Literature DB >> 27332140

Toward Hamiltonian Adaptive QM/MM: Accurate Solvent Structures Using Many-Body Potentials.

Jelle M Boereboom1, Raffaello Potestio2, Davide Donadio2,3,4,5, Rosa E Bulo1.   

Abstract

Adaptive quantum mechanical (QM)/molecular mechanical (MM) methods enable efficient molecular simulations of chemistry in solution. Reactive subregions are modeled with an accurate QM potential energy expression while the rest of the system is described in a more approximate manner (MM). As solvent molecules diffuse in and out of the reactive region, they are gradually included into (and excluded from) the QM expression. It would be desirable to model such a system with a single adaptive Hamiltonian, but thus far this has resulted in distorted structures at the boundary between the two regions. Solving this long outstanding problem will allow microcanonical adaptive QM/MM simulations that can be used to obtain vibrational spectra and dynamical properties. The difficulty lies in the complex QM potential energy expression, with a many-body expansion that contains higher order terms. Here, we outline a Hamiltonian adaptive multiscale scheme within the framework of many-body potentials. The adaptive expressions are entirely general, and complementary to all standard (nonadaptive) QM/MM embedding schemes available. We demonstrate the merit of our approach on a molecular system defined by two different MM potentials (MM/MM'). For the long-range interactions a numerical scheme is used (particle mesh Ewald), which yields energy expressions that are many-body in nature. Our Hamiltonian approach is the first to provide both energy conservation and the correct solvent structure everywhere in this system.

Year:  2016        PMID: 27332140     DOI: 10.1021/acs.jctc.6b00205

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


  7 in total

1.  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

2.  Computational methods and theory for ion channel research.

Authors:  C Guardiani; F Cecconi; L Chiodo; G Cottone; P Malgaretti; L Maragliano; M L Barabash; G Camisasca; M Ceccarelli; B Corry; R Roth; A Giacomello; B Roux
Journal:  Adv Phys X       Date:  2022

3.  Adaptive-Partitioning Multilayer Dynamics Simulations: 1. On-the-Fly Switch between Two Quantum Levels of Theory.

Authors:  Joani Mato; Adam W Duster; Emilie B Guidez; Hai Lin
Journal:  J Chem Theory Comput       Date:  2021-08-27       Impact factor: 6.578

4.  Explicit Solvation Matters: Performance of QM/MM Solvation Models in Nucleophilic Addition.

Authors:  Jelle M Boereboom; Paul Fleurat-Lessard; Rosa E Bulo
Journal:  J Chem Theory Comput       Date:  2018-03-16       Impact factor: 6.006

5.  Adaptive QM/MM for Molecular Dynamics Simulations: 5. On the Energy-Conserved Permuted Adaptive-Partitioning Schemes.

Authors:  Adam W Duster; Chun-Hung Wang; Hai Lin
Journal:  Molecules       Date:  2018-08-28       Impact factor: 4.411

6.  Estimating computational limits on theoretical descriptions of biological cells.

Authors:  Roland R Netz; William A Eaton
Journal:  Proc Natl Acad Sci U S A       Date:  2021-02-09       Impact factor: 11.205

Review 7.  From adaptive resolution to molecular dynamics of open systems.

Authors:  Robinson Cortes-Huerto; Matej Praprotnik; Kurt Kremer; Luigi Delle Site
Journal:  Eur Phys J B       Date:  2021-09-23       Impact factor: 1.500

  7 in total

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