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Kříž K, van Maaren PJ, van der Spoel D. Impact of Combination Rules, Level of Theory, and Potential Function on the Modeling of Gas- and Condensed-Phase Properties of Noble Gases. J Chem Theory Comput 2024; 20:2362-2376. [PMID: 38477573 DOI: 10.1021/acs.jctc.3c01257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/14/2024]
Abstract
The systems of noble gases are particularly instructive for molecular modeling due to the elemental nature of their interactions. They do not normally form bonds nor possess a (permanent) dipole moment, and the only forces determining their bonding/clustering stems from van der Waals forces─dispersion and Pauli repulsion, which can be modeled by empirical potential functions. Combination rules, that is, formulas to derive parameters for pair potentials of heterodimers from parameters of corresponding homodimers, have been studied at length for the Lennard-Jones 12-6 potentials but not in great detail for other, more accurate, potentials. In this work, we examine the usefulness of nine empirical potentials in their ability to reproduce quantum mechanical (QM) benchmark dissociation curves of noble gas dimers (He, Ne, Ar, Kr, and Xe homo- and heterodimers), and we systematically study the efficacy of different permutations of combination relations for each parameter of the potentials. Our QM benchmark comprises dissociation curves computed by several different coupled cluster implementations as well as symmetry-adapted perturbation theory. The two-parameter Lennard-Jones potentials were decisively outperformed by more elaborate potentials that sport a 25-30 times lower root-mean-square error (RMSE) when fitted to QM dissociation curves. Very good fits to the QM dissociation curves can be achieved with relatively inexpensive four- or even three-parameter potentials, for instance, the damped 14-7 potential (Halgren, J. Am. Chem. Soc. 1992, 114, 7827-7843), a four-parameter Buckingham potential (Werhahn et al., Chem. Phys. Lett. 2015, 619, 133-138), or the three-parameter Morse potential (Morse, Phys. Rev. 1929, 34, 57-64). Potentials for heterodimers that are generated from combination rules have an RMSE that is up to 20 times higher than potentials that are directly fitted to the QM dissociation curves. This means that the RMSE, in particular, for light atoms, is comparable in magnitude to the well-depth of the potential. Based on a systematic permutation of combination rules, we present one or more combination rules for each potential tested that yield a relatively low RMSE. Two new combination rules are introduced that perform well, one for the van der Waals radius σij as ( 1 2 ( σ i 3 + σ j 3 ) ) 1 / 3 and one for the well-depth ϵij as ( 1 2 ( ϵ i - 2 + ϵ j - 2 ) ) - 1 / 2 . The QM data and the fitted potentials were evaluated in the gas phase against experimental second virial coefficients for homo- and heterodimers, the latter of which allowed evaluation of the combination rules. The fitted models were used to perform condensed phase molecular dynamics simulations to verify the melting points, liquid densities at the melting point, and the enthalpies of vaporization produced by the models for pure substances. Subtle differences in the benchmark potentials, in particular, the well-depth, due to the level of theory used were found here to have a profound effect on the macroscopic properties of noble gases: second virial coefficients or the bulk properties in simulations. By explicitly including three-body dispersion in molecular simulations employing the best pair potential, we were able to obtain accurate melting points as well as satisfactory densities and enthalpies of vaporization.
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Affiliation(s)
- Kristian Kříž
- Department of Cell and Molecular Biology, Uppsala University, Box 596, Uppsala SE-75124, Sweden
| | - Paul J van Maaren
- Department of Cell and Molecular Biology, Uppsala University, Box 596, Uppsala SE-75124, Sweden
| | - David van der Spoel
- Department of Cell and Molecular Biology, Uppsala University, Box 596, Uppsala SE-75124, Sweden
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2
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Li M, Liu M, Qi F, Lin FR, Jen AKY. Self-Assembled Monolayers for Interfacial Engineering in Solution-Processed Thin-Film Electronic Devices: Design, Fabrication, and Applications. Chem Rev 2024; 124:2138-2204. [PMID: 38421811 DOI: 10.1021/acs.chemrev.3c00396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2024]
Abstract
Interfacial engineering has long been a vital means of improving thin-film device performance, especially for organic electronics, perovskites, and hybrid devices. It greatly facilitates the fabrication and performance of solution-processed thin-film devices, including organic field effect transistors (OFETs), organic solar cells (OSCs), perovskite solar cells (PVSCs), and organic light-emitting diodes (OLEDs). However, due to the limitation of traditional interfacial materials, further progress of these thin-film devices is hampered particularly in terms of stability, flexibility, and sensitivity. The deadlock has gradually been broken through the development of self-assembled monolayers (SAMs), which possess distinct benefits in transparency, diversity, stability, sensitivity, selectivity, and surface passivation ability. In this review, we first showed the evolution of SAMs, elucidating their working mechanisms and structure-property relationships by assessing a wide range of SAM materials reported to date. A comprehensive comparison of various SAM growth, fabrication, and characterization methods was presented to help readers interested in applying SAM to their works. Moreover, the recent progress of the SAM design and applications in mainstream thin-film electronic devices, including OFETs, OSCs, PVSCs and OLEDs, was summarized. Finally, an outlook and prospects section summarizes the major challenges for the further development of SAMs used in thin-film devices.
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Affiliation(s)
- Mingliang Li
- Department of Materials Science and Engineering, City University of Hong Kong, Kowloon, Hong Kong 999077, China
- Hong Kong Institute for Clean Energy, City University of Hong Kong, Kowloon, Hong Kong 999077, China
| | - Ming Liu
- Department of Materials Science and Engineering, City University of Hong Kong, Kowloon, Hong Kong 999077, China
- Hong Kong Institute for Clean Energy, City University of Hong Kong, Kowloon, Hong Kong 999077, China
| | - Feng Qi
- Department of Chemistry, City University of Hong Kong, Kowloon, Hong Kong 999077, China
- Hong Kong Institute for Clean Energy, City University of Hong Kong, Kowloon, Hong Kong 999077, China
| | - Francis R Lin
- Department of Materials Science and Engineering, City University of Hong Kong, Kowloon, Hong Kong 999077, China
- Department of Chemistry, City University of Hong Kong, Kowloon, Hong Kong 999077, China
- Hong Kong Institute for Clean Energy, City University of Hong Kong, Kowloon, Hong Kong 999077, China
| | - Alex K-Y Jen
- Department of Materials Science and Engineering, City University of Hong Kong, Kowloon, Hong Kong 999077, China
- Department of Chemistry, City University of Hong Kong, Kowloon, Hong Kong 999077, China
- Hong Kong Institute for Clean Energy, City University of Hong Kong, Kowloon, Hong Kong 999077, China
- Department of Materials Science and Engineering, University of Washington, Seattle, Washington 98195, United States
- State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon, Hong Kong 999077, China
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Demir Gİ, Tekin A. NICE-FF: A non-empirical, intermolecular, consistent, and extensible force field for nucleic acids and beyond. J Chem Phys 2023; 159:244117. [PMID: 38153156 DOI: 10.1063/5.0176641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 12/04/2023] [Indexed: 12/29/2023] Open
Abstract
A new non-empirical ab initio intermolecular force field (NICE-FF in buffered 14-7 potential form) has been developed for nucleic acids and beyond based on the dimer interaction energies (IEs) calculated at the spin component scaled-MI-second order Møller-Plesset perturbation theory. A fully automatic framework has been implemented for this purpose, capable of generating well-polished computational grids, performing the necessary ab initio calculations, conducting machine learning (ML) assisted force field (FF) parametrization, and extending existing FF parameters by incorporating new atom types. For the ML-assisted parametrization of NICE-FF, interaction energies of ∼18 000 dimer geometries (with IE < 0) were used, and the best fit gave a mean square deviation of about 0.46 kcal/mol. During this parametrization, atom types apparent in four deoxyribonucleic acid (DNA) bases have been first trained using the generated DNA base datasets. Both uracil and hypoxanthine, which contain the same atom types found in DNA bases, have been considered as test molecules. Three new atom types have been added to the DNA atom types by using IE datasets of both pyrazinamide and 9-methylhypoxanthine. Finally, the last test molecule, theophylline, has been selected, which contains already-fitted atom-type parameters. The performance of NICE-FF has been investigated on the S22 dataset, and it has been found that NICE-FF outperforms the well-known FFs by generating the most consistent IEs with the high-level ab initio ones. Moreover, NICE-FF has been integrated into our in-house developed crystal structure prediction (CSP) tool [called FFCASP (Fast and Flexible CrystAl Structure Predictor)], aiming to find the experimental crystal structures of all considered molecules. CSPs, which were performed up to 4 formula units (Z), resulted in NICE-FF being able to locate almost all the known experimental crystal structures with sufficiently low RMSD20 values to provide good starting points for density functional theory optimizations.
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Affiliation(s)
- Gözde İniş Demir
- Informatics Institute, Istanbul Technical University, 34469 Maslak, Istanbul, Türkiye
| | - Adem Tekin
- Informatics Institute, Istanbul Technical University, 34469 Maslak, Istanbul, Türkiye
- Research Institute for Fundamental Sciences (TÜBİTAK-TBAE), Kocaeli, Türkiye
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Wang W, Yan D, Cai Y, Xu D, Ma J, Wang Q. General Charge Transfer Dipole Model for AMOEBA-Like Force Fields. J Chem Theory Comput 2023; 19:2518-2534. [PMID: 37125725 DOI: 10.1021/acs.jctc.2c01084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
The development of highly accurate force fields is always an importance aspect in molecular modeling. In this work, we introduce a general damping-based charge transfer dipole (D-CTD) model to describe the charge transfer energy and the corresponding charge flow for H, C, N, O, P, S, F, Cl, and Br elements in common bio-organic systems. Then, two effective schemes to evaluate the charge flow from the corresponding induced dipole moment between the interacting molecules were also proposed and discussed. The potential applicability of the D-CTD model in ion-containing systems was also demonstrated in a series of ion-water complexes including Li+, Na+, K+, Mg2+, Ca2+, Fe2+, Zn2+, Pt2+, F-, Cl-, Br-, and I- ions. In general, the D-CTD model demonstrated good accuracy and good transferability in both charge transfer energy and the corresponding charge flow for a wide range of model systems. By distinguishing the intermolecular charge redistribution (charge transfer) under the influence of an external electric field from the accompanying intramolecular charge redistribution (polarization), the D-CTD model is theoretically consistent with current induced dipole-based polarizable dipole models and hence can be easily implemented and parameterized. Along with our previous work in charge penetration-corrected electrostatics, a bottom-up approach constructed water model was also proposed and demonstrated. The structure-maker and structure-breaker roles of cations and anions were also correctly reproduced using Na+, K+, Cl-, and I- ions in the new water model, respectively. This work demonstrates a cost-effective approach to describe the charge transfer phenomena. The water and ion models also show the feasibility of a modulated development approach for future force fields.
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Affiliation(s)
- Wei Wang
- Institute of Atomic and Molecular Physics, Sichuan University, Chengdu 610065, China
| | - Dengjie Yan
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610041, China
| | - Yao Cai
- College of Chemistry, Sichuan University, Chengdu 610064, China
| | - Dingguo Xu
- College of Chemistry, Sichuan University, Chengdu 610064, China
| | - Jianyi Ma
- Institute of Atomic and Molecular Physics, Sichuan University, Chengdu 610065, China
| | - Qiantao Wang
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610041, China
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Oliveira MP, Gonçalves YMH, Ol Gheta SK, Rieder SR, Horta BAC, Hünenberger PH. Comparison of the United- and All-Atom Representations of (Halo)alkanes Based on Two Condensed-Phase Force Fields Optimized against the Same Experimental Data Set. J Chem Theory Comput 2022; 18:6757-6778. [PMID: 36190354 DOI: 10.1021/acs.jctc.2c00524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The level of accuracy that can be achieved by a force field is influenced by choices made in the interaction-function representation and in the relevant simulation parameters. These choices, referred to here as functional-form variants (FFVs), include for example the model resolution, the charge-derivation procedure, the van der Waals combination rules, the cutoff distance, and the treatment of the long-range interactions. Ideally, assessing the effect of a given FFV on the intrinsic accuracy of the force-field representation requires that only the specific FFV is changed and that this change is performed at an optimal level of parametrization, a requirement that may prove extremely challenging to achieve in practice. Here, we present a first attempt at such a comparison for one specific FFV, namely the choice of a united-atom (UA) versus an all-atom (AA) resolution in a force field for saturated acyclic (halo)alkanes. Two force-field versions (UA vs AA) are optimized in an automated way using the CombiFF approach against 961 experimental values for the pure-liquid densities ρliq and vaporization enthalpies ΔHvap of 591 compounds. For the AA force field, the torsional and third-neighbor Lennard-Jones parameters are also refined based on quantum-mechanical rotational-energy profiles. The comparison between the UA and AA resolutions is also extended to properties that have not been included as parameterization targets, namely the surface-tension coefficient γ, the isothermal compressibility κT, the isobaric thermal-expansion coefficient αP, the isobaric heat capacity cP, the static relative dielectric permittivity ϵ, the self-diffusion coefficient D, the shear viscosity η, the hydration free energy ΔGwat, and the free energy of solvation ΔGche in cyclohexane. For the target properties ρliq and ΔHvap, the UA and AA resolutions reach very similar levels of accuracy after optimization. For the nine other properties, the AA representation leads to more accurate results in terms of η; comparably accurate results in terms of γ, κT, αP, ϵ, D, and ΔGche; and less accurate results in terms of cP and ΔGwat. This work also represents a first step toward the calibration of a GROMOS-compatible force field at the AA resolution.
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Affiliation(s)
- Marina P Oliveira
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Hönggerberg, HCI, CH-8093 Zürich, Switzerland
| | - Yan M H Gonçalves
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Hönggerberg, HCI, CH-8093 Zürich, Switzerland
| | - S Kashef Ol Gheta
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Hönggerberg, HCI, CH-8093 Zürich, Switzerland
| | - Salomé R Rieder
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Hönggerberg, HCI, CH-8093 Zürich, Switzerland
| | - Bruno A C Horta
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Hönggerberg, HCI, CH-8093 Zürich, Switzerland
| | - Philippe H Hünenberger
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Hönggerberg, HCI, CH-8093 Zürich, Switzerland
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6
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Chen H, Skylaris CK. Energy decomposition analysis method for metallic systems. Phys Chem Chem Phys 2022; 24:1702-1711. [PMID: 34982081 DOI: 10.1039/d1cp05112a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this work, we present the first extension of an energy decomposition analysis (EDA) method to metallic systems. We extend the theory of our Hybrid Absolutely Localized Molecular Orbitals (HALMO) EDA to take into account that molecular orbitals in metallic systems are partially occupied, which is done by weighted orthogonalization (WO) of the molecular orbitals using their associated fractional occupancies as weights in the construction of the projection operators. These operators are needed for the self-consistent field for molecular interaction (SCF MI) computation of the polarization-energy contribution to the interaction. The method gives more weight to orbitals that have higher occupancies and treats each fragment as metallic. The resulting HALMO EDA for metallic systems naturally reduces to the insulator version and produces the same results when applied to an insulating system. We present the theory and implementation of our new approach, and we demonstrate it with sample calculations of relevance to industrial materials. This work provides a new EDA paradigm and tool for the study and analysis of interactions in metallic systems within large-scale DFT calculations.
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Affiliation(s)
- Han Chen
- School of Chemistry, University of Southampton, Highfield, Southampton, SO17 1BJ, UK.
| | - Chris-Kriton Skylaris
- School of Chemistry, University of Southampton, Highfield, Southampton, SO17 1BJ, UK.
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Meinnel J, Zeroual S, Mahboub MS, Boucekkine A, Juranyi F, Carlile C, Mimouni M, Hamadneh I, Boudjada A. Calculations of the molecular interactions in 1,3-dibromo-2,4,6-trimethyl-benzene: which methyl groups are quasi-free rotors in the crystal? Phys Chem Chem Phys 2021; 23:21272-21285. [PMID: 34543373 DOI: 10.1039/d1cp02581c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Dibromomesitylene (DBMH) is one of the few molecules in which a methyl group is a quasi-free rotor in the crystal state. Density functional theory calculations - using the Born-Oppenheimer approximation (BOa) - indicate that in isolated DBMH, Me4 and Me6 are highly hindered in a 3-fold potential V3 > 55 meV while Me2 symmetrically located between two Br atoms has a small 6-fold rotation hindering potential: V6 ∼ 8 meV. Inelastic neutron scattering studies have shown that this is also true in the crystal, the Me2 tunneling gap being 390 μeV at 4.2 K and V6 ∼ 18 meV. In the monoclinic DBMH crystal, molecules are packed in an anti-ferroelectric manner along the oblique a axis, favoring strong van der Waals interactions, while in the corrugated bc planes each molecule has a quasi hexagonal environment and weaker interactions. This results in the nearby environment of Me2 only being composed of hydrogen atoms. This explains why the Me2 rotation barrier remains small in the crystal and mainly 6-fold. Using the same potentials in the Schrödinger equation for a -CD3 rotor has allowed predicting a tunneling gap of 69 μeV for deuterated Me2 in very good agreement with inelastic neutron scattering measurements. Therefore, because of a rare and unexpected local symmetry in the crystal, the Me2 rotation barrier remains small and 6-fold and hydrogen nuclei are highly delocalized and not relevant to the Born-Oppenheimer approximation. This and the neglect of spin states explain the failure of density functional theory calculations for finding the rotation energy levels of Me2.
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Affiliation(s)
- Jean Meinnel
- Univ Rennes 1, CNRS, ISCR - UMR 6226, ssF-35000 Rennes, France
| | - Soria Zeroual
- LEVRES Laboratory, University of El Oued, 39000 El Oued, Algeria.
| | | | | | - Fanni Juranyi
- Paul Scherrer Institute, Forschungsstrasse 111, 5232 Villigen PSI, Switzerland
| | - Colin Carlile
- Department of Physics and Astronomy, Uppsala University, Uppsala, Sweden
| | - Mourad Mimouni
- LEVRES Laboratory, University of El Oued, 39000 El Oued, Algeria.
| | - Imad Hamadneh
- Department of Chemistry, Faculty of Science, University of Jordan, Amman 11942, Jordan
| | - Ali Boudjada
- Laboratoire de Cristallographie, Département de Physique, Faculté des Sciences Exactes, Université des Frères Mentouri Constantine-1, 25000, Algeria
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Jing Z, Liu C, Ren P. Advanced Electrostatic Model for Monovalent Ions Based on Ab Initio Energy Decomposition. J Chem Inf Model 2021; 61:2806-2817. [PMID: 34096706 PMCID: PMC8323402 DOI: 10.1021/acs.jcim.1c00426] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Ions play important roles in the structures and functions of biomolecules. In biomolecular simulations, ions either directly interact with biomolecules or provide an ionic environment that influences electrostatic interactions of solutes. The AMOEBA+ water model has demonstrated significant advancement of the classical force field for describing molecular interactions due to its improvements on the functional forms to account for essential physics. This work expands the applicability of the AMOEBA+ model toward alkali metal (Li, Na, K, Rb, and Cs) and halogen (F, Cl, Br, and I) ions. Various quantum chemical data on ion-ion and ion-water interactions, experimental ion hydration free energies, and lattice energies of salt crystals are used in the parametrization. The final parameters are verified with other properties outside of the parametrization data, including lattice energies of additional salt crystals and ionic activity coefficients in solution. The new model captures a wide range of ion properties from the gas phase to solution phase and crystals. More importantly, AMOEBA+ provides energy components that are consistent with ab initio energy decomposition. Thus, we expect AMOEBA+ to be more general, transferable, and valuable for the interpretation of intermolecular forces in efficient classical simulations.
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Affiliation(s)
- Zhifeng Jing
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX 78712
| | - Chengwen Liu
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX 78712
| | - Pengyu Ren
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX 78712
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Dong X, Yuan X, Song Z, Wang Q. The development of an Amber-compatible organosilane force field for drug-like small molecules. Phys Chem Chem Phys 2021; 23:12582-12591. [PMID: 34037028 DOI: 10.1039/d1cp01169c] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
As members of the group IVA elements, silicon and carbon have long been thought of as isosteres of each other in drug design. However, the lack of silicon parameters in current main stream force fields hinders the computational study of this important element in drug discovery. Thus, in this study, we attempted to supplement the parameters of organosilanes in the General Amber Force Field (GAFF2). The parameters have been designed following the principles of GAFF2 to make it compatible with the Amber force field family. The accuracy of the parameters was discussed by comparing the pair interaction energy, the liquid properties, and the structures and alchemical binding free energy differences for a set of protein-ligand complexes.
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Affiliation(s)
- Xue Dong
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu, 610041, P. R. China.
| | - Xinghang Yuan
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu, 610041, P. R. China.
| | - Zhenlei Song
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu, 610041, P. R. China.
| | - Qiantao Wang
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu, 610041, P. R. China.
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10
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Zhu H, Wang W, Li Z, Ma D, Lin X, Li J, Wang Q, Ma J. Calculation of Transport Parameters Using ab initio and AMOEBA Polarizable Force Field Methods. J Phys Chem A 2021; 125:4918-4927. [PMID: 34038116 DOI: 10.1021/acs.jpca.1c03028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The transport properties of chemical species such as coefficients of diffusion, thermal conductivity, and viscosity have been widely used in combustion modeling. Lennard-Jones parameters fitted from the accurate intermolecular potential energy surfaces are crucial to obtain such information. Hence, a fast and accurate energy function is always desired for this purpose. In this study, the quality of a widely used polarizable force field AMOEBA was examined for the interaction between noble gases and n-alkanes. First, the intermolecular energy was compared between AMOEBA, MP2/CBS, MP2/aug'-cc-pVDZ, and QCISD(T)/CBS. The root mean squared error of the original AMOEBA was 10.31 cm-1 against QCISD(T)/CBS for all conformations. This was comparable with the errors of 10.84 and 7.75 cm-1 for MP2/aug'-cc-pVDZ and MP2/CBS, respectively. Further optimizing the van der Waals parameters of noble gases, the error of the force field against QCISD(T)/CBS was reduced to 6.24 cm-1, even better than the MP2/CBS results. Based on the optimized force field parameters, the intermolecular Lennard-Jones parameters were derived using the spherically averaged method and one-dimensional minimization method for a set of (n-alkanes, noble gases) pairs. The discrepancy of the one-dimensional minimization predicted Lennard-Jones collision rates from the tabulated values was typically within 10%, while it could be as large as 20-30% for the spherically averaged method. Additionally, the binary diffusion coefficients were calculated using the present Lennard-Jones parameters. In this case, the parameters derived from the spherically averaged method perform better. The mean unsigned error of the diffusion coefficients is usually within 5%, which is in good agreement with the experimental results. The results demonstrate that the AMOEBA force field can be used to generate the transport parameters systematically.
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Affiliation(s)
- Heyuan Zhu
- Institute of Atomic and Molecular Physics, Sichuan University, Chengdu 610065, P. R. China.,Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610041, P. R. China
| | - Wei Wang
- Institute of Atomic and Molecular Physics, Sichuan University, Chengdu 610065, P. R. China
| | - Zhiwei Li
- Institute of Atomic and Molecular Physics, Sichuan University, Chengdu 610065, P. R. China
| | - Dandan Ma
- Institute of Atomic and Molecular Physics, Sichuan University, Chengdu 610065, P. R. China
| | - Xiaomin Lin
- Institute of Atomic and Molecular Physics, Sichuan University, Chengdu 610065, P. R. China
| | - Jun Li
- School of Chemistry and Chemical Engineering, Chongqing University, Chongqing 400044, P. R. China
| | - Qiantao Wang
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610041, P. R. China
| | - Jianyi Ma
- Institute of Atomic and Molecular Physics, Sichuan University, Chengdu 610065, P. R. China
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11
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Chen H, Skylaris CK. Analysis of DNA interactions and GC content with energy decomposition in large-scale quantum mechanical calculations. Phys Chem Chem Phys 2021; 23:8891-8899. [PMID: 33876048 DOI: 10.1039/d0cp06630c] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
GC content is a contributing factor to the stability of nucleic acids due to hydrogen bonding. More hydrogen bonding generally results in greater stability. Empirical evidence, however, has suggested that the GC content of a nucleic acid is a poor predictor of its stability, implying that there are sequence-dependent interactions besides what its GC content indicates. To examine how much such sequence-dependent interactions affect the interaction energies of double-stranded DNA (dsDNA) molecules, dsDNA molecules of different sequences are generated and examined in silico for variabilities in the interaction energies within each group of dsDNA molecules of the same GC content. Since the amount of hydrogen bonding depends on the GC content, holding the GC content fixed when examining the differences in interaction energies allows sequence-dependent interactions to be isolated. The nature of sequence-dependent interactions is then dissected using energy decomposition analysis (EDA). By using EDA, the components of the interactions that depend on the neighboring base pairs help explain some of the variability in the interaction energies of the dsDNA molecules despite having the same GC content. This work provides a new paradigm and tool for the study and analysis of the distributions of interaction components in dsDNA with the same GC content using EDA within large-scale quantum chemistry calculations.
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Affiliation(s)
- Han Chen
- School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, UK.
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Thorning F, Strunge K, Jensen F, Ogilby PR. The complex between molecular oxygen and an organic molecule: modeling optical transitions to the intermolecular charge-transfer state. Phys Chem Chem Phys 2021; 23:15038-15048. [PMID: 34212959 DOI: 10.1039/d1cp01738a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The collision complex between the ground electronic state of an organic molecule, M, and ground state oxygen, O2(X3Σg-), can absorb light to produce an intermolecular charge transfer (CT) state, often represented simply as the M radical cation, M+˙, paired with the superoxide radical anion, O2-˙. Aspects of this transition have been the subject of numerous studies for ∼70 years, many of which address fundamental concepts in chemistry and physics. We now examine the extent to which the combination of Molecular Dynamics simulations and electronic structure response methods can model transitions to the toluene-O2 CT state. To account for the experimental spectra, we consider (a) the distribution of toluene-O2 geometries that contribute to the transitions, (b) a quantitative description of intermolecular CT, and (c) oxygen-induced local transitions in toluene that complement the CT transitions, specifically transitions that populate toluene triplet states. We find that the latter oxygen-induced local transitions play a prominent role on the long wavelength side of the spectrum commonly attributed to the intermolecular CT transition. Our calculations provide a new perspective on the seminal discussion between R. S. Mulliken and D. F. Evans on the nature of O2-dependent transitions in organic molecules, and bode well for modeling transitions to excited states with CT character in noncovalent weakly-bonded molecular complexes.
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Affiliation(s)
| | - Kris Strunge
- Chemistry Department, Aarhus University, DK-8000, Aarhus, Denmark.
| | - Frank Jensen
- Chemistry Department, Aarhus University, DK-8000, Aarhus, Denmark.
| | - Peter R Ogilby
- Chemistry Department, Aarhus University, DK-8000, Aarhus, Denmark.
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13
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Liu C, Piquemal JP, Ren P. Implementation of Geometry-Dependent Charge Flux into the Polarizable AMOEBA+ Potential. J Phys Chem Lett 2020; 11:419-426. [PMID: 31865706 PMCID: PMC7384396 DOI: 10.1021/acs.jpclett.9b03489] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Molecular dynamics (MD) simulations employing classical force fields (FFs) have been widely used to model molecular systems. The important ingredient of the current FFs, atomic charge, remains fixed during MD simulations despite the atomic environment or local geometry changes. This approximation hinders the transferability of the potential being used in multiple phases. Here we implement a geometry-dependent charge flux (GDCF) model into the multipole-based AMOEBA+ polarizable potential. The CF in the current work explicitly depends on the local geometry (bond and angle) of the molecule. To our knowledge, this is the first study that derives energy and force expressions due to GDCF in a multipole-based polarizable FF framework. Due to the inclusion of GDCF, the AMOEBA+ water model is noticeably improved in terms of describing the monomer properties, cluster binding/interaction energy, and a variety of liquid properties, including the infrared spectra that previous flexible water models were not able to capture.
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Affiliation(s)
- Chengwen Liu
- Department of Biomedical Engineering , The University of Texas at Austin , Austin , Texas 78712 , United States
| | - Jean-Philip Piquemal
- Department of Biomedical Engineering , The University of Texas at Austin , Austin , Texas 78712 , United States
- Laboratoire de Chimie Théorique , Sorbonne Université, UMR7616 CNRS , 75252 Paris , France
- Institut Universitaire de France , 75005 , Paris , France
| | - Pengyu Ren
- Department of Biomedical Engineering , The University of Texas at Austin , Austin , Texas 78712 , United States
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14
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Zeferino RC, Mota NSRS, Grinevicius VMAS, Filipe KB, Sulis PM, Silva FRMB, Filho DW, Pich CT, Pedrosa RC. Targeting ROS overgeneration by N-benzyl-2-nitro-1-imidazole-acetamide as a potential therapeutic reposition approach for cancer therapy. Invest New Drugs 2019; 38:785-799. [PMID: 31257554 DOI: 10.1007/s10637-019-00820-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Accepted: 06/17/2019] [Indexed: 11/25/2022]
Abstract
BackgroundWe investigated the role of reactive oxygen species (ROS) in the anticancer mechanism of N-benzyl-2-nitro-1-imidazole-acetamide (BZN), a drug used in Chagas' disease treatment. MethodsBALB/c mice, inoculated with Ehrlich ascites carcinoma (EAC), were treated with BZN or BZN + Nacylcysteine (NAC) or NAC for 9 days. Subsequently, the inhibition of tumor growth and angiogenesis as well as animal survival were evaluated. Apoptosis and the cell cycle were evaluated using fluorescence microscopy and flow cytometry, while oxidative stress was evaluated by measuring TBARS content, DNA damage, calcium influx and ROS generation and antioxidant defenses (CAT, SOD, GPx, GST and GR). Immunoblotting was used to evaluate key death and cell cycle proteins. Results BZN treatment inhibited tumor progression (79%), angiogenesis (2.8-fold) and increased animal survival (29%). Moreover, BZN increased ROS levels (42%), calcium influx (55%), TBARS contents (1.9-fold), SOD (4.4-fold), GPx (17.5-fold) and GST (3-fold) activities and GSH depletion (2.5-fold) also caused DNA fragmentation (7.6-fold), increased cleaved PARP and promoted the trapping of cells in the G1 phase, as corroborated by the reduction in cyclin A and increased CDK2 protein levels. In silico DNA and molecular dynamic simulations showed H-bonds and hydrophobic interactions that were confirmed by circular dichroism. Increased apoptosis (232%), induced by treatment with BZN, was demonstrated by apoptotic cell staining and p53 level. Conclusion The current findings indicate that BZN acts as a tumor growth inhibitor and anti-angiogenic agent by ROS overgeneration, which interact with DNA causing damage and triggering apoptosis.
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Affiliation(s)
- Rodrigo C Zeferino
- Biochemistry Department, Federal University of Santa Catarina (UFSC), Florianópolis, SC, Brazil
| | - Nádia S R S Mota
- Biochemistry Department, Federal University of Santa Catarina (UFSC), Florianópolis, SC, Brazil
| | | | - Karina B Filipe
- Department of Clinical Analysis, Federal University of Paraná (UFPR), Curitiba, PR, Brazil
| | - Paola M Sulis
- Biochemistry Department, Federal University of Santa Catarina (UFSC), Florianópolis, SC, Brazil
| | - Fátima R M B Silva
- Biochemistry Department, Federal University of Santa Catarina (UFSC), Florianópolis, SC, Brazil
| | - Danilo W Filho
- Ecology and Zoology Department, Federal University of Santa Catarina (UFSC), Florianópolis, SC, Brazil
| | - Claus T Pich
- Center for Sciences, Technologies and Health, Federal University of Santa Catarina (UFSC), Araranguá, SC, Brazil
| | - Rozangela C Pedrosa
- Biochemistry Department, Federal University of Santa Catarina (UFSC), Florianópolis, SC, Brazil.
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15
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Liu C, Piquemal JP, Ren P. AMOEBA+ Classical Potential for Modeling Molecular Interactions. J Chem Theory Comput 2019; 15:4122-4139. [PMID: 31136175 DOI: 10.1021/acs.jctc.9b00261] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Classical potentials based on isotropic and additive atomic charges have been widely used to model molecules in computers for the past few decades. The crude approximations in the underlying physics are hindering both their accuracy and transferability across chemical and physical environments. Here we present a new classical potential, AMOEBA+, to capture essential intermolecular forces, including permanent electrostatics, repulsion, dispersion, many-body polarization, short-range charge penetration, and charge transfer, by extending the polarizable multipole-based AMOEBA (Atomic Multipole Optimized Energetics for Biomolecular Applications) model. For a set of common organic molecules, we show that AMOEBA+ with general parameters can reproduce both quantum mechanical interactions and energy decompositions according to Symmetry-Adapted Perturbation Theory (SAPT). Additionally, a new water model based on the AMOEBA+ framework captures various liquid-phase properties in molecular dynamics simulations while remaining consistent with SAPT energy decompositions, utilizing both ab initio data and experimental liquid properties. Our results demonstrate that it is possible to improve the physical basis of classical force fields to advance their accuracy and general applicability.
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Affiliation(s)
- Chengwen Liu
- Department of Biomedical Engineering , The University of Texas at Austin , Austin , Texas 78712 , United States
| | - Jean-Philip Piquemal
- Department of Biomedical Engineering , The University of Texas at Austin , Austin , Texas 78712 , United States.,Laboratoire de Chimie Théorique , Sorbonne Université, UMR7616 CNRS , Paris 75252 , France.,Institut Universitaire de France , Paris Cedex 05, 75005 , France
| | - Pengyu Ren
- Department of Biomedical Engineering , The University of Texas at Austin , Austin , Texas 78712 , United States
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16
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Jing Z, Liu C, Cheng SY, Qi R, Walker BD, Piquemal JP, Ren P. Polarizable Force Fields for Biomolecular Simulations: Recent Advances and Applications. Annu Rev Biophys 2019; 48:371-394. [PMID: 30916997 DOI: 10.1146/annurev-biophys-070317-033349] [Citation(s) in RCA: 217] [Impact Index Per Article: 43.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Realistic modeling of biomolecular systems requires an accurate treatment of electrostatics, including electronic polarization. Due to recent advances in physical models, simulation algorithms, and computing hardware, biomolecular simulations with advanced force fields at biologically relevant timescales are becoming increasingly promising. These advancements have not only led to new biophysical insights but also afforded opportunities to advance our understanding of fundamental intermolecular forces. This article describes the recent advances and applications, as well as future directions, of polarizable force fields in biomolecular simulations.
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Affiliation(s)
- Zhifeng Jing
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, USA;
| | - Chengwen Liu
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, USA;
| | - Sara Y Cheng
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, USA;
| | - Rui Qi
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, USA;
| | - Brandon D Walker
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, USA;
| | - Jean-Philip Piquemal
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, USA; .,Sorbonne Université, CNRS, Laboratoire de Chimie Theórique, 75252 Paris CEDEX 05, France.,Institut Universitaire de France, 75005 Paris, France
| | - Pengyu Ren
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, USA;
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17
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Rackers JA, Ponder JW. Classical Pauli repulsion: An anisotropic, atomic multipole model. J Chem Phys 2019; 150:084104. [PMID: 30823770 DOI: 10.1063/1.5081060] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Pauli repulsion is a key component of any theory of intermolecular interactions. Although Pauli or exchange repulsion has its origin in the quantum mechanical nature of electrons, it is possible to describe the resulting energetic effects via a classical model in terms of the overlap of electron densities. In fact, closed shell intermolecular repulsion can be explained as a diminution of election density in the internuclear region resulting in decreased screening of nuclear charges and increased nuclear-nuclear repulsion. We provide a concise anisotropic repulsion formulation using the atomic multipoles from the Atomic Multipole Optimized Energetics for Biomolecular Applications force field to describe the electron density at each atom in a larger system. Mathematically, the proposed model consists of damped pairwise exponential multipolar repulsion interactions truncated at short range, which are suitable for use in compute-intensive biomolecular force fields and molecular dynamics simulations. Parameters for 26 atom classes encompassing most organic molecules are derived from a fit to Symmetry Adapted Perturbation Theory exchange repulsion energies for the S101 dimer database. Several applications of the multipolar Pauli repulsion model are discussed, including noble gas interactions, analysis of stationary points on the water dimer potential surface, and the directionality of several halogen bonding interactions.
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Affiliation(s)
- Joshua A Rackers
- Program in Computational and Molecular Biophysics, Washington University, School of Medicine, Saint Louis, Missouri 63110, USA
| | - Jay W Ponder
- Department of Chemistry, Washington University in Saint Louis, Saint Louis, Missouri 63130, USA
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18
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Zanette C, Bannan CC, Bayly CI, Fass J, Gilson MK, Shirts MR, Chodera JD, Mobley DL. Toward Learned Chemical Perception of Force Field Typing Rules. J Chem Theory Comput 2019; 15:402-423. [PMID: 30512951 PMCID: PMC6467725 DOI: 10.1021/acs.jctc.8b00821] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Molecular mechanics force fields define how the energy and forces in a molecular system are computed from its atomic positions, thus enabling the study of such systems through computational methods like molecular dynamics and Monte Carlo simulations. Despite progress toward automated force field parametrization, considerable human expertise is required to develop or extend force fields. In particular, human input has long been required to define atom types, which encode chemically unique environments that determine which parameters will be assigned. However, relying on humans to establish atom types is suboptimal. Human-created atom types are often developed without statistical justification, leading to over- or under-fitting of data. Human-created types are also difficult to extend in a systematic and consistent manner when new chemistries must be modeled or new data becomes available. Finally, human effort is not scalable when force fields must be generated for new (bio)polymers, compound classes, or materials. To remedy these deficiencies, our long-term goal is to replace human specification of atom types with an automated approach, based on rigorous statistics and driven by experimental and/or quantum chemical reference data. In this work, we describe novel methods that automate the discovery of appropriate chemical perception: SMARTY allows for the creation of atom types, while SMIRKY goes further by automating the creation of fragment (nonbonded, bonds, angles, and torsions) types. These approaches enable the creation of move sets in atom or fragment type space, which are used within a Monte Carlo optimization approach. We demonstrate the power of these new methods by automating the rediscovery of human defined atom types (SMARTY) or fragment types (SMIRKY) in existing small molecule force fields. We assess these approaches using several molecular data sets, including one which covers a diverse subset of the DrugBank database.
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Affiliation(s)
- Camila Zanette
- Department of Pharmaceutical Sciences, University of California, Irvine
| | | | | | - Josh Fass
- Tri-Institutional Training Program in Computational Biology and Medicine, New York, NY 10065
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Michael K. Gilson
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego
| | - Michael R. Shirts
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO 80309
| | - John D. Chodera
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - David L. Mobley
- Department of Pharmaceutical Sciences, University of California, Irvine
- Department of Chemistry, University of California, Irvine
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19
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Sun CQ. Aqueous charge injection: solvation bonding dynamics, molecular nonbond interactions, and extraordinary solute capabilities. INT REV PHYS CHEM 2018. [DOI: 10.1080/0144235x.2018.1544446] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Chang Q. Sun
- EBEAM, Yangtze Normal University, Chongqing, People's Republic of China
- NOVITAS, EEE, Nanyang Technological University, Singapore, Singapore
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20
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Hagler AT. Force field development phase II: Relaxation of physics-based criteria… or inclusion of more rigorous physics into the representation of molecular energetics. J Comput Aided Mol Des 2018; 33:205-264. [DOI: 10.1007/s10822-018-0134-x] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 07/18/2018] [Indexed: 01/04/2023]
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21
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Rackers JA, Liu C, Ren P, Ponder JW. A physically grounded damped dispersion model with particle mesh Ewald summation. J Chem Phys 2018; 149:084115. [PMID: 30193468 DOI: 10.1063/1.5030434] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Accurate modeling of dispersion is critical to the goal of predictive biomolecular simulations. To achieve this accuracy, a model must be able to correctly capture both the short-range and asymptotic behavior of dispersion interactions. We present here a damped dispersion model based on the overlap of charge densities that correctly captures both regimes. The overlap damped dispersion model represents a classical physical interpretation of dispersion: the interaction between the instantaneous induced dipoles of two distinct charge distributions. This model is shown to be an excellent fit with symmetry adapted perturbation theory dispersion energy calculations, yielding an RMS error on the S101x7 database of 0.5 kcal/mol. Moreover, the damping function used in this model is wholly derived and parameterized from the electrostatic dipole-dipole interaction, making it not only physically grounded but transferable as well.
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Affiliation(s)
- Joshua A Rackers
- Program in Computational and Molecular Biophysics, Washington University School of Medicine, Saint Louis, Missouri 63110, USA
| | - Chengwen Liu
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Pengyu Ren
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Jay W Ponder
- Program in Computational and Molecular Biophysics, Washington University School of Medicine, Saint Louis, Missouri 63110, USA
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22
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Demerdash O, Wang L, Head‐Gordon T. Advanced models for water simulations. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2017. [DOI: 10.1002/wcms.1355] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Omar Demerdash
- Kenneth S. Pitzer Center for Theoretical Chemistry University of California Berkeley CA USA
- Department of Chemistry University of California Berkeley CA USA
| | - Lee‐Ping Wang
- Department of Chemistry University of California, Davis Davis CA USA
| | - Teresa Head‐Gordon
- Kenneth S. Pitzer Center for Theoretical Chemistry University of California Berkeley CA USA
- Department of Chemistry University of California Berkeley CA USA
- Department of Bioengineering University of California Berkeley CA USA
- Department of Chemical and Biomolecular Engineering University of California Berkeley CA USA
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23
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Deng S, Wang Q, Ren P. Estimating and modeling charge transfer from the SAPT induction energy. J Comput Chem 2017; 38:2222-2231. [PMID: 28766729 DOI: 10.1002/jcc.24864] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Revised: 06/04/2017] [Accepted: 06/06/2017] [Indexed: 02/05/2023]
Abstract
Recent studies using quantum mechanics energy decomposition methods, for example, SAPT and ALMO, have revealed that the charge transfer energy may play an important role in short ranged inter-molecular interactions, and have a different distance dependence comparing with the polarization energy. However, the charge transfer energy component has been ignored in most current polarizable or non-polarizable force fields. In this work, first, we proposed an empirical decomposition of SAPT induction energy into charge transfer and polarization energy that mimics the regularized SAPT method (ED-SAPT). This empirical decomposition is free of the divergence issue, hence providing a good reference for force field development. Then, we further extended this concept in the context of AMOEBA polarizable force field, proposed a consistent approach to treat the charge transfer phenomenon. Current results show a promising application of this charge transfer model in future force field development. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Shi Deng
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Qiantao Wang
- Key Laboratory of Drug Targeting and Drug Delivery System of Education Ministry, West China School of Pharmacy, Sichuan University, Chengdu, 610041, China
| | - Pengyu Ren
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas, 78712
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24
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Vandenbrande S, Waroquier M, Speybroeck VV, Verstraelen T. The Monomer Electron Density Force Field (MEDFF): A Physically Inspired Model for Noncovalent Interactions. J Chem Theory Comput 2016; 13:161-179. [DOI: 10.1021/acs.jctc.6b00969] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Steven Vandenbrande
- Center for Molecular Modeling
(CMM), QCMM Ghent−Brussels Alliance, Ghent University, Technologiepark
903, B9000 Ghent, Belgium
| | - Michel Waroquier
- Center for Molecular Modeling
(CMM), QCMM Ghent−Brussels Alliance, Ghent University, Technologiepark
903, B9000 Ghent, Belgium
| | - Veronique Van Speybroeck
- Center for Molecular Modeling
(CMM), QCMM Ghent−Brussels Alliance, Ghent University, Technologiepark
903, B9000 Ghent, Belgium
| | - Toon Verstraelen
- Center for Molecular Modeling
(CMM), QCMM Ghent−Brussels Alliance, Ghent University, Technologiepark
903, B9000 Ghent, Belgium
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