Literature DB >> 34096706

Advanced Electrostatic Model for Monovalent Ions Based on Ab Initio Energy Decomposition.

Zhifeng Jing1, Chengwen Liu1, Pengyu Ren1.   

Abstract

Ions play important roles in the structures and functions of biomolecules. In biomolecular simulations, ions either directly interact with biomolecules or provide an ionic environment that influences electrostatic interactions of solutes. The AMOEBA+ water model has demonstrated significant advancement of the classical force field for describing molecular interactions due to its improvements on the functional forms to account for essential physics. This work expands the applicability of the AMOEBA+ model toward alkali metal (Li, Na, K, Rb, and Cs) and halogen (F, Cl, Br, and I) ions. Various quantum chemical data on ion-ion and ion-water interactions, experimental ion hydration free energies, and lattice energies of salt crystals are used in the parametrization. The final parameters are verified with other properties outside of the parametrization data, including lattice energies of additional salt crystals and ionic activity coefficients in solution. The new model captures a wide range of ion properties from the gas phase to solution phase and crystals. More importantly, AMOEBA+ provides energy components that are consistent with ab initio energy decomposition. Thus, we expect AMOEBA+ to be more general, transferable, and valuable for the interpretation of intermolecular forces in efficient classical simulations.

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Year:  2021        PMID: 34096706      PMCID: PMC8323402          DOI: 10.1021/acs.jcim.1c00426

Source DB:  PubMed          Journal:  J Chem Inf Model        ISSN: 1549-9596            Impact factor:   6.162


  37 in total

1.  Accurate description of intermolecular interactions involving ions using symmetry-adapted perturbation theory.

Authors:  Ka Un Lao; Rainer Schäffer; Georg Jansen; John M Herbert
Journal:  J Chem Theory Comput       Date:  2015-05-04       Impact factor: 6.006

Review 2.  Recent advances in molecular simulations of ion solvation at liquid interfaces.

Authors:  Tsun-Mei Chang; Liem X Dang
Journal:  Chem Rev       Date:  2006-04       Impact factor: 60.622

3.  Polarizable Force Field for Molecular Ions Based on the Classical Drude Oscillator.

Authors:  Fang-Yu Lin; Pedro E M Lopes; Edward Harder; Benoît Roux; Alexander D MacKerell
Journal:  J Chem Inf Model       Date:  2018-04-17       Impact factor: 4.956

Review 4.  Role of zinc and copper ions in the pathogenetic mechanisms of Alzheimer's and Parkinson's diseases.

Authors:  E V Stelmashook; N K Isaev; E E Genrikhs; G A Amelkina; L G Khaspekov; V G Skrebitsky; S N Illarioshkin
Journal:  Biochemistry (Mosc)       Date:  2014-05       Impact factor: 2.487

5.  Study of interactions between metal ions and protein model compounds by energy decomposition analyses and the AMOEBA force field.

Authors:  Zhifeng Jing; Rui Qi; Chengwen Liu; Pengyu Ren
Journal:  J Chem Phys       Date:  2017-10-28       Impact factor: 3.488

6.  Psi4 1.4: Open-source software for high-throughput quantum chemistry.

Authors:  Daniel G A Smith; Lori A Burns; Andrew C Simmonett; Robert M Parrish; Matthew C Schieber; Raimondas Galvelis; Peter Kraus; Holger Kruse; Roberto Di Remigio; Asem Alenaizan; Andrew M James; Susi Lehtola; Jonathon P Misiewicz; Maximilian Scheurer; Robert A Shaw; Jeffrey B Schriber; Yi Xie; Zachary L Glick; Dominic A Sirianni; Joseph Senan O'Brien; Jonathan M Waldrop; Ashutosh Kumar; Edward G Hohenstein; Benjamin P Pritchard; Bernard R Brooks; Henry F Schaefer; Alexander Yu Sokolov; Konrad Patkowski; A Eugene DePrince; Uğur Bozkaya; Rollin A King; Francesco A Evangelista; Justin M Turney; T Daniel Crawford; C David Sherrill
Journal:  J Chem Phys       Date:  2020-05-14       Impact factor: 3.488

7.  Tinker-OpenMM: Absolute and relative alchemical free energies using AMOEBA on GPUs.

Authors:  Matthew Harger; Daniel Li; Zhi Wang; Kevin Dalby; Louis Lagardère; Jean-Philip Piquemal; Jay Ponder; Pengyu Ren
Journal:  J Comput Chem       Date:  2017-06-10       Impact factor: 3.376

8.  Energy Decomposition Analysis with a Stable Charge-Transfer Term for Interpreting Intermolecular Interactions.

Authors:  Ka Un Lao; John M Herbert
Journal:  J Chem Theory Comput       Date:  2016-05-06       Impact factor: 6.006

9.  Implementation of Geometry-Dependent Charge Flux into the Polarizable AMOEBA+ Potential.

Authors:  Chengwen Liu; Jean-Philip Piquemal; Pengyu Ren
Journal:  J Phys Chem Lett       Date:  2019-12-30       Impact factor: 6.475

10.  Optimized Magnesium Force Field Parameters for Biomolecular Simulations with Accurate Solvation, Ion-Binding, and Water-Exchange Properties.

Authors:  Kara K Grotz; Sergio Cruz-León; Nadine Schwierz
Journal:  J Chem Theory Comput       Date:  2021-03-15       Impact factor: 6.006

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