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Naseem-Khan S, Lagardère L, Narth C, Cisneros GA, Ren P, Gresh N, Piquemal JP. Development of the Quantum-Inspired SIBFA Many-Body Polarizable Force Field: Enabling Condensed-Phase Molecular Dynamics Simulations. J Chem Theory Comput 2022; 18:3607-3621. [PMID: 35575306 PMCID: PMC10851344 DOI: 10.1021/acs.jctc.2c00029] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
We present the extension of the Sum of Interactions Between Fragments Ab initio Computed (SIBFA) many-body polarizable force field to condensed-phase molecular dynamics (MD) simulations. The quantum-inspired SIBFA procedure is grounded on simplified integrals obtained from localized molecular orbital theory and achieves full separability of its intermolecular potential. It embodies long-range multipolar electrostatics (up to quadrupole) coupled to a short-range penetration correction (up to charge-quadrupole), exchange repulsion, many-body polarization, many-body charge transfer/delocalization, exchange dispersion, and dispersion (up to C10). This enables the reproduction of all energy contributions of ab initio symmetry-adapted perturbation theory (SAPT(DFT)) gas-phase reference computations. The SIBFA approach has been integrated within the Tinker-HP massively parallel MD package. To do so, all SIBFA energy gradients have been derived and the approach has been extended to enable periodic boundary conditions simulations using smooth particle mesh Ewald. This novel implementation also notably includes a computationally tractable simplification of the many-body charge transfer/delocalization contribution. As a proof of concept, we perform a first computational experiment defining a water model fitted on a limited set of SAPT(DFT) data. SIBFA is shown to enable a satisfactory reproduction of both gas-phase energetic contributions and condensed-phase properties highlighting the importance of its physically motivated functional form.
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Affiliation(s)
- Sehr Naseem-Khan
- LCT, UMR 7616 CNRS, Sorbonne Université, 75005 Paris, France
- Department of Chemistry, University of North Texas, Denton, Texas 76201, United States
| | - Louis Lagardère
- LCT, UMR 7616 CNRS, Sorbonne Université, 75005 Paris, France
- IP2CT, FR 2622, CNRS, Sorbonne Université, 75005 Paris, France
| | | | - G Andrés Cisneros
- Department of Chemistry, University of North Texas, Denton, Texas 76201, United States
| | - Pengyu Ren
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Nohad Gresh
- LCT, UMR 7616 CNRS, Sorbonne Université, 75005 Paris, France
| | - Jean-Philip Piquemal
- LCT, UMR 7616 CNRS, Sorbonne Université, 75005 Paris, France
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
- Institut Universitaire de France, 75005 Paris, France
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Gresh N, Perahia D. Multimolecular complexes of the phosphodiester anion with Zn(II) or Mg(II) and water molecules-Preliminary validations of a polarizable potential by ab initio quantum chemistry. J Comput Chem 2021; 42:1430-1446. [PMID: 34101861 DOI: 10.1002/jcc.26555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 04/26/2021] [Accepted: 04/27/2021] [Indexed: 11/06/2022]
Abstract
Dimethyl phosphate (DMP- ) is a model for the phosphodiester backbone of DNA, RNA, and phospholipids. It is central for the binding of divalent cations and water along the backbone of nucleic acids. Significant polarization and charge-transfer contributions and nonadditivity come into play in the multimolecular complexes organized around phosphate. Prior to large-scale molecular dynamics (MD) with advanced polarizable potentials, it is essential to evaluate how well the values and trends of intermolecular interaction energies (ΔE) from ab initio quantum chemistry (QC) and their individual contributions are reproduced in a diversity of such complexes. These differ by the starting binding modes of a divalent cation, Zn(II), namely direct, bi- or mono-dentate to anionic and/or ester oxygens, versus through-water binding. We present first the results from automated refinements of the individual contributions of the SIBFA potential with respect to their QC counterparts using a Zn(II) or a water probe. This is followed by validations on eight relaxed multimolecular complexes of DMP- with Zn(II) or Mg(II) and seven waters, then on sixteen complexes of DMP- with Zn(II) and eight waters in arrangements extracted from MD or energy-minimization on a droplet of sixty-four waters. This monitors the compared evolutions of SIBFA and QC ΔE and their individual contributions in the competing arrangements. Some waters, bridging Zn(II) and DMP- , were found to have exceptionally large dipole moments, of up to 3.8 Debye. The perspectives of extension to a flexible phosphodiester backbone are discussed in the context of the SIBFA potential for DNA and RNA.
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Affiliation(s)
- Nohad Gresh
- Laboratoire de Chimie Théorique, UMR 7616 CNRS, Sorbonne Université, Paris, France
| | - David Perahia
- Laboratoire de Biologie et Pharmacologie Appliquées, UMR 8113 CNRS, Ecole Normale Supérieure Paris-Saclay, Gif-sur-Yvette, France
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Kwapien K, Gavara L, Docquier J, Berthomieu D, Hernandez J, Gresh N. Intermolecular interactions of the extended recognition site of
VIM
‐2
metallo‐β‐lactamase
with 1,2,4‐triazole‐3‐thione inhibitors. Validations of a polarizable molecular mechanics potential by ab initio
QC. J Comput Chem 2020; 42:86-106. [DOI: 10.1002/jcc.26437] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 09/30/2020] [Accepted: 10/01/2020] [Indexed: 12/12/2022]
Affiliation(s)
- Karolina Kwapien
- Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques Université de Paris UMR 8601 Paris France
- Laboratoire de Chimie Théorique Paris France
- Institut Charles Gerhardt, UMR 5253, CNRS, Université de Montpellier, ENSCM Montpellier France
| | - Laurent Gavara
- Institut des Biomolécules Max Mousseron, UMR 5247 CNRS, Université de Montpellier, ENSCM, Faculté de Pharmacie Montpellier France
| | | | - Dorothée Berthomieu
- Institut Charles Gerhardt, UMR 5253, CNRS, Université de Montpellier, ENSCM Montpellier France
| | - Jean‐François Hernandez
- Institut des Biomolécules Max Mousseron, UMR 5247 CNRS, Université de Montpellier, ENSCM, Faculté de Pharmacie Montpellier France
| | - Nohad Gresh
- Laboratoire de Chimie Théorique Paris France
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