Multiscale modeling of enzymes: QM-cluster, QM/MM, and QM/MM/MD: A tutorial review

被引：127

作者：

Ahmadi, Shideh ^{[1
,2
]}

Herrera, Lizandra Barrios ^{[1
,2
]}

Chehelamirani, Morteza ^{[1
,2
]}

Hostas, Jiri ^{[1
,2
]}

Jalife, Said ^{[1
,2
,3
]}

Salahub, Dennis R. ^{[1
,2
,4
]}

机构：

[1] Univ Calgary, Dept Chem, CMS, IQST, 2500 Univ Dr NW, Calgary, AB T2N 1N4, Canada

[2] Univ Calgary, Quantum Alberta, 2500 Univ Dr NW, Calgary, AB T2N 1N4, Canada

[3] Ctr Invest & Estudios Avanzados, Dept Fis Aplicada, Unidad Merida, Km 6 Antigua Carretera Progreso,Apdo Postal 73, Mexico City 97310, DF, Mexico

[4] Henan Univ Technol, Coll Chem & Chem Engn, 100 Lian Hua St, Zhengzhou 450001, Henan, Peoples R China

来源：

INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY | 2018年 / 118卷 / 09期

基金：

加拿大自然科学与工程研究理事会;

关键词：

density functional theory; multiscale modeling of enzymes; QM-cluster models; QM; MM models; MM; MD models; FREE-ENERGY CALCULATIONS; MOLECULAR-DYNAMICS SIMULATIONS; COUPLED ELECTRON-TRANSFER; O BOND FORMATION; PHOSPHORYL-TRANSFER-REACTIONS; PLESSET PERTURBATION-THEORY; DENSITY-FUNCTIONAL THEORY; OXYGEN-EVOLVING COMPLEX; LYS CATALYTIC TRIAD; ORBITAL GHO METHOD;

D O I：

10.1002/qua.25558

中图分类号：

O64 [物理化学（理论化学）、化学物理学];

学科分类号：

070304 ; 081704 ;

摘要：

Exemplars of the state of the art in modeling enzymes are reviewed through a selection of works from leading schools using QM-only cluster models, QM/MM models and QM/MM/MD models. A computational protocol is proposed, intended to guide neophytes through the myriad of methodological choices that are necessary for the successful study of chemical reactions in the complex enzymatic environment.

引用

页数：34

共 271 条

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