QM/MM Methods for Biomolecular Systems

被引：2076

作者：

Senn, Hans Martin ^{[1
,2
,3
,4
]}

Thiel, Walter ^{[4
,5
]}

机构：

[1] Univ Dusseldorf, D-4000 Dusseldorf, Germany

[2] Univ Texas Austin, Austin, TX 78712 USA

[3] Univ Wuppertal, Wuppertal, Germany

[4] Max Planck Inst Kohlenforsch, D-45470 Mulheim, Germany

[5] Univ Calgary, Calgary, AB T2N 1N4, Canada

来源：

ANGEWANDTE CHEMIE-INTERNATIONAL EDITION | 2009年 / 48卷 / 07期

关键词：

enzyme catalysis; molecular simulations; QM/MM calculations; theoretical chemistry; QUANTUM-MECHANICS/MOLECULAR-MECHANICS; MOLECULAR-DYNAMICS SIMULATIONS; TRANSITION-STATE STABILIZATION; DENSITY-FUNCTIONAL THEORY; COMBINED AB-INITIO; ELECTRON CORRELATION METHODS; POLARIZABLE FORCE-FIELD; POTENTIAL-ENERGY SURFACE; COLOR-TUNING MECHANISM; CARBONIC-ANHYDRASE-II;

D O I：

10.1002/anie.200802019

中图分类号：

O6 [化学];

学科分类号：

0703 ;

摘要：

Two are better than one: Quantum mechanics/molecular mechanics (QM/MM) methods are the state-of-the-art computational technique for treating reactive and other electronic processes in biomolecular systems. This Review presents the general methodological aspects of the QM/MM approach, its use within optimization and simulation techniques, and its areas of application, always with a biomolecular focus. © 2009 Wiley-VCH Verlag GmbH & Co. KGaA.

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页码：1198 / 1229

页数：32

相关论文

共 636 条

[1] Cope elimination: Elucidation of solvent effects from QM/MM simulations [J].

Acevedo, Orlando ;

Jorgensen, William L. .

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 2006, 128 (18) :6141-6146

[2] Understanding rate accelerations for Diels-Alder reactions in solution using enhanced QM/MM methodology [J].

Acevedo, Orlando ;

Jorgensen, William L. .

JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 2007, 3 (04) :1412-1419

[3] Elucidation of rate variations for a Diels-Alder reaction in ionic liquids from QM/MM simulations [J].

Acevedo, Orlando ;

Jorgensen, William L. ;

Evanseck, Jeffrey D. .

JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 2007, 3 (01) :132-138

[4] Medium effects on the decarboxylation of a biotin model in pure and mixed solvents from QM/MM simulations [J].

Acevedo, Orlando ;

Jorgensen, William L. .

JOURNAL OF ORGANIC CHEMISTRY, 2006, 71 (13) :4896-4902

[5] DNA polymerase β catalysis:: Are different mechanisms possible? [J].

Alberts, Ian L. ;

Wang, Yanli ;

Schlick, Tamar .

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 2007, 129 (36) :11100-11110

[6] Why urea eliminates ammonia rather than hydrolyzes in aqueous solution [J].

Alexandrova, Anastassia N. ;

Jorgensen, William L. .

JOURNAL OF PHYSICAL CHEMISTRY B, 2007, 111 (04) :720-730

[7] The structures and electronic configuration of compound I intermediates of Helicobacter pylori and Penicillium vitale catalases determined by X-ray crystallography and QM/MM density functional theory calculations [J].

Alfonso-Prieto, Mercedes ;

Borovik, Anton ;

Carpena, Xavier ;

Murshudov, Garib ;

Melik-Adamyan, William ;

Fita, Ignacio ;

Rovira, Carme ;

Loewen, Peter C. .

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 2007, 129 (14) :4193-4205

[8] The effect of heme environment on the hydrogen abstraction reaction of camphor in P450cam catalysis:: A QM/MM study [J].

Altun, A ;

Guallar, V ;

Friesner, RA ;

Shaik, S ;

Thiel, W .

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 2006, 128 (12) :3924-3925

[9] Combined quantum mechanical/molecular mechanical study on the pentacoordinated ferric and ferrous cytochrome P450cam complexes [J].

Altun, A ;

Thiel, W .

JOURNAL OF PHYSICAL CHEMISTRY B, 2005, 109 (03) :1268-1280

[10] What is the active species of cytochrome p450 during camphor hydroxylation? QM/MM studies of different electronic states of compound I and of reduced and oxidized iron-oxo intermediates [J].

Altun, Ahmet ;

Shaik, Sason ;

Thiel, Walter .

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 2007, 129 (29) :8978-8987

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