1
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Chung JK, Brown ML, Popelier PLA. Transferability of Buckingham Parameters for Short-Range Repulsion between Topological Atoms. J Phys Chem A 2024; 128:4561-4572. [PMID: 38805440 PMCID: PMC11163427 DOI: 10.1021/acs.jpca.4c02048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 05/16/2024] [Accepted: 05/20/2024] [Indexed: 05/30/2024]
Abstract
The repulsive part of the Buckingham potential, with parameters A and B, can be used to model deformation energies and steric energies. Both are calculated using the interacting quantum atom energy decomposition scheme where the latter is obtained from the former by a charge-transfer-based energy correction. These energies relate to short-range interactions, specifically the deformation of electron density and steric hindrance, respectively, when topological atoms approach each other. In this work, we calculate and fit the energies of carbonyl carbon, carbonyl oxygen, and, where possible, amine nitrogen atoms to the repulsive part of the Buckingham potential for 26 molecules. We find that while the steric energies of all atom pairs studied display exponential behavior with respect to distance, some deformation energy data do not. The obtained parameters are shown to be transferable by calculating root-mean-square errors of fitted potentials with respect to energy data of the same atom in, as far as possible, all other molecules from our data set. We observed that 36% and 10% of these errors were smaller than 4 kJ mol-1 for steric and deformation energy, respectively. Thus, we find that steric energy parameters are more transferable than deformation energy parameters. Finally, we speculate about the physical meaning of the A and B parameters and the implications of the strong exponential and exponential-linear piecewise relationships that we observe between them.
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Affiliation(s)
- Jaiming
J. K. Chung
- Department of Chemistry, The University of Manchester, Oxford Road, Manchester M13 9PL, Great
Britain
| | - Matthew L. Brown
- Department of Chemistry, The University of Manchester, Oxford Road, Manchester M13 9PL, Great
Britain
| | - Paul L. A. Popelier
- Department of Chemistry, The University of Manchester, Oxford Road, Manchester M13 9PL, Great
Britain
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2
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Elhatisari S, Bovermann L, Ma YZ, Epelbaum E, Frame D, Hildenbrand F, Kim M, Kim Y, Krebs H, Lähde TA, Lee D, Li N, Lu BN, Meißner UG, Rupak G, Shen S, Song YH, Stellin G. Wavefunction matching for solving quantum many-body problems. Nature 2024; 630:59-63. [PMID: 38750357 PMCID: PMC11153134 DOI: 10.1038/s41586-024-07422-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 04/15/2024] [Indexed: 06/07/2024]
Abstract
Ab initio calculations have an essential role in our fundamental understanding of quantum many-body systems across many subfields, from strongly correlated fermions1-3 to quantum chemistry4-6 and from atomic and molecular systems7-9 to nuclear physics10-14. One of the primary challenges is to perform accurate calculations for systems where the interactions may be complicated and difficult for the chosen computational method to handle. Here we address the problem by introducing an approach called wavefunction matching. Wavefunction matching transforms the interaction between particles so that the wavefunctions up to some finite range match that of an easily computable interaction. This allows for calculations of systems that would otherwise be impossible owing to problems such as Monte Carlo sign cancellations. We apply the method to lattice Monte Carlo simulations15,16 of light nuclei, medium-mass nuclei, neutron matter and nuclear matter. We use high-fidelity chiral effective field theory interactions17,18 and find good agreement with empirical data. These results are accompanied by insights on the nuclear interactions that may help to resolve long-standing challenges in accurately reproducing nuclear binding energies, charge radii and nuclear-matter saturation in ab initio calculations19,20.
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Affiliation(s)
- Serdar Elhatisari
- Faculty of Natural Sciences and Engineering, Gaziantep Islam Science and Technology University, Gaziantep, Turkey
- Helmholtz-Institut für Strahlen- und Kernphysik and Bethe Center for Theoretical Physics, Universität Bonn, Bonn, Germany
| | - Lukas Bovermann
- Institut für Theoretische Physik II, Ruhr-Universität Bochum, Bochum, Germany
| | - Yuan-Zhuo Ma
- Facility for Rare Isotope Beams and Department of Physics and Astronomy, Michigan State University, East Lansing, MI, USA
- Guangdong Provincial Key Laboratory of Nuclear Science, Institute of Quantum Matter, South China Normal University, Guangzhou, China
| | - Evgeny Epelbaum
- Institut für Theoretische Physik II, Ruhr-Universität Bochum, Bochum, Germany
| | - Dillon Frame
- Institut für Kernphysik, Institute for Advanced Simulation, Jülich Center for Hadron Physics, Jülich, Germany
- Center for Advanced Simulation and Analytics (CASA), Forschungszentrum Jülich, Jülich, Germany
| | - Fabian Hildenbrand
- Institut für Kernphysik, Institute for Advanced Simulation, Jülich Center for Hadron Physics, Jülich, Germany
- Center for Advanced Simulation and Analytics (CASA), Forschungszentrum Jülich, Jülich, Germany
| | - Myungkuk Kim
- Center for Exotic Nuclear Studies, Institute for Basic Science, Daejeon, Korea
| | - Youngman Kim
- Center for Exotic Nuclear Studies, Institute for Basic Science, Daejeon, Korea
| | - Hermann Krebs
- Institut für Theoretische Physik II, Ruhr-Universität Bochum, Bochum, Germany
| | - Timo A Lähde
- Institut für Kernphysik, Institute for Advanced Simulation, Jülich Center for Hadron Physics, Jülich, Germany
- Center for Advanced Simulation and Analytics (CASA), Forschungszentrum Jülich, Jülich, Germany
| | - Dean Lee
- Facility for Rare Isotope Beams and Department of Physics and Astronomy, Michigan State University, East Lansing, MI, USA.
| | - Ning Li
- School of Physics, Sun Yat-Sen University, Guangzhou, China
| | - Bing-Nan Lu
- Graduate School of China Academy of Engineering Physics, Beijing, China
| | - Ulf-G Meißner
- Helmholtz-Institut für Strahlen- und Kernphysik and Bethe Center for Theoretical Physics, Universität Bonn, Bonn, Germany
- Institut für Kernphysik, Institute for Advanced Simulation, Jülich Center for Hadron Physics, Jülich, Germany
- Center for Advanced Simulation and Analytics (CASA), Forschungszentrum Jülich, Jülich, Germany
- Tbilisi State University, Tbilisi, Georgia
| | - Gautam Rupak
- Department of Physics and Astronomy and HPC2 Center for Computational Sciences, Mississippi State University, Mississippi State, MI, USA
| | - Shihang Shen
- Institut für Kernphysik, Institute for Advanced Simulation, Jülich Center for Hadron Physics, Jülich, Germany
- Center for Advanced Simulation and Analytics (CASA), Forschungszentrum Jülich, Jülich, Germany
| | - Young-Ho Song
- Institute for Rare Isotope Science, Institute for Basic Science (IBS), Daejeon, Korea
| | - Gianluca Stellin
- ESNT, DRF/IRFU/DPhN/LENA, CEA Paris-Saclay and Université Paris-Saclay, Gif-sur-Yvette, France
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3
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Beran GJO. Frontiers of molecular crystal structure prediction for pharmaceuticals and functional organic materials. Chem Sci 2023; 14:13290-13312. [PMID: 38033897 PMCID: PMC10685338 DOI: 10.1039/d3sc03903j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 11/02/2023] [Indexed: 12/02/2023] Open
Abstract
The reliability of organic molecular crystal structure prediction has improved tremendously in recent years. Crystal structure predictions for small, mostly rigid molecules are quickly becoming routine. Structure predictions for larger, highly flexible molecules are more challenging, but their crystal structures can also now be predicted with increasing rates of success. These advances are ushering in a new era where crystal structure prediction drives the experimental discovery of new solid forms. After briefly discussing the computational methods that enable successful crystal structure prediction, this perspective presents case studies from the literature that demonstrate how state-of-the-art crystal structure prediction can transform how scientists approach problems involving the organic solid state. Applications to pharmaceuticals, porous organic materials, photomechanical crystals, organic semi-conductors, and nuclear magnetic resonance crystallography are included. Finally, efforts to improve our understanding of which predicted crystal structures can actually be produced experimentally and other outstanding challenges are discussed.
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Affiliation(s)
- Gregory J O Beran
- Department of Chemistry, University of California Riverside Riverside CA 92521 USA
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4
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Jensen F. Unifying Charge-Flow Polarization Models. J Chem Theory Comput 2023. [PMID: 37365806 DOI: 10.1021/acs.jctc.3c00341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/28/2023]
Abstract
We show that several models where electric polarization in molecular systems is modeled by charge-flow between atoms can all be considered as different manifestations of a general underlying mathematical structure. The models can be classified according to whether they employ atomic or bond parameters and whether they employ atom/bond hardness or softness. We show that an ab initio calculated charge response kernel can be considered as the inverse screened Coulombic matrix projected onto the zero-charge subspace, and this may provide a method for deriving charge screening functions to be used in force fields. The analysis suggests that some models contain redundancies, and we argue that a parameterization of charge-flow models in terms of bond softness is preferable as it depends on local quantities and decay to zero upon bond dissociation, while bond hardness depends on global quantities and increases toward infinity upon bond dissociation.
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Affiliation(s)
- Frank Jensen
- Department of Chemistry, Aarhus University, Langelandsgade 140, Aarhus DK-8000, Denmark
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5
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Janicki TD, Van Vleet MJ, Schmidt JR. Development and Implementation of Atomically Anisotropic First-Principles Force Fields: A Benzene Case Study. J Phys Chem A 2023; 127:1736-1749. [PMID: 36780209 DOI: 10.1021/acs.jpca.2c07244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/14/2023]
Abstract
π-interactions are an important motif in chemical and biochemical systems. However, due to their anisotropic electron densities and complex balance of intermolecular interactions, aromatic molecules represent an ongoing challenge for accurate and transferable force field development. Historically, ab initio force fields for aromatics have not exhibited good accuracy with respect to bulk properties or have only been used to study gas-phase dimers. Using benzene as a proof of concept, herein we show how our own ab initio MASTIFF force field incorporates an atomically anisotropic description of intermolecular interactions to yield an accurate and robust model for aromatic interactions irrespective of phase. Compared to existing models, the MASTIFF benzene force field not only is accurate for liquid phase properties but also offers transferability to the gas and solid phases. Additionally, we introduce a computationally efficient OpenMM plugin which enables customizable anisotropic intermolecular functional forms and which can be generically used in any MD simulation where a model for nonspherical atomic features is required. Overall, our results demonstrate the importance of atomic-level anisotropy in enabling next-generation ab initio force field development.
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Affiliation(s)
- Tesia D Janicki
- Department of Chemistry, University of Wisconsin─Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Mary J Van Vleet
- Department of Chemistry and Biochemistry, Spelman College, 350 Spelman Ln SW, Atlanta, Georgia 30314, United States
| | - J R Schmidt
- Department of Chemistry, University of Wisconsin─Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
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6
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Szalewicz K, Jeziorski B. Physical mechanisms of intermolecular interactions from symmetry-adapted perturbation theory. J Mol Model 2022; 28:273. [PMID: 36006512 DOI: 10.1007/s00894-022-05190-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 05/12/2022] [Indexed: 10/15/2022]
Abstract
Symmetry-adapted perturbation theory (SAPT) is a method for computational studies of noncovalent interactions between molecules. This method will be discussed here from the perspective of establishing the paradigm for understanding mechanisms of intermolecular interactions. SAPT interaction energies are obtained as sums of several contributions. Each contribution possesses a clear physical interpretation as it results from some specific physical process. It also exhibits a specific dependence on the intermolecular separation R. The four major contributions are the electrostatic, induction, dispersion, and exchange energies, each due to a different mechanism, valid at any R. In addition, at large R, SAPT interaction energies are seamlessly connected with the corresponding terms in the asymptotic multipole expansion of interaction energy in inverse powers of R. Since such expansion explicitly depends on monomers' multipole moments and polarizabilities, this connection provides additional insights by rigorously relating interaction energies to monomers' properties.
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Affiliation(s)
- Krzysztof Szalewicz
- Department of Physics and Astronomy, University of Delaware, Newark, DE, 19716, USA.
| | - Bogumił Jeziorski
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02093, Warsaw, Poland
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7
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Non-covalent interactions from a Quantum Chemical Topology perspective. J Mol Model 2022; 28:276. [PMID: 36006513 PMCID: PMC9411098 DOI: 10.1007/s00894-022-05188-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 02/07/2022] [Indexed: 11/12/2022]
Abstract
About half a century after its little-known beginnings, the quantum topological approach called QTAIM has grown into a widespread, but still not mainstream, methodology of interpretational quantum chemistry. Although often confused in textbooks with yet another population analysis, be it perhaps an elegant but somewhat esoteric one, QTAIM has been enriched with about a dozen other research areas sharing its main mathematical language, such as Interacting Quantum Atoms (IQA) or Electron Localisation Function (ELF), to form an overarching approach called Quantum Chemical Topology (QCT). Instead of reviewing the latter’s role in understanding non-covalent interactions, we propose a number of ideas emerging from the full consequences of the space-filling nature of topological atoms, and discuss how they (will) impact on interatomic interactions, including non-covalent ones. The architecture of a force field called FFLUX, which is based on these ideas, is outlined. A new method called Relative Energy Gradient (REG) is put forward, which is able, by computation, to detect which fragments of a given molecular assembly govern the energetic behaviour of this whole assembly. This method can offer insight into the typical balance of competing atomic energies both in covalent and non-covalent case studies. A brief discussion on so-called bond critical points is given, highlighting concerns about their meaning, mainly in the arena of non-covalent interactions.
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8
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James A, Swathi RS. Modeling the Adsorption of Polycyclic Aromatic Hydrocarbons on Graphynes: An Improved Lennard-Jones Formulation. J Phys Chem A 2022; 126:3472-3485. [PMID: 35609299 DOI: 10.1021/acs.jpca.2c01777] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Research on the development of theoretical methodologies for modeling noncovalent interactions governing the adsorption of polycyclic aromatic hydrocarbons (PAHs) on graphene and other two-dimensional materials is being intensely pursued in recent times. Highly accurate empirical potentials have emerged as a viable alternative to first-principles calculations for performing large-scale simulations. Herein, we report exploration of the potential energy surfaces for the adsorption of cata-condensed and peri-condensed PAHs on graphynes (GYs) using the improved Lennard-Jones (ILJ) potential. Initially, the ILJ potential is parametrized against benchmark electronic structure calculations performed on a selected set of PAH-GY complexes using dispersion-corrected density functional theory. The accuracy of the parametrization scheme is then assessed by a comparison of the adsorption features predicted from the ILJ potential with those computed using electronic structure calculations. The potential energy profiles as well as the single point energy calculations and geometry reoptimizations performed on the minimum-energy configurations predicted by the ILJ potential for a broader range of PAH-GY complexes provided a validation of the parametrization scheme. Finally, by an extrapolation of the PAH adsorption energies on various GYs, we estimated the interlayer cohesion energies for the van der Waals bilayer heterostructures of GYs with graphene to be in the range of 25-50 meV/atom.
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Affiliation(s)
- Anto James
- School of Chemistry, Indian Institute of Science Education and Research Thiruvananthapuram (IISER TVM), Vithura, Thiruvananthapuram 695551, India
| | - Rotti Srinivasamurthy Swathi
- School of Chemistry, Indian Institute of Science Education and Research Thiruvananthapuram (IISER TVM), Vithura, Thiruvananthapuram 695551, India
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9
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Abstract
We review different models for introducing electric polarization in force fields, with special focus on methods where polarization is modelled at the atomic charge level. While electric polarization has been included in several force fields, the common approach has been to focus on atomic dipole polarizability. Several approaches allow modelling electric polarization by using charge-flow between charge sites instead, but this has been less exploited, despite that atomic charges and charge-flow is expected to be more important than atomic dipoles and dipole polarizability. A number of challenges are required to be solved for charge-flow models to be incorporated into polarizable force fields, for example how to parameterize the models and how to make them computational efficient.
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Affiliation(s)
- Frank Jensen
- Department of Chemistry, Aarhus University, Denmark.
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10
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P. Oliveira M, Hünenberger PH. Systematic optimization of a fragment-based force field against experimental pure-liquid properties considering large compound families: application to oxygen and nitrogen compounds. Phys Chem Chem Phys 2021; 23:17774-17793. [PMID: 34350931 PMCID: PMC8386690 DOI: 10.1039/d1cp02001c] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 06/30/2021] [Indexed: 12/04/2022]
Abstract
The CombiFF approach is a workflow for the automated refinement of force-field parameters against experimental condensed-phase data, considering entire classes of organic molecules constructed using a fragment library via combinatorial isomer enumeration. One peculiarity of this approach is that it relies on an electronegativity-equalization scheme to account for induction effects within molecules, with values of the atomic hardness and electronegativity as electrostatic parameters, rather than the partial charges themselves. In a previous article [M. P. Oliveira, M. Andrey, S. R. Rieder, L. Kern, D. F. Hahn, S. Riniker, B. A. C. Horta and P. H. Hünenberger, J. Chem. Theory. Comput. 2020, 16, 7525], CombiFF was introduced and applied to calibrate a GROMOS-compatible united-atom force field for the saturated acyclic (halo-)alkane family. Here, this scheme is employed for the construction of a corresponding force field for saturated acyclic compounds encompassing eight common chemical functional groups involving oxygen and/or nitrogen atoms, namely: ether, aldehyde, ketone, ester, alcohol, carboxylic acid, amine, and amide. Monofunctional as well as homo-polyfunctional compounds are considered. A total of 1712 experimental liquid densities ρliq and vaporization enthalpies ΔHvap concerning 1175 molecules are used for the calibration (339 molecules) and validation (836 molecules) of the 102 non-bonded interaction parameters of the force field. Using initial parameter values based on the GROMOS 2016H66 parameter set, convergence is reached after five iterations. Given access to one processor per simulated system, this operation only requires a few days of wall-clock computing time. After optimization, the root-mean-square deviations from experiment are 29.9 (22.4) kg m-3 for ρliq and 4.1 (5.5) kJ mol-1 for ΔHvap for the calibration (validation) set. Thus, a very good level of agreement with experiment is achieved in terms of these two properties, although the errors are inhomogeneously distributed across the different chemical functional groups.
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Affiliation(s)
- Marina P. Oliveira
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Hönggerberg, HCICH-8093 ZürichSwitzerland+41 44 632 5503
| | - Philippe H. Hünenberger
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Hönggerberg, HCICH-8093 ZürichSwitzerland+41 44 632 5503
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11
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Konrad M, Wenzel W. CONI-Net: Machine Learning of Separable Intermolecular Force Fields. J Chem Theory Comput 2021; 17:4996-5006. [PMID: 34247485 DOI: 10.1021/acs.jctc.1c00328] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Noncovalent interactions (NCIs) play an essential role in soft matter and biomolecular simulations. The ab initio method symmetry-adapted perturbation theory allows a precise quantitative analysis of NCIs and offers an inherent energy decomposition, enabling a deeper understanding of the nature of intermolecular interactions. However, this method is limited to small systems, for instance, dimers of molecules. Here, we present a scale-bridging approach to systematically derive an intermolecular force field from ab initio data while preserving the energy decomposition of the underlying method. We apply the model in molecular dynamics simulations of several solvents and compare two predicted thermodynamic observables-mass density and enthalpy of vaporization-to experiments and established force fields. For a data set limited to hydrocarbons, we investigate the extrapolation capabilities to molecules absent from the training set. Overall, despite the affordable moderate quality of the reference ab initio data, we find promising results. With the straightforward data set generation procedure and the lack of target data in the fitting process, we have developed a method that enables the rapid development of predictive force fields with an extra dimension of insights into the balance of NCIs.
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Affiliation(s)
- Manuel Konrad
- Institute of Nanotechnology, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, Eggenstein-Leopoldshafen 76344, Germany
| | - Wolfgang Wenzel
- Institute of Nanotechnology, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, Eggenstein-Leopoldshafen 76344, Germany
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12
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Loukhovitski BI, Sharipov AS. Molecular Collision Diameters and Electronic Polarizabilities: Inherent Relationship and Fast Evaluation. J Phys Chem A 2021; 125:5117-5123. [PMID: 34077208 DOI: 10.1021/acs.jpca.1c02201] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The collision diameter σ for a large set of molecular species is related to the static electronic polarizability αel. A remarkable correlation between these quantities conceptually similar to the analogous one previously identified for atoms is revealed. Our recommended model is the function σ(αel) = p1 + p2αel1/3, where p1 = 0.768 Å and p2 = 2.168 are the fitting parameters providing the best overall match to the reference data for collision diameter (181 data points). The obtained correlation allows one to easily find the collision diameter of molecules from the known polarizability and vice versa. These findings can be useful for many applications, where there is a need for inexpensive assessments of the collision diameters or electronic polarizabilities, for example, when developing the transport property databases for modeling of chemically reacting flows.
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13
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Schriber JB, Nascimento DR, Koutsoukas A, Spronk SA, Cheney DL, Sherrill CD. CLIFF: A component-based, machine-learned, intermolecular force field. J Chem Phys 2021; 154:184110. [PMID: 34241025 DOI: 10.1063/5.0042989] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Computation of intermolecular interactions is a challenge in drug discovery because accurate ab initio techniques are too computationally expensive to be routinely applied to drug-protein models. Classical force fields are more computationally feasible, and force fields designed to match symmetry adapted perturbation theory (SAPT) interaction energies can remain accurate in this context. Unfortunately, the application of such force fields is complicated by the laborious parameterization required for computations on new molecules. Here, we introduce the component-based machine-learned intermolecular force field (CLIFF), which combines accurate, physics-based equations for intermolecular interaction energies with machine-learning models to enable automatic parameterization. The CLIFF uses functional forms corresponding to electrostatic, exchange-repulsion, induction/polarization, and London dispersion components in SAPT. Molecule-independent parameters are fit with respect to SAPT2+(3)δMP2/aug-cc-pVTZ, and molecule-dependent atomic parameters (atomic widths, atomic multipoles, and Hirshfeld ratios) are obtained from machine learning models developed for C, N, O, H, S, F, Cl, and Br. The CLIFF achieves mean absolute errors (MAEs) no worse than 0.70 kcal mol-1 in both total and component energies across a diverse dimer test set. For the side chain-side chain interaction database derived from protein fragments, the CLIFF produces total interaction energies with an MAE of 0.27 kcal mol-1 with respect to reference data, outperforming similar and even more expensive methods. In applications to a set of model drug-protein interactions, the CLIFF is able to accurately rank-order ligand binding strengths and achieves less than 10% error with respect to SAPT reference values for most complexes.
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Affiliation(s)
- Jeffrey B Schriber
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30318, USA
| | - Daniel R Nascimento
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30318, USA
| | - Alexios Koutsoukas
- Molecular Structure and Design, Bristol Myers Squibb Company, P.O. Box 5400, Princeton, New Jersey 08543, USA
| | - Steven A Spronk
- Molecular Structure and Design, Bristol Myers Squibb Company, P.O. Box 5400, Princeton, New Jersey 08543, USA
| | - Daniel L Cheney
- Molecular Structure and Design, Bristol Myers Squibb Company, P.O. Box 5400, Princeton, New Jersey 08543, USA
| | - C David Sherrill
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry and School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30318, USA
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14
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Hogan A, Space B. Next-Generation Accurate, Transferable, and Polarizable Potentials for Material Simulations. J Chem Theory Comput 2020; 16:7632-7644. [PMID: 33251798 DOI: 10.1021/acs.jctc.0c00837] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
PHAHST (potentials with high accuracy, high speed, and transferability) intermolecular potential energy functions have been developed from first principles for H2, N2, the noble gases, and a metal-organic material, HKUST-1. The potentials are designed from the outset to be transferable to heterogeneous environments including porous materials, interfaces, and material simulations. This is accomplished by theoretically justified choices for all functional forms, parameters, and mixing rules, including explicit polarization in every environment and fitting to high quality electronic structure calculations using methods that are tractable for real systems. The models have been validated in neat systems by comparison to second virial coefficients and bulk pressure-density isotherms. For inhomogeneous applications, our main target, comparisons are presented to previously published experimental studies on the metal-organic material HKUST-1 including adsorption, isosteric heats of adsorption, binding site locations, and binding site energies. A systematic prescription is provided for developing compatible potentials for additional small molecules and materials. The resulting models are recommended for use in complex heterogeneous simulations where existing potentials may be inadequate.
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Affiliation(s)
- Adam Hogan
- Department of Chemistry, University of South Florida, 4202 E. Fowler Ave., CHE205, Tampa, Florida 33620-5250, United States
| | - Brian Space
- Department of Chemistry, University of South Florida, 4202 E. Fowler Ave., CHE205, Tampa, Florida 33620-5250, United States
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15
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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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16
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Kashefolgheta S, Oliveira MP, Rieder SR, Horta BAC, Acree WE, Hünenberger PH. Evaluating Classical Force Fields against Experimental Cross-Solvation Free Energies. J Chem Theory Comput 2020; 16:7556-7580. [DOI: 10.1021/acs.jctc.0c00688] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Sadra Kashefolgheta
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Hönggerberg, HCI, CH-8093 Zürich, Switzerland
| | - Marina P. Oliveira
- 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
- Instituto de Química, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-909, Brazil
| | - William E. Acree
- Department of Chemistry, University of North Texas, 1155 Union Circle Drive #305070, Denton, Texas 76203, United States
| | - Philippe H. Hünenberger
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Hönggerberg, HCI, CH-8093 Zürich, Switzerland
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17
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Glick ZL, Metcalf DP, Koutsoukas A, Spronk SA, Cheney DL, Sherrill CD. AP-Net: An atomic-pairwise neural network for smooth and transferable interaction potentials. J Chem Phys 2020; 153:044112. [DOI: 10.1063/5.0011521] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Affiliation(s)
- Zachary L. Glick
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, and School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, USA
| | - Derek P. Metcalf
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, and School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, USA
| | - Alexios Koutsoukas
- Molecular Structure and Design, Bristol Myers Squibb Company, P.O. Box 5400, Princeton, New Jersey 08543, USA
| | - Steven A. Spronk
- Molecular Structure and Design, Bristol Myers Squibb Company, P.O. Box 5400, Princeton, New Jersey 08543, USA
| | - Daniel L. Cheney
- Molecular Structure and Design, Bristol Myers Squibb Company, P.O. Box 5400, Princeton, New Jersey 08543, USA
| | - C. David Sherrill
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, and School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, USA
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18
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Gilmore RAJ, Dove MT, Misquitta AJ. First-Principles Many-Body Nonadditive Polarization Energies from Monomer and Dimer Calculations Only: A Case Study on Water. J Chem Theory Comput 2020; 16:224-242. [PMID: 31769980 DOI: 10.1021/acs.jctc.9b00819] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The many-body polarization energy is the major source of nonadditivity in strongly polar systems such as water. This nonadditivity is often considerable and must be included, if only in an average manner, to correctly describe the physical properties of the system. Models for the polarization energy are usually parametrized using experimental data, or theoretical estimates of the many-body effects. Here we show how many-body polarization models can be developed for water complexes using data for the monomer and dimer only using ideas recently developed in the field of intermolecular perturbation theory and state-of-the-art approaches for calculating distributed molecular properties based on the iterated stockholder atoms (ISA) algorithm. We show how these models can be calculated, and we validate their accuracy in describing the many-body nonadditive energies of a range of water clusters. We further investigate their sensitivity to the details of the polarization damping models used. We show how our very best polarization models yield many-body energies that agree with those computed with coupled-cluster methods, but at a fraction of the computational cost.
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Affiliation(s)
- Rory A J Gilmore
- School of Physics and Astronomy and the Thomas Young Centre for Theory and Simulation of Materials at Queen Mary University of London , London E1 4NS , U.K
| | - Martin T Dove
- School of Physics and Astronomy and the Thomas Young Centre for Theory and Simulation of Materials at Queen Mary University of London , London E1 4NS , U.K
| | - Alston J Misquitta
- School of Physics and Astronomy and the Thomas Young Centre for Theory and Simulation of Materials at Queen Mary University of London , London E1 4NS , U.K
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19
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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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20
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Allen AA, Robertson MJ, Payne MC, Cole DJ. Development and Validation of the Quantum Mechanical Bespoke Protein Force Field. ACS OMEGA 2019; 4:14537-14550. [PMID: 31528808 PMCID: PMC6740169 DOI: 10.1021/acsomega.9b01769] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 07/30/2019] [Indexed: 06/10/2023]
Abstract
Molecular mechanics force field parameters for macromolecules, such as proteins, are traditionally fit to reproduce experimental properties of small molecules, and thus, they neglect system-specific polarization. In this paper, we introduce a complete protein force field that is designed to be compatible with the quantum mechanical bespoke (QUBE) force field by deriving nonbonded parameters directly from the electron density of the specific protein under study. The main backbone and sidechain protein torsional parameters are rederived in this work by fitting to quantum mechanical dihedral scans for compatibility with QUBE nonbonded parameters. Software is provided for the preparation of QUBE input files. The accuracy of the new force field, and the derived torsional parameters, is tested by comparing the conformational preferences of a range of peptides and proteins with experimental measurements. Accurate backbone and sidechain conformations are obtained in molecular dynamics simulations of dipeptides, with NMR J coupling errors comparable to the widely used OPLS force field. In simulations of five folded proteins, the secondary structure is generally retained, and the NMR J coupling errors are similar to standard transferable force fields, although some loss of the experimental structure is observed in certain regions of the proteins. With several avenues for further development, the use of system-specific nonbonded force field parameters is a promising approach for next-generation simulations of biological molecules.
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Affiliation(s)
- Alice
E. A. Allen
- TCM
Group, Cavendish Laboratory, 19 JJ Thomson Ave, Cambridge CB3 0HE, United Kingdom
| | - Michael J. Robertson
- Department of Molecular and Cellular Physiology and Department of Structural Biology Stanford University School of Medicine, 279 Campus Drive, Stanford, California 94305, United States
| | - Michael C. Payne
- TCM
Group, Cavendish Laboratory, 19 JJ Thomson Ave, Cambridge CB3 0HE, United Kingdom
| | - Daniel J. Cole
- School
of Natural and Environmental Sciences, Newcastle
University, Newcastle
upon Tyne NE1 7RU, United
Kingdom
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21
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Abstract
We review recent work on property decomposition techniques using quantum chemical methods and discuss some topical applications in terms of quantum mechanics-molecular mechanics calculations and the constructing of properties of large molecules and clusters. Starting out from the so-called LoProp decomposition scheme [Gagliardi et al., J. Chem. Phys., 2004, 121, 4994] for extracting atomic and inter-atomic contributions to molecular properties we show how this method can be generalized to localized frequency-dependent polarizabilities, to localized hyperpolarizabilities and to localized dispersion coefficients. Some applications of the generalized decomposition technique are reviewed - calculations of frequency-dependent polarizabilities, Rayleigh scattering of large clusters, and calculations of hyperpolarizabilities of proteins.
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Affiliation(s)
- Hans Ågren
- KTH Royal Institute of Technology, School of Engineering Sciences in Chemistry, Biotechnology and Health, Department of Theoretical Chemistry and Biology, SE-106 91 Stockholm, Sweden.
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22
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Stöhr M, Van Voorhis T, Tkatchenko A. Theory and practice of modeling van der Waals interactions in electronic-structure calculations. Chem Soc Rev 2019; 48:4118-4154. [PMID: 31190037 DOI: 10.1039/c9cs00060g] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The accurate description of long-range electron correlation, most prominently including van der Waals (vdW) dispersion interactions, represents a particularly challenging task in the modeling of molecules and materials. vdW forces arise from the interaction of quantum-mechanical fluctuations in the electronic charge density. Within (semi-)local density functional approximations or Hartree-Fock theory such interactions are neglected altogether. Non-covalent vdW interactions, however, are ubiquitous in nature and play a key role for the understanding and accurate description of the stability, dynamics, structure, and response properties in a plethora of systems. During the last decade, many promising methods have been developed for modeling vdW interactions in electronic-structure calculations. These methods include vdW-inclusive Density Functional Theory and correlated post-Hartree-Fock approaches. Here, we focus on the methods within the framework of Density Functional Theory, including non-local van der Waals density functionals, interatomic dispersion models within many-body and pairwise formulation, and random phase approximation-based approaches. This review aims to guide the reader through the theoretical foundations of these methods in a tutorial-style manner and, in particular, highlight practical aspects such as the applicability and the advantages and shortcomings of current vdW-inclusive approaches. In addition, we give an overview of complementary experimental approaches, and discuss tools for the qualitative understanding of non-covalent interactions as well as energy decomposition techniques. Besides representing a reference for the current state-of-the-art, this work is thus also designed as a concise and detailed introduction to vdW-inclusive electronic structure calculations for a general and broad audience.
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Affiliation(s)
- Martin Stöhr
- Physics and Materials Science Research Unit, University of Luxembourg, L-1511 Luxembourg, Luxembourg.
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23
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Misquitta AJ, Stone AJ. ISA-Pol: distributed polarizabilities and dispersion models from a basis-space implementation of the iterated stockholder atoms procedure. Theor Chem Acc 2018. [DOI: 10.1007/s00214-018-2371-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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24
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Price SL. Control and prediction of the organic solid state: a challenge to theory and experiment †. Proc Math Phys Eng Sci 2018; 474:20180351. [PMID: 30333710 PMCID: PMC6189584 DOI: 10.1098/rspa.2018.0351] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 08/15/2018] [Indexed: 11/12/2022] Open
Abstract
The ability of theoretical chemists to quantitatively model the weak forces between organic molecules is being exploited to predict their crystal structures and estimate their physical properties. Evolving crystal structure prediction methods are increasingly being used to aid the design of organic functional materials and provide information about thermodynamically plausible polymorphs of speciality organic materials to aid, for example, pharmaceutical development. However, the increasingly sophisticated experimental studies for detecting the range of organic solid-state behaviours provide many challenges for improving quantitative theories that form the basis for the computer modelling. It is challenging to calculate the relative thermodynamic stability of different organic crystal structures, let alone understand the kinetic effects that determine which polymorphs can be observed and are practically important. However, collaborations between experiment and theory are reaching the stage of devising experiments to target the first crystallization of new polymorphs or create novel organic molecular materials.
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Affiliation(s)
- Sarah L. Price
- Department of Chemistry, University College London, 20 Gordon St, London WC1H 0AJ, UK
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25
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Walters ET, Mohebifar M, Johnson ER, Rowley CN. Evaluating the London Dispersion Coefficients of Protein Force Fields Using the Exchange-Hole Dipole Moment Model. J Phys Chem B 2018; 122:6690-6701. [DOI: 10.1021/acs.jpcb.8b02814] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Evan T. Walters
- Department of Chemistry, Memorial University of Newfoundland, St. John’s A1C 5S7, Newfoundland and Labrador, Canada
| | - Mohamad Mohebifar
- Department of Chemistry, Memorial University of Newfoundland, St. John’s A1C 5S7, Newfoundland and Labrador, Canada
| | - Erin R. Johnson
- Department of Chemistry, Dalhousie University, Halifax B3H 4R2, Nova Scotia, Canada
| | - Christopher N. Rowley
- Department of Chemistry, Memorial University of Newfoundland, St. John’s A1C 5S7, Newfoundland and Labrador, Canada
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26
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Xu P, Guidez EB, Bertoni C, Gordon MS. Perspective:Ab initioforce field methods derived from quantum mechanics. J Chem Phys 2018. [DOI: 10.1063/1.5009551] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Affiliation(s)
- Peng Xu
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, USA
| | - Emilie B. Guidez
- Department of Chemistry, University of Colorado Denver, Denver, Colorado 80217, USA
| | - Colleen Bertoni
- Argonne Leadership Computing Facility, Argonne, Illinois 60439, USA
| | - Mark S. Gordon
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, USA
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27
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Van Vleet MJ, Misquitta AJ, Schmidt JR. New Angles on Standard Force Fields: Toward a General Approach for Treating Atomic-Level Anisotropy. J Chem Theory Comput 2018; 14:739-758. [DOI: 10.1021/acs.jctc.7b00851] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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
| | - J. R. Schmidt
- Theoretical
Chemistry Institute and Department of Chemistry, University of Wisconsin−Madison, Madison, Wisconsin 53706, United States
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28
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Mohebifar M, Johnson ER, Rowley CN. Evaluating Force-Field London Dispersion Coefficients Using the Exchange-Hole Dipole Moment Model. J Chem Theory Comput 2017; 13:6146-6157. [DOI: 10.1021/acs.jctc.7b00522] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Mohamad Mohebifar
- Department
of Chemistry, Memorial University of Newfoundland, St. John’s, Newfoundland
and Labrador, Canada
| | - Erin R. Johnson
- Department
of Chemistry, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Christopher N. Rowley
- Department
of Chemistry, Memorial University of Newfoundland, St. John’s, Newfoundland
and Labrador, Canada
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29
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Ho YC, Wang YS, Chao SD. Molecular dynamics simulations of fluid cyclopropane with MP2/CBS-fitted intermolecular interaction potentials. J Chem Phys 2017; 147:064507. [PMID: 28810796 DOI: 10.1063/1.4998149] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Modeling fluid cycloalkanes with molecular dynamics simulations has proven to be a very challenging task partly because of lacking a reliable force field based on quantum chemistry calculations. In this paper, we construct an ab initio force field for fluid cyclopropane using the second-order Møller-Plesset perturbation theory. We consider 15 conformers of the cyclopropane dimer for the orientation sampling. Single-point energies at important geometries are calibrated by the coupled cluster with single, double, and perturbative triple excitation method. Dunning's correlation consistent basis sets (up to aug-cc-pVTZ) are used in extrapolating the interaction energies at the complete basis set limit. The force field parameters in a 9-site Lennard-Jones model are regressed by the calculated interaction energies without using empirical data. With this ab initio force field, we perform molecular dynamics simulations of fluid cyclopropane and calculate both the structural and dynamical properties. We compare the simulation results with those using an empirical force field and obtain a quantitative agreement for the detailed atom-wise radial distribution functions. The experimentally observed gross radial distribution function (extracted from the neutron scattering measurements) is well reproduced in our simulation. Moreover, the calculated self-diffusion coefficients and shear viscosities are in good agreement with the experimental data over a wide range of thermodynamic conditions. To the best of our knowledge, this is the first ab initio force field which is capable of competing with empirical force fields for simulating fluid cyclopropane.
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Affiliation(s)
- Yen-Ching Ho
- Institute of Applied Mechanics, National Taiwan University, Taipei 106, Taiwan
| | - Yi-Siang Wang
- Institute of Applied Mechanics, National Taiwan University, Taipei 106, Taiwan
| | - Sheng D Chao
- Institute of Applied Mechanics, National Taiwan University, Taipei 106, Taiwan
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30
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31
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Nocito D, Beran GJO. Averaged Condensed Phase Model for Simulating Molecules in Complex Environments. J Chem Theory Comput 2017; 13:1117-1129. [PMID: 28170251 DOI: 10.1021/acs.jctc.6b00890] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The need for configurational sampling dramatically increases the cost of combined quantum mechanics/molecular mechanics (QM/MM) simulations of chemical processes in solution. We developed an averaged condensed phase environment (ACPE) model that constructs an effective polarizable environment directly from explicitly sampled molecular dynamics configurations via the K-means++ algorithm and a mathematically rigorous translation of the molecular mechanics parameters. The model captures detailed heterogeneous features in the environment that may be difficult to describe using a conventional polarizable continuum model. Instead of performing repeated QM/MM calculations for each new configuration of the environment, the ACPE approach allows one to perform a single QM calculation on an averaged configuration. Here, we demonstrate the model by computing electronic excitation energies for several small molecules in solution. The ACPE model predicts the excitation energies in excellent agreement with conventional configurational averaging yet with orders of magnitude of reduction in the computational cost.
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Affiliation(s)
- Dominique Nocito
- Department of Chemistry, University of California , Riverside, California 92521, United States
| | - Gregory J O Beran
- Department of Chemistry, University of California , Riverside, California 92521, United States
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32
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Harczuk I, Nagy B, Jensen F, Vahtras O, Ågren H. Local decomposition of imaginary polarizabilities and dispersion coefficients. Phys Chem Chem Phys 2017; 19:20241-20250. [DOI: 10.1039/c7cp02399e] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
We present a new way to compute the two-body contribution to the dispersion energy using ab initio theory.
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Affiliation(s)
- Ignat Harczuk
- KTH Royal Institute of Technology
- School of Biotechnology
- Division of Theoretical Chemistry and Biology
- SE-106 91 Stockholm
- Sweden
| | - Balazs Nagy
- Department of Chemistry
- Aarhus University
- Langelandsgade 140
- 8000 Aarhus C
- Denmark
| | - Frank Jensen
- Department of Chemistry
- Aarhus University
- Langelandsgade 140
- 8000 Aarhus C
- Denmark
| | - Olav Vahtras
- KTH Royal Institute of Technology
- School of Biotechnology
- Division of Theoretical Chemistry and Biology
- SE-106 91 Stockholm
- Sweden
| | - Hans Ågren
- KTH Royal Institute of Technology
- School of Biotechnology
- Division of Theoretical Chemistry and Biology
- SE-106 91 Stockholm
- Sweden
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33
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Metz MP, Piszczatowski K, Szalewicz K. Automatic Generation of Intermolecular Potential Energy Surfaces. J Chem Theory Comput 2016; 12:5895-5919. [DOI: 10.1021/acs.jctc.6b00913] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Michael P. Metz
- Department of Physics and
Astronomy, University of Delaware, Newark, Delaware 19716, United States
| | - Konrad Piszczatowski
- Department of Physics and
Astronomy, University of Delaware, Newark, Delaware 19716, United States
| | - Krzysztof Szalewicz
- Department of Physics and
Astronomy, University of Delaware, Newark, Delaware 19716, United States
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34
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Prampolini G, Campetella M, De Mitri N, Livotto PR, Cacelli I. Systematic and Automated Development of Quantum Mechanically Derived Force Fields: The Challenging Case of Halogenated Hydrocarbons. J Chem Theory Comput 2016; 12:5525-5540. [DOI: 10.1021/acs.jctc.6b00705] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Giacomo Prampolini
- Istituto di Chimica dei Composti OrganoMetallici (ICCOM-CNR), Area della Ricerca, Via G. Moruzzi 1, I-56124 Pisa, Italy
| | - Marco Campetella
- Dipartimento
di Chimica e Chimica Industriale, Università di Pisa, Via G. Moruzzi
13, I-56124 Pisa, Italy
| | - Nicola De Mitri
- Department
of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Paolo Roberto Livotto
- Instituto
de Química, Universidade Federal do Rio Grande do Sul, Avenida Bento Gonçalves 9500, CEP 91501-970 Porto Alegre, Brazil
| | - Ivo Cacelli
- Istituto di Chimica dei Composti OrganoMetallici (ICCOM-CNR), Area della Ricerca, Via G. Moruzzi 1, I-56124 Pisa, Italy
- Dipartimento
di Chimica e Chimica Industriale, Università di Pisa, Via G. Moruzzi
13, I-56124 Pisa, Italy
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35
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Misquitta AJ, Stone AJ. Ab Initio Atom–Atom Potentials Using CamCASP: Theory and Application to Many-Body Models for the Pyridine Dimer. J Chem Theory Comput 2016; 12:4184-208. [DOI: 10.1021/acs.jctc.5b01241] [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)
- Alston J. Misquitta
- School
of Physics and Astronomy, Queen Mary, University of London, London E1 4NS, United Kingdom
| | - Anthony J. Stone
- University Chemical Laboratory, Lensfield Road, Cambridge, CB2 1EW, United Kingdom
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36
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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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37
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Cole DJ, Vilseck JZ, Tirado-Rives J, Payne MC, Jorgensen WL. Biomolecular Force Field Parameterization via Atoms-in-Molecule Electron Density Partitioning. J Chem Theory Comput 2016; 12:2312-23. [PMID: 27057643 PMCID: PMC4864407 DOI: 10.1021/acs.jctc.6b00027] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
![]()
Molecular mechanics
force fields, which are commonly used in biomolecular
modeling and computer-aided drug design, typically treat nonbonded
interactions using a limited library of empirical parameters that
are developed for small molecules. This approach does not account
for polarization in larger molecules or proteins, and the parametrization
process is labor-intensive. Using linear-scaling density functional
theory and atoms-in-molecule electron density partitioning, environment-specific
charges and Lennard-Jones parameters are derived directly from quantum
mechanical calculations for use in biomolecular modeling of organic
and biomolecular systems. The proposed methods significantly reduce
the number of empirical parameters needed to construct molecular mechanics
force fields, naturally include polarization effects in charge and
Lennard-Jones parameters, and scale well to systems comprised of thousands
of atoms, including proteins. The feasibility and benefits of this
approach are demonstrated by computing free energies of hydration,
properties of pure liquids, and the relative binding free energies
of indole and benzofuran to the L99A mutant of T4 lysozyme.
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Affiliation(s)
- Daniel J Cole
- Department of Chemistry, Yale University , New Haven, Connecticut 06520-8107, United States.,TCM Group, Cavendish Laboratory, 19 JJ Thomson Avenue, Cambridge CB3 0HE, United Kingdom
| | - Jonah Z Vilseck
- Department of Chemistry, Yale University , New Haven, Connecticut 06520-8107, United States
| | - Julian Tirado-Rives
- Department of Chemistry, Yale University , New Haven, Connecticut 06520-8107, United States
| | - Mike C Payne
- TCM Group, Cavendish Laboratory, 19 JJ Thomson Avenue, Cambridge CB3 0HE, United Kingdom
| | - William L Jorgensen
- Department of Chemistry, Yale University , New Haven, Connecticut 06520-8107, United States
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38
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Abstract
Symmetry-adapted perturbation theory (SAPT) provides a unique set of advantages for parameterizing next-generation force fields from first principles. SAPT provides a direct, basis-set superposition error free estimate of molecular interaction energies, a physically intuitive energy decomposition, and a seamless transition to an asymptotic picture of intermolecular interactions. These properties have been exploited throughout the literature to develop next-generation force fields for a variety of applications, including classical molecular dynamics simulations, crystal structure prediction, and quantum dynamics/spectroscopy. This review provides a brief overview of the formalism and theory of SAPT, along with a practical discussion of the various methodologies utilized to parameterize force fields from SAPT calculations. It also highlights a number of applications of SAPT-based force fields for chemical systems of particular interest. Finally, the review ends with a brief outlook on the future opportunities and challenges that remain for next-generation force fields based on SAPT.
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Affiliation(s)
- Jesse G McDaniel
- Theoretical Chemistry Institute and Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706;
| | - J R Schmidt
- Theoretical Chemistry Institute and Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706;
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39
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Řezáč J, Huang Y, Hobza P, Beran GJO. Benchmark Calculations of Three-Body Intermolecular Interactions and the Performance of Low-Cost Electronic Structure Methods. J Chem Theory Comput 2016; 11:3065-79. [PMID: 26575743 DOI: 10.1021/acs.jctc.5b00281] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Many-body noncovalent interactions are increasingly important in large and/or condensed-phase systems, but the current understanding of how well various models predict these interactions is limited. Here, benchmark complete-basis set coupled cluster singles, doubles, and perturbative triples (CCSD(T)) calculations have been performed to generate a new test set for three-body intermolecular interactions. This "3B-69" benchmark set includes three-body interaction energies for 69 total trimer structures, consisting of three structures from each of 23 different molecular crystals. By including structures that exhibit a variety of intermolecular interactions and packing arrangements, this set provides a stringent test for the ability of electronic structure methods to describe the correct physics involved in the interactions. Both MP2.5 (the average of second- and third-order Møller-Plesset perturbation theory) and spin-component-scaled CCSD for noncovalent interactions (SCS-MI-CCSD) perform well. MP2 handles the polarization aspects reasonably well, but it omits three-body dispersion. In contrast, many widely used density functionals corrected with three-body D3 dispersion correction perform comparatively poorly. The primary difficulty stems from the treatment of exchange and polarization in the functionals rather than from the dispersion correction, though the three-body dispersion may also be moderately underestimated by the D3 correction.
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Affiliation(s)
- Jan Řezáč
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic , 166 10 Prague, Czech Republic
| | - Yuanhang Huang
- Department of Chemistry, University of California , Riverside, California 92521 United States
| | - Pavel Hobza
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic , 166 10 Prague, Czech Republic.,Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Palacký University , 771 46 Olomouc, Czech Republic
| | - Gregory J O Beran
- Department of Chemistry, University of California , Riverside, California 92521 United States
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40
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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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41
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Misquitta AJ, Stone AJ. Accurate Induction Energies for Small Organic Molecules: 1. Theory. J Chem Theory Comput 2015; 4:7-18. [PMID: 26619975 DOI: 10.1021/ct700104t] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The induction energy often plays a very important role in determining the structure and properties of clusters of organic molecules, but only in recent years has an effort been made to include this energy in such calculations, notably in the field of organic crystal structure prediction. In this paper and the following one in this issue we provide ab initio methods suitable for the accurate inclusion of the induction energy for molecules containing as many as 30 atoms or so. These techniques are based on Symmetry-Adapted Perturbation Theory using Density Functional Theory [SAPT(DFT)] and use distributed polarizabilities computed using the recently developed density-fitting algorithm with constrained refinement. With this approach we are able to obtain induction models of varying complexity and study the effects of overlap and related numerical issues. Basis set effects on the exact and asymptotic induction energies are investigated, and the roles of higher-order induction energies and many-body effects are explored.
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Affiliation(s)
- Alston J Misquitta
- University Chemical Laboratory, Lensfield Road, Cambridge CB2 1EW, U.K., and University College London, 20 Gordon Street, London WC1H 0AJ, U.K
| | - Anthony J Stone
- University Chemical Laboratory, Lensfield Road, Cambridge CB2 1EW, U.K., and University College London, 20 Gordon Street, London WC1H 0AJ, U.K
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42
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Prampolini G, Livotto PR, Cacelli I. Accuracy of Quantum Mechanically Derived Force-Fields Parameterized from Dispersion-Corrected DFT Data: The Benzene Dimer as a Prototype for Aromatic Interactions. J Chem Theory Comput 2015; 11:5182-96. [DOI: 10.1021/acs.jctc.5b00642] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Giacomo Prampolini
- Istituto di Chimica dei Composti OrganoMetallici (ICCOM-CNR), Area della Ricerca, via G. Moruzzi 1, I-56124, Pisa, Italy
| | - Paolo Roberto Livotto
- Instituto de Química, Universidade
Federal do Rio Grande do Sul, Avenida
Bento Gonçalves 9500, CEP 91501-970 Porto Alegre, Rio Grande do Sul, Brazil
| | - Ivo Cacelli
- Istituto di Chimica dei Composti OrganoMetallici (ICCOM-CNR), Area della Ricerca, via G. Moruzzi 1, I-56124, Pisa, Italy
- Dipartimento di Chimica e Chimica Industriale, Universitá di Pisa, Via G. Moruzzi 13, I-56124, Pisa, Italy
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43
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Huang Y, Beran GJO. Reliable prediction of three-body intermolecular interactions using dispersion-corrected second-order Møller-Plesset perturbation theory. J Chem Phys 2015; 143:044113. [DOI: 10.1063/1.4927304] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Yuanhang Huang
- Department of Chemistry, University of California, Riverside, California 92521, USA
| | - Gregory J. O. Beran
- Department of Chemistry, University of California, Riverside, California 92521, USA
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44
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Mei Y, Simmonett AC, Pickard FC, DiStasio RA, Brooks BR, Shao Y. Numerical study on the partitioning of the molecular polarizability into fluctuating charge and induced atomic dipole contributions. J Phys Chem A 2015; 119:5865-82. [PMID: 25945749 DOI: 10.1021/acs.jpca.5b03159] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In order to carry out a detailed analysis of the molecular static polarizability, which is the response of the molecule to a uniform external electric field, the molecular polarizability was computed using the finite-difference method for 21 small molecules, using density functional theory. Within nine charge population schemes (Löwdin, Mulliken, Becke, Hirshfeld, CM5, Hirshfeld-I, NPA, CHELPG, MK-ESP) in common use, the charge fluctuation contribution is found to dominate the molecular polarizability, with its ratio ranging from 59.9% with the Hirshfeld or CM5 scheme to 96.2% with the Mulliken scheme. The Hirshfeld-I scheme is also used to compute the other contribution to the molecular polarizability coming from the induced atomic dipoles, and the atomic polarizabilities in eight small molecules and water pentamer are found to be highly anisotropic for most atoms. Overall, the results suggest that (a) more emphasis probably should be placed on the charge fluctuation terms in future polarizable force field development and (b) an anisotropic polarizability might be more suitable than an isotropic one in polarizable force fields based entirely or partially on the induced atomic dipoles.
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Affiliation(s)
- Ye Mei
- †State Key Laboratory of Precision Spectroscopy, Department of Physics and Institute of Theoretical and Computational Science, East China Normal University, Shanghai 200062, China.,‡NYU-ECNU Center for Computational Chemistry, NYU Shanghai, Shanghai 200062, China.,⊥Laboratory of Computational Biology, National Institutes of Health, National Heart, Lung and Blood Institute, 5635 Fishers Lane, T-900 Suite, Rockville, Maryland 20852, United States
| | - Andrew C Simmonett
- ⊥Laboratory of Computational Biology, National Institutes of Health, National Heart, Lung and Blood Institute, 5635 Fishers Lane, T-900 Suite, Rockville, Maryland 20852, United States
| | - Frank C Pickard
- ⊥Laboratory of Computational Biology, National Institutes of Health, National Heart, Lung and Blood Institute, 5635 Fishers Lane, T-900 Suite, Rockville, Maryland 20852, United States
| | - Robert A DiStasio
- §Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Bernard R Brooks
- ⊥Laboratory of Computational Biology, National Institutes of Health, National Heart, Lung and Blood Institute, 5635 Fishers Lane, T-900 Suite, Rockville, Maryland 20852, United States
| | - Yihan Shao
- ∥Q-Chem Inc., 6601 Owens Drive, Suite 105, Pleasanton, California 94588, United States
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45
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Schmidt JR, Yu K, McDaniel JG. Transferable next-generation force fields from simple liquids to complex materials. Acc Chem Res 2015; 48:548-56. [PMID: 25688596 DOI: 10.1021/ar500272n] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Molecular simulations have had a transformative impact on chemists' understanding of the structure and dynamics of molecular systems. Simulations can both explain and predict chemical phenomena, and they provide a unique bridge between the microscopic and macroscopic regimes. The input for such simulations is the intermolecular interactions, which then determine the forces on the constituent atoms and therefore the time evolution and equilibrium properties of the system. However, in practice, accuracy and reliability are often limited by the fidelity of the description of those very same interactions, most typically embodied approximately in mathematical form in what are known as force fields. Force fields most often utilize conceptually simple functional forms that have been parametrized to reproduce existing experimental gas phase or bulk data. Yet, reliance on empirical parametrization can sometimes introduce limitations with respect to novel chemical systems or uncontrolled errors when moving to temperatures, pressures, or environments that differ from those for which they were developed. Alternatively, it is possible to develop force fields entirely from first principles, using accurate electronic structure calculations to determine the intermolecular interactions. This introduces a new set of challenges, including the transferability of the resulting force field to related chemical systems. In response, we recently developed an alternative approach to develop force fields entirely from first-principles electronic structure calculations based on intermolecular perturbation theory. Making use of an energy decomposition analysis ensures, by construction, that the resulting force fields contain the correct balance of the various components of intermolecular interaction (exchange repulsion, electrostatics, induction, and dispersion), each treated by a functional form that reflects the underlying physics. We therefore refer to the resulting force fields as physically motivated. We find that these physically motivated force fields exhibit both high accuracy and transferability, with the latter deriving from the universality of the fundamental physical laws governing intermolecular interactions. This basic methodology has been applied to a diverse set of systems, ranging from simple liquids to nanoporous metal-organic framework materials. A key conclusion is that, in many cases, it is feasible to account for nearly all of the relevant physics of intermolecular interactions within the context of the force field. In such cases, the structural, thermodynamic, and dynamic properties of the system become naturally emergent, even in the absence of explicit parameterization to bulk properties. We also find that, quite generally, the three-body contributions to the dispersion and exchange energies in bulk liquids are crucial for quantitative accuracy in a first-principles force field, although these contributions are almost universally neglected in existing empirical force fields.
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Affiliation(s)
- J. R. Schmidt
- Theoretical Chemistry Institute
and Department of Chemistry, University of Wisconsin−Madison, Madison, Wisconsin 53706, United States
| | - Kuang Yu
- Theoretical Chemistry Institute
and Department of Chemistry, University of Wisconsin−Madison, Madison, Wisconsin 53706, United States
| | - Jesse G. McDaniel
- Theoretical Chemistry Institute
and Department of Chemistry, University of Wisconsin−Madison, Madison, Wisconsin 53706, United States
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46
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Uzoh OG, Galek PTA, Price SL. Analysis of the conformational profiles of fenamates shows route towards novel, higher accuracy, force-fields for pharmaceuticals. Phys Chem Chem Phys 2015; 17:7936-48. [DOI: 10.1039/c4cp05525j] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The conformational barriers of the fenamates which lead to conformational polymorphism can be represented by a novel, physically motivated, model intramolecular potential suitable for extension to other pharmaceuticals.
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Affiliation(s)
- Ogaga G. Uzoh
- Department of Chemistry
- University College London
- London
- UK
| | | | - Sarah L. Price
- Department of Chemistry
- University College London
- London
- UK
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47
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Misquitta AJ, Stone AJ, Fazeli F. Distributed Multipoles from a Robust Basis-Space Implementation of the Iterated Stockholder Atoms Procedure. J Chem Theory Comput 2014; 10:5405-18. [DOI: 10.1021/ct5008444] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Alston J. Misquitta
- School
of Physics and Astronomy, Queen Mary University of London, London E1 4NS, United Kingdom
| | - Anthony J. Stone
- University Chemical Laboratory, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Farhang Fazeli
- School
of Physics and Astronomy, Queen Mary University of London, London E1 4NS, United Kingdom
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48
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Rob F, Misquitta AJ, Podeszwa R, Szalewicz K. Localized overlap algorithm for unexpanded dispersion energies. J Chem Phys 2014; 140:114304. [DOI: 10.1063/1.4867969] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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49
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Albertí M, Aguilar A, Huarte-Larrañaga F, Lucas JM, Pirani F. Benzene–Hydrogen Bond (C6H6–HX) Interactions: The Influence of the X Nature on their Strength and Anisotropy. J Phys Chem A 2014; 118:1651-62. [DOI: 10.1021/jp410917x] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- M. Albertí
- IQTCUB,
Departament de Química Física, Universitat de Barcelona, Barcelona, Spain
| | - A. Aguilar
- IQTCUB,
Departament de Química Física, Universitat de Barcelona, Barcelona, Spain
| | - F. Huarte-Larrañaga
- IQTCUB,
Departament de Química Física, Universitat de Barcelona, Barcelona, Spain
| | - J. M. Lucas
- IQTCUB,
Departament de Química Física, Universitat de Barcelona, Barcelona, Spain
| | - F. Pirani
- Dipartimento
di Chimica, Università di Perugia, Perugia, Italy
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50
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Pantelides CC, Adjiman CS, Kazantsev AV. General Computational Algorithms for Ab Initio Crystal Structure Prediction for Organic Molecules. Top Curr Chem (Cham) 2014; 345:25-58. [DOI: 10.1007/128_2013_497] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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