Sequential quadratic programming method for determining the minimum energy path

被引:33
作者
Burger, Steven K. [1 ]
Yang, Weitao [1 ]
机构
[1] Duke Univ, Dept Chem, Durham, NC 27708 USA
关键词
D O I
10.1063/1.2780147
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
A new method, referred to as the sequential quadratic programming method, is presented for determining minimum energy paths. The method is based on minimizing the points representing the path in the subspace perpendicular to the tangent of the path while using a penalty term to prevent kinks from forming. Rather than taking one full step, the minimization is divided into a number of sequential steps on an approximate quadratic surface. The resulting method can efficiently determine the reaction mechanism, from which transition state can be easily identified and refined with other methods. To improve the resolution of the path close to the transition state, points are clustered close to this region with a reparametrization scheme. The usefulness of the algorithm is demonstrated for the Muller-Brown potential, amide hydrolysis, and an 89 atom cluster taken from the active site of 4-oxalocrotonate tautomerase for the reaction which catalyzes 2-oxo-4-hexenedioate to the intermediate 2-hydroxy-2,4-hexadienedioate. (C) 2007 American Institute of Physics.
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页数:7
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共 31 条
[11]   Simplified and improved string method for computing the minimum energy paths in barrier-crossing events [J].
E, Weinan ;
Ren, Weiqing ;
Vanden-Eijnden, Eric .
JOURNAL OF CHEMICAL PHYSICS, 2007, 126 (16)
[12]  
Fletcher R., 1981, PRACTICAL METHODS OP
[13]  
Frisch M. J., 2004, GAUSSIAN 03 REVISION
[14]   THE PATH OF CHEMICAL-REACTIONS - THE IRC APPROACH [J].
FUKUI, K .
ACCOUNTS OF CHEMICAL RESEARCH, 1981, 14 (12) :363-368
[15]   REACTION-PATH FOLLOWING IN MASS-WEIGHTED INTERNAL COORDINATES [J].
GONZALEZ, C ;
SCHLEGEL, HB .
JOURNAL OF PHYSICAL CHEMISTRY, 1990, 94 (14) :5523-5527
[16]   A climbing image nudged elastic band method for finding saddle points and minimum energy paths [J].
Henkelman, G ;
Uberuaga, BP ;
Jónsson, H .
JOURNAL OF CHEMICAL PHYSICS, 2000, 113 (22) :9901-9904
[17]   QM/MM minimum free-energy path: Methodology and application to triosephosphate isomerase [J].
Hu, Hao ;
Lu, Zhenyu ;
Yang, Weitao .
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 2007, 3 (02) :390-406
[18]   The MaxFlux algorithm for calculating variationally optimized reaction paths for conformational transitions in many body systems at finite temperature [J].
Huo, SH ;
Straub, JE .
JOURNAL OF CHEMICAL PHYSICS, 1997, 107 (13) :5000-5006
[19]  
Jonsson H., 1998, CLASSICAL QUANTUM DY
[20]   Adaptive knot placement in B-spline curve approximation [J].
Li, WS ;
Xu, SH ;
Zhao, G ;
Goh, LP .
COMPUTER-AIDED DESIGN, 2005, 37 (08) :791-797