Suppr超能文献

贯穿20世纪90年代的量子力学/分子力学方法:方法发展与应用的头二十年

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

作者信息

Liu Meiyi, Wang Yingjie, Chen Yakun, Field Martin J, Gao Jiali

机构信息

State Key Laboratory of Theoretical and Computational Chemistry, Theoretical Chemistry Institute, Jilin University, Changchun, Jilin Province (China).

Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis MN 55455 (USA).

出版信息

Isr J Chem. 2014 Aug;54(8-9):1250-1263. doi: 10.1002/ijch.201400036. Epub 2014 Jul 31.

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.

摘要

2013年诺贝尔化学奖授予了最早运用量子力学与分子力学相结合(QM/MM)方法概念的两篇论文的作者。在庆祝计算化学这一重大事件之际,我们回顾了QM/MM组合技术的早期发展以及直至20世纪90年代中期所发生的相关事件。我们还对用于大分子系统的量子力学技术的未来发展提供了一些展望。

相似文献

1
QM/MM through the 1990s: The First Twenty Years of Method Development and Applications.
Isr J Chem. 2014 Aug;54(8-9):1250-1263. doi: 10.1002/ijch.201400036. Epub 2014 Jul 31.
2
QM/ELMO: A Multi-Purpose Fully Quantum Mechanical Embedding Scheme Based on Extremely Localized Molecular Orbitals.
J Phys Chem A. 2021 Apr 8;125(13):2709-2726. doi: 10.1021/acs.jpca.0c11450. Epub 2021 Mar 5.
3
Hybrid Quantum Mechanics/Molecular Mechanics (QM/MM) Simulation: A Tool for Structure-Based Drug Design and Discovery.
Mini Rev Med Chem. 2022;22(8):1096-1107. doi: 10.2174/1389557521666211007115250.
4
Recent advances toward a general purpose linear-scaling quantum force field.
Acc Chem Res. 2014 Sep 16;47(9):2812-20. doi: 10.1021/ar500103g. Epub 2014 Jun 17.
6
QM/MM methods for biomolecular systems.
Angew Chem Int Ed Engl. 2009;48(7):1198-229. doi: 10.1002/anie.200802019.
7
Fragment quantum mechanical calculation of proteins and its applications.
Acc Chem Res. 2014 Sep 16;47(9):2748-57. doi: 10.1021/ar500077t. Epub 2014 May 22.
8
Combined quantum mechanics/molecular mechanics (QM/MM) methods in computational enzymology.
Biochemistry. 2013 Apr 23;52(16):2708-28. doi: 10.1021/bi400215w. Epub 2013 Apr 12.
9
Macromolecular crowding: chemistry and physics meet biology (Ascona, Switzerland, 10-14 June 2012).
Phys Biol. 2013 Aug;10(4):040301. doi: 10.1088/1478-3975/10/4/040301. Epub 2013 Aug 2.
10
Quantum mechanics/coarse-grained molecular mechanics (QM/CG-MM).
J Chem Phys. 2018 Jan 7;148(1):014102. doi: 10.1063/1.5006810.

引用本文的文献

1
: A program for combined quantum mechanical and molecular mechanical modeling and simulations.
Comput Phys Commun. 2024 Feb;295. doi: 10.1016/j.cpc.2023.108987. Epub 2023 Oct 26.
2
Radical SAM Enzymes and Metallocofactor Assembly: A Structural Point of View.
ACS Bio Med Chem Au. 2021 Nov 20;2(1):36-52. doi: 10.1021/acsbiomedchemau.1c00044. eCollection 2022 Feb 16.
3
MiMiCPy: An Efficient Toolkit for MiMiC-Based QM/MM Simulations.
J Chem Inf Model. 2023 Mar 13;63(5):1406-1412. doi: 10.1021/acs.jcim.2c01620. Epub 2023 Feb 22.
5
Optimizing the Calculation of Free Energy Differences in Nonequilibrium Work SQM/MM Switching Simulations.
J Phys Chem B. 2022 Apr 21;126(15):2798-2811. doi: 10.1021/acs.jpcb.2c00696. Epub 2022 Apr 11.
6
Tuning Proton Transfer Thermodynamics in SARS-CoV-2 Main Protease: Implications for Catalysis and Inhibitor Design.
J Phys Chem Lett. 2021 May 6;12(17):4195-4202. doi: 10.1021/acs.jpclett.1c00425. Epub 2021 Apr 26.
7
Theoretical Characterization of the Reduction Potentials of Nucleic Acids in Solution.
J Chem Theory Comput. 2021 Mar 9;17(3):1301-1307. doi: 10.1021/acs.jctc.0c00728. Epub 2021 Feb 23.
9
Solvation Free Energy Calculations with Quantum Mechanics/Molecular Mechanics and Machine Learning Models.
J Phys Chem B. 2019 Jan 31;123(4):901-908. doi: 10.1021/acs.jpcb.8b11905. Epub 2019 Jan 15.

本文引用的文献

3
Analytical second derivatives of the energy in MNDO methods.
J Comput Chem. 1996 Aug;17(11):1318-27. doi: 10.1002/(SICI)1096-987X(199608)17:11<1318::AID-JCC4>3.0.CO;2-P.
4
Quantum mechanical force field for water with explicit electronic polarization.
J Chem Phys. 2013 Aug 7;139(5):054503. doi: 10.1063/1.4816280.
5
Mature HIV-1 capsid structure by cryo-electron microscopy and all-atom molecular dynamics.
Nature. 2013 May 30;497(7451):643-6. doi: 10.1038/nature12162.
8
The Design of a Next Generation Force Field: The X-POL Potential.
J Chem Theory Comput. 2007 Nov;3(6):1890-1900. doi: 10.1021/ct700167b.
10
Mechanisms and free energies of enzymatic reactions.
Chem Rev. 2006 Aug;106(8):3188-209. doi: 10.1021/cr050293k.

文献AI研究员

20分钟写一篇综述,助力文献阅读效率提升50倍。

立即体验

用中文搜PubMed

大模型驱动的PubMed中文搜索引擎

马上搜索

文档翻译

学术文献翻译模型,支持多种主流文档格式。

立即体验