☆ 4.5 Article

Toward Identification of the Reaction Coordinate Directly from the Transition State Ensemble Using the Kernel PCA Method

JOURNAL OF PHYSICAL CHEMISTRY B (2011)

Journal

JOURNAL OF PHYSICAL CHEMISTRY B

Volume 115, Issue 10, Pages 2465-2469

Publisher

AMER CHEMICAL SOC

DOI: 10.1021/jp111682x

Keywords

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Categories

Chemistry, Physical

Funding

National Institutes of Health [GM068036]
National Science Foundation [CHE-0714118]

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Abstract

We propose a new method for analyzing an ensemble of transition states to extract components of the reaction coordinate. We use the kernel principal component analysis (kPCA), which is a generalization of the ordinary PCA that does not make a linearization approximation We applied this method to a TPS study of human LDH we had previously published [Quaytman, S.; Schwartz, S. D. Proc. Natl. Acad. Sci. U.S.A. 2007, 104, 12253] and extracted a reasonable representation for the reaction coordinate.

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