Applicability of Effective Fragment Potential Version 2-Molecular Dynamics (EFP2-MD) Simulations for Predicting Dynamic Liquid Properties Including the Supercritical Fluid Phase
- Nahoko KurokiNahoko KurokiDepartment of Chemistry and Biochemistry, Graduate School of Humanities and Sciences, Ochanomizu University, 2-1-1 Otsuka, Bunkyo-ku, Tokyo 112-8610, JapanMore by Nahoko Kuroki
- and
- Hirotoshi Mori*Hirotoshi Mori*E-mail: [email protected]. Tel: +81-3-5978-5718. Fax: +81-3-5978-5717.Faculty of Core Research Natural Science Division, Ochanomizu University, 2-1-1 Otsuka, Bunkyo-ku, Tokyo 112-8610, JapanMore by Hirotoshi Mori
Copyright © 2022 American Chemical Society. This publication is licensed under these Terms of Use.
This publication is Open Access under the license indicated. Learn More
Abstract
Effective fragment potential version 2-molecular dynamics (EFP2-MD) simulations, where the EFP2 is a polarizable force field based on ab initio electronic structure calculations, were applied to predict the static and dynamic liquid properties of compressed liquid NH3. By analyzing the temperature dependence of the radial distribution function, the autocorrelation functions of velocity (Cv(t)) and reorientation (Cr(t)), and the self-diffusion constant, we clarified that the ab initio EFP2 force field can effectively describe the properties of compressed liquids. These descriptions can be performed with at least semiquantitative accuracy and at a sufficiently low computational cost. In the EFP2-MD protocol, no force field training is required. This training is mandatory when simulating liquid properties with classical MD techniques (especially in extreme conditions with high pressures and temperatures). EFP2-MD is a promising technique for predicting the physicochemical properties of novel functional compressed liquids, including supercritical fluid phase properties.
1. Introduction
ARTICLE SECTIONS
Molecular-level insights into the transporting properties of liquid materials (particularly under extreme conditions involving high pressures and temperatures) are important in the fields of chemical engineering and physical solution chemistry. (1) For example, supercritical fluids made up of small organic molecules are used both as extraction solvents and as novel organic synthesis environments. (2,3) Supercritical fluids can be mixed with the other supercritical fluids or gases because intermolecular interactions among their constituent molecules are weak, i.e., their diffusion constants are very large. With these backgrounds, prediction of the physicochemical nature of functional compressed liquids (including supercritical fluids) has attracted the interest of many engineers. The self-diffusion constant is one of the most important dynamic properties of liquid materials. Researchers have used classical molecular dynamics (MD) simulations to evaluate the self-diffusion constants of functional liquids under various extreme conditions. (4−10) As is well known, however, classical MD simulations are based on classical force fields (FFs), which describe the intra/intermolecular interaction potential of the target systems. Generally, classical force fields are optimized for reproducing (1) experimentally observed target material properties or (2) intermolecular interactions evaluated by high-level quantum chemical calculations for various molecular configurations. Without a great effort, it is very difficult to obtain sufficiently accurate classical force field parameters for novel (unknown) functional liquid materials, especially under extreme conditions. To predict functional liquid’s properties, it is mandatory to apply ab initio MD (AIMD) calculations (e.g., Car–Parrinello MD, CPMD; (11,12) fragment molecular orbital based MD, FMO-MD (13−18)), in which intermolecular interaction is evaluated on a quantum mechanical level. However, because the computational costs of AIMD are much higher than those of classical MDs, it had been difficult to perform AIMD simulations to predict novel functions of compressed liquid materials, including supercritical fluids.
Recently, we showed that it is possible to predict mixed solvent properties using effective fragment potential version 2-MD simulations (EFP2-MD). (19) In the EFP2-MD protocol, where internal degrees of freedom in the target molecules are fixed, we focus only on relative molecular motions. The intermolecular potential is evaluated by describing each interaction term (i.e., electrostatic, exchange-repulsion, polarization, and dispersion interactions) by compactly pre-expanding each monomer wave function (for details, see the next section). (20,21) Because the EFP2-MD method is based on a quantum mechanical wave function for monomer fragments, it is possible to apply the method to various liquid systems as a relatively cheap AIMD simulation with predictive accuracy. (19,22−25) EFP2-MD has well-balanced characteristics of low computational cost and semiquantitative chemical accuracy. These characteristics make EFP2-MD promising for applications involving the prediction of the physicochemical nature of novel compressed liquids. In this paper, we discuss the applicability of EFP2-MD simulations to the prediction of static and dynamic liquid properties under high-pressure conditions, including the properties of supercritical fluids. As a test system, we focus on highly compressed liquid NH3.
2. Details of Effective Fragment Potential Version 2 (EFP2) Theory
ARTICLE SECTIONS
Here, we explain the EFP2 theory in more detail. The original version of the EFP, which is often called EFP1, was developed by Day and Gordon et al. (20,26) Focusing on only hydrating systems, in the EFP1 theory, intermolecular interactions in the target systems were described by the compactly expanded localized wave function of constituent monomer fragment molecules, in which repulsive interaction term was modeled with some empirical parameters. The EFP2 is an upgraded theory of the original EFP1 to suit for not only water solvent but also general solvents without using any empirical parameters. (20,21)
In the EFP2 theory, total interfragment interaction is evaluated as the sum of the four energy components.
where EES, EEXREP, EPOL, and EDISP are electrostatic, exchange-repulsion, polarization, and dispersion energies, respectively.
(1)
Electrostatic interaction is calculated by multipole expansion, for which expansion points are at the atoms and bond-midpoints generated by means of Stone distributed multipolar analysis. (27) In the case of short ranges, Coulomb interactions are damped in consideration of the overlap of the fragments to avoid excessive instability. (28−30) Exchange-repulsion is evaluated as an intermolecular overlap truncated at the quadratic term. (31−33) Kinetic and overlap integrals are calculated between each pair of fragments on the fly using wave function for each fragment.
where i, j, k, and l are localized molecular orbitals; I and J are nuclei, S and T are the overlap and kinetic energy integrals, respectively; and F is the intramolecular Fock matrix. Polarization interaction is treated as induced dipoles of one fragment with static multipole field and the induced field of the other fragment. The truncated polarizability term is evaluated as a tensor sum of anisotropic localized molecular orbital polarizabilities. (34) Dispersion interaction, which is an interaction among the induced dipoles, is expressed by an inverse R expansion.
where the 1/R6 term is the so-called van der Waals interaction term and the 1/R8 term is added to correct short-range interactions. (35)
(2)
(3)
As seen in the above equations, EFP2 theory is based on well-defined molecular fragmentation with no chemical reaction. In EFP2-MD simulations, the EFP2 was applied to describe intermolecular potentials in an ab initio manner.
3. Computational Details
ARTICLE SECTIONS
The purpose of this study is to assess whether EFP2-MD simulations can predict compressed liquids properties. First, the molecular structure of NH3 was optimized using quantum chemical calculations at the MP2/aug-cc-pVTZ level of theory. (36) With respect to the optimum structures, an ab initio polarizable EFP2 force field was determined using the “MAKEFP” module implemented in the GAMESS-US (Aug 2016 version) quantum chemical program package. (37)
Before performing MD simulations, we evaluated EFP2 force field accuracy by comparing the intermolecular interaction potential-energy surfaces obtained by a set of EFP2 and quantum chemical calculations at the CCSD(T)/aug-cc-pVTZ level of theory. The structural parameters used in the potential-surface evaluation are shown in Figure 1. To compare EFP2 and CCSD(T) (in terms of both their total interaction energies and their physicochemical components, i.e., electrostatic, exchange-repulsion, polarization, and dispersion components), the CCSD(T) interaction energies were decomposed using a localized molecular orbital energy decomposition analysis (LMO-EDA) method. (38) In the LMO-EDA calculations, we applied a counterpoise method to correct basis set superposition errors.
Figure 1
Figure 1. Coordinate system of an NH3 dimer.
After the EFP2 accuracy evaluation, we subsequently performed a set of EFP2-MD simulations for the supercritical and compressed liquid phases of NH3. In the EFP2-MD simulations, we used a set of cubic periodic boxes containing 500 NH3 molecules having an isothermal–isobaric (NPT) ensemble, with a cutoff distance of 10 Å. The time step was set to 1 fs per step for the EFP2-MD simulations. The pressure condition was set to a constant value of 500 bar. Although the temperature conditions were varied as 203, 243, 323, 373, 423, 473, and 700 K, we theoretically evaluated the density and diffusion constant of NH3. The Nosé–Hoover and Hoover’s equations were applied for thermal and pressure controls, respectively. With the above conditions, a set of 0.8 ns equilibration and 1.0 ns production runs were performed to evaluate the radial distribution functions (RDFs), autocorrelation velocity functions (Cv(t)), reorientation functions (Cr(t)), and self-diffusion constants.
4. Results and Discussion
ARTICLE SECTIONS
4.1. Accuracy of the EFP2 Force Field
Figure 2 depicts intermolecular interaction potential-energy surfaces for NH3 dimers (at R = 3.5 Å and φ = 0 degree; see the definitions of R and φ in Figure 2). The figure also gives the mean error (in kcal mol–1) for the EFP2 force field from the highly accurate quantum chemical CCSD(T)/aug-cc-pVTZ level of theory. Figure 2 clearly shows that the EFP2 force field follows the corresponding CCSD(T) results within chemical accuracy. If we examine the potential data in more detail, EFP2 overestimates instability around the structure of (θ1, θ2) = (150 degree, 40 degree) relative to the CCSD(T) results. This occurs because of the EFP2’s tendency to underestimate dispersion interaction, which originates from the fact that the EFP2 dispersion interaction is expanded by the Hartree–Fock wave function of interacting monomer fragments. However, the difference in interaction potential between EFP2 and CCSD(T) is less than 1.5 kcal mol–1. This means that the EFP2 force field has sufficient accuracy for evaluating intermolecular interactions in the condensed phase of NH3.
Figure 2
Figure 2. Two-dimensional potential-energy surfaces obtained by LMO-EDA and EFP2 methods. For the LMO-EDA, we applied an ab initio CCSD(T)/aug-cc-pVTZ level of quantum chemical calculation.
4.2. Static and Dynamic Properties of Compressed/Supercritical NH3 Described with EFP2-MD Simulations
A set of N–N RDFs for different temperature conditions are depicted in Figure 3. To obtain the RDFs, we statistically averaged trajectory data along 150 ps EFP2-MD simulations. Compared with that of the previous classical MD report using specially parametrized force fields for reproducing intermolecular interaction potential by quantum chemistry calculations, (7) our RDFs gave basically similar structures. In the RDFs, the NH3 distributions (N atom) around other N atoms are given for the temperature conditions. Under relatively low temperature conditions, we observed a set of apparent peaks assigned to the first and second NH3 hydration shells. With increasing temperatures, the second RDF peak vanishes, resulting in a very broad band. With the temperature ascension, we also observed a decrease in the NH3 coordination number (nNN), which is evaluated as the integral of the RDF along the radial coordinate (see Table 1). These observations indicate that increasing temperatures lead to a phase transition from a compressed liquid to a supercritical fluid.
Figure 3
Figure 3. Temperature dependence of N–N radial distribution functions (RDFs) for compressed NH3.
Table 1. Temperature Dependencies of NH3 Coordination Numbers (nNN(r)) for the First Solvation Shell (in the Region of r = 2.0–5.0 Å)
| T (K) | nNN(r) |
|---|---|
| 203 | 11.6 |
| 243 | 10.6 |
| 323 | 8.2 |
| 373 | 6.6 |
| 423 | 5.2 |
| 473 | 4.2 |
| 700 | 2.2 |
The liquid-supercritical NH3 densities in the temperature range of 203–700 K were 0.741–0.164 and 0.652–0.134 g cm–3 by experimental methods (7) and EFP2-MD, respectively. EFP2-MD gave ca. −10% systematic error. It should be reminded that rigid rotor approximation was applied in the EFP2 theory. Thus, theoretical densities obtained by the EFP2-MD should be smaller than the experimental values because all molecules in the system have frozen degrees of freedom. On the other hand, the corresponding density change by OPLS3-MD was 0.820–0.143 g cm–3. That is, OPLS3-MD gave ca. +10% overestimation and −10% underestimation with varying temperature conditions. In the case of density prediction for novel liquids including supercritical fluids, EFP2-MD with a set of systematic error that can be explained by proper physicochemical reasons would be preferred.
NH3 confined in a high-pressure box is polarized because the average intermolecular distance is shorter than it is under physicochemically mild conditions. Figure 4 depicts variations in the temporal dipole moment of NH3 simulated by EFP2-MD simulations (T = 203, 473, and 700 K). We observed that almost all NH3 molecules were strongly polarized in the compressed liquid phase (T = 203 K). The average variation in dipole moment was +0.65 Debye under these conditions, meaning that the strong polarization of NH3 must be considered. When heating the system to induce a transition into the supercritical fluid phase (T = 473 and 700 K), the distribution of the strongly polarized NH3 was observed to be sparse with the elongation of averaged intermolecular distance. It should be noted that several NH3 molecules in supercritical fluid phase remained strongly polarized. This can be explained by the fact that microscopic density fluctuates in supercritical fluids (i.e., several NH3 molecules form microclusters). When higher temperature conditions were simulated, the population of strongly polarized NH3 molecules decreased.
Figure 4
Figure 4. Temporal dipole moment variations for NH3 simulated by EFP2-MD simulations (T = 203, 473, and 700 K). The variations were defined as differences from the dipole moment of free NH3 molecules predicted by the EFP2 theory (1.61 Debye, which agrees well with experimental data of 1.47 Debye (39)). For clarity, NH3 molecules are depicted as single atoms placed at their centers of mass, and a set of representative snapshot structures with time evolution are depicted.
The temperature dependencies of the autocorrelation functions for velocity (Cv(t)) and reorientation (Cr(t)) are given in Figure 5. Defining u as a unit vector along the principal C3 axis of NH3, Cr(t) can be represented by the following equation
where θ(t) is the angle formed by the principal C3 axes of NH3 at t = 0 and t. From Figure 5a, we observed that the rate of Cr(t) decay increases with ascending temperatures. This can be well explained by the fact that liquid density decreases with increasing temperatures. In low-density conditions, Cr(t) diminishes more rapidly because molecular rotation is easy. The temperature dependence of Cr(t) simulated by our EFP2-MD method appropriately followed previous classical MD reports by Vyalov. (40) The following equation defines the autocorrelation function for velocity (Cv(t))
Cv(t) is a function that describes the relative translational motion of the target molecule in its condensed phase. For an ideal gas, Cv(t) is always equal to 1 because of the lack of molecular collision. As shown in Figure 5b, a set of exponential decays of Cv(t) is observed for relatively high temperature (i.e., low density) conditions (323–700 K). In contrast, according to our simulations, Cv(t) becomes negative for t = 0.1–0.5 ps in the compressed liquid phase at a low temperature (203 K). The negative value of Cv(t) means that the translation direction is scattered by molecular collision because of the high density of the compressed liquid. By analyzing dynamic molecular motion, it was clarified that we successfully modeled two different condensed phases (the compressed liquid phase and the supercritical fluid phase), using an EFP2-MD simulation with changing temperature conditions.
(4)
(5)
Figure 5
Figure 5. Temperature dependencies of Cr(t) and Cv(t) for compressed NH3.
Finally, it would be useful to demonstrate the merits of applying the EFP2-MD scheme to further study liquid materials. In Figure 6, the self-diffusion constants of NH3 predicted by the EFP2-MD simulation were shown as functions of temperature. In this study, the self-diffusion constants (D) were defined according to the following equation, using the long-time limits of the mean-square displacement.
As shown in Figure 6, classical MD with optimized FF, which is specially optimized for reproducing intermolecular interaction potential by quantum chemistry calculations, well followed the experimental self-diffusion constants by Groß et al. (41) On the other hand, EFP2-MD and OPLS3-MD (42) gave slight overestimates of self-diffusion constants compared with the experimental results. It should be noted that our object in this study is not to reproduce experimental data in an exact manner but to predict a dynamic physicochemical property such as self-diffusion constant prior to performing experiments with semiquantitative accuracy and low computational costs. Generally speaking, evaluation of diffusion constants is difficult even to reproduce their order without applying well-trained force fields. Figure 6 shows that EFP2-MD has succeeded in reproducing the order of diffusion constants with no effort for optimizing such empirical parameters. The overall results presented in this report indicate that a new stage of functional compressed liquid design (including the supercritical fluid phase) can be developed with EFP2-MD, a simple and sufficiently accurate ab initio MD scheme. It is well known that a set of long-term MD simulations (at least sub-ns order) is mandatory for predicting dynamic molecular properties like self-diffusion constants. Although there is significant need in the chemical engineering field to perform ab initio MD simulations for predicting liquid functionality (particularly for compressed liquids including supercritical fluids), it is currently very difficult to perform such predictive simulations because of their high computational costs relative to classical simulations. Thus, classical MD simulations with well-trained force field parameters have been used for engineering applications. Considering the balance between accuracy and computational and simulation setup costs, EFP2-MD is a promising protocol for designing functional liquids (including the physicochemical properties of such liquids) under high pressures and temperatures. The computational cost of EFP2-MD to obtain 1 ns trajectory for the target system is half week with modern in-house computers (32 CPU cores), which is much faster than so-called ab initio MD (e.g., CPMD, FMO-MD). In our group, physicochemical property predictions for various supercritical fluids are now in progress.
(6)
Figure 6
Figure 6. Dependence of the self-diffusion constant of NH3 on temperature. Experimental and classical MD (optimized FF) data were those reported by Orabi et al. (7)
5. Concluding Remarks
ARTICLE SECTIONS
In this paper, the applicability of simulating strongly compressed liquids using EFP2-MD, including the supercritical fluid phase, was reported for NH3 using a set of numerical examples. Although the EFP2 force field was constructed only on the basis of the ab initio wave function for a monomer (NH3) fragment, we showed that both static (RDFs) and dynamic condensed phase properties (autocorrelation functions and self-diffusion constants) could be evaluated with sufficient accuracy compared with the previous experimental and theoretical data. No empirical parameterization, which is mandatory in classical MD simulations, was required before performing MD simulations with the EFP2-MD protocol, even for compressed liquids and supercritical fluids. Overall, we showed that it is possible to predict the dynamic liquid properties of compressed liquids, at least semiquantitatively, using the simple EFP2-MD protocol described in this report.
Author Information
ARTICLE SECTIONS
- Hirotoshi Mori - Faculty of Core Research Natural Science Division and , Ochanomizu University, 2-1-1 Otsuka, Bunkyo-ku, Tokyo 112-8610, Japan;
http://orcid.org/0000-0002-7662-9636;
Acknowledgments
ARTICLE SECTIONS
Some of the presented calculations were performed at the Research Center for Computational Science (RCCS), the Okazaki Research Facilities, and the National Institutes of Natural Sciences (NINS), and TSUBAME3.0 supercomputer at Tokyo Institute of Technology. This study was supported in part by the Advanced Information and Communication Technology for Innovation (ACT-I; Grant number: JPMJPR16UB), Precursory Research for Embryonic Science and Technology programs (PRESTO; Grant number: JPMJPR16NC) from the Japan Science and Technology (JST) Agency, and JSPS KAKENHI (Grant Numbers: 16K13928 and 18J11490).
References
ARTICLE SECTIONS
This article references 42 other publications.
- 1Hendriks, E.; Kontogeorgis, G. M.; Dohrn, R.; de Hemptinne, J.-C.; Economou, I. G.; Zilnik, L. F.; Vesovic, V. Industrial Requirements for Thermodynamics and Transport Properties. Ind. Eng. Chem. Res. 2010, 49, 11131– 11141, DOI: 10.1021/ie101231b[ACS Full Text
], [CAS], Google Scholar1https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3cXht1OnurnN&md5=b76e6b5e01a794ce5b88066b9beebb22Industrial Requirements for Thermodynamics and Transport PropertiesHendriks, Eric; Kontogeorgis, Georgios M.; Dohrn, Ralf; de Hemptinne, Jean-Charles; Economou, Ioannis G.; Zilnik, Ljudmila Fele; Vesovic, VelisaIndustrial & Engineering Chemistry Research (2010), 49 (22), 11131-11141CODEN: IECRED; ISSN:0888-5885. (American Chemical Society)A review. This work reports the results of an investigation on industrial requirements for thermodn. and transport properties carried out by the Working Party on Thermodn. and Transport properties (http://www.wp-ttp.dk/) of the European Federation of Chem. Engineering, EFCE (http://www.efce.info/). A carefully designed questionnaire was sent to a no. of key tech. people in companies in the oil and gas, chems., and pharmaceutical/biotechnol. sectors. Twenty-eight companies have provided answers which formed the basis for the anal. presented here. A no. of previous reviews, specifically addressed to or written by industrial colleagues, are discussed initially. This provides the context of the survey and material with which the results of the survey can be compared. The results of the survey have been divided into the themes: data, models, systems, properties, education, and collaboration. The main results are as follows. There is (still) an acute need for accurate, reliable, and thermodynamically consistent exptl. data. Quality is more important than quantity. Similarly, there is a great need for reliable predictive, rather than correlative, models covering a wide range of compns., temps., and pressures and capable of predicting primary (phase equil.) and secondary (enthalpy, heat capacity, etc.) properties. It is clear that the ideal of a single model covering all requirements is not achievable, but there is a consensus that this ideal should still provide the direction for future development. The use of new methods, such as SAFT, is increasing, but they are not yet in position to replace traditional methods such as cubic equations of state (esp. in oil and gas industry) and the UNIFAC group contribution approach. A common problem with novel methods is lack of standardization, ref. data, and correct and transparent implementations, esp. in com. available simulation programs. The survey indicates a great variety of systems where further work is required. For instance, for electrolyte systems better models are needed, capable of describing all types of phase behavior and mixts. with other types of components. There is also a lack of data and methods for larger complex mols. Compared with the previous reviews, complex mixts. contg. carbon dioxide assocd. with a wide range of applications, such as capture, transport, and storage are becoming interesting to a no. of survey participants. Despite the academic success of mol. simulation techniques, the survey does not indicate great interest in it or its future development. Algorithms appear to be a neglected area, but improvements are still needed esp. for multiphase reactive systems (simultaneous chem. and phys. equil.). Education in thermodn. is perceived as key, for the future application of thermodn. in the industry. A no. of suggestions for improvement were made at all three levels (undergraduate, postgraduate, and professional development) indicating that the education is correctly perceived as an ongoing process. - 2Vyhmeister, E.; Valdes-Gonzalez, H.; Muscat, A. J.; Suleiman, D.; Estevez, L. A. Surface Modification of Porous Silicon-Based Films Using Dichlorosilanes Dissolved in Supercritical Carbon Dioxide. Ind. Eng. Chem. Res. 2013, 52, 4762– 4771, DOI: 10.1021/ie302686e
- 3Tomita, K.; Machmudah, S.; Quitain, A. T.; Sasaki, M.; Fukuzato, R.; Goto, M. Extraction and Solubility Evaluation of Functional Seed Oil in Supercritical Carbon Dioxide. J. Supercrit. Fluids 2013, 79, 109– 113, DOI: 10.1016/j.supflu.2013.02.011[Crossref], [CAS], Google Scholar3https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3sXktFWit7Y%253D&md5=f11a410dbeed1562ea95743181dae13fExtraction and solubility evaluation of functional seed oil in supercritical carbon dioxideTomita, Karin; Machmudah, Siti; Quitain, Armando T.; Sasaki, Mitsuru; Fukuzato, Ryuichi; Goto, MotonobuJournal of Supercritical Fluids (2013), 79 (), 109-113CODEN: JSFLEH; ISSN:0896-8446. (Elsevier B.V.)Hemp (Cannabis sativa L.) seed oil is valued for its nutritional properties and for the health benefits assocd. with it. Its greatest feature is that the ratio of linoleic acid and linolenic acid is the desirable value of 3:1. In this research, supercrit. carbon dioxide was applied to extn. of functional oil from hemp seed. In order to det. the effect of temp. and pressure on the yield of extd. components, the oil was extd. from hemp seed at temps. between 40 and 80°C, pressures of 20-40 MPa and a CO2 flow rate of 3 mL/min. The soly. of hemp seed oil in SCCO2 detd. exptl. was fitted to the Chrastil equation to det. the model parameters. The soly. calcd. by Chrastil equation was compared with the exptl. data. Finally, the fatty acid profile of the oil was evaluated by gas chromatog.-flame ionization detection (GC-FID). There are no significant differences in the compns. of five abundant fatty acid components of the oil obtained at different sampling times with SCCO2 extn. and other extn. methods.
- 4Feng, H.; Liu, X.; Gao, W.; Chen, X.; Wang, J.; Chen, L.; Lüdemann, H.-D. Evolution of Self-Diffusion and Local Structure in Some Amines over a Wide Temperature Range at High Pressures: A Molecular Dynamics Simulation Study. Phys. Chem. Chem. Phys. 2010, 12, 15007– 15017, DOI: 10.1039/c0cp00337a
- 5Idrissi, A.; Vyalov, I.; Kiselev, M.; Fedorov, M. V.; Jedlovszky, P. Heterogeneity of the Local Structure in Sub- and Supercritical Ammonia: A Voronoi Polyhedra Analysis. J. Phys. Chem. B 2011, 115, 9646– 9652, DOI: 10.1021/jp204078u[ACS Full Text], [CAS], Google Scholar5https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3MXovFKmsLc%253D&md5=37b7b7e185d26c8eb1199d70515bd1ccHeterogeneity of the Local Structure in Sub- and Supercritical Ammonia: A Voronoi Polyhedra AnalysisIdrissi, A.; Vyalov, I.; Kiselev, M.; Fedorov, M. V.; Jedlovszky, P.Journal of Physical Chemistry B (2011), 115 (31), 9646-9652CODEN: JPCBFK; ISSN:1520-5207. (American Chemical Society)We report results of mol. dynamics simulations and detailed anal. of the local structure of sub- and supercrit. ammonia in the range of temp. between 250 and 500 K along the 135 bar isobar. This anal. is based on the behavior of distributions of metric and topol. properties of the Voronoi polyhedra (VP). We show that by increasing the temp., the vol., surface, and face area distributions of the Voronoi polyhedra as well as the vacancy radius distribution broaden, particularly near the temp. Tα, where the calcd. thermal expansion coeff. has its max. The rate of increase of the corresponding mean values and fluctuations increases drastically when approaching Tα. This behavior clearly indicates that the local structure, as described by the VP, becomes increasingly heterogeneous upon approaching this temp. This heterogeneous distribution of ammonia mols. is traced back to the increase of the large voids with increasing temp., and is also clearly seen in the behavior of the fluctuation of the local d., as measured by the VP. More interestingly, the max. in the heterogeneity coincides with the max. of the fluctuation in the d. of the VP.
- 6Guevara-Carrion, G.; Vrabec, J.; Hasse, H. Prediction of Transport Properties of Liquid Ammonia and Its Binary Mixture with Methanol by Molecular Simulation. Int. J. Thermophys. 2012, 33, 449– 468, DOI: 10.1007/s10765-012-1166-4[Crossref], [CAS], Google Scholar6https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC38XktVagtb8%253D&md5=87b8fbd21f36031110c0e374928e7262Prediction of transport properties of liquid ammonia and its binary mixture with methanol by molecular simulationGuevara-Carrion, Gabriela; Vrabec, Jadran; Hasse, HansInternational Journal of Thermophysics (2012), 33 (3), 449-468CODEN: IJTHDY; ISSN:0195-928X. (Springer)Transport properties of NH3 and of the binary mixt. NH3 + MeOH are predicted for a broad range of liq. states by mol. dynamics (MD) simulation on the basis of rigid, non-polarizable mol. models of the united-atom type. These models were parameterized in preceding work using only exptl. vapor-liq. equil. data. The self- and the Maxwell-Stefan (MS) diffusion coeffs. as well as the shear viscosity are obtained by equil. MD and the Green-Kubo formalism. Non-equil. MD is used for the thermal cond. The transport properties of liq. NH3 are predicted for temps. between 223-473 K up to pressures of 200 MPa and are compared to exptl. data and correlations thereof. Generally, good agreement is achieved. The predicted self-diffusion coeff. as well as the shear viscosity deviates on av. by <15 % from the expt. and the thermal cond. by <6 %. Furthermore, the self- and the MS transport diffusion coeffs. as well as the shear viscosity of the liq. mixt. NH3 + MeOH were studied at different compns. and compared to the available exptl. data.
- 7Orabi, E. A.; Lamoureux, G. Polarizable Interaction Model for Liquid, Supercritical, and Aqueous Ammonia. J. Chem. Theory Comput. 2013, 9, 2035– 2051, DOI: 10.1021/ct301123j[ACS Full Text], [CAS], Google Scholar7https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3sXjtVCns70%253D&md5=5a0e5a649d626b39232f245e364c1f74Polarizable Interaction Model for Liquid, Supercritical, and Aqueous AmmoniaOrabi, Esam A.; Lamoureux, GuillaumeJournal of Chemical Theory and Computation (2013), 9 (4), 2035-2051CODEN: JCTCCE; ISSN:1549-9618. (American Chemical Society)A polarizable model for ammonia is optimized based on the ab initio properties of the NH3 mol. and the NH3-NH3 and NH3-H2O dimers calcd. at the MP2 level. For larger (NH3)m, NH3(H2O)n, and H2O(NH3)n clusters (m = 2-7 and n = 1-4), the model yields structural and binding energies in good agreement with ab initio calcns. without further adjustments. It also reproduces the structure, d., heat of vaporization, self-diffusion coeff., heat capacity, and isothermal compressibility of liq. ammonia at the b.p. The model is further validated by calcg. some of these properties at various temps. and pressures spanning the liq. and supercrit. phases of the fluid (up to 700 K and 200 MPa). The excellent transferability of the model suggests that it can be used to investigate properties of fluid ammonia under conditions for which expts. are not easy to perform. For aq. ammonia solns., the model yields liq. structures and densities in good agreement with exptl. data and allows the nonlinearity in the d.-compn. plot to be interpreted in terms of structural changes with compn. Finally, the model is used to investigate the solvation structure of ammonia in liq. water and of water in liq. ammonia and to calc. the solvation free energy of NH3 and H2O in aq. ammonia as a function of soln. compn. and temp. The simulation results suggest the presence of a transition around 50% molar NH3/H2O compns., above which water mols. are preferably solvated by ammonia.
- 8Albertí, M.; Amat, A.; Farrera, L.; Pirani, F. From the (NH3)2-5 Clusters to Liquid Ammonia: Molecular Dynamics Simulations Using the NVE and NpT Ensembles. J. Mol. Liq. 2015, 212, 307– 315, DOI: 10.1016/j.molliq.2015.09.016[Crossref], [CAS], Google Scholar8https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2MXhsFOjsLzJ&md5=5e24542c24d9bad1cb500d60865ee267From the (NH3)2-5 clusters to liquid ammonia: Molecular dynamics simulations using the NVE and NpT ensemblesAlberti, M.; Amat, A.; Farrera, Ll.; Pirani, F.Journal of Molecular Liquids (2015), 212 (), 307-315CODEN: JMLIDT; ISSN:0167-7322. (Elsevier B.V.)A force field for the intermol. NH 3-NH 3 interaction has been constructed and applied to characterize in detail the ammonia behavior in different environments. In particular, the dynamics of the (NH 3) 2 - 5 small clusters have been investigated and the isomerization processes analyzed as a function of the temp. considering a microcanonical (NVE) ensemble. The predicted (NH 3) 2 - 5 binding energies are in good agreement with exptl. data and/or ab initio calcns. Liq. ammonia has been studied, by considering an isothermic-isobaric ensemble (NpT) of 512 mols. at different conditions of temp. and pressure. In particular, the temp. dependence of the d. and of the mean diffusion coeffs. has been analyzed at 1 atm of pressure. Six different p-T conditions, at which the coexistence of vapor and liq. is possible, have been also taken into account. Finally, the radial distribution functions and the coordination no. have been calcd. at the same conditions used in neutron diffraction expts. The model predictions have been compared successfully with exptl. results, confirming the reliability of the force field formulation.
- 9Ushiki, I.; Ota, M.; Sato, Y.; Inomata, H. A Kinetic Study of Organic Compounds (Acetone, Toluene, n-Hexane and n-Decane) Adsorption Behavior on Activated Carbon Under Supercritical Carbon Dioxide Conditions at Temperature from 313 to 353 K and at Pressure from 4.2 to 15.0 MPa. J. Supercrit. Fluids 2014, 95, 187– 194, DOI: 10.1016/j.supflu.2014.08.021[Crossref], [CAS], Google Scholar9https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2cXhsV2ntrrI&md5=0b8eb1bf2fe28a354ce9ce921eea1898A kinetic study of organic compounds (acetone, toluene, n-hexane and n-decane) adsorption behavior on activated carbon under supercritical carbon dioxide conditions at temperature from 313 to 353 K and at pressure from 4.2 to 15.0 MPaUshiki, Ikuo; Ota, Masaki; Sato, Yoshiyuki; Inomata, HiroshiJournal of Supercritical Fluids (2014), 95 (), 187-194CODEN: JSFLEH; ISSN:0896-8446. (Elsevier B.V.)Adsorption kinetics of four volatile org. compds. (VOCs) (acetone, toluene, n-hexane and n-decane) on activated carbon under supercrit. carbon dioxide (scCO2) conditions was studied. Breakthrough curve measurements of VOCs in scCO2 were performed with a fixed bed method for activated carbon (ca. mean particles diam.: 100 μm, sp. surface area: 1300 m2/g and mean pore diam.: 0.687 nm, resp.). The measured breakthrough curves could be correlated with a kinetic model by using only one fitting parameter (effective diffusion coeff. in pore) within 10% of av. relative deviation. The detd. effective diffusion coeff. decreased with decreasing temps. and increasing pressures at all conditions. Addnl., a generalized model of the detd. effective diffusion coeffs. was developed, and the proposed model could satisfactorily describe temp. and pressure dependence at all VOCs conditions.
- 10Sohrevardi, N.; Bozorgmehr, M. R.; Heravi, M. M.; Khanpour, M. Transport Properties of Mixtures Composed of Acetone, Water, and Supercritical Carbon Dioxide by Molecular Dynamics Simulation. J. Supercrit. Fluids 2017, 130, 321– 326, DOI: 10.1016/j.supflu.2017.06.017[Crossref], [CAS], Google Scholar10https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2sXhtFOju7fO&md5=7e11abbf69bcbb312a8f001a33a96677Transport properties of mixtures composed of acetone, water, and supercritical carbon dioxide by molecular dynamics simulationSohrevardi, Nahid; Bozorgmehr, Mohammad Reza; Heravi, Mohammad Momen; Khanpour, MehrdadJournal of Supercritical Fluids (2017), 130 (), 321-326CODEN: JSFLEH; ISSN:0896-8446. (Elsevier B.V.)Transport properties of various mixts. of supercrit. carbon dioxide, acetone, and water at different concns. are evaluated at temps. 313.15 K and pressure 150 bar by mol. dynamics simulations. The results show that the self-diffusion (viscosity) coeff. is increased (decreased) for all various mixts. studied when the concn. of the acetone is increased. In addn., the densities of the mixts. will rise (lower), when the supercrit. carbon dioxide (acetone) concns. is increased. We have obsd. that the first peak heights of the radial distribution functions will rise at very low mole fraction of water (xw = 0.016) when the acetone and carbon dioxide concns. are increasing, and hence the self-diffusion coeffs. will decrease while its d. and viscosity will increase.
- 11Car, R.; Parrinello, M. Unified Approach for Molecular Dynamics and Density-Functional Theory. Phys. Rev. Lett. 1985, 55, 2471– 2474, DOI: 10.1103/PhysRevLett.55.2471[Crossref], [PubMed], [CAS], Google Scholar11https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaL28XhtVOlug%253D%253D&md5=ff5ef2fa5a1cf2c64bce1d5c052da979Unified approach for molecular dynamics and density-functional theoryCar, R.; Parrinello, M.Physical Review Letters (1985), 55 (22), 2471-4CODEN: PRLTAO; ISSN:0031-9007.A unified scheme is given that, by combining mol. dynamics and d.-functional theory, profoundly extends the range of both concepts. This approach extends mol. dynamics beyond the usual pair-potential approxn., thereby making possible the simulation of both covalently bonded and metallic systems. In addn., it permits the application of d.-functional theory to much larger systems than previously feasible. The new technique is demonstrated by the calcn. of some static and dynamic properties of cryst. Si within a self-consistent pseudopotential framework.
- 12Saharay, M.; Balasubramanian, S. Electron Donor-Acceptor Interactions in Ethanol-CO2 Mixtures: An Ab Initio Molecular Dynamics Study of Supercritical Carbon Dioxide. J. Phys. Chem. B 2006, 110, 3782– 3790, DOI: 10.1021/jp053839f[ACS Full Text], [CAS], Google Scholar12https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2MXht1WisLvF&md5=36a062eca2602cc4a9ad7c71d7e9d1a3Electron Donor-Acceptor Interactions in Ethanol-CO2 Mixtures: An Ab Initio Molecular Dynamics Study of Supercritical Carbon DioxideSaharay, Moumita; Balasubramanian, SundaramJournal of Physical Chemistry B (2006), 110 (8), 3782-3790CODEN: JPCBFK; ISSN:1520-6106. (American Chemical Society)The nature of interactions between ethanol and carbon dioxide has been characterized using simulations via the Car-Parrinello mol. dynamics (CPMD) method. Optimized geometries and energetics of free-standing ethanol-CO2 clusters exhibit evidence for a relatively more stable electron donor-acceptor (EDA) complex between these two species rather than a hydrogen-bonded configuration. This fact has also been confirmed by the higher formation rate of the EDA complex in supercrit. carbon dioxide-ethanol mixts. The probability d. distribution of CO2 mols. around ethanol in the supercrit. state shows two high probability regions along the direction of the lone pairs on the oxygen atom of ethanol. The EDA interaction between ethanol and CO2 as well as that between CO2 mols. themselves leads to significant deviations from linearity in the geometry of the CO2 mol. The vibrational spectra of carbon dioxide obtained from the at. velocity correlation functions in the bulk system as well as from isolated complexes show splitting of the ν2 bending mode that arises largely from CO2-CO2 interactions, with ethanol contributing only marginally because of its low concn. in the present study. The stretching frequency of the hydroxyl group of ethanol is shifted to lower frequencies in the bulk mixt. when compared to its gas-phase value, in agreement with expts.
- 13Kato, Y.; Fujiwara, T.; Komeiji, Y.; Nakano, T.; Mori, H.; Okiyama, Y.; Mochizuki, Y. Fragment Molecular Orbital-Based Molecular Dynamics (FMO-MD) Simulations on Hydrated Cu(II) Ion. Chem-Bio Inf. J. 2014, 14, 1– 13, DOI: 10.1273/cbij.14.1[Crossref], [CAS], Google Scholar13https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2cXhslaju7bK&md5=2519486b958cfb4b0bd94b3feb64d895Fragment molecular orbital-based molecular dynamics (FMO-MD) simulations on hydrated Cu(II) ionKato, Yuji; Fujiwara, Takayuki; Komeiji, Yuto; Nakano, Tatsuya; Mori, Hirotoshi; Okiyama, Yoshio; Mochizuki, YujiChem-Bio Informatics Journal (2014), 14 (), 1-13CODEN: CIJHBB; ISSN:1347-0442. (Chem-Bio Informatics Society)A simulation protocol based on fragment MO-based mol. dynamics (FMO-MD) was applied to a droplet model consisting of a divalent copper ion and 64 water mols. The total energy and forces were evaluated at the UHF (UHF) level with three-body fragment correction (FMO3). Two MD runs were performed: one with a six-coordination setting and the other with a five-coordination setting in the first hydration shell. Both runs resulted in the main peak position of the Cu-O radial distribution function at 2.02 Å, in reasonable agreement with the exptl. data. The O-Cu-O angular distribution function showed different characteristics between the two cases.
- 14Matsuda, A.; Mori, H. Theoretical Study on the Hydration Structure of Divalent Radium Ion Using Fragment Molecular Orbital-Molecular Dynamics (FMO-MD) Simulation. J. Solution Chem. 2014, 43, 1669– 1675, DOI: 10.1007/s10953-014-0235-7[Crossref], [CAS], Google Scholar14https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2cXhslels7jL&md5=47afd2fb6a90e02da740a14bf5435f4fTheoretical Study on the Hydration Structure of Divalent Radium Ion Using Fragment Molecular Orbital-Molecular Dynamics (FMO-MD) SimulationMatsuda, Aya; Mori, HirotoshiJournal of Solution Chemistry (2014), 43 (9-10), 1669-1675CODEN: JSLCAG; ISSN:0095-9782. (Springer)Using fragment MO-mol. dynamics (FMO-MD) simulation at the FMO3-HF/6-31G(d,p) level, the hydration of a Ra2+ ion was theor. investigated. The first peaks of the radial distribution function (RDF) for Ra-O and Ra-H lengths were predicted to be 2.85 and 3.45 Å with broad envelopes in the ranges of 2.5-3.5 and 2.8-4.3 Å, resp. The broad peaks shows that the first hydration shell of Ra2+ is much more flexible than those in the other hydrated divalent alk. earth metal ions, i.e., Ra2+ is a structure-breaking ion. The hydration no. of Ra2+ was predicted to be 8.1. From the angular distribution function (ADF), it was clarified that the octa hydrated Ra2+ ion has a flexible square antiprism structure at room temp.
- 15Mori, H.; Hirayama, N.; Komeiji, Y.; Mochizuki, Y. Differences in Hydration Between cis- and trans-Platin: Quantum Insights by Ab Initio Fragment Molecular Orbital-Based Molecular Dynamics (FMO-MD). Comput. Theor. Chem. 2012, 986, 30– 34, DOI: 10.1016/j.comptc.2012.02.008[Crossref], [CAS], Google Scholar15https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC38XksFaqt78%253D&md5=cf790e1372b1da59acc6166a29d4c580Differences in hydration between cis- and trans-platin: Quantum insights by ab initio fragment molecular orbital-based molecular dynamics (FMO-MD)Mori, Hirotoshi; Hirayama, Natsumi; Komeiji, Yuto; Mochizuki, YujiComputational & Theoretical Chemistry (2012), 986 (), 30-34CODEN: CTCOA5; ISSN:2210-271X. (Elsevier B.V.)Differences in hydration between cis- and trans-platin were investigated using ab initio fragment MO-based mol. dynamics (FMO-MD) simulations. Analyzing quantum charge fluctuation in water, we found that the Pt-Cl bond fluctuation of cis/trans-platin, which is important for activating their anticancer functions, was induced by charge transfer interaction between an anti-bonding π(Pt-Cl) orbital of platin complex and unoccupied orbital of solvent water mols. The hydration no. of Cl ligand in the first hydration shell was found to be larger for cis-platin than for trans-platin due to their difference in charge distribution. Our FMO-MD simulations showed that the amplitude of the Pt-Cl bond fluctuation is larger in hydrated cis-platin than in hydrated trans-platin.
- 16Komeiji, Y.; Mochizuki, Y.; Nakano, T.; Mori, H. Recent Advances in Fragment Molecular Orbital-Based Molecular Dynamics (FMO-MD) Simulations in Molecular Dynamics; InTech: Rijeka, Croatia, 2012.
- 17Fujiwara, T.; Mori, H.; Mochizuki, Y.; Osanai, Y.; Miyoshi, E. 4f-in-Core Model Core Potentials for Trivalent Lanthanides. Chem. Phys. Lett. 2011, 510, 261– 266, DOI: 10.1016/j.cplett.2011.05.028
- 18Fujiwara, T.; Mochizuki, Y.; Komeiji, Y.; Okiyama, Y.; Mori, H.; Nakano, T.; Miyoshi, E. Fragment Molecular Orbital-Based Molecular Dynamics (FMO-MD) Simulations on Hydrated Zn(II) Ion. Chem. Phys. Lett. 2010, 490, 41– 45, DOI: 10.1016/j.cplett.2010.03.020
- 19Kuroki, N.; Mori, H. Applicability of Effective Fragment Potential Version 2 - Molecular Dynamics (EFP2-MD) Simulations for Predicting Excess Properties of Mixed Solvents. Chem. Phys. Lett. 2018, 694, 82– 85, DOI: 10.1016/j.cplett.2018.01.042
- 20Day, P. N.; Jensen, J. H.; Gordon, M. S.; Webb, S. P.; Stevens, W. J.; Krauss, M.; Garmer, D.; Basch, H.; Cohen, D. An Effective Fragment Method for Modeling Solvent Effects in Quantum Mechanical Calculations. J. Chem. Phys. 1996, 105, 1968– 1986, DOI: 10.1063/1.472045[Crossref], [CAS], Google Scholar20https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaK28Xks1yktrY%253D&md5=c58a00728e94178578d70d3d07861f33An effective fragment method for modeling solvent effects in quantum mechanical calculationsDay, Paul N.; Jensen, Jan H.; Gordon, Mark S.; Webb, Simon P.; Stevens, Walter J.; Krauss, Morris; Garmer, David; Basch, Harold; Cohen, DroraJournal of Chemical Physics (1996), 105 (5), 1968-1986CODEN: JCPSA6; ISSN:0021-9606. (American Institute of Physics)An effective fragment model is developed to treat solvent effects on chem. properties and reactions. The solvent, which might consist of discrete water mols., protein, or other material, is treated explicitly using a model potential that incorporates electrostatics, polarization, and exchange repulsion effects. The solute, which one can most generally envision as including some no. of solvent mols. as well, is treated in a fully ab initio manner, using an appropriate level of electronic structure theory. In addn. to the fragment model itself, formulas are presented that permit the detn. of analytic energy gradients and, therefore, numerically detd. energy second derivs. (Hessians) for the complete system. Initial tests of the model for the water dimer and water-formamide are in good agreement with fully ab initio calcns.
- 21Gordon, M. S.; Fedorov, D. G.; Pruitt, S. R.; Slipchenko, L. V. Fragmentation Methods: A Route to Accurate Calculations on Large Systems. Chem. Rev. 2012, 112, 632– 672, DOI: 10.1021/cr200093j[ACS Full Text], [CAS], Google Scholar21https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3MXhtVyhurjJ&md5=7fa407f4c831f6c15c23d76fde206ba0Fragmentation Methods: A Route to Accurate Calculations on Large SystemsGordon, Mark S.; Fedorov, Dmitri G.; Pruitt, Spencer R.; Slipchenko, Lyudmila V.Chemical Reviews (Washington, DC, United States) (2012), 112 (1), 632-672CODEN: CHREAY; ISSN:0009-2665. (American Chemical Society)A review including the following topics: methodologies, software and parallel computing, applications, and conclusions and prognosis.
- 22Kuroki, N.; Mori, H. Effective Fragment Potential Version 2 - Molecular Dynamics (EFP2-MD) Simulation for Investigating Solution Structures of Ionic Liquids. Chem. Lett. 2016, 45, 1009– 1011, DOI: 10.1246/cl.160366
- 23Hands, M. D.; Slipchenko, L. V. Intermolecular Interactions in Complex Liquids: Effective Fragment Potential Investigation of Water-tert-Butanol Mixtures. J. Phys. Chem. B 2012, 116, 2775– 2786, DOI: 10.1021/jp2077566[ACS Full Text], [CAS], Google Scholar23https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC38XitFKltbw%253D&md5=b55574f040f72edda1854f5375b8762fIntermolecular Interactions in Complex Liquids: Effective Fragment Potential Investigation of Water-tert-Butanol MixturesHands, Michael D.; Slipchenko, Lyudmila V.Journal of Physical Chemistry B (2012), 116 (9), 2775-2786CODEN: JPCBFK; ISSN:1520-5207. (American Chemical Society)Structure and bonding patterns in tert-butanol (TBA)-water mixts. are investigated by using mol. dynamics simulations with the effective fragment potential (EFP) method. EFP is a model potential in which all parameters are obtained from a set of ab initio calcns. on isolated fragment mols. Mixed-basis EFP potentials (called "EFPm") for water and TBA mols. were prepd. and tested in this work. The accuracy of these EFP potentials is justified by comparison of structures and binding energies in water, TBA, and water-TBA dimers with MP2/6-311++G(d,p) data. It has been found that the discrepancies between EFP and MP2 do not exceed 0.1 Å in intermol. distances and 1 kcal/mol in binding energies. Structures of TBA-water solns. with 0.0, 0.06, 0.11, 0.16, and 0.50 TBA mole fractions were analyzed by using radial distribution functions (RDFs) and coordination nos. These results suggest that, at low TBA concns., the structure of water is enhanced and water and TBA are not homogeneously mixed at the mol. level. In the equimolar TBA-water soln., the microscopic mixing is more complete. Anal. of the energy components in TBA-water solns. shows that, while the electrostatic and exchange-repulsion terms provide the largest contributions to the total potential energy, the relative importance of the polarization and dispersion terms depends on the concn. of TBA. With an increase of TBA concn., the fraction of the dispersion energy increases, while the fraction of polarization energy diminishes. However, both polarization and dispersion terms are essential for accurate description of these systems.
- 24Ghosh, M. K.; Cho, S. G.; Choi, C. H. A Priori Prediction of Heats of Vaporization and Sublimation by EFP2-MD. J. Phys. Chem. B 2014, 118, 4876– 4882, DOI: 10.1021/jp500365z
- 25Ghosh, M. K.; Cho, S. G.; Choi, T. H.; Choi, C. H. A Priori Predictions of Molecular Density by EFP2-MD. Theor. Chem. Acc. 2016, 135, 254 DOI: 10.1007/s00214-016-2010-x
- 26Gordon, M. S.; Freitag, M. A.; Bandyopadhyay, P.; Jensen, J. H.; Kairys, V.; Stevens, W. J. The Effective Fragment Potential Method: A QM-Based MM Approach to Modeling Environmental Effects in Chemistry. J. Phys. Chem. A 2001, 105, 293– 307, DOI: 10.1021/jp002747h[ACS Full Text], [CAS], Google Scholar26https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD3cXoslKisro%253D&md5=1d864637cdd4fb21eec527d9e0051675The Effective Fragment Potential Method: A QM-Based MM Approach to Modeling Environmental Effects in ChemistryGordon, Mark S.; Freitag, Mark A.; Bandyopadhyay, Pradipta; Jensen, Jan H.; Kairys, Visvaldas; Stevens, Walter J.Journal of Physical Chemistry A (2001), 105 (2), 293-307CODEN: JPCAFH; ISSN:1089-5639. (American Chemical Society)A review, with 58 refs., describing the effective fragment potential (EFP) method, with illustration of its capabilities using several applications. The effective fragment potential (EFP) method is described and its capabilities illustrated using several applications. The original method, EFP1, was primarily developed to describe aq. solvation, by representing Coulombic, induction and repulsive interactions via one-electron terms in the ab initio Hamiltonian. It is demonstrated, using water clusters, the Menshutkin reaction, and the glycine neutral/zwitterion equil., that agreement with both fully ab initio calcns. and expt. are excellent. More recently, the model has been extended so that it can treat any solvent, as well as more difficult links across covalent bonds.
- 27Stone, A. J. Distributed Multipole Analysis, or How to Describe a Molecular Charge Distribution. Chem. Phys. Lett. 1981, 83, 233– 239, DOI: 10.1016/0009-2614(81)85452-8[Crossref], [CAS], Google Scholar27https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaL3MXmt1yitbY%253D&md5=1a7ac695fa444006688ea669d36a3d55Distributed multipole analysis, or how to describe a molecular charge distributionStone, A. J.Chemical Physics Letters (1981), 83 (2), 233-9CODEN: CHPLBC; ISSN:0009-2614.A method of analyzing mol. wavefunctions is described. It can be regarded as an extension of Mulliken population anal., and can be used both to give a qual. or quant. picture of the mol. charge distribution, and in the accurate evaluation of mol. multipole moments of arbitrary order with negligible computational effort.
- 28Slipchenko, L. V.; Gordon, M. S. Electrostatic Energy in the Effective Fragment Potential Method: Theory and Application to Benzene Dimer. J. Comput. Chem. 2007, 28, 276– 291, DOI: 10.1002/jcc.20520[Crossref], [PubMed], [CAS], Google Scholar28https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2sXktVKnsA%253D%253D&md5=3511c5e65075f2cb6fb4a71ae6dc21c9Electrostatic energy in the effective fragment potential method: theory and application to benzene dimerSlipchenko, Lyudmila V.; Gordon, Mark S.Journal of Computational Chemistry (2007), 28 (1), 276-291CODEN: JCCHDD; ISSN:0192-8651. (John Wiley & Sons, Inc.)Evaluation of the electrostatic energy within the effective fragment potential (EFP) method is presented. The performance of two variants of the distributed multipole anal. (DMA) together with two different models for estg. the charge penetration energies was studied using six homonuclear dimers. The importance of damping the higher order multipole terms, i.e. charge dipole, was also investigated. Damping corrections recover more than 70% of the charge penetration energy in all dimers, whereas higher order damping introduces only minor improvement. Electrostatic energies calcd. by the numerical DMA are less accurate than those calcd. by the analytic DMA. Anal. of bonding in the benzene dimer shows that EFP with inclusion of the electrostatic damping term performs very well compared to the high-level coupled cluster singles, doubles, and perturbative triples method. The largest error of 0.4 kcal/mol occurs for the sandwich dimer configuration. This error is about half the size of the corresponding error in second order perturbation theory. Thus, EFP in the current implementation is an accurate and computationally inexpensive method for calcg. interaction energies in weakly bonded mol. complexes.
- 29Freitag, M. A.; Gordon, M. S.; Jensen, J. H.; Stevens, W. J. Evaluation of Charge Penetration Between Distributed Multipolar Expansions. J. Chem. Phys. 2000, 112, 7300– 7306, DOI: 10.1063/1.481370[Crossref], [CAS], Google Scholar29https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD3cXis1ansrw%253D&md5=41338a58ecae70fd9d5fdd511983eb2dEvaluation of charge penetration between distributed multipolar expansionsFreitag, Mark A.; Gordon, Mark S.; Jensen, Jan H.; Stevens, Walter J.Journal of Chemical Physics (2000), 112 (17), 7300-7306CODEN: JCPSA6; ISSN:0021-9606. (American Institute of Physics)A formula to calc. the charge penetration energy that results when two charge densities overlap has been derived for mols. described by an effective fragment potential (EFP). The method has been compared with the ab initio charge penetration, taken to be the difference between the electrostatic energy from a Morokuma anal. and Stone's Distributed Multipole Anal. The av. abs. difference between the EFP method and the ab initio charge penetration for dimers of methanol, acetonitrile, acetone, DMSO, and dichloromethane at their resp. equil. geometries is 0.32 kcal mol-1.
- 30Slipchenko, L. V.; Gordon, M. S. Damping Functions in the Effective Fragment Potential Method. Mol. Phys. 2009, 107, 999– 1016, DOI: 10.1080/00268970802712449[Crossref], [CAS], Google Scholar30https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD1MXotlWlu7o%253D&md5=120d1f73dbb37866d4fa1ace1def54cbDamping functions in the effective fragment potential methodSlipchenko, Lyudmila V.; Gordon, Mark S.Molecular Physics (2009), 107 (8-12), 999-1016CODEN: MOPHAM; ISSN:0026-8976. (Taylor & Francis Ltd.)This work presents the implementation and anal. of several damping functions for Coulomb, induction, and dispersion interactions within the framework of the general effective fragment potential (EFP) method. Damping is necessary to obtain the correct asymptotic short-range behavior of these interactions. Correctly chosen damping functions allow a balanced description of different parts of intermol. potential energy surfaces and improve the accuracy of predicted intermol. distances and binding energies. The performance of different damping functions is tested by comparing the EFP energy terms with the symmetry adapted perturbation theory (SAPT) energy terms in a range of intermol. sepns. for ten mol. dimers. The total EFP binding energies in these dimers were compared with the binding energies obtained from SAPT and coupled cluster theory with single, double, and perturbative triple excitations [CCSD(T)]. A formula for electrostatic damping that was derived from first principles is recommended. This method employs the overlap of fragment localized MOs (LMO) within the spherical Gaussian approxn. The LMO overlap integrals are also used to det. the damping of dispersion. Gaussian polarization damping functions are recommended for use within the EFP framework. With this set of damping functions, the EFP binding energies are within 0.5 kcal/mol and intermol. equil. sepns. are within 0.2 Å of the corresponding CCSD(T) and SAPT values. This consistent accuracy of EFP is encouraging for future studies of more complicated mol. complexes.
- 31Jensen, J. H.; Gordon, M. S. An Approximate Formula for the Intermolecular Pauli Repulsion Between Closed Shell Molecules. Mol. Phys. 1996, 89, 1313– 1325, DOI: 10.1080/00268979609482543[Crossref], [CAS], Google Scholar31https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaK2sXhtVChsA%253D%253D&md5=a32c678e8136c9ed311592878a4ff49bAn approximate formula for the intermolecular Pauli repulsion between closed shell moleculesJensen, Jan H.; Gordon, Mark S.Molecular Physics (1996), 89 (5), 1313-1325CODEN: MOPHAM; ISSN:0026-8976. (Taylor & Francis)The exchange repulsion formula proposed by Murrell and co-workers (Proc. Roy. Soc. (Lond.), 1965 A284, 566; J. Chem. Phys., 1967, 47, 4916) is considered in detail. Potentially important terms missing in the formalism of Murrell and co-workers are identified and evaluated for the water dimer using several basis sets. Insights into the contributing terms are obtained by using localized MOs. The results point towards a relatively simple expression for intermol. exchange repulsion, based on the isolated wavefunctions of the two overlapping species.
- 32Jensen, J. H.; Gordon, M. S. An Approximate Formula for the Intermolecular Pauli Repulsion Between Closed Shell Molecules. II. Application to the Effective Fragment Potential Method. J. Chem. Phys. 1998, 108, 4772– 4782, DOI: 10.1063/1.475888[Crossref], [CAS], Google Scholar32https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaK1cXhvVamtLk%253D&md5=353c1793275a7c881ce121eeccb20b23An approximate formula for the intermolecular Pauli repulsion between closed shell molecules. II. Application to the effective fragment potential methodJensen, Jan H.; Gordon, Mark S.Journal of Chemical Physics (1998), 108 (12), 4772-4782CODEN: JCPSA6; ISSN:0021-9606. (American Institute of Physics)The accuracy and efficiency of an approx. formula for the intermol. Pauli repulsion between closed shell mols., derived earlier [Mol. Phys. 89, 1313(1996)], is demonstrated for dimers of H2O, MeOH, CH2Cl2, MeCN, Me2CO, and Me2SO. The energy deriv. with respect to a Cartesian coordinate and rigid rotation about the center-of-mass (torques) are presented. The Pauli repulsion energy term is then combined with the Coulomb and classical induction energy terms of the effective fragment potential method [J. Chem. Phys. 105, 1968, 11081(1996)] to give a general intermol. interaction potential. This potential is applied to H2O and MeOH clusters.
- 33Jensen, J. H. Modeling Intermolecular Exchange Integrals Between Nonorthogonal Molecular Orbitals. J. Chem. Phys. 1996, 104, 7795– 7796, DOI: 10.1063/1.471485[Crossref], [CAS], Google Scholar33https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaK28XivFGrur4%253D&md5=562320db08a8a75f23e91a1da2c968c0Modeling intermolecular exchange integrals between nonorthogonal molecular orbitalsJensen, Jan H.Journal of Chemical Physics (1996), 104 (19), 7795-7796CODEN: JCPSA6; ISSN:0021-9606. (American Institute of Physics)A simple way of approximating the integrals in the intermol. exchange energy is obtained by representing the nonorthogonal MOs on each mol. by spherical Gaussians centered on their resp. centroids of charge. This approxn. is compared to the Mulliken approxn. for a series of water dimer calcns.
- 34Li, H.; Netzloff, H. M.; Gordon, M. S. Gradients of the Polarization Energy in the Effective Fragment Potential Method. J. Chem. Phys. 2006, 125, 194103 DOI: 10.1063/1.2378767[Crossref], [PubMed], [CAS], Google Scholar34https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD28Xht1CnsrrL&md5=e7cc14841af2996ef937528ecdbca958Gradients of the polarization energy in the effective fragment potential methodLi, Hui; Netzloff, Heather M.; Gordon, Mark S.Journal of Chemical Physics (2006), 125 (19), 194103/1-194103/9CODEN: JCPSA6; ISSN:0021-9606. (American Institute of Physics)The effective fragment potential (EFP) method is an ab initio based polarizable classical method in which the intermol. interaction parameters are obtained from preparative ab initio calcns. on isolated mols. The polarization energy in the EFP method is modeled with asym. anisotropic dipole polarizability tensors located at the centroids of localized bond and lone pair orbitals of the mols. Analytic expressions for the translational and rotational gradients (forces and torques) of the EFP polarization energy have been derived and implemented. Periodic boundary conditions (the min. image convention) and switching functions have also been implemented for the polarization energy, as well as for other EFP interaction terms. With these improvements, mol. dynamics simulations can be performed with the EFP method for various chem. systems.
- 35Adamovic, I.; Gordon, M. S. Dynamic Polarizability, Dispersion Coefficient C6 and Dispersion Energy in the Effective Fragment Potential Method. Mol. Phys. 2005, 103, 379– 387, DOI: 10.1080/00268970512331317246[Crossref], [CAS], Google Scholar35https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2MXjs1ajsw%253D%253D&md5=9c315539b728c88f4b746902c5278084Dynamic polarizability, dispersion coefficient C6 and dispersion energy in the effective fragment potential methodAdamovic, Ivana; Gordon, Mark S.Molecular Physics (2005), 103 (2-3), 379-387CODEN: MOPHAM; ISSN:0026-8976. (Taylor & Francis Ltd.)The development of a fragment-fragment dispersion energy expression, for the general effective fragment potential (EFP2) method is presented. C6 dispersion coeffs., expressed in terms of the dynamic polarizabilities over the imaginary frequency range (α(iν)), were calcd. for a set of homo and hetero dimers. Using these coeffs. the dispersion energy has been calcd. The dispersion energy is expressed using a simple London series expansion terminated after the n = 6 term and implemented using distributed localized MOs (LMOs). The EFP2 dispersion energy is compared to symmetry adapted perturbation theory (SAPT) values. From this comparison, it is apparent that one needs to include higher order terms in the dispersion energy. Adding an estd. C8 term to the C6 energy greatly improves the agreement with the benchmark SAPT energies.
- 36Dunning, T. H., Jr. Gaussian Basis Sets for Use in Correlated Molecular Calculations. I. The Atoms Boron Through Neon and Hydrogen. J. Chem. Phys. 1989, 90, 1007– 1023, DOI: 10.1063/1.456153[Crossref], [CAS], Google Scholar36https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaL1MXksVGmtrk%253D&md5=c6cd67a3748dc61692a9cb622d2694a0Gaussian basis sets for use in correlated molecular calculations. I. The atoms boron through neon and hydrogenDunning, Thom H., Jr.Journal of Chemical Physics (1989), 90 (2), 1007-23CODEN: JCPSA6; ISSN:0021-9606.Guided by the calcns. on oxygen in the literature, basis sets for use in correlated at. and mol. calcns. were developed for all of the first row atoms from boron through neon, and for hydrogen. As in the oxygen atom calcns., the incremental energy lowerings, due to the addn. of correlating functions, fall into distinct groups. This leads to the concept of correlation-consistent basis sets, i.e., sets which include all functions in a given group as well as all functions in any higher groups. Correlation-consistent sets are given for all of the atoms considered. The most accurate sets detd. in this way, [5s4p3d2f1g], consistently yield 99% of the correlation energy obtained with the corresponding at.-natural-orbital sets, even though the latter contains 50% more primitive functions and twice as many primitive polarization functions. It is estd. that this set yields 94-97% of the total (HF + 1 + 2) correlation energy for the atoms neon through boron.
- 37Schmidt, M. W.; Baldridge, K. K.; Boatz, J. A.; Elbert, S. T.; Gordon, M. S.; Jensen, J. H.; Koseki, S.; Matsunaga, N.; Nguyen, K. A.; Su, S. General Atomic and Molecular Electronic Structure System. J. Comput. Chem. 1993, 14, 1347– 1363, DOI: 10.1002/jcc.540141112[Crossref], [CAS], Google Scholar37https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaK2cXhsFaqtQ%253D%253D&md5=4d9e37cd3ec67a92bdfb5b0c0084707cGeneral atomic and molecular electronic structure systemSchmidt, Michael W.; Baldridge, Kim K.; Boatz, Jerry A.; Elbert, Steven T.; Gordon, Mark S.; Jensen, Jan H.; Koseki, Shiro; Matsunaga, Nikita; Nguyen, Kiet A.; et al.Journal of Computational Chemistry (1993), 14 (11), 1347-63CODEN: JCCHDD; ISSN:0192-8651.A description of the ab initio quantum chem. package GAMESS is presented. Chem. systems contg. atoms through Rn can be treated with wave functions ranging from the simplest closed-shell case up to a general MCSCF case, permitting calcns. at the necessary level of sophistication. Emphasis is given to novel features of the program. The parallelization strategy used in the RHF, ROHF, UHF, and GVB sections of the program is described, and detailed speedup results are given. Parallel calcns. can be run on ordinary workstations as well as dedicated parallel machines.
- 38Su, P.; Li, H. Energy Decomposition Analysis of Covalent Bonds and Intermolecular Interactions. J. Chem. Phys. 2009, 131, 014102 DOI: 10.1063/1.3159673[Crossref], [PubMed], [CAS], Google Scholar38https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD1MXosFGhsbY%253D&md5=d7ee8efa3cbafd0c33b37f42f14b1a9bEnergy decomposition analysis of covalent bonds and intermolecular interactionsSu, Peifeng; Li, HuiJournal of Chemical Physics (2009), 131 (1), 014102/1-014102/15CODEN: JCPSA6; ISSN:0021-9606. (American Institute of Physics)An energy decompn. anal. method is implemented for the anal. of both covalent bonds and intermol. interactions on the basis of single-determinant Hartree-Fock (HF) (restricted closed shell HF, restricted open shell HF, and unrestricted open shell HF) wavefunctions and their d. functional theory analogs. For HF methods, the total interaction energy from a supermol. calcn. is decompd. into electrostatic, exchange, repulsion, and polarization terms. Dispersion energy is obtained from second-order Moller-Plesset perturbation theory and coupled-cluster methods such as CCSD and CCSD(T). Similar to the HF methods, Kohn-Sham d. functional interaction energy is decompd. into electrostatic, exchange, repulsion, polarization, and dispersion terms. Tests on various systems show that this algorithm is simple and robust. insights are provided by the energy decompn. anal. into H2, methane C-H, and ethane C-C covalent bond formation, CH3CH3 internal rotation barrier, water, ammonia, ammonium, and hydrogen fluoride hydrogen bonding, van der Waals interaction, DNA base pair formation, NH3NH3 and NH3CO coordinate bond formation, Cu-ligand interactions, as well as LiF, LiCl, NaF, and NaCl ionic interactions. (c) 2009 American Institute of Physics.
- 39Nelson, R. D., Jr.; Lide, D. R.; Maryott, A. A. Selected Values of Electric Dipole Moments for Molecules in the Gas Phase; NBS10; NSRDS: Washington, D. C., 1967.
- 40Vyalov, I.; Kiselev, M.; Tassaing, T.; Soetens, J. C.; Federov, M.; Damay, P.; Idrissi, A. Reorientation Relaxation in Supercritical Ammonia. J. Mol. Liq. 2011, 159, 31– 37, DOI: 10.1016/j.molliq.2010.09.012[Crossref], [CAS], Google Scholar40https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3MXisVOgsrw%253D&md5=7497109d3b2812e96fb1eaae8969906bReorientation relaxation in supercritical ammoniaVyalov, I.; Kiselev, M.; Tassaing, T.; Soetens, J. C.; Federov, M.; Damay, P.; Idrissi, A.Journal of Molecular Liquids (2011), 159 (1), 31-37CODEN: JMLIDT; ISSN:0167-7322. (Elsevier B.V.)In the present study, we investigate the reorientation and rotation relaxations of ammonia along the 135 bar isobar and in a range of d. between 0.666 g cm-3 and 0.074 g cm-3. One of our primary interests is in clarifying the changes in the intermediate time behavior of the reorientation correlation, which connects the inertial motion at short time and the diffusive one at long time. Our results show that at low temps. far from the crit. one, the intermediate time behavior of the reorientation correlation of the dipole axis is connected to the anisotropy of the angular velocity correlation around the principal mol. axes. Indeed, at these temps., the hydrogen bond interactions are strong enough to affect the angular velocity correlation which is less hindered around the dipole axis than that around its perpendicular one. As a consequence, the intermediate time behavior of the reorientation of the dipole axis is characterized by an occurrence of a kink. At higher temps. than the crit. one, the intermediate time behavior of reorientation of the dipole axis has a free rotor characteristic (a sudden increase of the correlation) and this was assocd. with the fact that the angular velocity along the mol. axes becomes almost free as a consequence of the weakening of hydrogen bonding.
- 41Groß, T.; Buchhauser, J.; Price, W. E.; Tarassov, I. N.; Lüdemann, H.-D. The p,T-Dependence of Self-Diffusion in Fluid Ammonia. J. Mol. Liq. 1997, 73–74, 433– 444, DOI: 10.1016/S0167-7322(97)00086-X[Crossref], [CAS], Google Scholar41https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaK2sXns1Kjtr0%253D&md5=1da857f3c7bb7ac65e18c15021dab0ccThe p,T-dependence of self-diffusion in fluid ammoniaGross, T.; Buchhauser, J.; Price, W. E.; Tarassov, I. N.; Luedemann, H.-D.Journal of Molecular Liquids (1997), 73,74 (), 433-444CODEN: JMLIDT; ISSN:0167-7322. (Elsevier Science B.V.)Self-diffusion coeffs. D for fluid NH3 have been obtained at high pressures by the NMR pulsed field gradient method for the first time between the melting pressure curve and 473 K at pressures up to 200 MPa. Compared to H2O and the lower alcs. D of NH3 shows a surprisingly weak T dependence. The data are analyzed in the rough-hard-sphere (RHS) model. The A-parameter of this model gives no indication for the influence of hydrogen bonding upon the translational dynamics in NH3.
- 42Harder, E.; Damm, W.; Maple, J.; Wu, C.; Reboul, M.; Xiang, J. Y.; Wang, L.; Lupyan, D.; Dahlgren, M. K.; Knight, J. L. OPLS3: A Force Field Providing Broad Coverage of Drug-like Small Molecules and Proteins. J. Chem. Theory Comput. 2016, 12, 281– 296, DOI: 10.1021/acs.jctc.5b00864[ACS Full Text], [CAS], Google Scholar42https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2MXhvVCjtbfE&md5=42663f8cfa84b80a67132bbb13b9b7ceOPLS3: A Force Field Providing Broad Coverage of Drug-like Small Molecules and ProteinsHarder, Edward; Damm, Wolfgang; Maple, Jon; Wu, Chuanjie; Reboul, Mark; Xiang, Jin Yu; Wang, Lingle; Lupyan, Dmitry; Dahlgren, Markus K.; Knight, Jennifer L.; Kaus, Joseph W.; Cerutti, David S.; Krilov, Goran; Jorgensen, William L.; Abel, Robert; Friesner, Richard A.Journal of Chemical Theory and Computation (2016), 12 (1), 281-296CODEN: JCTCCE; ISSN:1549-9618. (American Chemical Society)The parametrization and validation of the OPLS3 force field for small mols. and proteins are reported. Enhancements with respect to the previous version (OPLS2.1) include the addn. of off-atom charge sites to represent halogen bonding and aryl nitrogen lone pairs as well as a complete refit of peptide dihedral parameters to better model the native structure of proteins. To adequately cover medicinal chem. space, OPLS3 employs over an order of magnitude more ref. data and assocd. parameter types relative to other commonly used small mol. force fields (e.g., MMFF and OPLS_2005). As a consequence, OPLS3 achieves a high level of accuracy across performance benchmarks that assess small mol. conformational propensities and solvation. The newly fitted peptide dihedrals lead to significant improvements in the representation of secondary structure elements in simulated peptides and native structure stability over a no. of proteins. Together, the improvements made to both the small mol. and protein force field lead to a high level of accuracy in predicting protein-ligand binding measured over a wide range of targets and ligands (less than 1 kcal/mol RMS error) representing a 30% improvement over earlier variants of the OPLS force field.
Cited By
This article is cited by 3 publications.
- Nahoko Kuroki, Yukina Uchino, Tamon Funakura, Hirotoshi Mori. Electronic fluctuation difference between trimethylamine N-oxide and tert-butyl alcohol in water. Scientific Reports 2022, 12 (1) https://doi.org/10.1038/s41598-022-24049-0
- Bartosz Błasiak, Joanna D. Bednarska, Marta Chołuj, Robert W. Góra, Wojciech Bartkowiak. Ab initio effective one‐electron potential operators: Applications for charge‐transfer energy in effective fragment potentials. Journal of Computational Chemistry 2021, 42 (6) , 398-411. https://doi.org/10.1002/jcc.26462
- Chika MASUDA, Nahoko KUROKI. Statistical Thermodynamics Database Construction to Search for Novel Ionic Liquids with Gas Selectivity. Journal of Computer Chemistry, Japan 2019, 18 (5) , 217-220. https://doi.org/10.2477/jccj.2019-0046
Abstract
Figure 1
Figure 1. Coordinate system of an NH3 dimer.
Figure 2
Figure 2. Two-dimensional potential-energy surfaces obtained by LMO-EDA and EFP2 methods. For the LMO-EDA, we applied an ab initio CCSD(T)/aug-cc-pVTZ level of quantum chemical calculation.
Figure 3
Figure 3. Temperature dependence of N–N radial distribution functions (RDFs) for compressed NH3.
Figure 4
Figure 4. Temporal dipole moment variations for NH3 simulated by EFP2-MD simulations (T = 203, 473, and 700 K). The variations were defined as differences from the dipole moment of free NH3 molecules predicted by the EFP2 theory (1.61 Debye, which agrees well with experimental data of 1.47 Debye (39)). For clarity, NH3 molecules are depicted as single atoms placed at their centers of mass, and a set of representative snapshot structures with time evolution are depicted.
Figure 5
Figure 5. Temperature dependencies of Cr(t) and Cv(t) for compressed NH3.
Figure 6
Figure 6. Dependence of the self-diffusion constant of NH3 on temperature. Experimental and classical MD (optimized FF) data were those reported by Orabi et al. (7)
References
ARTICLE SECTIONSThis article references 42 other publications.
- 1Hendriks, E.; Kontogeorgis, G. M.; Dohrn, R.; de Hemptinne, J.-C.; Economou, I. G.; Zilnik, L. F.; Vesovic, V. Industrial Requirements for Thermodynamics and Transport Properties. Ind. Eng. Chem. Res. 2010, 49, 11131– 11141, DOI: 10.1021/ie101231b[ACS Full Text], [CAS], Google Scholar1https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3cXht1OnurnN&md5=b76e6b5e01a794ce5b88066b9beebb22Industrial Requirements for Thermodynamics and Transport PropertiesHendriks, Eric; Kontogeorgis, Georgios M.; Dohrn, Ralf; de Hemptinne, Jean-Charles; Economou, Ioannis G.; Zilnik, Ljudmila Fele; Vesovic, VelisaIndustrial & Engineering Chemistry Research (2010), 49 (22), 11131-11141CODEN: IECRED; ISSN:0888-5885. (American Chemical Society)A review. This work reports the results of an investigation on industrial requirements for thermodn. and transport properties carried out by the Working Party on Thermodn. and Transport properties (http://www.wp-ttp.dk/) of the European Federation of Chem. Engineering, EFCE (http://www.efce.info/). A carefully designed questionnaire was sent to a no. of key tech. people in companies in the oil and gas, chems., and pharmaceutical/biotechnol. sectors. Twenty-eight companies have provided answers which formed the basis for the anal. presented here. A no. of previous reviews, specifically addressed to or written by industrial colleagues, are discussed initially. This provides the context of the survey and material with which the results of the survey can be compared. The results of the survey have been divided into the themes: data, models, systems, properties, education, and collaboration. The main results are as follows. There is (still) an acute need for accurate, reliable, and thermodynamically consistent exptl. data. Quality is more important than quantity. Similarly, there is a great need for reliable predictive, rather than correlative, models covering a wide range of compns., temps., and pressures and capable of predicting primary (phase equil.) and secondary (enthalpy, heat capacity, etc.) properties. It is clear that the ideal of a single model covering all requirements is not achievable, but there is a consensus that this ideal should still provide the direction for future development. The use of new methods, such as SAFT, is increasing, but they are not yet in position to replace traditional methods such as cubic equations of state (esp. in oil and gas industry) and the UNIFAC group contribution approach. A common problem with novel methods is lack of standardization, ref. data, and correct and transparent implementations, esp. in com. available simulation programs. The survey indicates a great variety of systems where further work is required. For instance, for electrolyte systems better models are needed, capable of describing all types of phase behavior and mixts. with other types of components. There is also a lack of data and methods for larger complex mols. Compared with the previous reviews, complex mixts. contg. carbon dioxide assocd. with a wide range of applications, such as capture, transport, and storage are becoming interesting to a no. of survey participants. Despite the academic success of mol. simulation techniques, the survey does not indicate great interest in it or its future development. Algorithms appear to be a neglected area, but improvements are still needed esp. for multiphase reactive systems (simultaneous chem. and phys. equil.). Education in thermodn. is perceived as key, for the future application of thermodn. in the industry. A no. of suggestions for improvement were made at all three levels (undergraduate, postgraduate, and professional development) indicating that the education is correctly perceived as an ongoing process.
- 2Vyhmeister, E.; Valdes-Gonzalez, H.; Muscat, A. J.; Suleiman, D.; Estevez, L. A. Surface Modification of Porous Silicon-Based Films Using Dichlorosilanes Dissolved in Supercritical Carbon Dioxide. Ind. Eng. Chem. Res. 2013, 52, 4762– 4771, DOI: 10.1021/ie302686e
- 3Tomita, K.; Machmudah, S.; Quitain, A. T.; Sasaki, M.; Fukuzato, R.; Goto, M. Extraction and Solubility Evaluation of Functional Seed Oil in Supercritical Carbon Dioxide. J. Supercrit. Fluids 2013, 79, 109– 113, DOI: 10.1016/j.supflu.2013.02.011[Crossref], [CAS], Google Scholar3https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3sXktFWit7Y%253D&md5=f11a410dbeed1562ea95743181dae13fExtraction and solubility evaluation of functional seed oil in supercritical carbon dioxideTomita, Karin; Machmudah, Siti; Quitain, Armando T.; Sasaki, Mitsuru; Fukuzato, Ryuichi; Goto, MotonobuJournal of Supercritical Fluids (2013), 79 (), 109-113CODEN: JSFLEH; ISSN:0896-8446. (Elsevier B.V.)Hemp (Cannabis sativa L.) seed oil is valued for its nutritional properties and for the health benefits assocd. with it. Its greatest feature is that the ratio of linoleic acid and linolenic acid is the desirable value of 3:1. In this research, supercrit. carbon dioxide was applied to extn. of functional oil from hemp seed. In order to det. the effect of temp. and pressure on the yield of extd. components, the oil was extd. from hemp seed at temps. between 40 and 80°C, pressures of 20-40 MPa and a CO2 flow rate of 3 mL/min. The soly. of hemp seed oil in SCCO2 detd. exptl. was fitted to the Chrastil equation to det. the model parameters. The soly. calcd. by Chrastil equation was compared with the exptl. data. Finally, the fatty acid profile of the oil was evaluated by gas chromatog.-flame ionization detection (GC-FID). There are no significant differences in the compns. of five abundant fatty acid components of the oil obtained at different sampling times with SCCO2 extn. and other extn. methods.
- 4Feng, H.; Liu, X.; Gao, W.; Chen, X.; Wang, J.; Chen, L.; Lüdemann, H.-D. Evolution of Self-Diffusion and Local Structure in Some Amines over a Wide Temperature Range at High Pressures: A Molecular Dynamics Simulation Study. Phys. Chem. Chem. Phys. 2010, 12, 15007– 15017, DOI: 10.1039/c0cp00337a
- 5Idrissi, A.; Vyalov, I.; Kiselev, M.; Fedorov, M. V.; Jedlovszky, P. Heterogeneity of the Local Structure in Sub- and Supercritical Ammonia: A Voronoi Polyhedra Analysis. J. Phys. Chem. B 2011, 115, 9646– 9652, DOI: 10.1021/jp204078u[ACS Full Text], [CAS], Google Scholar5https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3MXovFKmsLc%253D&md5=37b7b7e185d26c8eb1199d70515bd1ccHeterogeneity of the Local Structure in Sub- and Supercritical Ammonia: A Voronoi Polyhedra AnalysisIdrissi, A.; Vyalov, I.; Kiselev, M.; Fedorov, M. V.; Jedlovszky, P.Journal of Physical Chemistry B (2011), 115 (31), 9646-9652CODEN: JPCBFK; ISSN:1520-5207. (American Chemical Society)We report results of mol. dynamics simulations and detailed anal. of the local structure of sub- and supercrit. ammonia in the range of temp. between 250 and 500 K along the 135 bar isobar. This anal. is based on the behavior of distributions of metric and topol. properties of the Voronoi polyhedra (VP). We show that by increasing the temp., the vol., surface, and face area distributions of the Voronoi polyhedra as well as the vacancy radius distribution broaden, particularly near the temp. Tα, where the calcd. thermal expansion coeff. has its max. The rate of increase of the corresponding mean values and fluctuations increases drastically when approaching Tα. This behavior clearly indicates that the local structure, as described by the VP, becomes increasingly heterogeneous upon approaching this temp. This heterogeneous distribution of ammonia mols. is traced back to the increase of the large voids with increasing temp., and is also clearly seen in the behavior of the fluctuation of the local d., as measured by the VP. More interestingly, the max. in the heterogeneity coincides with the max. of the fluctuation in the d. of the VP.
- 6Guevara-Carrion, G.; Vrabec, J.; Hasse, H. Prediction of Transport Properties of Liquid Ammonia and Its Binary Mixture with Methanol by Molecular Simulation. Int. J. Thermophys. 2012, 33, 449– 468, DOI: 10.1007/s10765-012-1166-4[Crossref], [CAS], Google Scholar6https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC38XktVagtb8%253D&md5=87b8fbd21f36031110c0e374928e7262Prediction of transport properties of liquid ammonia and its binary mixture with methanol by molecular simulationGuevara-Carrion, Gabriela; Vrabec, Jadran; Hasse, HansInternational Journal of Thermophysics (2012), 33 (3), 449-468CODEN: IJTHDY; ISSN:0195-928X. (Springer)Transport properties of NH3 and of the binary mixt. NH3 + MeOH are predicted for a broad range of liq. states by mol. dynamics (MD) simulation on the basis of rigid, non-polarizable mol. models of the united-atom type. These models were parameterized in preceding work using only exptl. vapor-liq. equil. data. The self- and the Maxwell-Stefan (MS) diffusion coeffs. as well as the shear viscosity are obtained by equil. MD and the Green-Kubo formalism. Non-equil. MD is used for the thermal cond. The transport properties of liq. NH3 are predicted for temps. between 223-473 K up to pressures of 200 MPa and are compared to exptl. data and correlations thereof. Generally, good agreement is achieved. The predicted self-diffusion coeff. as well as the shear viscosity deviates on av. by <15 % from the expt. and the thermal cond. by <6 %. Furthermore, the self- and the MS transport diffusion coeffs. as well as the shear viscosity of the liq. mixt. NH3 + MeOH were studied at different compns. and compared to the available exptl. data.
- 7Orabi, E. A.; Lamoureux, G. Polarizable Interaction Model for Liquid, Supercritical, and Aqueous Ammonia. J. Chem. Theory Comput. 2013, 9, 2035– 2051, DOI: 10.1021/ct301123j[ACS Full Text], [CAS], Google Scholar7https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3sXjtVCns70%253D&md5=5a0e5a649d626b39232f245e364c1f74Polarizable Interaction Model for Liquid, Supercritical, and Aqueous AmmoniaOrabi, Esam A.; Lamoureux, GuillaumeJournal of Chemical Theory and Computation (2013), 9 (4), 2035-2051CODEN: JCTCCE; ISSN:1549-9618. (American Chemical Society)A polarizable model for ammonia is optimized based on the ab initio properties of the NH3 mol. and the NH3-NH3 and NH3-H2O dimers calcd. at the MP2 level. For larger (NH3)m, NH3(H2O)n, and H2O(NH3)n clusters (m = 2-7 and n = 1-4), the model yields structural and binding energies in good agreement with ab initio calcns. without further adjustments. It also reproduces the structure, d., heat of vaporization, self-diffusion coeff., heat capacity, and isothermal compressibility of liq. ammonia at the b.p. The model is further validated by calcg. some of these properties at various temps. and pressures spanning the liq. and supercrit. phases of the fluid (up to 700 K and 200 MPa). The excellent transferability of the model suggests that it can be used to investigate properties of fluid ammonia under conditions for which expts. are not easy to perform. For aq. ammonia solns., the model yields liq. structures and densities in good agreement with exptl. data and allows the nonlinearity in the d.-compn. plot to be interpreted in terms of structural changes with compn. Finally, the model is used to investigate the solvation structure of ammonia in liq. water and of water in liq. ammonia and to calc. the solvation free energy of NH3 and H2O in aq. ammonia as a function of soln. compn. and temp. The simulation results suggest the presence of a transition around 50% molar NH3/H2O compns., above which water mols. are preferably solvated by ammonia.
- 8Albertí, M.; Amat, A.; Farrera, L.; Pirani, F. From the (NH3)2-5 Clusters to Liquid Ammonia: Molecular Dynamics Simulations Using the NVE and NpT Ensembles. J. Mol. Liq. 2015, 212, 307– 315, DOI: 10.1016/j.molliq.2015.09.016[Crossref], [CAS], Google Scholar8https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2MXhsFOjsLzJ&md5=5e24542c24d9bad1cb500d60865ee267From the (NH3)2-5 clusters to liquid ammonia: Molecular dynamics simulations using the NVE and NpT ensemblesAlberti, M.; Amat, A.; Farrera, Ll.; Pirani, F.Journal of Molecular Liquids (2015), 212 (), 307-315CODEN: JMLIDT; ISSN:0167-7322. (Elsevier B.V.)A force field for the intermol. NH 3-NH 3 interaction has been constructed and applied to characterize in detail the ammonia behavior in different environments. In particular, the dynamics of the (NH 3) 2 - 5 small clusters have been investigated and the isomerization processes analyzed as a function of the temp. considering a microcanonical (NVE) ensemble. The predicted (NH 3) 2 - 5 binding energies are in good agreement with exptl. data and/or ab initio calcns. Liq. ammonia has been studied, by considering an isothermic-isobaric ensemble (NpT) of 512 mols. at different conditions of temp. and pressure. In particular, the temp. dependence of the d. and of the mean diffusion coeffs. has been analyzed at 1 atm of pressure. Six different p-T conditions, at which the coexistence of vapor and liq. is possible, have been also taken into account. Finally, the radial distribution functions and the coordination no. have been calcd. at the same conditions used in neutron diffraction expts. The model predictions have been compared successfully with exptl. results, confirming the reliability of the force field formulation.
- 9Ushiki, I.; Ota, M.; Sato, Y.; Inomata, H. A Kinetic Study of Organic Compounds (Acetone, Toluene, n-Hexane and n-Decane) Adsorption Behavior on Activated Carbon Under Supercritical Carbon Dioxide Conditions at Temperature from 313 to 353 K and at Pressure from 4.2 to 15.0 MPa. J. Supercrit. Fluids 2014, 95, 187– 194, DOI: 10.1016/j.supflu.2014.08.021[Crossref], [CAS], Google Scholar9https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2cXhsV2ntrrI&md5=0b8eb1bf2fe28a354ce9ce921eea1898A kinetic study of organic compounds (acetone, toluene, n-hexane and n-decane) adsorption behavior on activated carbon under supercritical carbon dioxide conditions at temperature from 313 to 353 K and at pressure from 4.2 to 15.0 MPaUshiki, Ikuo; Ota, Masaki; Sato, Yoshiyuki; Inomata, HiroshiJournal of Supercritical Fluids (2014), 95 (), 187-194CODEN: JSFLEH; ISSN:0896-8446. (Elsevier B.V.)Adsorption kinetics of four volatile org. compds. (VOCs) (acetone, toluene, n-hexane and n-decane) on activated carbon under supercrit. carbon dioxide (scCO2) conditions was studied. Breakthrough curve measurements of VOCs in scCO2 were performed with a fixed bed method for activated carbon (ca. mean particles diam.: 100 μm, sp. surface area: 1300 m2/g and mean pore diam.: 0.687 nm, resp.). The measured breakthrough curves could be correlated with a kinetic model by using only one fitting parameter (effective diffusion coeff. in pore) within 10% of av. relative deviation. The detd. effective diffusion coeff. decreased with decreasing temps. and increasing pressures at all conditions. Addnl., a generalized model of the detd. effective diffusion coeffs. was developed, and the proposed model could satisfactorily describe temp. and pressure dependence at all VOCs conditions.
- 10Sohrevardi, N.; Bozorgmehr, M. R.; Heravi, M. M.; Khanpour, M. Transport Properties of Mixtures Composed of Acetone, Water, and Supercritical Carbon Dioxide by Molecular Dynamics Simulation. J. Supercrit. Fluids 2017, 130, 321– 326, DOI: 10.1016/j.supflu.2017.06.017[Crossref], [CAS], Google Scholar10https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2sXhtFOju7fO&md5=7e11abbf69bcbb312a8f001a33a96677Transport properties of mixtures composed of acetone, water, and supercritical carbon dioxide by molecular dynamics simulationSohrevardi, Nahid; Bozorgmehr, Mohammad Reza; Heravi, Mohammad Momen; Khanpour, MehrdadJournal of Supercritical Fluids (2017), 130 (), 321-326CODEN: JSFLEH; ISSN:0896-8446. (Elsevier B.V.)Transport properties of various mixts. of supercrit. carbon dioxide, acetone, and water at different concns. are evaluated at temps. 313.15 K and pressure 150 bar by mol. dynamics simulations. The results show that the self-diffusion (viscosity) coeff. is increased (decreased) for all various mixts. studied when the concn. of the acetone is increased. In addn., the densities of the mixts. will rise (lower), when the supercrit. carbon dioxide (acetone) concns. is increased. We have obsd. that the first peak heights of the radial distribution functions will rise at very low mole fraction of water (xw = 0.016) when the acetone and carbon dioxide concns. are increasing, and hence the self-diffusion coeffs. will decrease while its d. and viscosity will increase.
- 11Car, R.; Parrinello, M. Unified Approach for Molecular Dynamics and Density-Functional Theory. Phys. Rev. Lett. 1985, 55, 2471– 2474, DOI: 10.1103/PhysRevLett.55.2471[Crossref], [PubMed], [CAS], Google Scholar11https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaL28XhtVOlug%253D%253D&md5=ff5ef2fa5a1cf2c64bce1d5c052da979Unified approach for molecular dynamics and density-functional theoryCar, R.; Parrinello, M.Physical Review Letters (1985), 55 (22), 2471-4CODEN: PRLTAO; ISSN:0031-9007.A unified scheme is given that, by combining mol. dynamics and d.-functional theory, profoundly extends the range of both concepts. This approach extends mol. dynamics beyond the usual pair-potential approxn., thereby making possible the simulation of both covalently bonded and metallic systems. In addn., it permits the application of d.-functional theory to much larger systems than previously feasible. The new technique is demonstrated by the calcn. of some static and dynamic properties of cryst. Si within a self-consistent pseudopotential framework.
- 12Saharay, M.; Balasubramanian, S. Electron Donor-Acceptor Interactions in Ethanol-CO2 Mixtures: An Ab Initio Molecular Dynamics Study of Supercritical Carbon Dioxide. J. Phys. Chem. B 2006, 110, 3782– 3790, DOI: 10.1021/jp053839f[ACS Full Text], [CAS], Google Scholar12https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2MXht1WisLvF&md5=36a062eca2602cc4a9ad7c71d7e9d1a3Electron Donor-Acceptor Interactions in Ethanol-CO2 Mixtures: An Ab Initio Molecular Dynamics Study of Supercritical Carbon DioxideSaharay, Moumita; Balasubramanian, SundaramJournal of Physical Chemistry B (2006), 110 (8), 3782-3790CODEN: JPCBFK; ISSN:1520-6106. (American Chemical Society)The nature of interactions between ethanol and carbon dioxide has been characterized using simulations via the Car-Parrinello mol. dynamics (CPMD) method. Optimized geometries and energetics of free-standing ethanol-CO2 clusters exhibit evidence for a relatively more stable electron donor-acceptor (EDA) complex between these two species rather than a hydrogen-bonded configuration. This fact has also been confirmed by the higher formation rate of the EDA complex in supercrit. carbon dioxide-ethanol mixts. The probability d. distribution of CO2 mols. around ethanol in the supercrit. state shows two high probability regions along the direction of the lone pairs on the oxygen atom of ethanol. The EDA interaction between ethanol and CO2 as well as that between CO2 mols. themselves leads to significant deviations from linearity in the geometry of the CO2 mol. The vibrational spectra of carbon dioxide obtained from the at. velocity correlation functions in the bulk system as well as from isolated complexes show splitting of the ν2 bending mode that arises largely from CO2-CO2 interactions, with ethanol contributing only marginally because of its low concn. in the present study. The stretching frequency of the hydroxyl group of ethanol is shifted to lower frequencies in the bulk mixt. when compared to its gas-phase value, in agreement with expts.
- 13Kato, Y.; Fujiwara, T.; Komeiji, Y.; Nakano, T.; Mori, H.; Okiyama, Y.; Mochizuki, Y. Fragment Molecular Orbital-Based Molecular Dynamics (FMO-MD) Simulations on Hydrated Cu(II) Ion. Chem-Bio Inf. J. 2014, 14, 1– 13, DOI: 10.1273/cbij.14.1[Crossref], [CAS], Google Scholar13https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2cXhslaju7bK&md5=2519486b958cfb4b0bd94b3feb64d895Fragment molecular orbital-based molecular dynamics (FMO-MD) simulations on hydrated Cu(II) ionKato, Yuji; Fujiwara, Takayuki; Komeiji, Yuto; Nakano, Tatsuya; Mori, Hirotoshi; Okiyama, Yoshio; Mochizuki, YujiChem-Bio Informatics Journal (2014), 14 (), 1-13CODEN: CIJHBB; ISSN:1347-0442. (Chem-Bio Informatics Society)A simulation protocol based on fragment MO-based mol. dynamics (FMO-MD) was applied to a droplet model consisting of a divalent copper ion and 64 water mols. The total energy and forces were evaluated at the UHF (UHF) level with three-body fragment correction (FMO3). Two MD runs were performed: one with a six-coordination setting and the other with a five-coordination setting in the first hydration shell. Both runs resulted in the main peak position of the Cu-O radial distribution function at 2.02 Å, in reasonable agreement with the exptl. data. The O-Cu-O angular distribution function showed different characteristics between the two cases.
- 14Matsuda, A.; Mori, H. Theoretical Study on the Hydration Structure of Divalent Radium Ion Using Fragment Molecular Orbital-Molecular Dynamics (FMO-MD) Simulation. J. Solution Chem. 2014, 43, 1669– 1675, DOI: 10.1007/s10953-014-0235-7[Crossref], [CAS], Google Scholar14https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2cXhslels7jL&md5=47afd2fb6a90e02da740a14bf5435f4fTheoretical Study on the Hydration Structure of Divalent Radium Ion Using Fragment Molecular Orbital-Molecular Dynamics (FMO-MD) SimulationMatsuda, Aya; Mori, HirotoshiJournal of Solution Chemistry (2014), 43 (9-10), 1669-1675CODEN: JSLCAG; ISSN:0095-9782. (Springer)Using fragment MO-mol. dynamics (FMO-MD) simulation at the FMO3-HF/6-31G(d,p) level, the hydration of a Ra2+ ion was theor. investigated. The first peaks of the radial distribution function (RDF) for Ra-O and Ra-H lengths were predicted to be 2.85 and 3.45 Å with broad envelopes in the ranges of 2.5-3.5 and 2.8-4.3 Å, resp. The broad peaks shows that the first hydration shell of Ra2+ is much more flexible than those in the other hydrated divalent alk. earth metal ions, i.e., Ra2+ is a structure-breaking ion. The hydration no. of Ra2+ was predicted to be 8.1. From the angular distribution function (ADF), it was clarified that the octa hydrated Ra2+ ion has a flexible square antiprism structure at room temp.
- 15Mori, H.; Hirayama, N.; Komeiji, Y.; Mochizuki, Y. Differences in Hydration Between cis- and trans-Platin: Quantum Insights by Ab Initio Fragment Molecular Orbital-Based Molecular Dynamics (FMO-MD). Comput. Theor. Chem. 2012, 986, 30– 34, DOI: 10.1016/j.comptc.2012.02.008[Crossref], [CAS], Google Scholar15https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC38XksFaqt78%253D&md5=cf790e1372b1da59acc6166a29d4c580Differences in hydration between cis- and trans-platin: Quantum insights by ab initio fragment molecular orbital-based molecular dynamics (FMO-MD)Mori, Hirotoshi; Hirayama, Natsumi; Komeiji, Yuto; Mochizuki, YujiComputational & Theoretical Chemistry (2012), 986 (), 30-34CODEN: CTCOA5; ISSN:2210-271X. (Elsevier B.V.)Differences in hydration between cis- and trans-platin were investigated using ab initio fragment MO-based mol. dynamics (FMO-MD) simulations. Analyzing quantum charge fluctuation in water, we found that the Pt-Cl bond fluctuation of cis/trans-platin, which is important for activating their anticancer functions, was induced by charge transfer interaction between an anti-bonding π(Pt-Cl) orbital of platin complex and unoccupied orbital of solvent water mols. The hydration no. of Cl ligand in the first hydration shell was found to be larger for cis-platin than for trans-platin due to their difference in charge distribution. Our FMO-MD simulations showed that the amplitude of the Pt-Cl bond fluctuation is larger in hydrated cis-platin than in hydrated trans-platin.
- 16Komeiji, Y.; Mochizuki, Y.; Nakano, T.; Mori, H. Recent Advances in Fragment Molecular Orbital-Based Molecular Dynamics (FMO-MD) Simulations in Molecular Dynamics; InTech: Rijeka, Croatia, 2012.
- 17Fujiwara, T.; Mori, H.; Mochizuki, Y.; Osanai, Y.; Miyoshi, E. 4f-in-Core Model Core Potentials for Trivalent Lanthanides. Chem. Phys. Lett. 2011, 510, 261– 266, DOI: 10.1016/j.cplett.2011.05.028
- 18Fujiwara, T.; Mochizuki, Y.; Komeiji, Y.; Okiyama, Y.; Mori, H.; Nakano, T.; Miyoshi, E. Fragment Molecular Orbital-Based Molecular Dynamics (FMO-MD) Simulations on Hydrated Zn(II) Ion. Chem. Phys. Lett. 2010, 490, 41– 45, DOI: 10.1016/j.cplett.2010.03.020
- 19Kuroki, N.; Mori, H. Applicability of Effective Fragment Potential Version 2 - Molecular Dynamics (EFP2-MD) Simulations for Predicting Excess Properties of Mixed Solvents. Chem. Phys. Lett. 2018, 694, 82– 85, DOI: 10.1016/j.cplett.2018.01.042
- 20Day, P. N.; Jensen, J. H.; Gordon, M. S.; Webb, S. P.; Stevens, W. J.; Krauss, M.; Garmer, D.; Basch, H.; Cohen, D. An Effective Fragment Method for Modeling Solvent Effects in Quantum Mechanical Calculations. J. Chem. Phys. 1996, 105, 1968– 1986, DOI: 10.1063/1.472045[Crossref], [CAS], Google Scholar20https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaK28Xks1yktrY%253D&md5=c58a00728e94178578d70d3d07861f33An effective fragment method for modeling solvent effects in quantum mechanical calculationsDay, Paul N.; Jensen, Jan H.; Gordon, Mark S.; Webb, Simon P.; Stevens, Walter J.; Krauss, Morris; Garmer, David; Basch, Harold; Cohen, DroraJournal of Chemical Physics (1996), 105 (5), 1968-1986CODEN: JCPSA6; ISSN:0021-9606. (American Institute of Physics)An effective fragment model is developed to treat solvent effects on chem. properties and reactions. The solvent, which might consist of discrete water mols., protein, or other material, is treated explicitly using a model potential that incorporates electrostatics, polarization, and exchange repulsion effects. The solute, which one can most generally envision as including some no. of solvent mols. as well, is treated in a fully ab initio manner, using an appropriate level of electronic structure theory. In addn. to the fragment model itself, formulas are presented that permit the detn. of analytic energy gradients and, therefore, numerically detd. energy second derivs. (Hessians) for the complete system. Initial tests of the model for the water dimer and water-formamide are in good agreement with fully ab initio calcns.
- 21Gordon, M. S.; Fedorov, D. G.; Pruitt, S. R.; Slipchenko, L. V. Fragmentation Methods: A Route to Accurate Calculations on Large Systems. Chem. Rev. 2012, 112, 632– 672, DOI: 10.1021/cr200093j[ACS Full Text], [CAS], Google Scholar21https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3MXhtVyhurjJ&md5=7fa407f4c831f6c15c23d76fde206ba0Fragmentation Methods: A Route to Accurate Calculations on Large SystemsGordon, Mark S.; Fedorov, Dmitri G.; Pruitt, Spencer R.; Slipchenko, Lyudmila V.Chemical Reviews (Washington, DC, United States) (2012), 112 (1), 632-672CODEN: CHREAY; ISSN:0009-2665. (American Chemical Society)A review including the following topics: methodologies, software and parallel computing, applications, and conclusions and prognosis.
- 22Kuroki, N.; Mori, H. Effective Fragment Potential Version 2 - Molecular Dynamics (EFP2-MD) Simulation for Investigating Solution Structures of Ionic Liquids. Chem. Lett. 2016, 45, 1009– 1011, DOI: 10.1246/cl.160366
- 23Hands, M. D.; Slipchenko, L. V. Intermolecular Interactions in Complex Liquids: Effective Fragment Potential Investigation of Water-tert-Butanol Mixtures. J. Phys. Chem. B 2012, 116, 2775– 2786, DOI: 10.1021/jp2077566[ACS Full Text], [CAS], Google Scholar23https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC38XitFKltbw%253D&md5=b55574f040f72edda1854f5375b8762fIntermolecular Interactions in Complex Liquids: Effective Fragment Potential Investigation of Water-tert-Butanol MixturesHands, Michael D.; Slipchenko, Lyudmila V.Journal of Physical Chemistry B (2012), 116 (9), 2775-2786CODEN: JPCBFK; ISSN:1520-5207. (American Chemical Society)Structure and bonding patterns in tert-butanol (TBA)-water mixts. are investigated by using mol. dynamics simulations with the effective fragment potential (EFP) method. EFP is a model potential in which all parameters are obtained from a set of ab initio calcns. on isolated fragment mols. Mixed-basis EFP potentials (called "EFPm") for water and TBA mols. were prepd. and tested in this work. The accuracy of these EFP potentials is justified by comparison of structures and binding energies in water, TBA, and water-TBA dimers with MP2/6-311++G(d,p) data. It has been found that the discrepancies between EFP and MP2 do not exceed 0.1 Å in intermol. distances and 1 kcal/mol in binding energies. Structures of TBA-water solns. with 0.0, 0.06, 0.11, 0.16, and 0.50 TBA mole fractions were analyzed by using radial distribution functions (RDFs) and coordination nos. These results suggest that, at low TBA concns., the structure of water is enhanced and water and TBA are not homogeneously mixed at the mol. level. In the equimolar TBA-water soln., the microscopic mixing is more complete. Anal. of the energy components in TBA-water solns. shows that, while the electrostatic and exchange-repulsion terms provide the largest contributions to the total potential energy, the relative importance of the polarization and dispersion terms depends on the concn. of TBA. With an increase of TBA concn., the fraction of the dispersion energy increases, while the fraction of polarization energy diminishes. However, both polarization and dispersion terms are essential for accurate description of these systems.
- 24Ghosh, M. K.; Cho, S. G.; Choi, C. H. A Priori Prediction of Heats of Vaporization and Sublimation by EFP2-MD. J. Phys. Chem. B 2014, 118, 4876– 4882, DOI: 10.1021/jp500365z
- 25Ghosh, M. K.; Cho, S. G.; Choi, T. H.; Choi, C. H. A Priori Predictions of Molecular Density by EFP2-MD. Theor. Chem. Acc. 2016, 135, 254 DOI: 10.1007/s00214-016-2010-x
- 26Gordon, M. S.; Freitag, M. A.; Bandyopadhyay, P.; Jensen, J. H.; Kairys, V.; Stevens, W. J. The Effective Fragment Potential Method: A QM-Based MM Approach to Modeling Environmental Effects in Chemistry. J. Phys. Chem. A 2001, 105, 293– 307, DOI: 10.1021/jp002747h[ACS Full Text], [CAS], Google Scholar26https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD3cXoslKisro%253D&md5=1d864637cdd4fb21eec527d9e0051675The Effective Fragment Potential Method: A QM-Based MM Approach to Modeling Environmental Effects in ChemistryGordon, Mark S.; Freitag, Mark A.; Bandyopadhyay, Pradipta; Jensen, Jan H.; Kairys, Visvaldas; Stevens, Walter J.Journal of Physical Chemistry A (2001), 105 (2), 293-307CODEN: JPCAFH; ISSN:1089-5639. (American Chemical Society)A review, with 58 refs., describing the effective fragment potential (EFP) method, with illustration of its capabilities using several applications. The effective fragment potential (EFP) method is described and its capabilities illustrated using several applications. The original method, EFP1, was primarily developed to describe aq. solvation, by representing Coulombic, induction and repulsive interactions via one-electron terms in the ab initio Hamiltonian. It is demonstrated, using water clusters, the Menshutkin reaction, and the glycine neutral/zwitterion equil., that agreement with both fully ab initio calcns. and expt. are excellent. More recently, the model has been extended so that it can treat any solvent, as well as more difficult links across covalent bonds.
- 27Stone, A. J. Distributed Multipole Analysis, or How to Describe a Molecular Charge Distribution. Chem. Phys. Lett. 1981, 83, 233– 239, DOI: 10.1016/0009-2614(81)85452-8[Crossref], [CAS], Google Scholar27https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaL3MXmt1yitbY%253D&md5=1a7ac695fa444006688ea669d36a3d55Distributed multipole analysis, or how to describe a molecular charge distributionStone, A. J.Chemical Physics Letters (1981), 83 (2), 233-9CODEN: CHPLBC; ISSN:0009-2614.A method of analyzing mol. wavefunctions is described. It can be regarded as an extension of Mulliken population anal., and can be used both to give a qual. or quant. picture of the mol. charge distribution, and in the accurate evaluation of mol. multipole moments of arbitrary order with negligible computational effort.
- 28Slipchenko, L. V.; Gordon, M. S. Electrostatic Energy in the Effective Fragment Potential Method: Theory and Application to Benzene Dimer. J. Comput. Chem. 2007, 28, 276– 291, DOI: 10.1002/jcc.20520[Crossref], [PubMed], [CAS], Google Scholar28https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2sXktVKnsA%253D%253D&md5=3511c5e65075f2cb6fb4a71ae6dc21c9Electrostatic energy in the effective fragment potential method: theory and application to benzene dimerSlipchenko, Lyudmila V.; Gordon, Mark S.Journal of Computational Chemistry (2007), 28 (1), 276-291CODEN: JCCHDD; ISSN:0192-8651. (John Wiley & Sons, Inc.)Evaluation of the electrostatic energy within the effective fragment potential (EFP) method is presented. The performance of two variants of the distributed multipole anal. (DMA) together with two different models for estg. the charge penetration energies was studied using six homonuclear dimers. The importance of damping the higher order multipole terms, i.e. charge dipole, was also investigated. Damping corrections recover more than 70% of the charge penetration energy in all dimers, whereas higher order damping introduces only minor improvement. Electrostatic energies calcd. by the numerical DMA are less accurate than those calcd. by the analytic DMA. Anal. of bonding in the benzene dimer shows that EFP with inclusion of the electrostatic damping term performs very well compared to the high-level coupled cluster singles, doubles, and perturbative triples method. The largest error of 0.4 kcal/mol occurs for the sandwich dimer configuration. This error is about half the size of the corresponding error in second order perturbation theory. Thus, EFP in the current implementation is an accurate and computationally inexpensive method for calcg. interaction energies in weakly bonded mol. complexes.
- 29Freitag, M. A.; Gordon, M. S.; Jensen, J. H.; Stevens, W. J. Evaluation of Charge Penetration Between Distributed Multipolar Expansions. J. Chem. Phys. 2000, 112, 7300– 7306, DOI: 10.1063/1.481370[Crossref], [CAS], Google Scholar29https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD3cXis1ansrw%253D&md5=41338a58ecae70fd9d5fdd511983eb2dEvaluation of charge penetration between distributed multipolar expansionsFreitag, Mark A.; Gordon, Mark S.; Jensen, Jan H.; Stevens, Walter J.Journal of Chemical Physics (2000), 112 (17), 7300-7306CODEN: JCPSA6; ISSN:0021-9606. (American Institute of Physics)A formula to calc. the charge penetration energy that results when two charge densities overlap has been derived for mols. described by an effective fragment potential (EFP). The method has been compared with the ab initio charge penetration, taken to be the difference between the electrostatic energy from a Morokuma anal. and Stone's Distributed Multipole Anal. The av. abs. difference between the EFP method and the ab initio charge penetration for dimers of methanol, acetonitrile, acetone, DMSO, and dichloromethane at their resp. equil. geometries is 0.32 kcal mol-1.
- 30Slipchenko, L. V.; Gordon, M. S. Damping Functions in the Effective Fragment Potential Method. Mol. Phys. 2009, 107, 999– 1016, DOI: 10.1080/00268970802712449[Crossref], [CAS], Google Scholar30https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD1MXotlWlu7o%253D&md5=120d1f73dbb37866d4fa1ace1def54cbDamping functions in the effective fragment potential methodSlipchenko, Lyudmila V.; Gordon, Mark S.Molecular Physics (2009), 107 (8-12), 999-1016CODEN: MOPHAM; ISSN:0026-8976. (Taylor & Francis Ltd.)This work presents the implementation and anal. of several damping functions for Coulomb, induction, and dispersion interactions within the framework of the general effective fragment potential (EFP) method. Damping is necessary to obtain the correct asymptotic short-range behavior of these interactions. Correctly chosen damping functions allow a balanced description of different parts of intermol. potential energy surfaces and improve the accuracy of predicted intermol. distances and binding energies. The performance of different damping functions is tested by comparing the EFP energy terms with the symmetry adapted perturbation theory (SAPT) energy terms in a range of intermol. sepns. for ten mol. dimers. The total EFP binding energies in these dimers were compared with the binding energies obtained from SAPT and coupled cluster theory with single, double, and perturbative triple excitations [CCSD(T)]. A formula for electrostatic damping that was derived from first principles is recommended. This method employs the overlap of fragment localized MOs (LMO) within the spherical Gaussian approxn. The LMO overlap integrals are also used to det. the damping of dispersion. Gaussian polarization damping functions are recommended for use within the EFP framework. With this set of damping functions, the EFP binding energies are within 0.5 kcal/mol and intermol. equil. sepns. are within 0.2 Å of the corresponding CCSD(T) and SAPT values. This consistent accuracy of EFP is encouraging for future studies of more complicated mol. complexes.
- 31Jensen, J. H.; Gordon, M. S. An Approximate Formula for the Intermolecular Pauli Repulsion Between Closed Shell Molecules. Mol. Phys. 1996, 89, 1313– 1325, DOI: 10.1080/00268979609482543[Crossref], [CAS], Google Scholar31https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaK2sXhtVChsA%253D%253D&md5=a32c678e8136c9ed311592878a4ff49bAn approximate formula for the intermolecular Pauli repulsion between closed shell moleculesJensen, Jan H.; Gordon, Mark S.Molecular Physics (1996), 89 (5), 1313-1325CODEN: MOPHAM; ISSN:0026-8976. (Taylor & Francis)The exchange repulsion formula proposed by Murrell and co-workers (Proc. Roy. Soc. (Lond.), 1965 A284, 566; J. Chem. Phys., 1967, 47, 4916) is considered in detail. Potentially important terms missing in the formalism of Murrell and co-workers are identified and evaluated for the water dimer using several basis sets. Insights into the contributing terms are obtained by using localized MOs. The results point towards a relatively simple expression for intermol. exchange repulsion, based on the isolated wavefunctions of the two overlapping species.
- 32Jensen, J. H.; Gordon, M. S. An Approximate Formula for the Intermolecular Pauli Repulsion Between Closed Shell Molecules. II. Application to the Effective Fragment Potential Method. J. Chem. Phys. 1998, 108, 4772– 4782, DOI: 10.1063/1.475888[Crossref], [CAS], Google Scholar32https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaK1cXhvVamtLk%253D&md5=353c1793275a7c881ce121eeccb20b23An approximate formula for the intermolecular Pauli repulsion between closed shell molecules. II. Application to the effective fragment potential methodJensen, Jan H.; Gordon, Mark S.Journal of Chemical Physics (1998), 108 (12), 4772-4782CODEN: JCPSA6; ISSN:0021-9606. (American Institute of Physics)The accuracy and efficiency of an approx. formula for the intermol. Pauli repulsion between closed shell mols., derived earlier [Mol. Phys. 89, 1313(1996)], is demonstrated for dimers of H2O, MeOH, CH2Cl2, MeCN, Me2CO, and Me2SO. The energy deriv. with respect to a Cartesian coordinate and rigid rotation about the center-of-mass (torques) are presented. The Pauli repulsion energy term is then combined with the Coulomb and classical induction energy terms of the effective fragment potential method [J. Chem. Phys. 105, 1968, 11081(1996)] to give a general intermol. interaction potential. This potential is applied to H2O and MeOH clusters.
- 33Jensen, J. H. Modeling Intermolecular Exchange Integrals Between Nonorthogonal Molecular Orbitals. J. Chem. Phys. 1996, 104, 7795– 7796, DOI: 10.1063/1.471485[Crossref], [CAS], Google Scholar33https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaK28XivFGrur4%253D&md5=562320db08a8a75f23e91a1da2c968c0Modeling intermolecular exchange integrals between nonorthogonal molecular orbitalsJensen, Jan H.Journal of Chemical Physics (1996), 104 (19), 7795-7796CODEN: JCPSA6; ISSN:0021-9606. (American Institute of Physics)A simple way of approximating the integrals in the intermol. exchange energy is obtained by representing the nonorthogonal MOs on each mol. by spherical Gaussians centered on their resp. centroids of charge. This approxn. is compared to the Mulliken approxn. for a series of water dimer calcns.
- 34Li, H.; Netzloff, H. M.; Gordon, M. S. Gradients of the Polarization Energy in the Effective Fragment Potential Method. J. Chem. Phys. 2006, 125, 194103 DOI: 10.1063/1.2378767[Crossref], [PubMed], [CAS], Google Scholar34https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD28Xht1CnsrrL&md5=e7cc14841af2996ef937528ecdbca958Gradients of the polarization energy in the effective fragment potential methodLi, Hui; Netzloff, Heather M.; Gordon, Mark S.Journal of Chemical Physics (2006), 125 (19), 194103/1-194103/9CODEN: JCPSA6; ISSN:0021-9606. (American Institute of Physics)The effective fragment potential (EFP) method is an ab initio based polarizable classical method in which the intermol. interaction parameters are obtained from preparative ab initio calcns. on isolated mols. The polarization energy in the EFP method is modeled with asym. anisotropic dipole polarizability tensors located at the centroids of localized bond and lone pair orbitals of the mols. Analytic expressions for the translational and rotational gradients (forces and torques) of the EFP polarization energy have been derived and implemented. Periodic boundary conditions (the min. image convention) and switching functions have also been implemented for the polarization energy, as well as for other EFP interaction terms. With these improvements, mol. dynamics simulations can be performed with the EFP method for various chem. systems.
- 35Adamovic, I.; Gordon, M. S. Dynamic Polarizability, Dispersion Coefficient C6 and Dispersion Energy in the Effective Fragment Potential Method. Mol. Phys. 2005, 103, 379– 387, DOI: 10.1080/00268970512331317246[Crossref], [CAS], Google Scholar35https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2MXjs1ajsw%253D%253D&md5=9c315539b728c88f4b746902c5278084Dynamic polarizability, dispersion coefficient C6 and dispersion energy in the effective fragment potential methodAdamovic, Ivana; Gordon, Mark S.Molecular Physics (2005), 103 (2-3), 379-387CODEN: MOPHAM; ISSN:0026-8976. (Taylor & Francis Ltd.)The development of a fragment-fragment dispersion energy expression, for the general effective fragment potential (EFP2) method is presented. C6 dispersion coeffs., expressed in terms of the dynamic polarizabilities over the imaginary frequency range (α(iν)), were calcd. for a set of homo and hetero dimers. Using these coeffs. the dispersion energy has been calcd. The dispersion energy is expressed using a simple London series expansion terminated after the n = 6 term and implemented using distributed localized MOs (LMOs). The EFP2 dispersion energy is compared to symmetry adapted perturbation theory (SAPT) values. From this comparison, it is apparent that one needs to include higher order terms in the dispersion energy. Adding an estd. C8 term to the C6 energy greatly improves the agreement with the benchmark SAPT energies.
- 36Dunning, T. H., Jr. Gaussian Basis Sets for Use in Correlated Molecular Calculations. I. The Atoms Boron Through Neon and Hydrogen. J. Chem. Phys. 1989, 90, 1007– 1023, DOI: 10.1063/1.456153[Crossref], [CAS], Google Scholar36https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaL1MXksVGmtrk%253D&md5=c6cd67a3748dc61692a9cb622d2694a0Gaussian basis sets for use in correlated molecular calculations. I. The atoms boron through neon and hydrogenDunning, Thom H., Jr.Journal of Chemical Physics (1989), 90 (2), 1007-23CODEN: JCPSA6; ISSN:0021-9606.Guided by the calcns. on oxygen in the literature, basis sets for use in correlated at. and mol. calcns. were developed for all of the first row atoms from boron through neon, and for hydrogen. As in the oxygen atom calcns., the incremental energy lowerings, due to the addn. of correlating functions, fall into distinct groups. This leads to the concept of correlation-consistent basis sets, i.e., sets which include all functions in a given group as well as all functions in any higher groups. Correlation-consistent sets are given for all of the atoms considered. The most accurate sets detd. in this way, [5s4p3d2f1g], consistently yield 99% of the correlation energy obtained with the corresponding at.-natural-orbital sets, even though the latter contains 50% more primitive functions and twice as many primitive polarization functions. It is estd. that this set yields 94-97% of the total (HF + 1 + 2) correlation energy for the atoms neon through boron.
- 37Schmidt, M. W.; Baldridge, K. K.; Boatz, J. A.; Elbert, S. T.; Gordon, M. S.; Jensen, J. H.; Koseki, S.; Matsunaga, N.; Nguyen, K. A.; Su, S. General Atomic and Molecular Electronic Structure System. J. Comput. Chem. 1993, 14, 1347– 1363, DOI: 10.1002/jcc.540141112[Crossref], [CAS], Google Scholar37https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaK2cXhsFaqtQ%253D%253D&md5=4d9e37cd3ec67a92bdfb5b0c0084707cGeneral atomic and molecular electronic structure systemSchmidt, Michael W.; Baldridge, Kim K.; Boatz, Jerry A.; Elbert, Steven T.; Gordon, Mark S.; Jensen, Jan H.; Koseki, Shiro; Matsunaga, Nikita; Nguyen, Kiet A.; et al.Journal of Computational Chemistry (1993), 14 (11), 1347-63CODEN: JCCHDD; ISSN:0192-8651.A description of the ab initio quantum chem. package GAMESS is presented. Chem. systems contg. atoms through Rn can be treated with wave functions ranging from the simplest closed-shell case up to a general MCSCF case, permitting calcns. at the necessary level of sophistication. Emphasis is given to novel features of the program. The parallelization strategy used in the RHF, ROHF, UHF, and GVB sections of the program is described, and detailed speedup results are given. Parallel calcns. can be run on ordinary workstations as well as dedicated parallel machines.
- 38Su, P.; Li, H. Energy Decomposition Analysis of Covalent Bonds and Intermolecular Interactions. J. Chem. Phys. 2009, 131, 014102 DOI: 10.1063/1.3159673[Crossref], [PubMed], [CAS], Google Scholar38https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD1MXosFGhsbY%253D&md5=d7ee8efa3cbafd0c33b37f42f14b1a9bEnergy decomposition analysis of covalent bonds and intermolecular interactionsSu, Peifeng; Li, HuiJournal of Chemical Physics (2009), 131 (1), 014102/1-014102/15CODEN: JCPSA6; ISSN:0021-9606. (American Institute of Physics)An energy decompn. anal. method is implemented for the anal. of both covalent bonds and intermol. interactions on the basis of single-determinant Hartree-Fock (HF) (restricted closed shell HF, restricted open shell HF, and unrestricted open shell HF) wavefunctions and their d. functional theory analogs. For HF methods, the total interaction energy from a supermol. calcn. is decompd. into electrostatic, exchange, repulsion, and polarization terms. Dispersion energy is obtained from second-order Moller-Plesset perturbation theory and coupled-cluster methods such as CCSD and CCSD(T). Similar to the HF methods, Kohn-Sham d. functional interaction energy is decompd. into electrostatic, exchange, repulsion, polarization, and dispersion terms. Tests on various systems show that this algorithm is simple and robust. insights are provided by the energy decompn. anal. into H2, methane C-H, and ethane C-C covalent bond formation, CH3CH3 internal rotation barrier, water, ammonia, ammonium, and hydrogen fluoride hydrogen bonding, van der Waals interaction, DNA base pair formation, NH3NH3 and NH3CO coordinate bond formation, Cu-ligand interactions, as well as LiF, LiCl, NaF, and NaCl ionic interactions. (c) 2009 American Institute of Physics.
- 39Nelson, R. D., Jr.; Lide, D. R.; Maryott, A. A. Selected Values of Electric Dipole Moments for Molecules in the Gas Phase; NBS10; NSRDS: Washington, D. C., 1967.
- 40Vyalov, I.; Kiselev, M.; Tassaing, T.; Soetens, J. C.; Federov, M.; Damay, P.; Idrissi, A. Reorientation Relaxation in Supercritical Ammonia. J. Mol. Liq. 2011, 159, 31– 37, DOI: 10.1016/j.molliq.2010.09.012[Crossref], [CAS], Google Scholar40https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3MXisVOgsrw%253D&md5=7497109d3b2812e96fb1eaae8969906bReorientation relaxation in supercritical ammoniaVyalov, I.; Kiselev, M.; Tassaing, T.; Soetens, J. C.; Federov, M.; Damay, P.; Idrissi, A.Journal of Molecular Liquids (2011), 159 (1), 31-37CODEN: JMLIDT; ISSN:0167-7322. (Elsevier B.V.)In the present study, we investigate the reorientation and rotation relaxations of ammonia along the 135 bar isobar and in a range of d. between 0.666 g cm-3 and 0.074 g cm-3. One of our primary interests is in clarifying the changes in the intermediate time behavior of the reorientation correlation, which connects the inertial motion at short time and the diffusive one at long time. Our results show that at low temps. far from the crit. one, the intermediate time behavior of the reorientation correlation of the dipole axis is connected to the anisotropy of the angular velocity correlation around the principal mol. axes. Indeed, at these temps., the hydrogen bond interactions are strong enough to affect the angular velocity correlation which is less hindered around the dipole axis than that around its perpendicular one. As a consequence, the intermediate time behavior of the reorientation of the dipole axis is characterized by an occurrence of a kink. At higher temps. than the crit. one, the intermediate time behavior of reorientation of the dipole axis has a free rotor characteristic (a sudden increase of the correlation) and this was assocd. with the fact that the angular velocity along the mol. axes becomes almost free as a consequence of the weakening of hydrogen bonding.
- 41Groß, T.; Buchhauser, J.; Price, W. E.; Tarassov, I. N.; Lüdemann, H.-D. The p,T-Dependence of Self-Diffusion in Fluid Ammonia. J. Mol. Liq. 1997, 73–74, 433– 444, DOI: 10.1016/S0167-7322(97)00086-X[Crossref], [CAS], Google Scholar41https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaK2sXns1Kjtr0%253D&md5=1da857f3c7bb7ac65e18c15021dab0ccThe p,T-dependence of self-diffusion in fluid ammoniaGross, T.; Buchhauser, J.; Price, W. E.; Tarassov, I. N.; Luedemann, H.-D.Journal of Molecular Liquids (1997), 73,74 (), 433-444CODEN: JMLIDT; ISSN:0167-7322. (Elsevier Science B.V.)Self-diffusion coeffs. D for fluid NH3 have been obtained at high pressures by the NMR pulsed field gradient method for the first time between the melting pressure curve and 473 K at pressures up to 200 MPa. Compared to H2O and the lower alcs. D of NH3 shows a surprisingly weak T dependence. The data are analyzed in the rough-hard-sphere (RHS) model. The A-parameter of this model gives no indication for the influence of hydrogen bonding upon the translational dynamics in NH3.
- 42Harder, E.; Damm, W.; Maple, J.; Wu, C.; Reboul, M.; Xiang, J. Y.; Wang, L.; Lupyan, D.; Dahlgren, M. K.; Knight, J. L. OPLS3: A Force Field Providing Broad Coverage of Drug-like Small Molecules and Proteins. J. Chem. Theory Comput. 2016, 12, 281– 296, DOI: 10.1021/acs.jctc.5b00864[ACS Full Text], [CAS], Google Scholar42https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2MXhvVCjtbfE&md5=42663f8cfa84b80a67132bbb13b9b7ceOPLS3: A Force Field Providing Broad Coverage of Drug-like Small Molecules and ProteinsHarder, Edward; Damm, Wolfgang; Maple, Jon; Wu, Chuanjie; Reboul, Mark; Xiang, Jin Yu; Wang, Lingle; Lupyan, Dmitry; Dahlgren, Markus K.; Knight, Jennifer L.; Kaus, Joseph W.; Cerutti, David S.; Krilov, Goran; Jorgensen, William L.; Abel, Robert; Friesner, Richard A.Journal of Chemical Theory and Computation (2016), 12 (1), 281-296CODEN: JCTCCE; ISSN:1549-9618. (American Chemical Society)The parametrization and validation of the OPLS3 force field for small mols. and proteins are reported. Enhancements with respect to the previous version (OPLS2.1) include the addn. of off-atom charge sites to represent halogen bonding and aryl nitrogen lone pairs as well as a complete refit of peptide dihedral parameters to better model the native structure of proteins. To adequately cover medicinal chem. space, OPLS3 employs over an order of magnitude more ref. data and assocd. parameter types relative to other commonly used small mol. force fields (e.g., MMFF and OPLS_2005). As a consequence, OPLS3 achieves a high level of accuracy across performance benchmarks that assess small mol. conformational propensities and solvation. The newly fitted peptide dihedrals lead to significant improvements in the representation of secondary structure elements in simulated peptides and native structure stability over a no. of proteins. Together, the improvements made to both the small mol. and protein force field lead to a high level of accuracy in predicting protein-ligand binding measured over a wide range of targets and ligands (less than 1 kcal/mol RMS error) representing a 30% improvement over earlier variants of the OPLS force field.