Literature DB >> 29775314

QM/MM Simulations with the Gaussian Electrostatic Model: A Density-based Polarizable Potential.

Hatice Gökcan1, Eric Kratz2, Thomas A Darden3, Jean-Philip Piquemal4,5,6, G Andrés Cisneros1.   

Abstract

The use of advanced polarizable potentials in quantum mechanical/molecular mechanical (QM/MM) simulations has been shown to improve the overall accuracy of the calculation. We have developed a density-based potential called the Gaussian electrostatic model (GEM), which has been shown to provide very accurate environments for QM wave functions in QM/MM. In this contribution we present a new implementation of QM/GEM that extends our implementation to include all components (Coulomb, exchange-repulsion, polarization, and dispersion) for the total intermolecular interaction energy in QM/MM calculations, except for the charge-transfer term. The accuracy of the method is tested using a subset of water dimers from the water dimer potential energy surface reported by Babin et al. ( J. Chem. Theory Comput. 2013 9, 5395-5403). Additionally, results of the new implementation are contrasted with results obtained with the classical AMOEBA potential. Our results indicate that GEM provides an accurate MM environment with average root-mean-square error <0.15 kcal/mol for every intermolecular interaction energy component compared with SAPT2+3/aug-cc-pVTZ reference calculations.

Entities:  

Year:  2018        PMID: 29775314      PMCID: PMC6069983          DOI: 10.1021/acs.jpclett.8b01412

Source DB:  PubMed          Journal:  J Phys Chem Lett        ISSN: 1948-7185            Impact factor:   6.475


  39 in total

1.  Ion solvation thermodynamics from simulation with a polarizable force field.

Authors:  Alan Grossfield; Pengyu Ren; Jay W Ponder
Journal:  J Am Chem Soc       Date:  2003-12-17       Impact factor: 15.419

2.  Multiple high-level QM/MM reaction paths demonstrate transition-state stabilization in chorismate mutase: correlation of barrier height with transition-state stabilization.

Authors:  Frederik Claeyssens; Kara E Ranaghan; Frederick R Manby; Jeremy N Harvey; Adrian J Mulholland
Journal:  Chem Commun (Camb)       Date:  2005-09-07       Impact factor: 6.222

3.  A critical evaluation of different QM/MM frontier treatments with SCC-DFTB as the QM method.

Authors:  P H König; M Hoffmann; Th Frauenheim; Q Cui
Journal:  J Phys Chem B       Date:  2005-05-12       Impact factor: 2.991

4.  An efficient method for the calculation of quantum mechanics/molecular mechanics free energies.

Authors:  Christopher J Woods; Frederick R Manby; Adrian J Mulholland
Journal:  J Chem Phys       Date:  2008-01-07       Impact factor: 3.488

5.  Polarizable density embedding: a new QM/QM/MM-based computational strategy.

Authors:  Jógvan Magnus Haugaard Olsen; Casper Steinmann; Kenneth Ruud; Jacob Kongsted
Journal:  J Phys Chem A       Date:  2015-02-02       Impact factor: 2.781

6.  Hybrid QM/MM Molecular Dynamics with AMOEBA Polarizable Embedding.

Authors:  Daniele Loco; Louis Lagardère; Stefano Caprasecca; Filippo Lipparini; Benedetta Mennucci; Jean-Philip Piquemal
Journal:  J Chem Theory Comput       Date:  2017-08-14       Impact factor: 6.006

7.  Polarizable Density Embedding: A Solution to the Electron Spill-Out Problem in Multiscale Modeling.

Authors:  Peter Reinholdt; Jacob Kongsted; Jógvan Magnus Haugaard Olsen
Journal:  J Phys Chem Lett       Date:  2017-11-29       Impact factor: 6.475

8.  Testing high-level QM/MM methods for modeling enzyme reactions: acetyl-CoA deprotonation in citrate synthase.

Authors:  Marc W van der Kamp; Jolanta Zurek; Frederick R Manby; Jeremy N Harvey; Adrian J Mulholland
Journal:  J Phys Chem B       Date:  2010-09-02       Impact factor: 2.991

9.  GEM*: A Molecular Electronic Density-Based Force Field for Molecular Dynamics Simulations.

Authors:  Robert E Duke; Oleg N Starovoytov; Jean-Philip Piquemal; G Andrés Cisneros
Journal:  J Chem Theory Comput       Date:  2014-03-03       Impact factor: 6.006

10.  Tinker-HP: a massively parallel molecular dynamics package for multiscale simulations of large complex systems with advanced point dipole polarizable force fields.

Authors:  Louis Lagardère; Luc-Henri Jolly; Filippo Lipparini; Félix Aviat; Benjamin Stamm; Zhifeng F Jing; Matthew Harger; Hedieh Torabifard; G Andrés Cisneros; Michael J Schnieders; Nohad Gresh; Yvon Maday; Pengyu Y Ren; Jay W Ponder; Jean-Philip Piquemal
Journal:  Chem Sci       Date:  2017-11-27       Impact factor: 9.825

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  8 in total

1.  Classical Pauli repulsion: An anisotropic, atomic multipole model.

Authors:  Joshua A Rackers; Jay W Ponder
Journal:  J Chem Phys       Date:  2019-02-28       Impact factor: 3.488

2.  A Many-Body, Fully Polarizable Approach to QM/MM Simulations.

Authors:  Eleftherios Lambros; Filippo Lipparini; Gerardo Andrés Cisneros; Francesco Paesani
Journal:  J Chem Theory Comput       Date:  2020-11-19       Impact factor: 6.006

3.  LICHEM 1.1: Recent Improvements and New Capabilities.

Authors:  Hatice Gökcan; Erik Antonio Vázquez-Montelongo; G Andrés Cisneros
Journal:  J Chem Theory Comput       Date:  2019-04-02       Impact factor: 6.006

4.  A Minimum Quantum Chemistry CCSD(T)/CBS Data Set of Dimeric Interaction Energies for Small Organic Functional Groups: Heterodimers.

Authors:  Hsing-Hsiang Huang; Yi-Siang Wang; Sheng D Chao
Journal:  ACS Omega       Date:  2022-05-31

5.  Ewald-based methods for Gaussian integral evaluation: application to a new parameterization of GEM.

Authors:  Robert E Duke; G Andrés Cisneros
Journal:  J Mol Model       Date:  2019-09-09       Impact factor: 1.810

6.  A simplified charge projection scheme for long-range electrostatics in ab initio QM/MM calculations.

Authors:  Xiaoliang Pan; Kwangho Nam; Evgeny Epifanovsky; Andrew C Simmonett; Edina Rosta; Yihan Shao
Journal:  J Chem Phys       Date:  2021-01-14       Impact factor: 3.488

7.  Polarizable Water Potential Derived from a Model Electron Density.

Authors:  Joshua A Rackers; Roseane R Silva; Zhi Wang; Jay W Ponder
Journal:  J Chem Theory Comput       Date:  2021-10-26       Impact factor: 6.006

8.  Development and application of quantum mechanics/molecular mechanics methods with advanced polarizable potentials.

Authors:  Jorge Nochebuena; Sehr Naseem-Khan; G Andrés Cisneros
Journal:  Wiley Interdiscip Rev Comput Mol Sci       Date:  2021-01-12
  8 in total

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