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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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Structure and spectrum of the hydrated electron. A combined quantum chemical statistical mechanical simulation. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2019.111300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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3
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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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4
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Ghahremanpour MM, van Maaren PJ, Caleman C, Hutchison GR, van der Spoel D. Polarizable Drude Model with s-Type Gaussian or Slater Charge Density for General Molecular Mechanics Force Fields. J Chem Theory Comput 2018; 14:5553-5566. [PMID: 30281307 DOI: 10.1021/acs.jctc.8b00430] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Gas-phase electric properties of molecules can be computed routinely using wave function methods or density functional theory (DFT). However, these methods remain computationally expensive for high-throughput screening of the vast chemical space of virtual compounds. Therefore, empirical force fields are a more practical choice in many cases, particularly since force field methods allow one to routinely predict the physicochemical properties in the condensed phases. This work presents Drude polarizable models, to increase the physical realism in empirical force fields, where the core particle is treated as a point charge and the Drude particle is treated either as a 1 s-Gaussian or a ns-Slater ( n = 1, 2, 3) charge density. Systematic parametrization to large high-quality quantum chemistry data obtained from the open access Alexandria Library ( https://doi.org/10.5281/zenodo.1004711 ) ensures the transferability of these parameters. The dipole moments and isotropic polarizabilities of the isolated molecules predicted by the proposed Drude models are in agreement with experiment with accuracy similar to DFT calculations at the B3LYP/aug-cc-pVTZ level of theory. The results show that the inclusion of explicit polarization into the models reduces the root-mean-square deviation with respect to DFT calculations of the predicted dipole moments of 152 dimers and clusters by more than 50%. Finally, we show that the accuracy of the electrostatic interaction energy of the water dimers can be improved systematically by the introduction of polarizable smeared charges as a model for charge penetration.
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Affiliation(s)
- Mohammad Mehdi Ghahremanpour
- Uppsala Center for Computational Chemistry, Department of Cell and Molecular Biology , Uppsala University , Husargatan 3 , Box 596, SE-75124 Uppsala , Sweden
| | - Paul J van Maaren
- Uppsala Center for Computational Chemistry, Department of Cell and Molecular Biology , Uppsala University , Husargatan 3 , Box 596, SE-75124 Uppsala , Sweden
| | - Carl Caleman
- Department of Physics and Astronomy , Uppsala University , Box 516, SE-75120 Uppsala , Sweden.,Center for Free-Electron Laser Science , Deutsches Elektronen-Synchrotron , DE-22607 Hamburg , Germany
| | - Geoffrey R Hutchison
- Department of Chemistry , University of Pittsburgh , Pittsburgh , Pennsylvania 15260 , United States
| | - David van der Spoel
- Uppsala Center for Computational Chemistry, Department of Cell and Molecular Biology , Uppsala University , Husargatan 3 , Box 596, SE-75124 Uppsala , Sweden
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5
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Loboda O, Millot C. Geometry-dependent atomic multipole models for the water molecule. J Chem Phys 2017; 147:161718. [DOI: 10.1063/1.4995569] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- O. Loboda
- Karl-Franzens Universität, Institut für Chemie, Heinrichstraße 28/IV, Graz A-8010, Austria
| | - C. Millot
- Université de Lorraine, CNRS, SRSMC UMR 7565, Faculté des Sciences et Technologies, Boulevard des Aiguillettes BP 70239, Vandoeuvre-lès-Nancy Cedex F-54506, France
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6
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Verma P, Wang B, Fernandez LE, Truhlar DG. Physical Molecular Mechanics Method for Damped Dispersion. J Phys Chem A 2017; 121:2855-2862. [PMID: 28328203 DOI: 10.1021/acs.jpca.7b02384] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Damped dispersion can be a significant component of the interaction energy in many physical and chemical processes, for example, physisorption and noncovalent complexation. For physically interpreting and modeling such processes, it is convenient to have an analytic method to calculate damped dispersion that is readily applicable across the entire periodic table. Of the available methods to calculate damped dispersion energy for interacting systems with overlapping charge distributions, we select symmetry-adapted perturbation theory (SAPT) as providing a reasonable definition, and of the possible analytic forms, we choose the D3(BJ) method. However, the available parametrizations of D3(BJ) include not only damped dispersion energy but also corrections for errors in specific exchange-correlation functionals. Here we present a parametrization that provides a physical measure of damped dispersion without such density functional corrections. The method generalizes an earlier method of Pernal and co-workers to all elements from hydrogen to plutonium.
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Affiliation(s)
- Pragya Verma
- Department of Chemistry, Nanoporous Materials Genome Center, Chemical Theory Center, and Minnesota Supercomputing Institute, University of Minnesota , 207 Pleasant Street Southeast, Minneapolis, Minnesota 55455-0431, United States
| | - Bo Wang
- Department of Chemistry, Nanoporous Materials Genome Center, Chemical Theory Center, and Minnesota Supercomputing Institute, University of Minnesota , 207 Pleasant Street Southeast, Minneapolis, Minnesota 55455-0431, United States
| | - Laura E Fernandez
- Department of Chemistry, Nanoporous Materials Genome Center, Chemical Theory Center, and Minnesota Supercomputing Institute, University of Minnesota , 207 Pleasant Street Southeast, Minneapolis, Minnesota 55455-0431, United States
| | - Donald G Truhlar
- Department of Chemistry, Nanoporous Materials Genome Center, Chemical Theory Center, and Minnesota Supercomputing Institute, University of Minnesota , 207 Pleasant Street Southeast, Minneapolis, Minnesota 55455-0431, United States
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7
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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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Van Vleet MJ, Misquitta AJ, Stone AJ, Schmidt JR. Beyond Born-Mayer: Improved Models for Short-Range Repulsion in ab Initio Force Fields. J Chem Theory Comput 2016; 12:3851-70. [PMID: 27337546 DOI: 10.1021/acs.jctc.6b00209] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Short-range repulsion within intermolecular force fields is conventionally described by either Lennard-Jones (A/r(12)) or Born-Mayer (A exp(-Br)) forms. Despite their widespread use, these simple functional forms are often unable to describe the interaction energy accurately over a broad range of intermolecular distances, thus creating challenges in the development of ab initio force fields and potentially leading to decreased accuracy and transferability. Herein, we derive a novel short-range functional form based on a simple Slater-like model of overlapping atomic densities and an iterated stockholder atom (ISA) partitioning of the molecular electron density. We demonstrate that this Slater-ISA methodology yields a more accurate, transferable, and robust description of the short-range interactions at minimal additional computational cost compared to standard Lennard-Jones or Born-Mayer approaches. Finally, we show how this methodology can be adapted to yield the standard Born-Mayer functional form while still retaining many of the advantages of the Slater-ISA approach.
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Affiliation(s)
- Mary J Van Vleet
- Theoretical Chemistry Institute and Department of Chemistry, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
| | - Alston J Misquitta
- Department of Physics and Astronomy, Queen Mary University of London , London E1 4NS, United Kingdom
| | - Anthony J Stone
- Department of Chemistry, University of Cambridge , Cambridge CB2 1EW, United Kingdom
| | - J R Schmidt
- Theoretical Chemistry Institute and Department of Chemistry, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
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