Toward identification of the reaction coordinate directly from the transition state ensemble using the kernel PCA method

Dimitri Antoniou; Steven D. Schwartz

doi:10.1021/jp111682x

Toward identification of the reaction coordinate directly from the transition state ensemble using the kernel PCA method

Dimitri Antoniou, Steven D. Schwartz

Research output: Contribution to journal › Article › peer-review

42 Scopus citations

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.

Original language	English (US)
Pages (from-to)	2465-2469
Number of pages	5
Journal	Journal of Physical Chemistry B
Volume	115
Issue number	10
DOIs	https://doi.org/10.1021/jp111682x
State	Published - Mar 17 2011
Externally published	Yes

ASJC Scopus subject areas

Physical and Theoretical Chemistry
Surfaces, Coatings and Films
Materials Chemistry

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10.1021/jp111682x

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Toward identification of the reaction coordinate directly from the transition state ensemble using the kernel PCA method

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