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Echeverría J, Alvarez S. The borderless world of chemical bonding across the van der Waals crust and the valence region. Chem Sci 2023; 14:11647-11688. [PMID: 37920358 PMCID: PMC10619631 DOI: 10.1039/d3sc02238b] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 07/01/2023] [Indexed: 11/04/2023] Open
Abstract
The definition of the van der Waals crust as the spherical section between the atomic radius and the van der Waals radius of an element is discussed and a survey of the application of the penetration index between two interacting atoms in a wide variety of covalent, polar, coordinative or noncovalent bonding situations is presented. It is shown that this newly defined parameter permits the comparison of bonding between pairs of atoms in structural and computational studies independently of the atom sizes.
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Affiliation(s)
- Jorge Echeverría
- Instituto de Síntesis Química y Catalisis Homogénea (ISQCH) and Departmento de Química Inorgánica, Facultad de Ciencias, Universidad de Zaragoza Pedro Cerbuna 12 50009 Zaragoza Spain
| | - Santiago Alvarez
- Department de Química Inorgànica i Orgànica, Secció de Química Inorgànica, e Institut de Química Teòrica i Computacional, Universitat de Barcelona Martí i Franquès 1-11 08028 -Barcelona Spain
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Demerdash O, Mao Y, Liu T, Head-Gordon M, Head-Gordon T. Assessing many-body contributions to intermolecular interactions of the AMOEBA force field using energy decomposition analysis of electronic structure calculations. J Chem Phys 2018; 147:161721. [PMID: 29096520 DOI: 10.1063/1.4999905] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
In this work, we evaluate the accuracy of the classical AMOEBA model for representing many-body interactions, such as polarization, charge transfer, and Pauli repulsion and dispersion, through comparison against an energy decomposition method based on absolutely localized molecular orbitals (ALMO-EDA) for the water trimer and a variety of ion-water systems. When the 2- and 3-body contributions according to the many-body expansion are analyzed for the ion-water trimer systems examined here, the 3-body contributions to Pauli repulsion and dispersion are found to be negligible under ALMO-EDA, thereby supporting the validity of the pairwise-additive approximation in AMOEBA's 14-7 van der Waals term. However AMOEBA shows imperfect cancellation of errors for the missing effects of charge transfer and incorrectness in the distance dependence for polarization when compared with the corresponding ALMO-EDA terms. We trace the larger 2-body followed by 3-body polarization errors to the Thole damping scheme used in AMOEBA, and although the width parameter in Thole damping can be changed to improve agreement with the ALMO-EDA polarization for points about equilibrium, the correct profile of polarization as a function of intermolecular distance cannot be reproduced. The results suggest that there is a need for re-examining the damping and polarization model used in the AMOEBA force field and provide further insights into the formulations of polarizable force fields in general.
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Affiliation(s)
- Omar Demerdash
- Departments of Chemistry, University of California, Berkeley, California 94720, USA
| | - Yuezhi Mao
- Departments of Chemistry, University of California, Berkeley, California 94720, USA
| | - Tianyi Liu
- Departments of Chemistry, University of California, Berkeley, California 94720, USA
| | - Martin Head-Gordon
- Departments of Chemistry, University of California, Berkeley, California 94720, USA
| | - Teresa Head-Gordon
- Departments of Chemistry, University of California, Berkeley, California 94720, USA
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Vandenbrande S, Waroquier M, Speybroeck VV, Verstraelen T. The Monomer Electron Density Force Field (MEDFF): A Physically Inspired Model for Noncovalent Interactions. J Chem Theory Comput 2016; 13:161-179. [DOI: 10.1021/acs.jctc.6b00969] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Steven Vandenbrande
- Center for Molecular Modeling
(CMM), QCMM Ghent−Brussels Alliance, Ghent University, Technologiepark
903, B9000 Ghent, Belgium
| | - Michel Waroquier
- Center for Molecular Modeling
(CMM), QCMM Ghent−Brussels Alliance, Ghent University, Technologiepark
903, B9000 Ghent, Belgium
| | - Veronique Van Speybroeck
- Center for Molecular Modeling
(CMM), QCMM Ghent−Brussels Alliance, Ghent University, Technologiepark
903, B9000 Ghent, Belgium
| | - Toon Verstraelen
- Center for Molecular Modeling
(CMM), QCMM Ghent−Brussels Alliance, Ghent University, Technologiepark
903, B9000 Ghent, Belgium
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Wilson AL, Popelier PLA. Exponential Relationships Capturing Atomistic Short-Range Repulsion from the Interacting Quantum Atoms (IQA) Method. J Phys Chem A 2016; 120:9647-9659. [DOI: 10.1021/acs.jpca.6b10295] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Alex L. Wilson
- Manchester Institute of Biotechnology (MIB), 131 Princess Street, Manchester M1 7DN, U.K. and
- School of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, U.K
| | - Paul L. A. Popelier
- Manchester Institute of Biotechnology (MIB), 131 Princess Street, Manchester M1 7DN, U.K. and
- School of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, U.K
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Mao Y, Demerdash O, Head-Gordon M, Head-Gordon T. Assessing Ion-Water Interactions in the AMOEBA Force Field Using Energy Decomposition Analysis of Electronic Structure Calculations. J Chem Theory Comput 2016; 12:5422-5437. [PMID: 27709939 DOI: 10.1021/acs.jctc.6b00764] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
AMOEBA is a molecular mechanics force field that addresses some of the shortcomings of a fixed partial charge model, by including permanent atomic point multipoles through quadrupoles, as well as many-body polarization through the use of point inducible dipoles. In this work, we investigate how well AMOEBA formulates its non-bonded interactions, and how it implicitly incorporates quantum mechanical effects such as charge penetration (CP) and charge transfer (CT), for water-water and water-ion interactions. We find that AMOEBA's total interaction energies, as a function of distance and over angular scans for the water dimer and for a range of water-monovalent cations, agree well with an advanced density functional theory (DFT) model, whereas the water-halides and water-divalent cations show significant disagreement with the DFT result, especially in the compressed region when the two fragments overlap. We use a second-generation energy decomposition analysis (EDA) scheme based on absolutely localized molecular orbitals (ALMOs) to show that in the best cases AMOEBA relies on cancellation of errors by softening of the van der Waals (vdW) wall to balance permanent electrostatics that are too unfavorable, thereby compensating for the missing CP effect. CT, as another important stabilizing effect not explicitly taken into account in AMOEBA, is also found to be incorporated by the softened vdW interaction. For the water-halides and water-divalent cations, this compensatory approach is not as well executed by AMOEBA over all distances and angles, wherein permanent electrostatics remains too unfavorable and polarization is overdamped in the former while overestimated in the latter. We conclude that the DFT-based EDA approach can help refine a next-generation AMOEBA model that either realizes a better cancellation of errors for problematic cases like those illustrated here, or serves to guide the parametrization of explicit functional forms for short-range contributions from CP and/or CT.
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Affiliation(s)
- Yuezhi Mao
- Kenneth S. Pitzer Center for Theoretical Chemistry, and Department of Chemistry, University of California at Berkeley , Berkeley, California 94720, United States
| | - Omar Demerdash
- Kenneth S. Pitzer Center for Theoretical Chemistry, and Department of Chemistry, University of California at Berkeley , Berkeley, California 94720, United States
| | - Martin Head-Gordon
- Kenneth S. Pitzer Center for Theoretical Chemistry, and Department of Chemistry, University of California at Berkeley , Berkeley, California 94720, United States
| | - Teresa Head-Gordon
- Kenneth S. Pitzer Center for Theoretical Chemistry, and Department of Chemistry, University of California at Berkeley , Berkeley, California 94720, United States.,Department of Bioengineering, and Department of Chemical and Biomolecular Engineering, University of California at Berkeley , Berkeley, California 94720, United States
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Madarász Á, Berta D, Paton RS. Development of a True Transition State Force Field from Quantum Mechanical Calculations. J Chem Theory Comput 2016; 12:1833-44. [PMID: 26925858 DOI: 10.1021/acs.jctc.5b01237] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Transition state force fields (TSFF) treated the TS structure as an artificial minimum on the potential energy surface in the past decades. The necessary parameters were developed either manually or by the Quantum-to-molecular mechanics method (Q2MM). In contrast with these approaches, here we propose to model the TS structures as genuine saddle points at the molecular mechanics level. Different methods were tested on small model systems of general chemical reactions such as protonation, nucleophilic attack, and substitution, and the new procedure led to more accurate models than the Q2MM-type parametrization. To demonstrate the practicality of our approach, transferrable parameters have been developed for Mo-catalyzed olefin metathesis using quantum mechanical properties as reference data. Based on the proposed strategy, any force field can be extended with true transition state force field (TTSFF) parameters, and they can be readily applied in several molecular mechanics programs as well.
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Affiliation(s)
- Ádám Madarász
- Research Center for Natural Sciences, Hungarian Academy of Sciences , Magyar Tudosok Korutja 2, H-1117 Budapest, Hungary
| | - Dénes Berta
- Research Center for Natural Sciences, Hungarian Academy of Sciences , Magyar Tudosok Korutja 2, H-1117 Budapest, Hungary
| | - Robert S Paton
- Chemistry Research Laboratory, University of Oxford , Mansfield Road, Oxford OX1 3TA, U.K.,Physical and Theoretical Chemistry Laboratory, University of Oxford , South Parks Road, Oxford OX1 3QZ, U.K
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Wu Q. Variational nature of the frozen density energy in density-based energy decomposition analysis and its application to torsional potentials. J Chem Phys 2014; 140:244109. [DOI: 10.1063/1.4884961] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Qin Wu
- Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, New York 11973, USA
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