Literature DB >> 33445891

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

Xiaoliang Pan1, Kwangho Nam2, Evgeny Epifanovsky3, Andrew C Simmonett4, Edina Rosta5, Yihan Shao1.   

Abstract

In a previous work [Pan et al., Molecules 23, 2500 (2018)], a charge projection scheme was reported, where outer molecular mechanical (MM) charges [>10 Å from the quantum mechanical (QM) region] were projected onto the electrostatic potential (ESP) grid of the QM region to accurately and efficiently capture long-range electrostatics in ab initio QM/MM calculations. Here, a further simplification to the model is proposed, where the outer MM charges are projected onto inner MM atom positions (instead of ESP grid positions). This enables a representation of the long-range MM electrostatic potential via augmentary charges (AC) on inner MM atoms. Combined with the long-range electrostatic correction function from Cisneros et al. [J. Chem. Phys. 143, 044103 (2015)] to smoothly switch between inner and outer MM regions, this new QM/MM-AC electrostatic model yields accurate and continuous ab initio QM/MM electrostatic energies with a 10 Å cutoff between inner and outer MM regions. This model enables efficient QM/MM cluster calculations with a large number of MM atoms as well as QM/MM calculations with periodic boundary conditions.

Entities:  

Year:  2021        PMID: 33445891      PMCID: PMC7808763          DOI: 10.1063/5.0038120

Source DB:  PubMed          Journal:  J Chem Phys        ISSN: 0021-9606            Impact factor:   3.488


  77 in total

1.  Long-Range Electrostatic Effects in QM/MM Studies of Enzymatic Reactions: Application of the Solvated Macromolecule Boundary Potential.

Authors:  Tobias Benighaus; Walter Thiel
Journal:  J Chem Theory Comput       Date:  2010-12-03       Impact factor: 6.006

2.  Improved pseudobonds for combined ab initio quantum mechanical/molecular mechanical methods.

Authors:  Yingkai Zhang
Journal:  J Chem Phys       Date:  2005-01-08       Impact factor: 3.488

3.  Generalized hybrid-orbital method for combining density functional theory with molecular mechanicals.

Authors:  Jingzhi Pu; Jiali Gao; Donald G Truhlar
Journal:  Chemphyschem       Date:  2005-09-05       Impact factor: 3.102

4.  YinYang atom: a simple combined ab initio quantum mechanical molecular mechanical model.

Authors:  Yihan Shao; Jing Kong
Journal:  J Phys Chem A       Date:  2007-04-13       Impact factor: 2.781

5.  Acceleration of Semiempirical QM/MM Methods through Message Passage Interface (MPI), Hybrid MPI/Open Multiprocessing, and Self-Consistent Field Accelerator Implementations.

Authors:  Pedro Ojeda-May; Kwangho Nam
Journal:  J Chem Theory Comput       Date:  2017-07-06       Impact factor: 6.006

6.  Exchange-repulsion energy in QM/EFP.

Authors:  Claudia I Viquez Rojas; Jonathan Fine; Lyudmila V Slipchenko
Journal:  J Chem Phys       Date:  2018-09-07       Impact factor: 3.488

7.  Ambient-Potential Composite Ewald Method for ab Initio Quantum Mechanical/Molecular Mechanical Molecular Dynamics Simulation.

Authors:  Timothy J Giese; Darrin M York
Journal:  J Chem Theory Comput       Date:  2016-05-26       Impact factor: 6.006

8.  An Average Solvent Electrostatic Configuration Protocol for QM/MM Free Energy Optimization: Implementation and Application to Rhodopsin Systems.

Authors:  Yoelvis Orozco-Gonzalez; Madushanka Manathunga; María Del Carmen Marín; Damianos Agathangelou; Kwang-Hwan Jung; Federico Melaccio; Nicolas Ferré; Stefan Haacke; Kaline Coutinho; Sylvio Canuto; Massimo Olivucci
Journal:  J Chem Theory Comput       Date:  2017-11-21       Impact factor: 6.006

9.  The CHARMM-TURBOMOLE interface for efficient and accurate QM/MM molecular dynamics, free energies, and excited state properties.

Authors:  Saleh Riahi; Christopher N Rowley
Journal:  J Comput Chem       Date:  2014-09-01       Impact factor: 3.376

10.  Acceleration of Ab Initio QM/MM Calculations under Periodic Boundary Conditions by Multiscale and Multiple Time Step Approaches.

Authors:  Kwangho Nam
Journal:  J Chem Theory Comput       Date:  2014-09-15       Impact factor: 6.006

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  2 in total

1.  Machine-Learning-Assisted Free Energy Simulation of Solution-Phase and Enzyme Reactions.

Authors:  Xiaoliang Pan; Junjie Yang; Richard Van; Evgeny Epifanovsky; Junming Ho; Jing Huang; Jingzhi Pu; Ye Mei; Kwangho Nam; Yihan Shao
Journal:  J Chem Theory Comput       Date:  2021-09-01       Impact factor: 6.578

2.  Combined QM/MM, Machine Learning Path Integral Approach to Compute Free Energy Profiles and Kinetic Isotope Effects in RNA Cleavage Reactions.

Authors:  Timothy J Giese; Jinzhe Zeng; Şölen Ekesan; Darrin M York
Journal:  J Chem Theory Comput       Date:  2022-06-16       Impact factor: 6.578

  2 in total

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