Literature DB >> 33213149

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

Eleftherios Lambros1, Filippo Lipparini2, Gerardo Andrés Cisneros3, Francesco Paesani1,4,5.   

Abstract

We present a new development in quantum mechanics/molecular mechanics (QM/MM) methods by replacing conventional MM models with data-driven many-body (MB) representations rigorously derived from high-level QM calculations. The new QM/MM approach builds on top of mutually polarizable QM/MM schemes developed for polarizable force fields with inducible dipoles and uses permutationally invariant polynomials to effectively account for quantum-mechanical contributions (e.g., exchange-repulsion and charge transfer and penetration) that are difficult to describe by classical expressions adopted by conventional MM models. Using the many-body MB-pol and MB-DFT potential energy functions for water, which include explicit two-body and three-body terms fitted to reproduce the corresponding CCSD(T) and PBE0 two-body and three-body energies for water, we demonstrate a smooth energetic transition as molecules are transferred between QM and MM regions, without the need of a transition layer. By effectively elevating the accuracy of both the MM region and the QM/MM interface to that of the QM region, the new QM/MB-MM approach achieves an accuracy comparable to that obtained with a fully QM treatment of the entire system.

Entities:  

Year:  2020        PMID: 33213149      PMCID: PMC8131112          DOI: 10.1021/acs.jctc.0c00932

Source DB:  PubMed          Journal:  J Chem Theory Comput        ISSN: 1549-9618            Impact factor:   6.006


  69 in total

Review 1.  Force fields for protein simulations.

Authors:  Jay W Ponder; David A Case
Journal:  Adv Protein Chem       Date:  2003

2.  Variational calculation of quantum mechanical/molecular mechanical free energy with electronic polarization of solvent.

Authors:  Hiroshi Nakano; Takeshi Yamamoto
Journal:  J Chem Phys       Date:  2012-04-07       Impact factor: 3.488

3.  Analytical First and Second Derivatives for a Fully Polarizable QM/Classical Hamiltonian.

Authors:  Filippo Lipparini; Chiara Cappelli; Giovanni Scalmani; Nicola De Mitri; Vincenzo Barone
Journal:  J Chem Theory Comput       Date:  2012-10-11       Impact factor: 6.006

4.  LICHEM: A QM/MM program for simulations with multipolar and polarizable force fields.

Authors:  Eric G Kratz; Alice R Walker; Louis Lagardère; Filippo Lipparini; Jean-Philip Piquemal; G Andrés Cisneros
Journal:  J Comput Chem       Date:  2016-01-18       Impact factor: 3.376

5.  Adaptive partitioning in combined quantum mechanical and molecular mechanical calculations of potential energy functions for multiscale simulations.

Authors:  Andreas Heyden; Hai Lin; Donald G Truhlar
Journal:  J Phys Chem B       Date:  2007-02-09       Impact factor: 2.991

6.  Theoretical studies of enzymic reactions: dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme.

Authors:  A Warshel; M Levitt
Journal:  J Mol Biol       Date:  1976-05-15       Impact factor: 5.469

7.  Mutually polarizable QM/MM model with in situ optimized localized basis functions.

Authors:  Jacek Dziedzic; Teresa Head-Gordon; Martin Head-Gordon; Chris-Kriton Skylaris
Journal:  J Chem Phys       Date:  2019-02-21       Impact factor: 3.488

8.  Polarizable QM/MM Approach with Fluctuating Charges and Fluctuating Dipoles: The QM/FQFμ Model.

Authors:  Tommaso Giovannini; Alessandra Puglisi; Matteo Ambrosetti; Chiara Cappelli
Journal:  J Chem Theory Comput       Date:  2019-03-29       Impact factor: 6.006

9.  A gauge invariant multiscale approach to magnetic spectroscopies in condensed phase: general three-layer model, computational implementation and pilot applications.

Authors:  Filippo Lipparini; Chiara Cappelli; Vincenzo Barone
Journal:  J Chem Phys       Date:  2013-06-21       Impact factor: 3.488

10.  A Comparison of QM/MM Simulations with and without the Drude Oscillator Model Based on Hydration Free Energies of Simple Solutes.

Authors:  Gerhard König; Frank C Pickard; Jing Huang; Walter Thiel; Alexander D MacKerell; Bernard R Brooks; Darrin M York
Journal:  Molecules       Date:  2018-10-19       Impact factor: 4.411

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  3 in total

1.  Biomolecular QM/MM Simulations: What Are Some of the "Burning Issues"?

Authors:  Qiang Cui; Tanmoy Pal; Luke Xie
Journal:  J Phys Chem B       Date:  2021-01-06       Impact factor: 2.991

2.  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

3.  QM/MM Energy Decomposition Using the Interacting Quantum Atoms Approach.

Authors:  Roberto López; Natalia Díaz; Evelio Francisco; Angel Martín-Pendás; Dimas Suárez
Journal:  J Chem Inf Model       Date:  2022-02-25       Impact factor: 4.956

  3 in total

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