Literature DB >> 29386687

QM/MM through the 1990s: The First Twenty Years of Method Development and Applications.

Meiyi Liu1, Yingjie Wang2, Yakun Chen1, Martin J Field3, Jiali Gao1,2.   

Abstract

The 2013 Nobel Prize in Chemistry was awarded to the authors of the first two publications utilizing the concept of combined quantum mechanical and molecular mechanical (QM/MM) methods. In celebrating this great event in computational chemistry, we review the early development of combined QM/MM techniques and the associated events that took place through the mid-1990s. We also offer some prospects for the future development of quantum mechanical techniques for macromolecular systems.

Entities:  

Keywords:  biomolecular interactions; computational chemistry; electronic structure; molecular mechanics; quantum mechanics

Year:  2014        PMID: 29386687      PMCID: PMC5788202          DOI: 10.1002/ijch.201400036

Source DB:  PubMed          Journal:  Isr J Chem        ISSN: 0021-2148            Impact factor:   3.333


  22 in total

Review 1.  Mechanisms and free energies of enzymatic reactions.

Authors:  Jiali Gao; Shuhua Ma; Dan T Major; Kwangho Nam; Jingzhi Pu; Donald G Truhlar
Journal:  Chem Rev       Date:  2006-08       Impact factor: 60.622

2.  Design-atom approach for the quantum mechanical/molecular mechanical covalent boundary: a design-carbon atom with five valence electrons.

Authors:  Chuanyun Xiao; Yingkai Zhang
Journal:  J Chem Phys       Date:  2007-09-28       Impact factor: 3.488

3.  The Design of a Next Generation Force Field: The X-POL Potential.

Authors:  Wangshen Xie; Jiali Gao
Journal:  J Chem Theory Comput       Date:  2007-11       Impact factor: 6.006

4.  Quantum mechanical force field for water with explicit electronic polarization.

Authors:  Jaebeom Han; Michael J M Mazack; Peng Zhang; Donald G Truhlar; Jiali Gao
Journal:  J Chem Phys       Date:  2013-08-07       Impact factor: 3.488

5.  Quantum mechanical/molecular mechanical approaches to transition state structure: mechanism of sialidase action.

Authors:  J A Barnes; I H Williams
Journal:  Biochem Soc Trans       Date:  1996-02       Impact factor: 5.407

6.  Calculation of pi-pi excited state conformations and vibronic structure of retinal and related molecules.

Authors:  A Warshel; M Karplus
Journal:  J Am Chem Soc       Date:  1974-09-04       Impact factor: 15.419

7.  Implications of torsional potential of retinal isomers for visual excitation.

Authors:  B Honig; M Karplus
Journal:  Nature       Date:  1971-02-19       Impact factor: 49.962

8.  Structure of the triosephosphate isomerase-phosphoglycolohydroxamate complex: an analogue of the intermediate on the reaction pathway.

Authors:  R C Davenport; P A Bash; B A Seaton; M Karplus; G A Petsko; D Ringe
Journal:  Biochemistry       Date:  1991-06-18       Impact factor: 3.162

9.  X-Pol Potential: An Electronic Structure-Based Force Field for Molecular Dynamics Simulation of a Solvated Protein in Water.

Authors:  Wangshen Xie; Modesto Orozco; Donald G Truhlar; Jiali Gao
Journal:  J Chem Theory Comput       Date:  2009-02-17       Impact factor: 6.006

10.  Theoretical modeling of large molecular systems. Advances in the local self consistent field method for mixed quantum mechanics/molecular mechanics calculations.

Authors:  Antonio Monari; Jean-Louis Rivail; Xavier Assfeld
Journal:  Acc Chem Res       Date:  2012-12-18       Impact factor: 22.384

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  10 in total

1.  Enzymatic Kinetic Isotope Effects from Path-Integral Free Energy Perturbation Theory.

Authors:  J Gao
Journal:  Methods Enzymol       Date:  2016-07-22       Impact factor: 1.600

2.  Solvation Free Energy Calculations with Quantum Mechanics/Molecular Mechanics and Machine Learning Models.

Authors:  Pan Zhang; Lin Shen; Weitao Yang
Journal:  J Phys Chem B       Date:  2019-01-15       Impact factor: 2.991

3.  Accurate Quantum Mechanical/Molecular Mechanical Calculations of Reduction Potentials in Azurin Variants.

Authors:  Lin Shen; Xiancheng Zeng; Hao Hu; Xiangqian Hu; Weitao Yang
Journal:  J Chem Theory Comput       Date:  2018-08-10       Impact factor: 6.006

4.  Dual QM and MM Approach for Computing Equilibrium Isotope Fractionation Factor of Organic Species in Solution.

Authors:  Meiyi Liu; Katelyn N Youmans; Jiali Gao
Journal:  Molecules       Date:  2018-10-15       Impact factor: 4.411

5.  Do Better Quality Embedding Potentials Accelerate the Convergence of QM/MM Models? The Case of Solvated Acid Clusters.

Authors:  Junming Ho; Yihan Shao; Jin Kato
Journal:  Molecules       Date:  2018-09-26       Impact factor: 4.411

6.  Optimizing the Calculation of Free Energy Differences in Nonequilibrium Work SQM/MM Switching Simulations.

Authors:  Andreas Schöller; Fiona Kearns; H Lee Woodcock; Stefan Boresch
Journal:  J Phys Chem B       Date:  2022-04-11       Impact factor: 3.466

7.  Effects of Environmental and Electric Perturbations on the pKa of Thioredoxin Cysteine 35: A Computational Study.

Authors:  Valeria D'Annibale; Donatella Fracassi; Paolo Marracino; Guglielmo D'Inzeo; Marco D'Abramo
Journal:  Molecules       Date:  2022-09-30       Impact factor: 4.927

8.  High-throughput quantum-mechanics/molecular-mechanics (ONIOM) macromolecular crystallographic refinement with PHENIX/DivCon: the impact of mixed Hamiltonian methods on ligand and protein structure.

Authors:  Oleg Borbulevych; Roger I Martin; Lance M Westerhoff
Journal:  Acta Crystallogr D Struct Biol       Date:  2018-10-29       Impact factor: 7.652

9.  Tuning Proton Transfer Thermodynamics in SARS-Cov-2 Main Protease: Implications for Catalysis and Inhibitor Design.

Authors:  Laura Zanetti-Polzi; Micholas Dean Smith; Chris Chipot; James C Gumbart; Diane L Lynch; Anna Pavlova; Jeremy C Smith; Isabella Daidone
Journal:  ChemRxiv       Date:  2020-11-06

10.  Theoretical Characterization of the Reduction Potentials of Nucleic Acids in Solution.

Authors:  Valeria D'Annibale; Alessandro Nicola Nardi; Andrea Amadei; Marco D'Abramo
Journal:  J Chem Theory Comput       Date:  2021-02-23       Impact factor: 6.006

  10 in total

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