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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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2
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Rackers JA, Silva RR, Wang Z, Ponder JW. Polarizable Water Potential Derived from a Model Electron Density. J Chem Theory Comput 2021; 17:7056-7084. [PMID: 34699197 DOI: 10.1021/acs.jctc.1c00628] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A new empirical potential for efficient, large scale molecular dynamics simulation of water is presented. The HIPPO (Hydrogen-like Intermolecular Polarizable POtential) force field is based upon the model electron density of a hydrogen-like atom. This framework is used to derive and parametrize individual terms describing charge penetration damped permanent electrostatics, damped polarization, charge transfer, anisotropic Pauli repulsion, and damped dispersion interactions. Initial parameter values were fit to Symmetry Adapted Perturbation Theory (SAPT) energy components for ten water dimer configurations, as well as the radial and angular dependence of the canonical dimer. The SAPT-based parameters were then systematically refined to extend the treatment to water bulk phases. The final HIPPO water model provides a balanced representation of a wide variety of properties of gas phase clusters, liquid water, and ice polymorphs, across a range of temperatures and pressures. This water potential yields a rationalization of water structure, dynamics, and thermodynamics explicitly correlated with an ab initio energy decomposition, while providing a level of accuracy comparable or superior to previous polarizable atomic multipole force fields. The HIPPO water model serves as a cornerstone around which similarly detailed physics-based models can be developed for additional molecular species.
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Affiliation(s)
- Joshua A Rackers
- Program in Computational & Molecular Biophysics, Washington University School of Medicine, Saint Louis, Missouri 63110, United States.,Center for Computing Research, Sandia National Laboratories, Albuquerque, New Mexico 87123, United States
| | - Roseane R Silva
- Program in Computational & Molecular Biophysics, Washington University School of Medicine, Saint Louis, Missouri 63110, United States
| | - Zhi Wang
- Department of Chemistry, Washington University in Saint Louis, Saint Louis, Missouri 63130, United States
| | - Jay W Ponder
- Department of Chemistry, Washington University in Saint Louis, Saint Louis, Missouri 63130, United States.,Department of Biochemistry & Molecular Biophysics, Washington University School of Medicine, Saint Louis, Missouri 63110, United States
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3
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Naseem-Khan S, Gresh N, Misquitta AJ, Piquemal JP. Assessment of SAPT and Supermolecular EDA Approaches for the Development of Separable and Polarizable Force Fields. J Chem Theory Comput 2021; 17:2759-2774. [DOI: 10.1021/acs.jctc.0c01337] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Sehr Naseem-Khan
- Laboratoire de Chimie Théorique, Sorbonne Université, UMR 7616 CNRS, 75005 Paris, France
| | - Nohad Gresh
- Laboratoire de Chimie Théorique, Sorbonne Université, UMR 7616 CNRS, 75005 Paris, France
| | - 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
| | - Jean-Philip Piquemal
- Laboratoire de Chimie Théorique, Sorbonne Université, UMR 7616 CNRS, 75005 Paris, France
- Institut Universitaire de France, 75005 Paris, France
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
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4
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Melcr J, Piquemal JP. Accurate Biomolecular Simulations Account for Electronic Polarization. Front Mol Biosci 2019; 6:143. [PMID: 31867342 PMCID: PMC6904368 DOI: 10.3389/fmolb.2019.00143] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 11/20/2019] [Indexed: 11/29/2022] Open
Abstract
In this perspective, we discuss where and how accounting for electronic many-body polarization affects the accuracy of classical molecular dynamics simulations of biomolecules. While the effects of electronic polarization are highly pronounced for molecules with an opposite total charge, they are also non-negligible for interactions with overall neutral molecules. For instance, neglecting these effects in important biomolecules like amino acids and phospholipids affects the structure of proteins and membranes having a large impact on interpreting experimental data as well as building coarse grained models. With the combined advances in theory, algorithms and computational power it is currently realistic to perform simulations with explicit polarizable dipoles on systems with relevant sizes and complexity. Alternatively, the effects of electronic polarization can also be included at zero additional computational cost compared to standard fixed-charge force fields using the electronic continuum correction, as was recently demonstrated for several classes of biomolecules.
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Affiliation(s)
- Josef Melcr
- Groningen Biomolecular Sciences and Biotechnology Institute and the Zernike Institute for Advanced Materials, University of Groningen, Groningen, Netherlands
| | - Jean-Philip Piquemal
- Laboratoire de Chimie Théorique, Sorbonne Université, UMR7616 CNRS, Paris, France
- Institut Universitaire de France, Paris, France
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX, United States
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5
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Hagler AT. Force field development phase II: Relaxation of physics-based criteria… or inclusion of more rigorous physics into the representation of molecular energetics. J Comput Aided Mol Des 2018; 33:205-264. [DOI: 10.1007/s10822-018-0134-x] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 07/18/2018] [Indexed: 01/04/2023]
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6
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Bojarowski SA, Kumar P, Wandtke CM, Dittrich B, Dominiak PM. Universal Method for Electrostatic Interaction Energies Estimation with Charge Penetration and Easily Attainable Point Charges. J Chem Theory Comput 2018; 14:6336-6345. [PMID: 30359528 DOI: 10.1021/acs.jctc.8b00781] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Our new model of electron density augmented by point charges (aug-PROmol) provides an estimation of electrostatic interaction energies including penetration effects ( ChemPhysChem 2016, 17, 2455-2460). In this paper we prove that it can be applied using sources of point charges other than those from direct restrained fitting to electrostatic potential (RESP). We used a newly established databank of tabulated invariom point charges and a widely known semiempirical method. Both sources perform equivalently to the basic aug-PROmol method as well as to reference energies at the DFT-SAPT/aug-cc-pVTZ level of theory. This is possible due to the universal character of the penetration model included in the aug-PROmol. Aug-PROmol may become a basis for development of new nonbonded terms in force fields or a high success rate scoring function.
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Affiliation(s)
- Sławomir A Bojarowski
- Biological and Chemical Research Centre, Department of Chemistry , University of Warsaw , ul. Żwirki i Wigury 101 , 02-089 Warszawa , Poland
| | - Prashant Kumar
- Biological and Chemical Research Centre, Department of Chemistry , University of Warsaw , ul. Żwirki i Wigury 101 , 02-089 Warszawa , Poland
| | - Claudia M Wandtke
- Institut fur Anorganische Chemie , Georg-August-Universitat , Tammannstrasse 4 , 37077 Göttingen , Germany
| | - Birger Dittrich
- Anorganische Chemie und Strukturchemie , Heinrich-Heine Universitat Düsseldorf , Universitatsstrasse 1, Gëbaude 26.42.01.21 , 40225 Düsseldorf , Germany
| | - Paulina M Dominiak
- Biological and Chemical Research Centre, Department of Chemistry , University of Warsaw , ul. Żwirki i Wigury 101 , 02-089 Warszawa , Poland
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7
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Rackers JA, Wang Z, Lu C, Laury ML, Lagardère L, Schnieders MJ, Piquemal JP, Ren P, Ponder JW. Tinker 8: Software Tools for Molecular Design. J Chem Theory Comput 2018; 14:5273-5289. [PMID: 30176213 PMCID: PMC6335969 DOI: 10.1021/acs.jctc.8b00529] [Citation(s) in RCA: 290] [Impact Index Per Article: 48.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The Tinker software, currently released as version 8, is a modular molecular mechanics and dynamics package written primarily in a standard, easily portable dialect of Fortran 95 with OpenMP extensions. It supports a wide variety of force fields, including polarizable models such as the Atomic Multipole Optimized Energetics for Biomolecular Applications (AMOEBA) force field. The package runs on Linux, macOS, and Windows systems. In addition to canonical Tinker, there are branches, Tinker-HP and Tinker-OpenMM, designed for use on message passing interface (MPI) parallel distributed memory supercomputers and state-of-the-art graphical processing units (GPUs), respectively. The Tinker suite also includes a tightly integrated Java-based graphical user interface called Force Field Explorer (FFE), which provides molecular visualization capabilities as well as the ability to launch and control Tinker calculations.
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Affiliation(s)
- Joshua A. Rackers
- Program in Computational & Molecular Biophysics, Washington University School of Medicine, Saint Louis, Missouri 63110, United States
| | - Zhi Wang
- Department of Chemistry, Washington University in Saint Louis, Saint Louis, Missouri 63130, United States
| | - Chao Lu
- Department of Chemistry, Washington University in Saint Louis, Saint Louis, Missouri 63130, United States
| | - Marie L. Laury
- Department of Chemistry, Washington University in Saint Louis, Saint Louis, Missouri 63130, United States
| | - Louis Lagardère
- Laboratoire de Chimie Théorique, Sorbonne Universités, UPMC Paris 06, UMR 7616, case courrier 137, 4 place Jussieu, F-75005, Paris, France
| | - Michael J. Schnieders
- Department of Biomedical Engineering, The University of Iowa, Iowa City, IA 52242, United States
| | - Jean-Philip Piquemal
- Laboratoire de Chimie Théorique, Sorbonne Universités, UPMC Paris 06, UMR 7616, case courrier 137, 4 place Jussieu, F-75005, Paris, France
| | - Pengyu Ren
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Jay W. Ponder
- Program in Computational & Molecular Biophysics, Washington University School of Medicine, Saint Louis, Missouri 63110, United States
- Department of Chemistry, Washington University in Saint Louis, Saint Louis, Missouri 63130, United States
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8
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Rackers JA, Liu C, Ren P, Ponder JW. A physically grounded damped dispersion model with particle mesh Ewald summation. J Chem Phys 2018; 149:084115. [PMID: 30193468 DOI: 10.1063/1.5030434] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Accurate modeling of dispersion is critical to the goal of predictive biomolecular simulations. To achieve this accuracy, a model must be able to correctly capture both the short-range and asymptotic behavior of dispersion interactions. We present here a damped dispersion model based on the overlap of charge densities that correctly captures both regimes. The overlap damped dispersion model represents a classical physical interpretation of dispersion: the interaction between the instantaneous induced dipoles of two distinct charge distributions. This model is shown to be an excellent fit with symmetry adapted perturbation theory dispersion energy calculations, yielding an RMS error on the S101x7 database of 0.5 kcal/mol. Moreover, the damping function used in this model is wholly derived and parameterized from the electrostatic dipole-dipole interaction, making it not only physically grounded but transferable as well.
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Affiliation(s)
- Joshua A Rackers
- Program in Computational and Molecular Biophysics, Washington University School of Medicine, Saint Louis, Missouri 63110, USA
| | - Chengwen Liu
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Pengyu Ren
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Jay W Ponder
- Program in Computational and Molecular Biophysics, Washington University School of Medicine, Saint Louis, Missouri 63110, USA
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9
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Marefat Khah A, Karbalaei Khani S, Hättig C. Analytic Excited State Gradients for the QM/MM Polarizable Embedded Second-Order Algebraic Diagrammatic Construction for the Polarization Propagator PE-ADC(2). J Chem Theory Comput 2018; 14:4640-4650. [PMID: 30040882 DOI: 10.1021/acs.jctc.8b00396] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
An implementation of a QM/MM embedding in a polarizable environment is presented for second-order Møller-Plesset perturbation theory, MP2, for ground state energies and molecular gradients and for the second-order Algebraic Diagrammatic Construction, ADC(2), for excitation energies and excited state molecular gradients. In this implementation of PE-MP2 and PE-ADC(2), the polarizable embedded Hartree-Fock wave function is used as uncorrelated reference state. The polarization-correlation cross terms for the ground and excited states are included in this model via an approximate coupling density. A Lagrangian formulation is used to derive the relaxed electron densities and molecular gradients. The resolution-of-the-identity approximation speeds up the calculation of four-index electron repulsion integrals in the molecular orbital basis. As a first application, the method is used to study the photophysical properties of host-guest complexes where the accuracy and weaknesses of the model are also critically examined. It is demonstrated that the ground state geometries of the full quantum mechanical calculation for the supermolecule can be well reproduced. For excited state geometries, the deviations from the supermolecular calculation are slightly larger, but still the environment effects are captured qualitatively correctly, and energy gaps between the ground and excited states are obtained with sufficient accuracy.
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Affiliation(s)
- Alireza Marefat Khah
- Arbeitsgruppe Quantenchemie , Ruhr-Universität Bochum , Bochum D-44801 , Germany
| | | | - Christof Hättig
- Arbeitsgruppe Quantenchemie , Ruhr-Universität Bochum , Bochum D-44801 , Germany
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10
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Bereau T, DiStasio RA, Tkatchenko A, von Lilienfeld OA. Non-covalent interactions across organic and biological subsets of chemical space: Physics-based potentials parametrized from machine learning. J Chem Phys 2018; 148:241706. [DOI: 10.1063/1.5009502] [Citation(s) in RCA: 109] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Tristan Bereau
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Robert A. DiStasio
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, USA
| | - Alexandre Tkatchenko
- Physics and Materials Science Research Unit, University of Luxembourg, L-1511 Luxembourg,
Luxembourg
| | - O. Anatole von Lilienfeld
- Institute of Physical Chemistry and National Center for Computational Design and Discovery of Novel Materials (MARVEL), Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel,
Switzerland
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11
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Wu X, Clavaguera C, Lagardère L, Piquemal JP, de la Lande A. AMOEBA Polarizable Force Field Parameters of the Heme Cofactor in Its Ferrous and Ferric Forms. J Chem Theory Comput 2018; 14:2705-2720. [PMID: 29630819 DOI: 10.1021/acs.jctc.7b01128] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
We report the first parameters of the heme redox cofactors for the polarizable AMOEBA force field in both the ferric and ferrous forms. We consider two types of complexes, one with two histidine side chains as axial ligands and one with a histidine and a methionine side chain as ligands. We have derived permanent multipoles from second-order Møller-Plesset perturbation theory (MP2). The sets of parameters have been validated in a first step by comparison of AMOEBA interaction energies of heme and a collection of biologically relevant molecules with MP2 and Density Functional Theory (DFT) calculations. In a second validation step, we consider interaction energies with large aggregates comprising around 80 H2O molecules. These calculations are repeated for 30 structures extracted from semiempirical PM7 DM simulations. Very encouraging agreement is found between DFT and the AMOEBA force field, which results from an accurate treatment of electrostatic interactions. We finally report long (10 ns) MD simulations of cytochromes in two redox states with AMOEBA testing both the 2003 and 2014 AMOEBA water models. These simulations have been carried out with the TINKER-HP (High Performance) program. In conclusion, owing to their ubiquity in biology, we think the present work opens a wide array of applications of the polarizable AMOEBA force field on hemeproteins.
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Affiliation(s)
- Xiaojing Wu
- Laboratoire de Chimie Physique , Université Paris Sud - CNRS, Université Paris Saclay , 15 Avenue Jean Perrin , 91405 Orsay Cedex , France
| | - Carine Clavaguera
- Laboratoire de Chimie Physique , Université Paris Sud - CNRS, Université Paris Saclay , 15 Avenue Jean Perrin , 91405 Orsay Cedex , France
| | - Louis Lagardère
- Sorbonne Université, CNRS , Institut Parisien de Chimie Physique et Théorique (IP2CT) , 4 Place Jussieu , F-75005 , Paris , France.,Sorbonne Université , Institut des Sciences du Calcul et des Données (ISCD) , 4 place Jussieu , F-75005 , Paris , France
| | - Jean-Philip Piquemal
- Sorbonne Université, CNRS , Laboratoire de Chimie Théorique (LCT) , 4 Place Jussieu , F-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
| | - Aurélien de la Lande
- Laboratoire de Chimie Physique , Université Paris Sud - CNRS, Université Paris Saclay , 15 Avenue Jean Perrin , 91405 Orsay Cedex , France
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12
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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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13
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Esser A, Belsare S, Marx D, Head-Gordon T. Mode specific THz spectra of solvated amino acids using the AMOEBA polarizable force field. Phys Chem Chem Phys 2018; 19:5579-5590. [PMID: 28165073 DOI: 10.1039/c6cp07388c] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We have used the AMOEBA model to simulate the THz spectra of two zwitterionic amino acids in aqueous solution, which is compared to the results on these same systems using ab initio molecular dynamics (AIMD) simulations. Overall we find that the polarizable force field shows promising agreement with AIMD data for both glycine and valine in water. This includes the THz spectral assignments and the mode-specific spectral decomposition into intramolecular solute motions as well as distinct solute-water cross-correlation modes some of which cannot be captured by non-polarizable force fields that rely on fixed partial charges. This bodes well for future studies for simulating and decomposing the THz spectra for larger solutes such as proteins or polymers for which AIMD studies are presently intractable. Furthermore, we believe that the current study on rather simple aqueous solutions offers a way to systematically investigate the importance of charge transfer, nuclear quantum effects, and the validity of computationally practical density functionals, all of which are needed to fully quantitatively capture complex dynamical motions in the condensed phase.
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Affiliation(s)
- Alexander Esser
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, 44780 Bochum, Germany.
| | - Saurabh Belsare
- The UC Berkeley - UCSF Graduate Program in Bioengineering, University of California, Berkeley, CA, 94720, USA
| | - Dominik Marx
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, 44780 Bochum, Germany.
| | - Teresa Head-Gordon
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, Department of Bioengineering, Department of Chemical and Biomolecular Engineering, University of California Berkeley, CA 94720, USA.
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14
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Rackers JA, Wang Q, Liu C, Piquemal JP, Ren P, Ponder JW. An optimized charge penetration model for use with the AMOEBA force field. Phys Chem Chem Phys 2018; 19:276-291. [PMID: 27901142 DOI: 10.1039/c6cp06017j] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The principal challenge of using classical physics to model biomolecular interactions is capturing the nature of short-range interactions that drive biological processes from nucleic acid base stacking to protein-ligand binding. In particular most classical force fields suffer from an error in their electrostatic models that arises from an ability to account for the overlap between charge distributions occurring when molecules get close to each other, known as charge penetration. In this work we present a simple, physically motivated model for including charge penetration in the AMOEBA (Atomic Multipole Optimized Energetics for Biomolecular Applications) force field. With a function derived from the charge distribution of a hydrogen-like atom and a limited number of parameters, our charge penetration model dramatically improves the description of electrostatics at short range. On a database of 101 biomolecular dimers, the charge penetration model brings the error in the electrostatic interaction energy relative to the ab initio SAPT electrostatic interaction energy from 13.4 kcal mol-1 to 1.3 kcal mol-1. The model is shown not only to be robust and transferable for the AMOEBA model, but also physically meaningful as it universally improves the description of the electrostatic potential around a given molecule.
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Affiliation(s)
- Joshua A Rackers
- Program in Computational & Molecular Biophysics, Washington University, School of Medicine, Saint Louis, Missouri 63110, USA
| | - Qiantao Wang
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Chengwen Liu
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Jean-Philip Piquemal
- Laboratoire de Chimie Théorique, Sorbonne Universités, UPMC Paris 06, UMR 7616, case courrier 137, 4 place Jussieu, F-75005, Paris, France
| | - Pengyu Ren
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Jay W Ponder
- Department of Chemistry, Washington University in Saint Louis, Saint Louis, Missouri 63130, USA.
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15
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Lagardère L, Jolly LH, Lipparini F, Aviat F, Stamm B, Jing ZF, Harger M, Torabifard H, Cisneros GA, Schnieders MJ, Gresh N, Maday Y, Ren PY, Ponder JW, Piquemal JP. Tinker-HP: a massively parallel molecular dynamics package for multiscale simulations of large complex systems with advanced point dipole polarizable force fields. Chem Sci 2018; 9:956-972. [PMID: 29732110 PMCID: PMC5909332 DOI: 10.1039/c7sc04531j] [Citation(s) in RCA: 130] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 11/24/2017] [Indexed: 12/23/2022] Open
Abstract
We present Tinker-HP, a massively MPI parallel package dedicated to classical molecular dynamics (MD) and to multiscale simulations, using advanced polarizable force fields (PFF) encompassing distributed multipoles electrostatics. Tinker-HP is an evolution of the popular Tinker package code that conserves its simplicity of use and its reference double precision implementation for CPUs. Grounded on interdisciplinary efforts with applied mathematics, Tinker-HP allows for long polarizable MD simulations on large systems up to millions of atoms. We detail in the paper the newly developed extension of massively parallel 3D spatial decomposition to point dipole polarizable models as well as their coupling to efficient Krylov iterative and non-iterative polarization solvers. The design of the code allows the use of various computer systems ranging from laboratory workstations to modern petascale supercomputers with thousands of cores. Tinker-HP proposes therefore the first high-performance scalable CPU computing environment for the development of next generation point dipole PFFs and for production simulations. Strategies linking Tinker-HP to Quantum Mechanics (QM) in the framework of multiscale polarizable self-consistent QM/MD simulations are also provided. The possibilities, performances and scalability of the software are demonstrated via benchmarks calculations using the polarizable AMOEBA force field on systems ranging from large water boxes of increasing size and ionic liquids to (very) large biosystems encompassing several proteins as well as the complete satellite tobacco mosaic virus and ribosome structures. For small systems, Tinker-HP appears to be competitive with the Tinker-OpenMM GPU implementation of Tinker. As the system size grows, Tinker-HP remains operational thanks to its access to distributed memory and takes advantage of its new algorithmic enabling for stable long timescale polarizable simulations. Overall, a several thousand-fold acceleration over a single-core computation is observed for the largest systems. The extension of the present CPU implementation of Tinker-HP to other computational platforms is discussed.
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Affiliation(s)
- Louis Lagardère
- Sorbonne Université , Institut des Sciences du Calcul et des Données , Paris , France
- Sorbonne Université , Institut Parisien de Chimie Physique et Théorique , CNRS , FR 2622 , Paris , France
- Sorbonne Université , Laboratoire de Chimie Théorique , UMR 7616 , CNRS , Paris , France .
| | - Luc-Henri Jolly
- Sorbonne Université , Institut Parisien de Chimie Physique et Théorique , CNRS , FR 2622 , Paris , France
| | - Filippo Lipparini
- Universita di Pisa , Dipartimento di Chimica e Chimica Industriale , Pisa , Italy
| | - Félix Aviat
- Sorbonne Université , Laboratoire de Chimie Théorique , UMR 7616 , CNRS , Paris , France .
| | - Benjamin Stamm
- MATHCCES , Department of Mathematics , RWTH Aachen University , Aachen , Germany
| | - Zhifeng F Jing
- The University of Texas at Austin , Department of Biomedical Engineering , TX , USA
| | - Matthew Harger
- The University of Texas at Austin , Department of Biomedical Engineering , TX , USA
| | - Hedieh Torabifard
- Department of Chemistry , Wayne State University , Detroit , MI 48202 , USA
| | - G Andrés Cisneros
- Department of Chemistry , University of North Texas , Denton , TX 76202 , USA
| | - Michael J Schnieders
- The University of Iowa , Department of Biomedical Engineering , Iowa City , IA , USA
| | - Nohad Gresh
- Sorbonne Université , Laboratoire de Chimie Théorique , UMR 7616 , CNRS , Paris , France .
| | - Yvon Maday
- Sorbonne Université , Laboratoire Jacques-Louis Lions , UMR 7598 , CNRS , Paris , France
- Institut Universitaire de France , Paris , France
- Brown University , Division of Applied Maths , Providence , RI , USA
| | - Pengyu Y Ren
- The University of Texas at Austin , Department of Biomedical Engineering , TX , USA
| | - Jay W Ponder
- Washington University in Saint Louis , Department of Chemistry , Saint Louis , MI , USA
| | - Jean-Philip Piquemal
- Sorbonne Université , Laboratoire de Chimie Théorique , UMR 7616 , CNRS , Paris , France .
- The University of Texas at Austin , Department of Biomedical Engineering , TX , USA
- Institut Universitaire de France , Paris , France
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16
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Giese TJ, York DM. Quantum mechanical force fields for condensed phase molecular simulations. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2017; 29:383002. [PMID: 28817382 PMCID: PMC5821073 DOI: 10.1088/1361-648x/aa7c5c] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Molecular simulations are powerful tools for providing atomic-level details into complex chemical and physical processes that occur in the condensed phase. For strongly interacting systems where quantum many-body effects are known to play an important role, density-functional methods are often used to provide the model with the potential energy used to drive dynamics. These methods, however, suffer from two major drawbacks. First, they are often too computationally intensive to practically apply to large systems over long time scales, limiting their scope of application. Second, there remain challenges for these models to obtain the necessary level of accuracy for weak non-bonded interactions to obtain quantitative accuracy for a wide range of condensed phase properties. Quantum mechanical force fields (QMFFs) provide a potential solution to both of these limitations. In this review, we address recent advances in the development of QMFFs for condensed phase simulations. In particular, we examine the development of QMFF models using both approximate and ab initio density-functional models, the treatment of short-ranged non-bonded and long-ranged electrostatic interactions, and stability issues in molecular dynamics calculations. Example calculations are provided for crystalline systems, liquid water, and ionic liquids. We conclude with a perspective for emerging challenges and future research directions.
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17
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Loco D, Lagardère L, Caprasecca S, Lipparini F, Mennucci B, Piquemal JP. Hybrid QM/MM Molecular Dynamics with AMOEBA Polarizable Embedding. J Chem Theory Comput 2017; 13:4025-4033. [DOI: 10.1021/acs.jctc.7b00572] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Daniele Loco
- Dipartimento
di Chimica e Chimica Industriale, Università di Pisa, via G. Moruzzi 13, I-56124 Pisa, Italy
| | - Louis Lagardère
- UPMC Univ. Paris
06, Institut des Sciences du Calcul et des Données, F-75005, Paris, France
| | - Stefano Caprasecca
- Dipartimento
di Chimica e Chimica Industriale, Università di Pisa, via G. Moruzzi 13, I-56124 Pisa, Italy
| | - Filippo Lipparini
- Institut
für Physikalische Chemie, Universität Mainz, Duesbergweg 10-14, D-55128 Mainz, Germany
| | - Benedetta Mennucci
- Dipartimento
di Chimica e Chimica Industriale, Università di Pisa, via G. Moruzzi 13, I-56124 Pisa, Italy
| | - Jean-Philip Piquemal
- UPMC Univ. Paris
06, UMR7616, Laboratoire de Chimie Théorique, F-75005, Paris, France
- Institut Universitaire de France, Paris
Cedex 05, 75231, France
- Department
of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
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18
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Harger M, Li D, Wang Z, Dalby K, Lagardère L, Piquemal JP, Ponder J, Ren P. Tinker-OpenMM: Absolute and relative alchemical free energies using AMOEBA on GPUs. J Comput Chem 2017; 38:2047-2055. [PMID: 28600826 DOI: 10.1002/jcc.24853] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2017] [Accepted: 05/06/2017] [Indexed: 12/27/2022]
Abstract
The capabilities of the polarizable force fields for alchemical free energy calculations have been limited by the high computational cost and complexity of the underlying potential energy functions. In this work, we present a GPU-based general alchemical free energy simulation platform for polarizable potential AMOEBA. Tinker-OpenMM, the OpenMM implementation of the AMOEBA simulation engine has been modified to enable both absolute and relative alchemical simulations on GPUs, which leads to a ∼200-fold improvement in simulation speed over a single CPU core. We show that free energy values calculated using this platform agree with the results of Tinker simulations for the hydration of organic compounds and binding of host-guest systems within the statistical errors. In addition to absolute binding, we designed a relative alchemical approach for computing relative binding affinities of ligands to the same host, where a special path was applied to avoid numerical instability due to polarization between the different ligands that bind to the same site. This scheme is general and does not require ligands to have similar scaffolds. We show that relative hydration and binding free energy calculated using this approach match those computed from the absolute free energy approach. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Matthew Harger
- Department of Biomedical Engineering, University of Texas at Austin, Austin, Texas, 78712
| | - Daniel Li
- Department of Biomedical Engineering, University of Texas at Austin, Austin, Texas, 78712
| | - Zhi Wang
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri, 63130
| | - Kevin Dalby
- Division of Chemical Biology and Medicinal Chemistry, University of Texas at Austin, Austin, Texas, 78712
| | - Louis Lagardère
- Institut des Sciences du Calcul et des Données, UPMC Université Paris 06, F-75005, Paris, France
| | - Jean-Philip Piquemal
- Laboratoire de Chimie Théorique, Sorbonne Universités, UPMC, UMR7616 CNRS, Paris, France.,Institut Universitaire de France, Paris Cedex 05, 75231, France
| | - Jay Ponder
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri, 63130
| | - Pengyu Ren
- Department of Biomedical Engineering, University of Texas at Austin, Austin, Texas, 78712
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19
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Mao Y, Shao Y, Dziedzic J, Skylaris CK, Head-Gordon T, Head-Gordon M. Performance of the AMOEBA Water Model in the Vicinity of QM Solutes: A Diagnosis Using Energy Decomposition Analysis. J Chem Theory Comput 2017; 13:1963-1979. [PMID: 28430427 DOI: 10.1021/acs.jctc.7b00089] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The importance of incorporating solvent polarization effects into the modeling of solvation processes has been well-recognized, and therefore a new generation of hybrid quantum mechanics/molecular mechanics (QM/MM) approaches that accounts for this effect is desirable. We present a fully self-consistent, mutually polarizable QM/MM scheme using the AMOEBA force field, in which the total energy of the system is variationally minimized with respect to both the QM electronic density and the MM induced dipoles. This QM/AMOEBA model is implemented through the Q-Chem/LibEFP code interface and then applied to the evaluation of solute-solvent interaction energies for various systems ranging from the water dimer to neutral and ionic solutes (NH3, NH4+, CN-) surrounded by increasing numbers of water molecules (up to 100). In order to analyze the resulting interaction energies, we also utilize an energy decomposition analysis (EDA) scheme which identifies contributions from permanent electrostatics, polarization, and van der Waals (vdW) interaction for the interaction between the QM solute and the solvent molecules described by AMOEBA. This facilitates a component-wise comparison against full QM calculations where the corresponding energy components are obtained via a modified version of the absolutely localized molecular orbitals (ALMO)-EDA. The results show that the present QM/AMOEBA model can yield reasonable solute-solvent interaction energies for neutral and cationic species, while further scrutiny reveals that this accuracy highly relies on the delicate balance between insufficiently favorable permanent electrostatics and softened vdW interaction. For anionic solutes where the charge penetration effect becomes more pronounced, the QM/MM interface turns out to be unbalanced. These results are consistent with and further elucidate our findings in a previous study using a slightly different QM/AMOEBA model ( Dziedzic et al. J. Chem. Phys. 2016 , 145 , 124106 ). The implications of these results for further refinement of this model are also discussed.
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Affiliation(s)
| | - Yihan Shao
- Department of Chemistry and Biochemistry, University of Oklahoma , Norman, Oklahoma 73019, United States
| | - Jacek Dziedzic
- School of Chemistry, University of Southampton , Highfield, Southampton SO17 1BJ, U.K.,Faculty of Applied Physics and Mathematics, Gdańsk University of Technology , Gdańsk 80-233, Poland
| | - Chris-Kriton Skylaris
- School of Chemistry, University of Southampton , Highfield, Southampton SO17 1BJ, U.K
| | | | - Martin Head-Gordon
- Chemical Science Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
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20
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Wang H, Yang W. Determining polarizable force fields with electrostatic potentials from quantum mechanical linear response theory. J Chem Phys 2017; 144:224107. [PMID: 27305996 DOI: 10.1063/1.4953558] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We developed a new method to calculate the atomic polarizabilities by fitting to the electrostatic potentials (ESPs) obtained from quantum mechanical (QM) calculations within the linear response theory. This parallels the conventional approach of fitting atomic charges based on electrostatic potentials from the electron density. Our ESP fitting is combined with the induced dipole model under the perturbation of uniform external electric fields of all orientations. QM calculations for the linear response to the external electric fields are used as input, fully consistent with the induced dipole model, which itself is a linear response model. The orientation of the uniform external electric fields is integrated in all directions. The integration of orientation and QM linear response calculations together makes the fitting results independent of the orientations and magnitudes of the uniform external electric fields applied. Another advantage of our method is that QM calculation is only needed once, in contrast to the conventional approach, where many QM calculations are needed for many different applied electric fields. The molecular polarizabilities obtained from our method show comparable accuracy with those from fitting directly to the experimental or theoretical molecular polarizabilities. Since ESP is directly fitted, atomic polarizabilities obtained from our method are expected to reproduce the electrostatic interactions better. Our method was used to calculate both transferable atomic polarizabilities for polarizable molecular mechanics' force fields and nontransferable molecule-specific atomic polarizabilities.
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Affiliation(s)
- Hao Wang
- Department of Chemistry, Duke University, Durham, North Carolina 27708, USA
| | - Weitao Yang
- Department of Chemistry, Duke University, Durham, North Carolina 27708, USA
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21
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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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22
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Albaugh A, Bradshaw RT, Demerdash O, Dziedzic J, Mao Y, Margul DT, Swails J, Boateng HA, Case DA, Eastman P, Essex JW, Head-Gordon M, Pande VS, Ponder J, Shao Y, Skylaris C, Todorov IT, Tuckerman ME, Zeng Q, Head-Gordon T. Advanced Potential Energy Surfaces for Molecular Simulation. J Phys Chem B 2016; 120:9811-32. [PMID: 27513316 PMCID: PMC9113031 DOI: 10.1021/acs.jpcb.6b06414] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Advanced potential energy surfaces are defined as theoretical models that explicitly include many-body effects that transcend the standard fixed-charge, pairwise-additive paradigm typically used in molecular simulation. However, several factors relating to their software implementation have precluded their widespread use in condensed-phase simulations: the computational cost of the theoretical models, a paucity of approximate models and algorithmic improvements that can ameliorate their cost, underdeveloped interfaces and limited dissemination in computational code bases that are widely used in the computational chemistry community, and software implementations that have not kept pace with modern high-performance computing (HPC) architectures, such as multicore CPUs and modern graphics processing units (GPUs). In this Feature Article we review recent progress made in these areas, including well-defined polarization approximations and new multipole electrostatic formulations, novel methods for solving the mutual polarization equations and increasing the MD time step, combining linear-scaling electronic structure methods with new QM/MM methods that account for mutual polarization between the two regions, and the greatly improved software deployment of these models and methods onto GPU and CPU hardware platforms. We have now approached an era where multipole-based polarizable force fields can be routinely used to obtain computational results comparable to state-of-the-art density functional theory while reaching sampling statistics that are acceptable when compared to that obtained from simpler fixed partial charge force fields.
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Affiliation(s)
- Alex Albaugh
- Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94720
| | - Richard T. Bradshaw
- School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, UK
| | - Omar Demerdash
- Department of Chemistry, University of California, Berkeley, CA 94720
| | - Jacek Dziedzic
- School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, UK
- Faculty of Applied Physics and Mathematics, Gdansk University of Technology, Poland
| | - Yuezhi Mao
- Department of Chemistry, University of California, Berkeley, CA 94720
| | - Daniel T. Margul
- Department of Chemistry, New York University, New York, NY 10003, USA
| | - Jason Swails
- Department of Chemistry and Chemical Biology and BioMaPS Institute, Rutgers University, Piscataway, New Jersey 08854-8066, United States
| | - Henry A. Boateng
- Department of Mathematics, Bates College, 2 Andrews Road, Lewiston, ME 04240
| | - David A. Case
- Department of Chemistry and Chemical Biology and BioMaPS Institute, Rutgers University, Piscataway, New Jersey 08854-8066, United States
| | - Peter Eastman
- Department of Chemistry, Stanford University, Stanford, CA 94305
| | - Jonathan W. Essex
- School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, UK
| | | | - Vijay S. Pande
- Department of Chemistry, Stanford University, Stanford, CA 94305
| | - Jay Ponder
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri, 63130
| | - Yihan Shao
- Q-Chem Inc., 6601 Owens Drive, Suite 105, Pleasanton, California 94588
| | - Chris Skylaris
- School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, UK
| | - Illian T. Todorov
- STFC Daresbury Laboratory, Keckwick Lane, Daresbury, Warrington WA4 4AD, UK
| | - Mark E. Tuckerman
- Department of Chemistry, New York University, New York, NY 10003, USA
- Courant Institute of Mathematical Sciences, New York University, New York, NY 10003, USA
- NYU-ECNU, Center for Computational Chemistry at NYU, Shanghai, Shanghai 200062, China
| | - Qiao Zeng
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892
| | - Teresa Head-Gordon
- Department of Chemistry, University of California, Berkeley, CA 94720
- Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94720
- Bioengineering, University of California, Berkeley, CA 94720
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23
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Loco D, Polack É, Caprasecca S, Lagardère L, Lipparini F, Piquemal JP, Mennucci B. A QM/MM Approach Using the AMOEBA Polarizable Embedding: From Ground State Energies to Electronic Excitations. J Chem Theory Comput 2016; 12:3654-61. [DOI: 10.1021/acs.jctc.6b00385] [Citation(s) in RCA: 109] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Daniele Loco
- Dipartimento
di Chimica e Chimica Industriale, Università di Pisa, via G. Moruzzi
13, I-56124 Pisa, Italy
| | - Étienne Polack
- Sorbonne Universités,
UPMC Univ. Paris 06, UMR 7616, Laboratoire de Chimie Théorique, F-75005, Paris, France
- Sorbonne Universités,
UPMC Univ. Paris 06, UMR 7598, Laboratoire Jacques-Louis Lions, F-75005, Paris, France
| | - Stefano Caprasecca
- Dipartimento
di Chimica e Chimica Industriale, Università di Pisa, via G. Moruzzi
13, I-56124 Pisa, Italy
| | - Louis Lagardère
- Sorbonne Universités,
UPMC Univ. Paris 06, UMR 7616, Laboratoire de Chimie Théorique, F-75005, Paris, France
- Sorbonne Universités,
UPMC Univ. Paris 06, Institut du Calcul et de la Simulation, F-75005, Paris, France
| | - Filippo Lipparini
- Institut
für Physikalische Chemie, Universität Mainz, Duesbergweg 10-14, D-55128 Mainz, Germany
| | - Jean-Philip Piquemal
- Sorbonne Universités,
UPMC Univ. Paris 06, UMR 7616, Laboratoire de Chimie Théorique, F-75005, Paris, France
- CNRS, UMR 7598 and 7616, F-75005, Paris, France
- Department
of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Benedetta Mennucci
- Dipartimento
di Chimica e Chimica Industriale, Università di Pisa, via G. Moruzzi
13, I-56124 Pisa, Italy
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24
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Bojarowski SA, Kumar P, Dominiak PM. A Universal and Straightforward Approach to Include Penetration Effects in Electrostatic Interaction Energy Estimation. Chemphyschem 2016; 17:2455-60. [PMID: 27166026 DOI: 10.1002/cphc.201600390] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Indexed: 12/23/2022]
Abstract
To compensate for the lack of the explicit treatment of charge penetration in classical force fields, we propose a new charge-distribution model based on a promolecule augmented with point charges (aug-PROmol). It relies on a superposition of spherical atomic electron densities obtained for each chemical element from SCF energy optimized atomic orbitals. Atomic densities are further rescaled by partial point charges computed from fits to the molecular electrostatic potential. Aug-PROmol was tested on the S66 benchmark dataset extended to nonequilibrium geometries (J. Chem. Theory Comput., 2011, 7, 3466). The model does not need any additional parametrization other than point charges. Despite its simplicity, aug-PROmol approximates the electrostatic energy with good agreement (RMSE=0.76 kcal mol(-1) to DFT-SAPT with B3LYP/aug-cc-pVTZ).
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Affiliation(s)
- Sławomir A Bojarowski
- Department of Chemistry, Biological and Chemical Research Centre, University of Warsaw, ul. Żwirki i Wigury 101, 02-089, Warszawa, Poland
| | - Prashant Kumar
- Department of Chemistry, Biological and Chemical Research Centre, University of Warsaw, ul. Żwirki i Wigury 101, 02-089, Warszawa, Poland
| | - Paulina M Dominiak
- Department of Chemistry, Biological and Chemical Research Centre, University of Warsaw, ul. Żwirki i Wigury 101, 02-089, Warszawa, Poland.
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