1
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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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2
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Das AK, Liu M, Head-Gordon T. Development of a Many-Body Force Field for Aqueous Alkali Metal and Halogen Ions: An Energy Decomposition Analysis Guided Approach. J Chem Theory Comput 2022; 18:953-967. [DOI: 10.1021/acs.jctc.1c00537] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Akshaya Kumar Das
- Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States
| | - Meili Liu
- Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States
- Department of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Teresa Head-Gordon
- Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States
- Departments of Bioengineering and Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, California 94720, United States
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3
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Oliveira MP, Andrey M, Rieder SR, Kern L, Hahn DF, Riniker S, Horta BAC, Hünenberger PH. Systematic Optimization of a Fragment-Based Force Field against Experimental Pure-Liquid Properties Considering Large Compound Families: Application to Saturated Haloalkanes. J Chem Theory Comput 2020; 16:7525-7555. [DOI: 10.1021/acs.jctc.0c00683] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Marina P. Oliveira
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Honggerberg, HCI, CH-8093 Zürich, Switzerland
| | - Maurice Andrey
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Honggerberg, HCI, CH-8093 Zürich, Switzerland
| | - Salomé R. Rieder
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Honggerberg, HCI, CH-8093 Zürich, Switzerland
| | - Leyla Kern
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Honggerberg, HCI, CH-8093 Zürich, Switzerland
| | - David F. Hahn
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Honggerberg, HCI, CH-8093 Zürich, Switzerland
| | - Sereina Riniker
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Honggerberg, HCI, CH-8093 Zürich, Switzerland
| | - Bruno A. C. Horta
- Instituto de Química, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-909, Brazil
| | - Philippe H. Hünenberger
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Honggerberg, HCI, CH-8093 Zürich, Switzerland
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4
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Peels M, Knizia G. Fast Evaluation of Two-Center Integrals over Gaussian Charge Distributions and Gaussian Orbitals with General Interaction Kernels. J Chem Theory Comput 2020; 16:2570-2583. [PMID: 32040326 DOI: 10.1021/acs.jctc.9b01296] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
We present efficient algorithms for computing two-center integrals and integral derivatives, with general interaction kernels K(r12), over Gaussian charge distributions of general angular momenta l. While formulated in terms of traditional ab initio integration techniques, full derivations and required secondary information, as well as a reference implementation, are provided to make the content accessible to other fields. Concretely, the presented algorithms are based on an adaption of the McMurchie-Davidson Recurrence Relation (MDRR) combined with analytical properties of the solid harmonic transformation; this obviates all intermediate recurrences except the adapted MDRR itself, and allows it to be applied to fully contracted auxiliary kernel integrals. The technique is particularly well-suited for semiempirical molecular orbital methods, where it can serve as a more general and efficient replacement of Slater-Koster tables, and for first-principles quantum chemistry methods employing density fitting. But the formalism's high efficiency and ability of handling general interaction kernels K(r12) and multipolar Gaussian charge distributions may also be of interest for modeling electrostatic interactions and short-range exchange and charge penetration effects in classical force fields and model potentials. With the presented technique, a 4894 × 4894 univ-JKFIT Coulomb matrix JAB = (A|1/r12|B) (183 MiB) can be computed in 50 ms on a Q2'2018 notebook CPU, without any screening or approximations.
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Affiliation(s)
- Mieke Peels
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Gerald Knizia
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
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5
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Patkowski K. Recent developments in symmetry‐adapted perturbation theory. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2019. [DOI: 10.1002/wcms.1452] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Konrad Patkowski
- Department of Chemistry and Biochemistry Auburn University Auburn Alabama
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6
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Glova A, Larin SV, Nazarychev VM, Kenny JM, Lyulin AV, Lyulin SV. Toward Predictive Molecular Dynamics Simulations of Asphaltenes in Toluene and Heptane. ACS OMEGA 2019; 4:20005-20014. [PMID: 31788635 PMCID: PMC6882142 DOI: 10.1021/acsomega.9b02992] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 10/31/2019] [Indexed: 06/10/2023]
Abstract
The conventional definition of asphaltenes is based on their solubility in toluene and their insolubility in heptane. We have utilized this definition to study the influence of partial charge parametrization on the aggregation behavior of asphaltenes using classical atomistic molecular dynamics simulations performed on the microsecond time scale. Under consideration here are toluene- and heptane-based systems with different partial charges parametrized using the general AMBER force field (GAFF). Systems with standard GAFF partial charges calculated by the AM1-BCC and HF/6-31G*(RESP) methods were simulated alongside systems without partial charges. The partial charges implemented differ in terms of the resulting electrical negativity of the asphaltene polyaromatic core, with the AM1-BCC method giving the greatest magnitude of the total core charge. Based on our analysis of the molecular relaxation and orientation, and on the aggregation behavior of asphaltenes in toluene and heptane, we proposed to use the partial charges obtained by the AM1-BCC method for the study of asphaltene aggregates. A good agreement with available experimental data was observed on the sizes of the aggregates, their fractal dimensions, and the solvent entrainment for the model asphaltenes in toluene and heptane. From the results obtained, we conclude that for a better predictive ability, simulation parameters must be carefully chosen, with particular attention paid to the partial charges owing to their influence on the electrical negativity of the asphaltene core and on the asphaltenes aggregation.
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Affiliation(s)
- Artyom
D. Glova
- Institute
of Macromolecular Compounds, Russian Academy
of Sciences, Bolshoi
pr. 31 (V.O.), 199004 St. Petersburg, Russia
| | - Sergey V. Larin
- Institute
of Macromolecular Compounds, Russian Academy
of Sciences, Bolshoi
pr. 31 (V.O.), 199004 St. Petersburg, Russia
| | - Victor M. Nazarychev
- Institute
of Macromolecular Compounds, Russian Academy
of Sciences, Bolshoi
pr. 31 (V.O.), 199004 St. Petersburg, Russia
| | - Josè M. Kenny
- Institute
of Macromolecular Compounds, Russian Academy
of Sciences, Bolshoi
pr. 31 (V.O.), 199004 St. Petersburg, Russia
| | - Alexey V. Lyulin
- Institute
of Macromolecular Compounds, Russian Academy
of Sciences, Bolshoi
pr. 31 (V.O.), 199004 St. Petersburg, Russia
- Theory
of Polymers and Soft Matter Group, Technische
Universiteit Eindhoven, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Sergey V. Lyulin
- Institute
of Macromolecular Compounds, Russian Academy
of Sciences, Bolshoi
pr. 31 (V.O.), 199004 St. Petersburg, Russia
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7
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Das AK, Urban L, Leven I, Loipersberger M, Aldossary A, Head-Gordon M, Head-Gordon T. Development of an Advanced Force Field for Water Using Variational Energy Decomposition Analysis. J Chem Theory Comput 2019; 15:5001-5013. [DOI: 10.1021/acs.jctc.9b00478] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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8
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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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9
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Albaugh A, Tuckerman ME, Head-Gordon T. Combining Iteration-Free Polarization with Large Time Step Stochastic-Isokinetic Integration. J Chem Theory Comput 2019; 15:2195-2205. [PMID: 30830768 DOI: 10.1021/acs.jctc.9b00072] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In order to accelerate molecular dynamics simulations using polarizable force fields, we combine a new extended Lagrangian approach that eliminates the self-consistent field step (iEL/0-SCF) with a stochastic integration scheme that allows for a long time step using a multiple time scale algorithm (SIN(R)). We consider different algorithms for the combined scheme that places different components of the nonbonded forces into different time scales, as well as splitting individual nonbonded forces across time scales, to demonstrate that the combined method works well for bulk water as well as for a concentrated salt solution, aqueous peptide, and solvated protein. Depending on system and desired accuracy, the iEL/0-SCF and SIN(R) combination yields lower bound computational speed-ups of ∼6-8 relative to a molecular dynamics Verlet integration using a standard SCF solver implemented in the reference program TINKER 8.1. The combined approach embodies a significant advance for equilibrium simulations in the canonical ensemble of many-body potential energy surfaces for condensed phase systems with speed-ups that exceed what is possible by either method alone.
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Affiliation(s)
| | - Mark E Tuckerman
- NYU-ECNU , Center for Computational Chemistry at NYU, Shanghai , Shanghai 200062 , China
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10
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Lambrecht DS. Generalizing energy decomposition analysis to response properties to inform expedited predictive models. COMPUT THEOR CHEM 2019. [DOI: 10.1016/j.comptc.2018.12.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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11
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Bojarowski SA, Kumar P, Wandtke CM, Dittrich B, Dominiak PM. Universal Method for Electrostatic Interaction Energies Estimation with Charge Penetration and Easily Attainable Point Charges. J Chem Theory Comput 2018; 14:6336-6345. [PMID: 30359528 DOI: 10.1021/acs.jctc.8b00781] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Our new model of electron density augmented by point charges (aug-PROmol) provides an estimation of electrostatic interaction energies including penetration effects ( ChemPhysChem 2016, 17, 2455-2460). In this paper we prove that it can be applied using sources of point charges other than those from direct restrained fitting to electrostatic potential (RESP). We used a newly established databank of tabulated invariom point charges and a widely known semiempirical method. Both sources perform equivalently to the basic aug-PROmol method as well as to reference energies at the DFT-SAPT/aug-cc-pVTZ level of theory. This is possible due to the universal character of the penetration model included in the aug-PROmol. Aug-PROmol may become a basis for development of new nonbonded terms in force fields or a high success rate scoring function.
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Affiliation(s)
- Sławomir A Bojarowski
- Biological and Chemical Research Centre, Department of Chemistry , University of Warsaw , ul. Żwirki i Wigury 101 , 02-089 Warszawa , Poland
| | - Prashant Kumar
- Biological and Chemical Research Centre, Department of Chemistry , University of Warsaw , ul. Żwirki i Wigury 101 , 02-089 Warszawa , Poland
| | - Claudia M Wandtke
- Institut fur Anorganische Chemie , Georg-August-Universitat , Tammannstrasse 4 , 37077 Göttingen , Germany
| | - Birger Dittrich
- Anorganische Chemie und Strukturchemie , Heinrich-Heine Universitat Düsseldorf , Universitatsstrasse 1, Gëbaude 26.42.01.21 , 40225 Düsseldorf , Germany
| | - Paulina M Dominiak
- Biological and Chemical Research Centre, Department of Chemistry , University of Warsaw , ul. Żwirki i Wigury 101 , 02-089 Warszawa , Poland
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12
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Ang SJ, Mak AM, Wong MW. Nature of halogen bonding involving π-systems, nitroxide radicals and carbenes: a highlight of the importance of charge transfer. Phys Chem Chem Phys 2018; 20:26463-26478. [PMID: 30306972 DOI: 10.1039/c8cp04075c] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The recently developed adiabatic absolutely localized molecular orbital energy decomposition analysis (ALMO-EDA) has proven to be useful in determining the effects of different energy components on the geometries of complexes bound by intermolecular interactions. The authors have applied it to systems such as the water dimer, water-ion complexes, metallocenes and lone-pair type halogen-bonded (XB) dimers. In this study, we have extended the second-generation ALMO-EDA method to 40 different XB complexes by benchmarking against its classical counterpart and symmetry-adapted perturbation theory (SAPT). In addition, we have examined the nature of halogen bonding involving less studied XB acceptors, namely π-systems, radicals and carbenes, using the adiabatic ALMO-EDA analyses, particularly to shed light on how each energy component affects the geometries of the XB complexes. Our results show that the second-generation ALMO-EDA predicts a higher electrostatic energy contribution in all XB complexes compared to SAPT and classical ALMO-EDA schemes. On the other hand, when comparing across different XB acceptors, all three partition schemes produced the same qualitative finding. The adiabatic ALMO-EDA analyses indicate that while the inclusion of a charge transfer contribution is important in achieving accurate XB bond lengths and interaction energies, as well as recovering the binding site specificity of XB involving benzene and naphthalene acceptors, it is sufficient to obtain the linearity of the XB complexes in the frozen approximation.
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Affiliation(s)
- Shi Jun Ang
- NUS Graduate School for Integrative Sciences and Engineering, Centre for Life Sciences, #05-01, 28 Medical Drive, Singapore 117456, Singapore. and Institute of High Performance Computing, 1 Fusionopolis Way, #16-16 Connexis North, Singapore 138632, Singapore
| | - Adrian M Mak
- Institute of High Performance Computing, 1 Fusionopolis Way, #16-16 Connexis North, Singapore 138632, Singapore
| | - Ming Wah Wong
- NUS Graduate School for Integrative Sciences and Engineering, Centre for Life Sciences, #05-01, 28 Medical Drive, Singapore 117456, Singapore. and Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543
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13
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Gryn’ova G, Corminboeuf C. Steric "attraction": not by dispersion alone. Beilstein J Org Chem 2018; 14:1482-1490. [PMID: 30013675 PMCID: PMC6037011 DOI: 10.3762/bjoc.14.125] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 06/02/2018] [Indexed: 12/23/2022] Open
Abstract
Non-covalent interactions between neutral, sterically hindered organic molecules generally involve a strong stabilizing contribution from dispersion forces that in many systems turns the 'steric repulsion' into a 'steric attraction'. In addition to London dispersion, such systems benefit from electrostatic stabilization, which arises from a short-range effect of charge penetration and gets bigger with increasing steric bulk. In the present work, we quantify this contribution for a diverse set of molecular cores, ranging from unsubstituted benzene and cyclohexane to their derivatives carrying tert-butyl, phenyl, cyclohexyl and adamantyl substituents. While the importance of electrostatic interactions in the dimers of sp2-rich (e.g., π-conjugated) cores is well appreciated, less polarizable assemblies of sp3-rich systems with multiple short-range CH···HC contacts between the bulky cyclohexyl and adamantyl moieties are also significantly influenced by electrostatics. Charge penetration is drastically larger in absolute terms for the sp2-rich cores, but still has a non-negligible effect on the sp3-rich dimers, investigated herein, both in terms of their energetics and equilibrium interaction distances. These results emphasize the importance of this electrostatic effect, which has so far been less recognized in aliphatic systems compared to London dispersion, and are therefore likely to have implications for the development of force fields and methods for crystal structure prediction.
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Affiliation(s)
- Ganna Gryn’ova
- Institut des Sciences et Ingénierie Chimiques, École polytechnique fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Clémence Corminboeuf
- Institut des Sciences et Ingénierie Chimiques, École polytechnique fédérale de Lausanne, CH-1015 Lausanne, Switzerland
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14
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Albaugh A, Boateng HA, Bradshaw RT, Demerdash ON, Dziedzic J, Mao Y, Margul DT, Swails J, Zeng Q, Case DA, Eastman P, Wang LP, Essex JW, Head-Gordon M, Pande VS, Ponder JW, Shao Y, Skylaris CK, Todorov IT, Tuckerman ME, Head-Gordon T. Advanced Potential Energy Surfaces for Molecular Simulation. J Phys Chem B 2018; 120:9811-32. [PMID: 27513316 DOI: 10.1021/acs.jpcb.6b06414] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Advanced potential energy surfaces are defined as theoretical models that explicitly include many-body effects that transcend the standard fixed-charge, pairwise-additive paradigm typically used in molecular simulation. However, several factors relating to their software implementation have precluded their widespread use in condensed-phase simulations: the computational cost of the theoretical models, a paucity of approximate models and algorithmic improvements that can ameliorate their cost, underdeveloped interfaces and limited dissemination in computational code bases that are widely used in the computational chemistry community, and software implementations that have not kept pace with modern high-performance computing (HPC) architectures, such as multicore CPUs and modern graphics processing units (GPUs). In this Feature Article we review recent progress made in these areas, including well-defined polarization approximations and new multipole electrostatic formulations, novel methods for solving the mutual polarization equations and increasing the MD time step, combining linear-scaling electronic structure methods with new QM/MM methods that account for mutual polarization between the two regions, and the greatly improved software deployment of these models and methods onto GPU and CPU hardware platforms. We have now approached an era where multipole-based polarizable force fields can be routinely used to obtain computational results comparable to state-of-the-art density functional theory while reaching sampling statistics that are acceptable when compared to that obtained from simpler fixed partial charge force fields.
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Affiliation(s)
| | - Henry A Boateng
- Department of Mathematics, Bates College , 2 Andrews Road, Lewiston, Maine 04240, United States
| | - Richard T Bradshaw
- School of Chemistry, University of Southampton , Highfield, Southampton SO17 1BJ, United Kingdom
| | | | - Jacek Dziedzic
- School of Chemistry, University of Southampton , Highfield, Southampton SO17 1BJ, United Kingdom.,Faculty of Applied Physics and Mathematics, Gdansk University of Technology , 80-223 Gdansk, Poland
| | | | | | - Jason Swails
- Department of Chemistry and Chemical Biology, Rutgers University , Piscataway, New Jersey 08854-8066, United States
| | - Qiao Zeng
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health , Bethesda, Maryland 20892, United States
| | - David A Case
- Department of Chemistry and Chemical Biology, Rutgers University , Piscataway, New Jersey 08854-8066, United States
| | - Peter Eastman
- Department of Chemistry, Stanford University , Stanford, California 94305, United States
| | - Lee-Ping Wang
- Department of Chemistry, Stanford University , Stanford, California 94305, United States
| | - Jonathan W Essex
- School of Chemistry, University of Southampton , Highfield, Southampton SO17 1BJ, United Kingdom
| | | | - Vijay S Pande
- Department of Chemistry, Stanford University , Stanford, California 94305, United States
| | - Jay W Ponder
- Department of Chemistry, Washington University in St. Louis , St. Louis, Missouri 63130, United States
| | - Yihan Shao
- Q-Chem Inc. , 6601 Owens Drive, Suite 105, Pleasanton, California 94588, United States
| | - Chris-Kriton Skylaris
- School of Chemistry, University of Southampton , Highfield, Southampton SO17 1BJ, United Kingdom
| | - Ilian T Todorov
- STFC Daresbury Laboratory , Keckwick Lane, Daresbury, Warrington WA4 4AD, United Kingdom
| | - Mark E Tuckerman
- NYU-ECNU, Center for Computational Chemistry at NYU, Shanghai , Shanghai 200062, China
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15
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Nikolaienko TY, Bulavin LA. Atomic charges for conformationally rich molecules obtained through a modified principal component regression. Phys Chem Chem Phys 2018; 20:2890-2903. [PMID: 29327000 DOI: 10.1039/c7cp05703b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A modification of the principal component regression model is proposed for obtaining a fixed set of atomic charges (referred to as dipole-derived charges) optimized for reproducing the dipole moment of a conformationally rich molecule, i.e., a molecule with multiple local minima on the potential energy surface. The method does not require any adjustable parameters and requires the geometries of conformers, their dipole moments and atomic polar tensor (APT) charges as the only input data. The fixed atomic charges generated by the method not only reproduce the molecular dipole moment in all the conformers accurately, but are also numerically close to the APT charges, thereby ensuring accurate reproduction of the dipole moment variations caused by small geometrical distortions (e.g., by vibrations) of the conformers. The proposed method has been applied to canonical 2'-deoxyribonucleotides, the model DNA monomers, and the dipole-derived charges have been shown to outperform both the averaged APT and RESP charges in reproducing the dipole moments of large sets of conformers, thus demonstrating a potential usefulness of the dipole-derived charges as a 'reference point' for modeling polarization effects in conformationally rich molecules.
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Affiliation(s)
- Tymofii Yu Nikolaienko
- Taras Shevchenko National University of Kyiv, Faculty of Physics, 64/13, Volodymyrska Street, City of Kyiv, 01601, Ukraine.
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16
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Rackers JA, Wang Q, Liu C, Piquemal JP, Ren P, Ponder JW. An optimized charge penetration model for use with the AMOEBA force field. Phys Chem Chem Phys 2018; 19:276-291. [PMID: 27901142 DOI: 10.1039/c6cp06017j] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The principal challenge of using classical physics to model biomolecular interactions is capturing the nature of short-range interactions that drive biological processes from nucleic acid base stacking to protein-ligand binding. In particular most classical force fields suffer from an error in their electrostatic models that arises from an ability to account for the overlap between charge distributions occurring when molecules get close to each other, known as charge penetration. In this work we present a simple, physically motivated model for including charge penetration in the AMOEBA (Atomic Multipole Optimized Energetics for Biomolecular Applications) force field. With a function derived from the charge distribution of a hydrogen-like atom and a limited number of parameters, our charge penetration model dramatically improves the description of electrostatics at short range. On a database of 101 biomolecular dimers, the charge penetration model brings the error in the electrostatic interaction energy relative to the ab initio SAPT electrostatic interaction energy from 13.4 kcal mol-1 to 1.3 kcal mol-1. The model is shown not only to be robust and transferable for the AMOEBA model, but also physically meaningful as it universally improves the description of the electrostatic potential around a given molecule.
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Affiliation(s)
- Joshua A Rackers
- Program in Computational & Molecular Biophysics, Washington University, School of Medicine, Saint Louis, Missouri 63110, USA
| | - Qiantao Wang
- 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
| | - Jean-Philip Piquemal
- Laboratoire de Chimie Théorique, Sorbonne Universités, UPMC Paris 06, UMR 7616, case courrier 137, 4 place Jussieu, F-75005, Paris, France
| | - Pengyu Ren
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Jay W Ponder
- Department of Chemistry, Washington University in Saint Louis, Saint Louis, Missouri 63130, USA.
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17
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Ang SJ, Mak AM, Sullivan MB, Wong MW. Site specificity of halogen bonding involving aromatic acceptors. Phys Chem Chem Phys 2018. [DOI: 10.1039/c7cp08343b] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Based on Cambridge structural database survey and quantum chemical studies, aromatic halogen bond (XB) acceptors are found to have unique pattern of XB binding sites and rim specificity.
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Affiliation(s)
- Shi Jun Ang
- NUS Graduate School for Integrative Sciences and Engineering
- Centre for Life Sciences
- Singapore 117456
- Singapore
- Institute of High Performance Computing
| | - Adrian M. Mak
- Institute of High Performance Computing
- Singapore 138632
- Singapore
| | - Michael B. Sullivan
- Institute of High Performance Computing
- Singapore 138632
- Singapore
- Department of Chemistry
- National University of Singapore
| | - Ming Wah Wong
- NUS Graduate School for Integrative Sciences and Engineering
- Centre for Life Sciences
- Singapore 117456
- Singapore
- Department of Chemistry
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18
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Grimme S, Bannwarth C, Caldeweyher E, Pisarek J, Hansen A. A general intermolecular force field based on tight-binding quantum chemical calculations. J Chem Phys 2017; 147:161708. [DOI: 10.1063/1.4991798] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Stefan Grimme
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie der Universität Bonn, Beringstr. 4, D-53115 Bonn,
Germany
| | - Christoph Bannwarth
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie der Universität Bonn, Beringstr. 4, D-53115 Bonn,
Germany
| | - Eike Caldeweyher
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie der Universität Bonn, Beringstr. 4, D-53115 Bonn,
Germany
| | - Jana Pisarek
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie der Universität Bonn, Beringstr. 4, D-53115 Bonn,
Germany
| | - Andreas Hansen
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie der Universität Bonn, Beringstr. 4, D-53115 Bonn,
Germany
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19
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Bojarowski SA, Kumar P, Dominiak PM. Interplay of point multipole moments and charge penetration for intermolecular electrostatic interaction energies from the University at Buffalo pseudoatom databank model of electron density. ACTA CRYSTALLOGRAPHICA SECTION B, STRUCTURAL SCIENCE, CRYSTAL ENGINEERING AND MATERIALS 2017; 73:598-609. [PMID: 28762970 DOI: 10.1107/s2052520617005510] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 04/12/2017] [Indexed: 06/07/2023]
Abstract
The strength of the University at Buffalo DataBank (UBDB) in Ees estimation is mainly due to charge overlap effects because the UBDB offers continuous representation of charge density which allows for a direct account of charge penetration in the derivation of electrostatic energies. In the UBDB model, these effects begin to play an important role at distances below twice the equilibrium distance and significantly increase as distances decrease. At equilibrium distances they are responsible for 30-50% of Ees for polar molecules and around 90% of Ees for nonpolar molecules. When the energy estimation from the UBDB is reduced to point multipoles, the results are comparable to point charges fitted to electrostatic potentials. On the other hand, particular components of energy from point multipole moments from the UBDB model are sensitive to the type of interaction and might be helpful in the characterization of interactions.
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Affiliation(s)
- Sławomir A Bojarowski
- Biological and Chemical Research Center, Department of Chemistry, University of Warsaw, ul. Zwirki i Wigury 101, 02-089 Warszawa, Poland
| | - Prashant Kumar
- Biological and Chemical Research Center, Department of Chemistry, University of Warsaw, ul. Zwirki i Wigury 101, 02-089 Warszawa, Poland
| | - Paulina M Dominiak
- Biological and Chemical Research Center, Department of Chemistry, University of Warsaw, ul. Zwirki i Wigury 101, 02-089 Warszawa, Poland
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20
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Brückner C, Stolte M, Würthner F, Pflaum J, Engels B. QM/MM calculations combined with the dimer approach on the static disorder at organic-organic interfaces of thin-film organic solar cells composed of small molecules. J PHYS ORG CHEM 2017. [DOI: 10.1002/poc.3740] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Charlotte Brückner
- Institut für Theoretische Chemie, Universität Würzburg; Würzburg Germany
| | - Matthias Stolte
- Universität Würzburg, Institut für Organische Chemie and Center for Nanosystems Chemistry; Würzburg Germany
| | - Frank Würthner
- Universität Würzburg, Institut für Organische Chemie and Center for Nanosystems Chemistry; Würzburg Germany
| | - Jens Pflaum
- Experimentelle Physik VI; Universität Würzburg; Würzburg Germany
- Bayerisches Zentrum für Angewandte Energieforschung (ZAE Bayern e.V.); Würzburg Germany
| | - Bernd Engels
- Institut für Theoretische Chemie, Universität Würzburg; Würzburg Germany
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21
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Nikolaienko TY. Interaction of anticancer drug doxorubicin with sodium oleate bilayer: Insights from molecular dynamics simulations. J Mol Liq 2017. [DOI: 10.1016/j.molliq.2016.11.065] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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22
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Mao Y, Shao Y, Dziedzic J, Skylaris CK, Head-Gordon T, Head-Gordon M. Performance of the AMOEBA Water Model in the Vicinity of QM Solutes: A Diagnosis Using Energy Decomposition Analysis. J Chem Theory Comput 2017; 13:1963-1979. [PMID: 28430427 DOI: 10.1021/acs.jctc.7b00089] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The importance of incorporating solvent polarization effects into the modeling of solvation processes has been well-recognized, and therefore a new generation of hybrid quantum mechanics/molecular mechanics (QM/MM) approaches that accounts for this effect is desirable. We present a fully self-consistent, mutually polarizable QM/MM scheme using the AMOEBA force field, in which the total energy of the system is variationally minimized with respect to both the QM electronic density and the MM induced dipoles. This QM/AMOEBA model is implemented through the Q-Chem/LibEFP code interface and then applied to the evaluation of solute-solvent interaction energies for various systems ranging from the water dimer to neutral and ionic solutes (NH3, NH4+, CN-) surrounded by increasing numbers of water molecules (up to 100). In order to analyze the resulting interaction energies, we also utilize an energy decomposition analysis (EDA) scheme which identifies contributions from permanent electrostatics, polarization, and van der Waals (vdW) interaction for the interaction between the QM solute and the solvent molecules described by AMOEBA. This facilitates a component-wise comparison against full QM calculations where the corresponding energy components are obtained via a modified version of the absolutely localized molecular orbitals (ALMO)-EDA. The results show that the present QM/AMOEBA model can yield reasonable solute-solvent interaction energies for neutral and cationic species, while further scrutiny reveals that this accuracy highly relies on the delicate balance between insufficiently favorable permanent electrostatics and softened vdW interaction. For anionic solutes where the charge penetration effect becomes more pronounced, the QM/MM interface turns out to be unbalanced. These results are consistent with and further elucidate our findings in a previous study using a slightly different QM/AMOEBA model ( Dziedzic et al. J. Chem. Phys. 2016 , 145 , 124106 ). The implications of these results for further refinement of this model are also discussed.
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Affiliation(s)
| | - Yihan Shao
- Department of Chemistry and Biochemistry, University of Oklahoma , Norman, Oklahoma 73019, United States
| | - Jacek Dziedzic
- School of Chemistry, University of Southampton , Highfield, Southampton SO17 1BJ, U.K.,Faculty of Applied Physics and Mathematics, Gdańsk University of Technology , Gdańsk 80-233, Poland
| | - Chris-Kriton Skylaris
- School of Chemistry, University of Southampton , Highfield, Southampton SO17 1BJ, U.K
| | | | - Martin Head-Gordon
- Chemical Science Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
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23
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Fletcher TL, Popelier PLA. Toward amino acid typing for proteins in FFLUX. J Comput Chem 2017; 38:336-345. [PMID: 27991680 PMCID: PMC6681421 DOI: 10.1002/jcc.24686] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Revised: 11/14/2016] [Accepted: 11/14/2016] [Indexed: 01/18/2023]
Abstract
Continuing the development of the FFLUX, a multipolar polarizable force field driven by machine learning, we present a modern approach to atom-typing and building transferable models for predicting atomic properties in proteins. Amino acid atomic charges in a peptide chain respond to the substitution of a neighboring residue and this response can be categorized in a manner similar to atom-typing. Using a machine learning method called kriging, we are able to build predictive models for an atom that is defined, not only by its local environment, but also by its neighboring residues, for a minimal additional computational cost. We found that prediction errors were up to 11 times lower when using a model specific to the correct group of neighboring residues, with a mean prediction of ∼0.0015 au. This finding suggests that atoms in a force field should be defined by more than just their immediate atomic neighbors. When comparing an atom in a single alanine to an analogous atom in a deca-alanine helix, the mean difference in charge is 0.026 au. Meanwhile, the same difference between a trialanine and a deca-alanine helix is only 0.012 au. When compared to deca-alanine models, the transferable models are up to 20 times faster to train, and require significantly less ab initio calculation, providing a practical route to modeling large biological systems. © 2016 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.
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Affiliation(s)
- Timothy L. Fletcher
- Manchester Institute of Biotechnology (MIB), 131 Princess StreetManchesterM1 7DNUnited Kingdom
| | - Paul L. A. Popelier
- School of ChemistryUniversity of Manchester, Oxford RoadManchesterM13 9PLUnited Kingdom
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24
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Engels B, Engel V. The dimer-approach to characterize opto-electronic properties of and exciton trapping and diffusion in organic semiconductor aggregates and crystals. Phys Chem Chem Phys 2017; 19:12604-12619. [DOI: 10.1039/c7cp01599b] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
We present the recently developed dimer approach which seems to include all main effects determining the photo-physics of organic semiconductor aggregates.
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Affiliation(s)
- Bernd Engels
- Universität Würzburg
- Institut für Physikalische und Theoretische Chemie
- Am Hubland
- 97074 Würzburg
- Germany
| | - Volker Engel
- Universität Würzburg
- Institut für Physikalische und Theoretische Chemie
- Am Hubland
- 97074 Würzburg
- Germany
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25
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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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26
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Demerdash O, Head-Gordon T. Parallel implementation of approximate atomistic models of the AMOEBA polarizable model. Chem Phys Lett 2016. [DOI: 10.1016/j.cplett.2016.10.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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27
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Mao Y, Demerdash O, Head-Gordon M, Head-Gordon T. Assessing Ion-Water Interactions in the AMOEBA Force Field Using Energy Decomposition Analysis of Electronic Structure Calculations. J Chem Theory Comput 2016; 12:5422-5437. [PMID: 27709939 DOI: 10.1021/acs.jctc.6b00764] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
AMOEBA is a molecular mechanics force field that addresses some of the shortcomings of a fixed partial charge model, by including permanent atomic point multipoles through quadrupoles, as well as many-body polarization through the use of point inducible dipoles. In this work, we investigate how well AMOEBA formulates its non-bonded interactions, and how it implicitly incorporates quantum mechanical effects such as charge penetration (CP) and charge transfer (CT), for water-water and water-ion interactions. We find that AMOEBA's total interaction energies, as a function of distance and over angular scans for the water dimer and for a range of water-monovalent cations, agree well with an advanced density functional theory (DFT) model, whereas the water-halides and water-divalent cations show significant disagreement with the DFT result, especially in the compressed region when the two fragments overlap. We use a second-generation energy decomposition analysis (EDA) scheme based on absolutely localized molecular orbitals (ALMOs) to show that in the best cases AMOEBA relies on cancellation of errors by softening of the van der Waals (vdW) wall to balance permanent electrostatics that are too unfavorable, thereby compensating for the missing CP effect. CT, as another important stabilizing effect not explicitly taken into account in AMOEBA, is also found to be incorporated by the softened vdW interaction. For the water-halides and water-divalent cations, this compensatory approach is not as well executed by AMOEBA over all distances and angles, wherein permanent electrostatics remains too unfavorable and polarization is overdamped in the former while overestimated in the latter. We conclude that the DFT-based EDA approach can help refine a next-generation AMOEBA model that either realizes a better cancellation of errors for problematic cases like those illustrated here, or serves to guide the parametrization of explicit functional forms for short-range contributions from CP and/or CT.
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Affiliation(s)
- Yuezhi Mao
- Kenneth S. Pitzer Center for Theoretical Chemistry, and Department of Chemistry, University of California at Berkeley , Berkeley, California 94720, United States
| | - Omar Demerdash
- Kenneth S. Pitzer Center for Theoretical Chemistry, and Department of Chemistry, University of California at Berkeley , Berkeley, California 94720, United States
| | - Martin Head-Gordon
- Kenneth S. Pitzer Center for Theoretical Chemistry, and Department of Chemistry, University of California at Berkeley , Berkeley, California 94720, United States
| | - Teresa Head-Gordon
- Kenneth S. Pitzer Center for Theoretical Chemistry, and Department of Chemistry, University of California at Berkeley , Berkeley, California 94720, United States.,Department of Bioengineering, and Department of Chemical and Biomolecular Engineering, University of California at Berkeley , Berkeley, California 94720, United States
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28
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Qi R, Wang Q, Ren P. General van der Waals potential for common organic molecules. Bioorg Med Chem 2016; 24:4911-4919. [PMID: 27519463 DOI: 10.1016/j.bmc.2016.07.062] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Revised: 07/27/2016] [Accepted: 07/28/2016] [Indexed: 11/18/2022]
Abstract
This work presents a systematic development of a new van der Waals potential (vdW2016) for common organic molecules based on symmetry-adapted perturbation theory (SAPT) energy decomposition. The Buf-14-7 function, as well as Cubic-mean and Waldman-Hagler mixing rules were chosen given their best performance among other popular potentials. A database containing 39 organic molecules and 108 dimers was utilized to derive a general set of vdW parameters, which were further validated on nucleobase stacking systems and testing organic dimers. The vdW2016 potential is anticipated to significantly improve the accuracy and transferability of new generations of force fields for organic molecules.
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Affiliation(s)
- Rui Qi
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX 78712, United States
| | - Qiantao Wang
- West China School of Pharmacy, Sichuan University, Chengdu 610041, China
| | - Pengyu Ren
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX 78712, United States.
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29
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30
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Verstraelen T, Vandenbrande S, Heidar-Zadeh F, Vanduyfhuys L, Van Speybroeck V, Waroquier M, Ayers PW. Minimal Basis Iterative Stockholder: Atoms in Molecules for Force-Field Development. J Chem Theory Comput 2016; 12:3894-912. [DOI: 10.1021/acs.jctc.6b00456] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Toon Verstraelen
- Center
for Molecular Modeling (CMM), Member of the QCMM Ghent−Brussels
Alliance, Ghent University, Technologiepark 903, B9000 Ghent, Belgium
| | - Steven Vandenbrande
- Center
for Molecular Modeling (CMM), Member of the QCMM Ghent−Brussels
Alliance, Ghent University, Technologiepark 903, B9000 Ghent, Belgium
| | - Farnaz Heidar-Zadeh
- Department
of Chemistry and Chemical Biology, McMaster University, 1280 West
Main Street, Hamilton, Ontario L8S 4M1, Canada
| | - Louis Vanduyfhuys
- Center
for Molecular Modeling (CMM), Member of the QCMM Ghent−Brussels
Alliance, Ghent University, Technologiepark 903, B9000 Ghent, Belgium
| | - Veronique Van Speybroeck
- Center
for Molecular Modeling (CMM), Member of the QCMM Ghent−Brussels
Alliance, Ghent University, Technologiepark 903, B9000 Ghent, Belgium
| | - Michel Waroquier
- Center
for Molecular Modeling (CMM), Member of the QCMM Ghent−Brussels
Alliance, Ghent University, Technologiepark 903, B9000 Ghent, Belgium
| | - Paul W. Ayers
- Department
of Chemistry and Chemical Biology, McMaster University, 1280 West
Main Street, Hamilton, Ontario L8S 4M1, Canada
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31
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Bojarowski SA, Kumar P, Dominiak PM. A Universal and Straightforward Approach to Include Penetration Effects in Electrostatic Interaction Energy Estimation. Chemphyschem 2016; 17:2455-60. [PMID: 27166026 DOI: 10.1002/cphc.201600390] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Indexed: 12/23/2022]
Abstract
To compensate for the lack of the explicit treatment of charge penetration in classical force fields, we propose a new charge-distribution model based on a promolecule augmented with point charges (aug-PROmol). It relies on a superposition of spherical atomic electron densities obtained for each chemical element from SCF energy optimized atomic orbitals. Atomic densities are further rescaled by partial point charges computed from fits to the molecular electrostatic potential. Aug-PROmol was tested on the S66 benchmark dataset extended to nonequilibrium geometries (J. Chem. Theory Comput., 2011, 7, 3466). The model does not need any additional parametrization other than point charges. Despite its simplicity, aug-PROmol approximates the electrostatic energy with good agreement (RMSE=0.76 kcal mol(-1) to DFT-SAPT with B3LYP/aug-cc-pVTZ).
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Affiliation(s)
- Sławomir A Bojarowski
- Department of Chemistry, Biological and Chemical Research Centre, University of Warsaw, ul. Żwirki i Wigury 101, 02-089, Warszawa, Poland
| | - Prashant Kumar
- Department of Chemistry, Biological and Chemical Research Centre, University of Warsaw, ul. Żwirki i Wigury 101, 02-089, Warszawa, Poland
| | - Paulina M Dominiak
- Department of Chemistry, Biological and Chemical Research Centre, University of Warsaw, ul. Żwirki i Wigury 101, 02-089, Warszawa, Poland.
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32
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Fletcher TL, Popelier PLA. Multipolar Electrostatic Energy Prediction for all 20 Natural Amino Acids Using Kriging Machine Learning. J Chem Theory Comput 2016; 12:2742-51. [DOI: 10.1021/acs.jctc.6b00457] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Timothy L. Fletcher
- Manchester Institute of Biotechnology (MIB), 131 Princess Street, Manchester M1 7DN, Great Britain
- School
of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, Great Britain
| | - Paul L. A. Popelier
- Manchester Institute of Biotechnology (MIB), 131 Princess Street, Manchester M1 7DN, Great Britain
- School
of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, Great Britain
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33
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Tafipolsky M, Ansorg K. Toward a Physically Motivated Force Field: Hydrogen Bond Directionality from a Symmetry-Adapted Perturbation Theory Perspective. J Chem Theory Comput 2016; 12:1267-79. [DOI: 10.1021/acs.jctc.5b01057] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Maxim Tafipolsky
- Institut
für Physikalische
und Theoretische Chemie, Universität Würzburg, Campus
Hubland Nord, Emil-Fischer-Strasse 42, D-97074 Würzburg, Germany
| | - Kay Ansorg
- Institut
für Physikalische
und Theoretische Chemie, Universität Würzburg, Campus
Hubland Nord, Emil-Fischer-Strasse 42, D-97074 Würzburg, Germany
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34
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Fletcher TL, Davie SJ, Popelier PLA. Prediction of Intramolecular Polarization of Aromatic Amino Acids Using Kriging Machine Learning. J Chem Theory Comput 2015; 10:3708-19. [PMID: 26588516 DOI: 10.1021/ct500416k] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Present computing power enables novel ways of modeling polarization. Here we show that the machine learning method kriging accurately captures the way the electron density of a topological atom responds to a change in the positions of the surrounding atoms. The success of this method is demonstrated on the four aromatic amino acids histidine, phenylalanine, tryptophan, and tyrosine. A new technique of varying training set sizes to vastly reduce training times while maintaining accuracy is described and applied to each amino acid. Each amino acid has its geometry distorted via normal modes of vibration over all local energy minima in the Ramachandran map. These geometries are then used to train the kriging models. Total electrostatic energies predicted by the kriging models for previously unseen geometries are compared to the true energies, yielding mean absolute errors of 2.9, 5.1, 4.2, and 2.8 kJ mol(-1) for histidine, phenylalanine, tryptophan, and tyrosine, respectively.
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Affiliation(s)
- Timothy L Fletcher
- Manchester Institute of Biotechnology (MIB) , 131 Princess Street, Manchester, M1 7DN, Great Britain.,School of Chemistry, University of Manchester , Oxford Road, Manchester, M13 9PL, Great Britain
| | - Stuart J Davie
- Manchester Institute of Biotechnology (MIB) , 131 Princess Street, Manchester, M1 7DN, Great Britain.,School of Chemistry, University of Manchester , Oxford Road, Manchester, M13 9PL, Great Britain
| | - Paul L A Popelier
- Manchester Institute of Biotechnology (MIB) , 131 Princess Street, Manchester, M1 7DN, Great Britain.,School of Chemistry, University of Manchester , Oxford Road, Manchester, M13 9PL, Great Britain
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35
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Wang B, Truhlar DG. Screened Electrostatic Interactions in Molecular Mechanics. J Chem Theory Comput 2015; 10:4480-7. [PMID: 26588144 DOI: 10.1021/ct5005142] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
In a typical application of molecular mechanics (MM), the electrostatic interactions are calculated from parametrized partial atomic charges treated as point charges interacting by radial Coulomb potentials. This does not usually yield accurate electrostatic interactions at van der Waals distances, but this is compensated by additional parametrized terms, for example Lennard-Jones potentials. In the present work, we present a scheme involving radial screened Coulomb potentials that reproduces the accurate electrostatics much more accurately. The screening accounts for charge penetration of one subsystem's charge cloud into that of another subsystem, and it is incorporated into the interaction potential in a way similar to what we proposed in a previous article (J. Chem. Theory Comput. 2010, 6, 3330) for combined quantum mechanical and molecular mechanical (QM/MM) simulations, but the screening parameters are reoptimized for MM. The optimization is carried out with electrostatic-potential-fitted partial atomic charges, but the optimized parameters should be useful with any realistic charge model. In the model we employ, the charge density of an atom is approximated as the sum of a point charge representing the nucleus and inner electrons and a smeared charge representing the outermost electrons; in particular, for all atoms except hydrogens, the smeared charge represents the two outermost electrons in the present model. We find that the charge penetration effect can cause very significant deviations from the popular point-charge model, and by comparison to electrostatic interactions calculated by symmetry-adapted perturbation theory, we find that the present results are considerably more accurate than point-charge electrostatic interactions. The mean unsigned error in electrostatics for a large and diverse data set (192 interaction energies) decreases from 9.2 to 3.3 kcal/mol, and the error in the electrostatics for 10 water dimers decreases from 1.7 to 0.5 kcal/mol. We could have decreased the average errors further, but at the cost of sometimes significantly overestimating the screening; instead we chose a more conservative (safer) parametrization that systematically underestimates the screening (which by definition means it improves over point charges) and only occasionally overestimates it. Despite this conservative choice, we find that the screened MM method is even more accurate for the electrostatics than unscreened QM/MM calculations. This new method is easy to implement in any MM program, and it can be used to develop more physical force fields for molecular simulations.
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Affiliation(s)
- Bo Wang
- Department of Chemistry, Chemical Theory Center, and Supercomputing Institute, University of Minnesota , 207 Pleasant Street SE, Minneapolis, Minnesota 55455-0431, United States
| | - Donald G Truhlar
- Department of Chemistry, Chemical Theory Center, and Supercomputing Institute, University of Minnesota , 207 Pleasant Street SE, Minneapolis, Minnesota 55455-0431, United States
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36
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Zgarbová M, Rosnik AM, Luque FJ, Curutchet C, Jurečka P. Transferability and additivity of dihedral parameters in polarizable and nonpolarizable empirical force fields. J Comput Chem 2015. [DOI: 10.1002/jcc.24012] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Marie Zgarbová
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science; Palacky University; 17. listopadu 12 Olomouc 77146 Czech Republic
| | - Andreana M. Rosnik
- Department de Fisicoquímica; Facultat de Farmàcia, Universitat de Barcelona; Av. Joan XXIII s/n Barcelona 08028 Spain
| | - F. Javier Luque
- Department de Fisicoquímica and Institut de Biomedicina (IBUB); Facultat de Farmàcia, Universitat de Barcelona; Avgda Prat de la Riba 171, Santa Coloma de Gramenet 08921 Spain
| | - Carles Curutchet
- Department de Fisicoquímica; Facultat de Farmàcia, Universitat de Barcelona; Av. Joan XXIII s/n Barcelona 08028 Spain
| | - Petr Jurečka
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science; Palacky University; 17. listopadu 12 Olomouc 77146 Czech Republic
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37
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Konieczny JK, Sokalski WA. Universal short-range ab initio atom–atom potentials for interaction energy contributions with an optimal repulsion functional form. J Mol Model 2015; 21:197. [DOI: 10.1007/s00894-015-2729-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2015] [Accepted: 06/08/2015] [Indexed: 11/28/2022]
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38
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Wang Q, Rackers JA, He C, Qi R, Narth C, Lagardere L, Gresh N, Ponder JW, Piquemal JP, Ren P. General Model for Treating Short-Range Electrostatic Penetration in a Molecular Mechanics Force Field. J Chem Theory Comput 2015; 11:2609-2618. [PMID: 26413036 PMCID: PMC4570253 DOI: 10.1021/acs.jctc.5b00267] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Indexed: 11/30/2022]
Abstract
Classical molecular mechanics force fields typically model interatomic electrostatic interactions with point charges or multipole expansions, which can fail for atoms in close contact due to the lack of a description of penetration effects between their electron clouds. These short-range penetration effects can be significant and are essential for accurate modeling of intermolecular interactions. In this work we report parametrization of an empirical charge-charge function previously reported (Piquemal J.-P.; J. Phys. Chem. A2003, 107, 10353) to correct for the missing penetration term in standard molecular mechanics force fields. For this purpose, we have developed a database (S101×7) of 101 unique molecular dimers, each at 7 different intermolecular distances. Electrostatic, induction/polarization, repulsion, and dispersion energies, as well as the total interaction energy for each complex in the database are calculated using the SAPT2+ method (Parker T. M.; J. Chem. Phys.2014, 140, 094106). This empirical penetration model significantly improves agreement between point multipole and quantum mechanical electrostatic energies across the set of dimers and distances, while using only a limited set of parameters for each chemical element. Given the simplicity and effectiveness of the model, we expect the electrostatic penetration correction will become a standard component of future molecular mechanics force fields.
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Affiliation(s)
- Qiantao Wang
- Department of Biomedical Engineering and Division of Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin , Austin, Texas 78712, United States ; Department of Biomedical Engineering and Division of Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin , Austin, Texas 78712, United States
| | - Joshua A Rackers
- Computational and Molecular Biophysics Program, Division of Biology & Biomedical Sciences, Washington University in St. Louis , St. Louis, Missouri 63110, United States
| | - Chenfeng He
- Department of Biomedical Engineering and Division of Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin , Austin, Texas 78712, United States
| | - Rui Qi
- Department of Biomedical Engineering and Division of Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin , Austin, Texas 78712, United States
| | - Christophe Narth
- Laboratoire de Chimie Théorique, Sorbonne Universités, UPMC Paris 06, UMR 7616 , Case Courrier 137, 4 Place Jussieu, F-75005 Paris, France
| | - Louis Lagardere
- Laboratoire de Chimie Théorique, Sorbonne Universités, UPMC Paris 06, UMR 7616 , Case Courrier 137, 4 Place Jussieu, F-75005 Paris, France
| | - Nohad Gresh
- Laboratoire de Chimie Théorique, Sorbonne Universités, UPMC Paris 06, UMR 7616 , Case Courrier 137, 4 Place Jussieu, F-75005 Paris, France
| | - Jay W Ponder
- Department of Chemistry, Washington University in St. Louis , St. Louis, Missouri 63130, United States
| | - Jean-Philip Piquemal
- Laboratoire de Chimie Théorique, Sorbonne Universités, UPMC Paris 06, UMR 7616 , Case Courrier 137, 4 Place Jussieu, F-75005 Paris, France
| | - Pengyu Ren
- Department of Biomedical Engineering and Division of Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin , Austin, Texas 78712, United States
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39
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Laury ML, Wang LP, Pande VS, Head-Gordon T, Ponder JW. Revised Parameters for the AMOEBA Polarizable Atomic Multipole Water Model. J Phys Chem B 2015; 119:9423-9437. [PMID: 25683601 DOI: 10.1021/jp510896n] [Citation(s) in RCA: 154] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
A set of improved parameters for the AMOEBA polarizable atomic multipole water model is developed. An automated procedure, ForceBalance, is used to adjust model parameters to enforce agreement with ab initio-derived results for water clusters and experimental data for a variety of liquid phase properties across a broad temperature range. The values reported here for the new AMOEBA14 water model represent a substantial improvement over the previous AMOEBA03 model. The AMOEBA14 model accurately predicts the temperature of maximum density and qualitatively matches the experimental density curve across temperatures from 249 to 373 K. Excellent agreement is observed for the AMOEBA14 model in comparison to experimental properties as a function of temperature, including the second virial coefficient, enthalpy of vaporization, isothermal compressibility, thermal expansion coefficient, and dielectric constant. The viscosity, self-diffusion constant, and surface tension are also well reproduced. In comparison to high-level ab initio results for clusters of 2-20 water molecules, the AMOEBA14 model yields results similar to AMOEBA03 and the direct polarization iAMOEBA models. With advances in computing power, calibration data, and optimization techniques, we recommend the use of the AMOEBA14 water model for future studies employing a polarizable water model.
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Affiliation(s)
- Marie L Laury
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63105
| | - Lee-Ping Wang
- Department of Chemistry, Stanford University, Stanford, CA 94305
| | - Vijay S Pande
- Department of Chemistry, Stanford University, Stanford, CA 94305
| | | | - Jay W Ponder
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63105
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40
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Grimme S. A General Quantum Mechanically Derived Force Field (QMDFF) for Molecules and Condensed Phase Simulations. J Chem Theory Comput 2014; 10:4497-514. [DOI: 10.1021/ct500573f] [Citation(s) in RCA: 134] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Stefan Grimme
- Mulliken Center for Theoretical
Chemistry, Institut für Physikalische und Theoretische Chemie der Universität Bonn, Beringstr. 4, D-53115 Bonn, Germany
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41
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Grebner C, Becker J, Weber D, Bellinger D, Tafipolski M, Brückner C, Engels B. CAST: A new program package for the accurate characterization of large and flexible molecular systems. J Comput Chem 2014; 35:1801-7. [DOI: 10.1002/jcc.23687] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2014] [Revised: 06/13/2014] [Accepted: 06/19/2014] [Indexed: 01/03/2023]
Affiliation(s)
- Christoph Grebner
- Julius-Maximilians-Universität Würzburg, Institut für Physikalische und Theoretische Chemie; Emil-Fischer-Straße 42 97074 Würzburg Germany
| | - Johannes Becker
- Julius-Maximilians-Universität Würzburg, Institut für Physikalische und Theoretische Chemie; Emil-Fischer-Straße 42 97074 Würzburg Germany
| | - Daniel Weber
- Julius-Maximilians-Universität Würzburg, Institut für Physikalische und Theoretische Chemie; Emil-Fischer-Straße 42 97074 Würzburg Germany
| | - Daniel Bellinger
- Julius-Maximilians-Universität Würzburg, Institut für Physikalische und Theoretische Chemie; Emil-Fischer-Straße 42 97074 Würzburg Germany
| | - Maxim Tafipolski
- Julius-Maximilians-Universität Würzburg, Institut für Physikalische und Theoretische Chemie; Emil-Fischer-Straße 42 97074 Würzburg Germany
| | - Charlotte Brückner
- Julius-Maximilians-Universität Würzburg, Institut für Physikalische und Theoretische Chemie; Emil-Fischer-Straße 42 97074 Würzburg Germany
| | - Bernd Engels
- Julius-Maximilians-Universität Würzburg, Institut für Physikalische und Theoretische Chemie; Emil-Fischer-Straße 42 97074 Würzburg Germany
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42
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Settels V, Schubert A, Tafipolski M, Liu W, Stehr V, Topczak AK, Pflaum J, Deibel C, Fink RF, Engel V, Engels B. Identification of Ultrafast Relaxation Processes As a Major Reason for Inefficient Exciton Diffusion in Perylene-Based Organic Semiconductors. J Am Chem Soc 2014; 136:9327-37. [DOI: 10.1021/ja413115h] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Volker Settels
- Institut
für Physikalische und Theoretische Chemie, Universität Würzburg, Emil-Fischer-Str. 42, 97074 Würzburg, Germany
| | - Alexander Schubert
- Institut
für Physikalische und Theoretische Chemie, Universität Würzburg, Emil-Fischer-Str. 42, 97074 Würzburg, Germany
| | - Maxim Tafipolski
- Institut
für Physikalische und Theoretische Chemie, Universität Würzburg, Emil-Fischer-Str. 42, 97074 Würzburg, Germany
| | - Wenlan Liu
- Institut
für Physikalische und Theoretische Chemie, Universität Würzburg, Emil-Fischer-Str. 42, 97074 Würzburg, Germany
| | - Vera Stehr
- Lehrstuhl
für Experimentelle Physik VI, Universität Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Anna K. Topczak
- Lehrstuhl
für Experimentelle Physik VI, Universität Würzburg, Am Hubland, 97074 Würzburg, Germany
- ZAE Bayern e.V., Am Galgenberg 87, 97074 Würzburg, Germany
| | - Jens Pflaum
- Lehrstuhl
für Experimentelle Physik VI, Universität Würzburg, Am Hubland, 97074 Würzburg, Germany
- ZAE Bayern e.V., Am Galgenberg 87, 97074 Würzburg, Germany
| | - Carsten Deibel
- Lehrstuhl
für Experimentelle Physik VI, Universität Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Reinhold F. Fink
- Institut
für Physikalische und Theoretische Chemie, Universität Würzburg, Emil-Fischer-Str. 42, 97074 Würzburg, Germany
| | - Volker Engel
- Institut
für Physikalische und Theoretische Chemie, Universität Würzburg, Emil-Fischer-Str. 42, 97074 Würzburg, Germany
| | - Bernd Engels
- Institut
für Physikalische und Theoretische Chemie, Universität Würzburg, Emil-Fischer-Str. 42, 97074 Würzburg, Germany
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43
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Zhou N, Lu Z, Wu Q, Zhang Y. Improved parameterization of interatomic potentials for rare gas dimers with density-based energy decomposition analysis. J Chem Phys 2014; 140:214117. [PMID: 24908000 PMCID: PMC4048451 DOI: 10.1063/1.4881255] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Accepted: 05/21/2014] [Indexed: 11/14/2022] Open
Abstract
We examine interatomic interactions for rare gas dimers using the density-based energy decomposition analysis (DEDA) in conjunction with computational results from CCSD(T) at the complete basis set (CBS) limit. The unique DEDA capability of separating frozen density interactions from density relaxation contributions is employed to yield clean interaction components, and the results are found to be consistent with the typical physical picture that density relaxations play a very minimal role in rare gas interactions. Equipped with each interaction component as reference, we develop a new three-term molecular mechanical force field to describe rare gas dimers: a smeared charge multipole model for electrostatics with charge penetration effects, a B3LYP-D3 dispersion term for asymptotically correct long-range attractions that is screened at short-range, and a Born-Mayer exponential function for the repulsion. The resulted force field not only reproduces rare gas interaction energies calculated at the CCSD(T)/CBS level, but also yields each interaction component (electrostatic or van der Waals) which agrees very well with its corresponding reference value.
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Affiliation(s)
- Nengjie Zhou
- Department of Chemistry, New York University, New York, New York 10003, USA
| | - Zhenyu Lu
- Department of Chemistry, New York University, New York, New York 10003, USA
| | - Qin Wu
- Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, New York 11973, USA
| | - Yingkai Zhang
- Department of Chemistry, New York University, New York, New York 10003, USA
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44
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Mu X, Wang Q, Wang LP, Fried SD, Piquemal JP, Dalby KN, Ren P. Modeling organochlorine compounds and the σ-hole effect using a polarizable multipole force field. J Phys Chem B 2014; 118:6456-65. [PMID: 24484473 PMCID: PMC4065202 DOI: 10.1021/jp411671a] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
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The charge distribution of halogen
atoms on organochlorine compounds
can be highly anisotropic and even display a so-called σ-hole,
which leads to strong halogen bonds with electron donors. In this
paper, we have systematically investigated a series of chloromethanes
with one to four chloro substituents using a polarizable multipole-based
molecular mechanics model. The atomic multipoles accurately reproduced
the ab initio electrostatic potential around chloromethanes, including
CCl4, which has a prominent σ-hole on the Cl atom.
The van der Waals parameters for Cl were fitted to the experimental
density and heat of vaporization. The calculated hydration free energy,
solvent reaction fields, and interaction energies of several homo-
and heterodimer of chloromethanes are in good agreement with experimental
and ab initio data. This study suggests that sophisticated electrostatic
models, such as polarizable atomic multipoles, are needed for accurate
description of electrostatics in organochlorine compounds and halogen
bonds, although further improvement is necessary for better transferability.
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Affiliation(s)
- Xiaojiao Mu
- Department of Biomedical Engineering, ‡Division of Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin , Texas 78712, United States
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45
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Cisneros GA, Karttunen M, Ren P, Sagui C. Classical electrostatics for biomolecular simulations. Chem Rev 2014; 114:779-814. [PMID: 23981057 PMCID: PMC3947274 DOI: 10.1021/cr300461d] [Citation(s) in RCA: 192] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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46
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Schmidt TC, Paasche A, Grebner C, Ansorg K, Becker J, Lee W, Engels B. QM/MM investigations of organic chemistry oriented questions. Top Curr Chem (Cham) 2014; 351:25-101. [PMID: 22392477 DOI: 10.1007/128_2011_309] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
About 35 years after its first suggestion, QM/MM became the standard theoretical approach to investigate enzymatic structures and processes. The success is due to the ability of QM/MM to provide an accurate atomistic picture of enzymes and related processes. This picture can even be turned into a movie if nuclei-dynamics is taken into account to describe enzymatic processes. In the field of organic chemistry, QM/MM methods are used to a much lesser extent although almost all relevant processes happen in condensed matter or are influenced by complicated interactions between substrate and catalyst. There is less importance for theoretical organic chemistry since the influence of nonpolar solvents is rather weak and the effect of polar solvents can often be accurately described by continuum approaches. Catalytic processes (homogeneous and heterogeneous) can often be reduced to truncated model systems, which are so small that pure quantum-mechanical approaches can be employed. However, since QM/MM becomes more and more efficient due to the success in software and hardware developments, it is more and more used in theoretical organic chemistry to study effects which result from the molecular nature of the environment. It is shown by many examples discussed in this review that the influence can be tremendous, even for nonpolar reactions. The importance of environmental effects in theoretical spectroscopy was already known. Due to its benefits, QM/MM can be expected to experience ongoing growth for the next decade.In the present chapter we give an overview of QM/MM developments and their importance in theoretical organic chemistry, and review applications which give impressions of the possibilities and the importance of the relevant effects. Since there is already a bunch of excellent reviews dealing with QM/MM, we will discuss fundamental ingredients and developments of QM/MM very briefly with a focus on very recent progress. For the applications we follow a similar strategy.
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Affiliation(s)
- Thomas C Schmidt
- Institut für Phys. und Theor. Chemie, Emil-Fischer-Strasse 42, Campus Hubland Nord, 97074, Würzburg, Germany
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48
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Ansorg K, Tafipolsky M, Engels B. Cation−π Interactions: Accurate Intermolecular Potential from Symmetry-Adapted Perturbation Theory. J Phys Chem B 2013; 117:10093-102. [DOI: 10.1021/jp403578r] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Kay Ansorg
- Institut
für Physikalische und Theoretische
Chemie, Universität Würzburg, Campus Hubland Nord, Emil-Fischer-Strasse 42, D-97074 Würzburg,
Germany
| | - Maxim Tafipolsky
- Institut
für Physikalische und Theoretische
Chemie, Universität Würzburg, Campus Hubland Nord, Emil-Fischer-Strasse 42, D-97074 Würzburg,
Germany
| | - Bernd Engels
- Institut
für Physikalische und Theoretische
Chemie, Universität Würzburg, Campus Hubland Nord, Emil-Fischer-Strasse 42, D-97074 Würzburg,
Germany
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49
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Kandathil SM, Fletcher TL, Yuan Y, Knowles J, Popelier PLA. Accuracy and tractability of a kriging model of intramolecular polarizable multipolar electrostatics and its application to histidine. J Comput Chem 2013; 34:1850-61. [PMID: 23720381 DOI: 10.1002/jcc.23333] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2013] [Revised: 04/23/2013] [Accepted: 04/24/2013] [Indexed: 11/05/2022]
Abstract
We propose a generic method to model polarization in the context of high-rank multipolar electrostatics. This method involves the machine learning technique kriging, here used to capture the response of an atomic multipole moment of a given atom to a change in the positions of the atoms surrounding this atom. The atoms are malleable boxes with sharp boundaries, they do not overlap and exhaust space. The method is applied to histidine where it is able to predict atomic multipole moments (up to hexadecapole) for unseen configurations, after training on 600 geometries distorted using normal modes of each of its 24 local energy minima at B3LYP/apc-1 level. The quality of the predictions is assessed by calculating the Coulomb energy between an atom for which the moments have been predicted and the surrounding atoms (having exact moments). Only interactions between atoms separated by three or more bonds ("1, 4 and higher" interactions) are included in this energy error. This energy is compared with that of a central atom with exact multipole moments interacting with the same environment. The resulting energy discrepancies are summed for 328 atom-atom interactions, for each of the 29 atoms of histidine being a central atom in turn. For 80% of the 539 test configurations (outside the training set), this summed energy deviates by less than 1 kcal mol(-1).
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Affiliation(s)
- Shaun M Kandathil
- Manchester Institute of Biotechnology, 131 Princess Street, Manchester, M1 7DN, United Kingdom
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50
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Oltean M, Mile G, Vidrighin M, Leopold N, Chiş V. Weakly bound PTCDI and PTCDA dimers studied by using MP2 and DFT methods with dispersion correction. Phys Chem Chem Phys 2013; 15:13978-90. [DOI: 10.1039/c3cp44644a] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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