible. On the basis of this theorem, three schemes are derived to calc. the d.: a set of hydrodynamical equations, a stationary action principle, and an effective single-particle Schroedinger equation.
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    35. 35
      Becke, A. D. Density-Functional Thermochemistry. III. The Role of Exact Exchange. J. Chem. Phys. 1993, 98, 5648– 5652,  DOI: 10.1063/1.464913
      35
      Density-functional thermochemistry. III. The role of exact exchange
      Becke, Axel D.
      Journal of Chemical Physics (1993), 98 (7), 5648-52CODEN: JCPSA6; ISSN:0021-9606.
      Despite the remarkable thermochem. accuracy of Kohn-Sham d.-functional theories with gradient corrections for exchange-correlation, the author believes that further improvements are unlikely unless exact-exchange information is considered. Arguments to support this view are presented, and a semiempirical exchange-correlation functional (contg. local-spin-d., gradient, and exact-exchange terms) is tested for 56 atomization energies, 42 ionization potentials, 8 proton affinities, and 10 total at. energies of first- and second-row systems. This functional performs better than previous functionals with gradient corrections only, and fits expt. atomization energies with an impressively small av. abs. deviation of 2.4 kcal/mol.
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      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaK3sXisVWgtrw%253D&md5=291bbfc119095338bb1624f0c21c7ca8
    36. 36
      Lee, C.; Yang, W.; Parr, R. G. Development of the Colle-Salvetti Correlation-Energy Formula into a Functional of the Electron Density. Phys. Rev. B 1988, 37, 785– 789,  DOI: 10.1103/physrevb.37.785
      36
      Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density
      Lee, Chengteh; Yang, Weitao; Parr, Robert G.
      Physical Review B: Condensed Matter and Materials Physics (1988), 37 (2), 785-9CODEN: PRBMDO; ISSN:0163-1829.
      A correlation-energy formula due to R. Colle and D. Salvetti (1975), in which the correlation energy d. is expressed in terms of the electron d. and a Laplacian of the 2nd-order Hartree-Fock d. matrix, is restated as a formula involving the d. and local kinetic-energy d. On insertion of gradient expansions for the local kinetic-energy d., d.-functional formulas for the correlation energy and correlation potential are then obtained. Through numerical calcns. on a no. of atoms, pos. ions, and mols., of both open- and closed-shell type, it is demonstrated that these formulas, like the original Colle-Salvetti formulas, give correlation energies within a few percent.
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    37. 37
      Stephens, P. J.; Devlin, F. J.; Chabalowski, C. F.; Frisch, M. J. Ab Initio Calculation of Vibrational Absorption and Circular Dichroism Spectra Using Density Functional Force Fields. J. Phys. Chem. 1994, 98, 11623– 11627,  DOI: 10.1021/j100096a001
      37
      Ab Initio Calculation of Vibrational Absorption and Circular Dichroism Spectra Using Density Functional Force Fields
      Stephens, P. J.; Devlin, F. J.; Chabalowski, C. F.; Frisch, M. J.
      Journal of Physical Chemistry (1994), 98 (45), 11623-7CODEN: JPCHAX; ISSN:0022-3654.
      The unpolarized absorption and CD spectra of the fundamental vibrational transitions of the chiral mol. 4-methyl-2-oxetanone are calcd. ab initio. Harmonic force fields are obtained using d. functional theory (DFT), MP2 and SCF methodologies, and a [5s4p2d/3s2p] (TZ2P) basis set. DFT calcns. use the LSDA, BLYP, and Becke3LYP (B3LYP) d. functionals. Mid-IR spectra predicted using LSDA, BLYP, and B3LYP force fields are of significantly different quality, the B3LYP force field yielding spectra in clearly superior, and overall excellent, agreement with expt. The MP2 force field yields spectra in slightly worse agreement with expt. than the B3LYP force field. The SCF force field yields spectra in poor agreement with expt. The basis set dependence of B3LYP force fields is also explored: the 6-31G* and TZ2P basis sets give very similar results while the 3-21G basis set yields spectra in substantially worse agreement with expt.
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    38. 38
      Glendening, E. D.; Landis, C. R.; Weinhold, F. Natural Bond Orbital Methods. Wiley Interdiscip. Rev. Comput. Mol. Sci. 2012, 2, 1– 42,  DOI: 10.1002/wcms.51
      38
      Natural bond orbital methods
      Glendening, Eric D.; Landis, Clark R.; Weinhold, Frank
      Wiley Interdisciplinary Reviews: Computational Molecular Science (2012), 2 (1), 1-43CODEN: WIRCAH; ISSN:1759-0884. (Wiley-Blackwell)
      A review. Natural bond orbital (NBO) methods encompass a suite of algorithms that enable fundamental bonding concepts to be extd. from Hartree-Fock (HF), D. Functional Theory (DFT), and post-HF computations. NBO terminol. and general math. formulations for atoms and polyat. species are presented. NBO analyses of selected mols. that span the periodic table illustrate the deciphering of the mol. wavefunction in terms commonly understood by chemists: Lewis structures, charge, bond order, bond type, hybridization, resonance, donor-acceptor interactions, etc. Upcoming features in the NBO program address ongoing advances in ab initio computing technol. and burgeoning demands of its user community by introducing major new methods, keywords, and electronic structure system/NBO communication enhancements.
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    39. 39
      Hariharan, C.; Vijaysree, V.; Mishra, A. K. Quenching of 2,5-Diphenyloxazole (PPO) Fluorescence by Metal Ions. J. Lumin. 1997, 75, 205– 211,  DOI: 10.1016/s0022-2313(97)00126-9
      39
      Quenching of 2,5-diphenyloxazole (PPO) fluorescence by metal ions
      Hariharan, Chithra; Vijaysree, V.; Mishra, A. K.
      Journal of Luminescence (1997), 75 (3), 205-211CODEN: JLUMA8; ISSN:0022-2313. (Elsevier)
      The quenching of 2, 5-diphenyloxazole (PPO) fluorescence by transition metal ions (Mn2+, Fe2+, Co2+, Ni2+, Cu2+, Zn2+, Cd2+, Hg2+, Pb2+) were studied. From a reasonably linear fit of the logarithm of the bimol. quenching const. (log kq) with the half-wave redn. potential (E1/2 in V vs. SCE) of the various metal ions, the quenching probably proceeds via the formation of a non-emissive exciplex with charge transfer taking place from the excited fluorophore (PPO) to the metal ions. Ions like Fe2+, Hg2+ and Pb2+ are extremely efficient quenchers, Cu2+ and Ni2+ are moderate quenchers and Co2+, Zn2+, Cd2+ and Mn2+ are very poor quenchers of PPO fluorescence. Various other probable mechanisms like ground-state complex formation, heavy atom quenching, paramagnetic effect, resonance energy transfer, etc., do not appear to be important in the fluorescence quenching of (PPO) though their presence cannot be completely excluded.
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    40. 40
      Ueno, N.; Wakabayashi, T.; Sato, H.; Morisawa, Y. Changes in the Electronic Transitions of Polyethylene Glycol upon the Formation of a Coordinate Bond with Li+, Studied by ATR Far-Ultraviolet Spectroscopy. J. Phys. Chem. A 2019, 123, 10746– 10756,  DOI: 10.1021/acs.jpca.9b09274
      40
      Changes in the Electronic Transitions of Polyethylene Glycol upon the Formation of a Coordinate Bond with Li+, Studied by ATR Far-Ultraviolet Spectroscopy
      Ueno, Nami; Wakabayashi, Tomonari; Sato, Harumi; Morisawa, Yusuke
      Journal of Physical Chemistry A (2019), 123 (50), 10746-10756CODEN: JPCAFH; ISSN:1089-5639. (American Chemical Society)
      This study investigates the electronic transitions of complexes of lithium with polyethylene glycol (PEG) by the absorption bands of solvent mols. via attenuated total reflectance spectroscopy in the far-UV region (ATR-FUV). Alkali-metal complexes are interesting materials because of their functional characteristics such as good ionic cond. These complexes are used as polymer electrolytes for Li batteries and as one of the new types of room-temp. ionic liqs., termed solvation ionic liqs. Considering these applications, alkali-metal complexes have been studied mainly for their electrochem. characteristics; there is no fundamental study providing a clear understanding of electronic states in terms of electronic structures for the ground and excitation states near the HOMO-lowest occupied MO transitions. This study explores the electronic transitions of ligand mols. in alkali-metal complexes. In the ATR-FUV spectra of the Li-PEG complex, a decrease in intensity and a large blue shift (over 4 nm) were obsd. to result from an increase in the concn. of Li salts. This observation suggests the formation of a complex, with coordinate bonding between Li+ and the O atoms in PEG. Comparison of the exptl. spectrum with a simulated spectrum of the Li-PEG complex calcd. by time-dependent d. functional theory indicated that changes in the intensities and peak positions of bands at approx. 155 and 177 nm (pure PEG shows bands at 155, 163, and 177 nm) are due to the formation of coordinate bonding between Li+ and the O atoms in the ether mol. The intensity of the 177 nm band depends on the no. of residual free O atoms in the ether, and the peak wavelength at approx. 177 nm changes with the expansion of the electron clouds of PEG. We assign a band in the 145-155 nm region to the alkali-metal complex because we obsd. a new band at approx. 150 nm in the ATR-FUV spectra of very highly concd. binary mixts.
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    41. 41
      Ensing, B.; Tiwari, A.; Tros, M.; Hunger, J.; Domingos, S. R.; Pérez, C.; Smits, G.; Bonn, M.; Bonn, D.; Woutersen, S. On the Origin of the Extremely Different Solubilities of Polyethers in Water. Nat. Commun. 2019, 10, 2893,  DOI: 10.1038/s41467-019-10783-z
      41
      On the origin of the extremely different solubilities of polyethers in water
      Ensing Bernd; Tiwari Ambuj; Tros Martijn; Woutersen Sander; Hunger Johannes; Bonn Mischa; Domingos Sergio R; Perez Cristobal; Smits Gertien; Bonn Daniel
      Nature communications (2019), 10 (1), 2893 ISSN:.
      The solubilities of polyethers are surprisingly counter-intuitive. The best-known example is the difference between polyethylene glycol ([-CH2-CH2-O-]n) which is infinitely soluble, and polyoxymethylene ([-CH2-O-]n) which is completely insoluble in water, exactly the opposite of what one expects from the C/O ratios of these molecules. Similar anomalies exist for oligomeric and cyclic polyethers. To solve this apparent mystery, we use femtosecond vibrational and GHz dielectric spectroscopy with complementary ab initio calculations and molecular dynamics simulations. We find that the dynamics of water molecules solvating polyethers is fundamentally different depending on their C/O composition. The ab initio calculations and simulations show that this is not because of steric effects (as is commonly believed), but because the partial charge on the O atoms depends on the number of C atoms by which they are separated. Our results thus show that inductive effects can have a major impact on aqueous solubilities.
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    42. 42
      Walker, M.; Harvey, A. J. A.; Sen, A.; Dessent, C. E. H. Performance of M06, M06-2X, and M06-HF Density Functionals for Conformationally Flexible Anionic Clusters: M06 Functionals Perform Better than B3LYP for a Model System with Dispersion and Ionic Hydrogen-Bonding Interactions. J. Phys. Chem. A 2013, 117, 12590– 12600,  DOI: 10.1021/jp408166m
      42
      Performance of M06, M06-2X, and M06-HF Density Functionals for Conformationally Flexible Anionic Clusters: M06 Functionals Perform Better than B3LYP for a Model System with Dispersion and Ionic Hydrogen-Bonding Interactions
      Walker, Martin; Harvey, Andrew J. A.; Sen, Ananya; Dessent, Caroline E. H.
      Journal of Physical Chemistry A (2013), 117 (47), 12590-12600CODEN: JPCAFH; ISSN:1089-5639. (American Chemical Society)
      We present a comparative assessment of the performance of the M06 suite of d. functionals (M06, M06-2X, and M06-HF) against an MP2 benchmark for calcg. the relative energies and geometric structures of the Cl-·arginine and Br-·arginine halide ion-amino acid clusters. Addnl. results are presented for the popular B3LYP d. functional. The Cl-·arginine and Br-·arginine complexes are important prototypes for the phenomenon of anion-induced zwitterion formation. Results are presented for the canonical (noncharge sepd.) and zwitterionic (charge sepd.) tautomers of the clusters, as well as the numerous conformational isomers of the clusters. We find that all of the M06 functions perform well in terms of predicting the general trends in the conformer relative energies and identifying the global min. conformer. This is in contrast to the B3LYP functional, which performed significantly less well for the canonical tautomers of the clusters where dispersion interactions contribute more significantly to the conformer energetics. We find that the M06 functional gave the lowest mean unsigned error for the relative energies of the canonical conformers (2.10 and 2.36 kJ/mol for Br-·arginine and Cl-·arginine), while M06-2X gave the lowest mean unsigned error for the zwitterionic conformers (0.85 and 1.23 kJ/mol for Br-·arginine and Cl-·arginine), thus providing insight into the types of phys. systems where each of these functionals should perform best.
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    43. 43
      SpectraBase; John Wiley & Sons, Inc. Https://Spectrabase.Com/.
      There is no corresponding record for this reference.

  • Supporting Information

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    • Comparative decrease in fluorescence due to metal ions for PEG 20k vs 3-BHA, emission spectra of PEG 20k and PEG of different molecular weights, AFM images, and UV–vis spectrum of PEG 20k (PDF)


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