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A compound QM/MM procedure: Comparative performance on a pyruvate formate‐lyase model system
Author(s) -
CondicJurkic Karmen,
Zipse Hendrik,
Smith David M.
Publication year - 2009
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/jcc.21389
Subject(s) - qm/mm , oniom , context (archaeology) , formate , chemistry , computational chemistry , mechanism (biology) , abstraction , computer science , molecule , organic chemistry , physics , molecular dynamics , catalysis , paleontology , philosophy , epistemology , quantum mechanics , biology
We present an ONIOM(G3:MM) method as an example of a technique capable of producing chemical accuracy in the quantum mechanical (QM) treatment with a molecular mechanical description context. By applying the method to small model systems, in which we are also able to calculate the pure QM G3‐type results, it is possible to establish the reliability of the method as it applies to evaluating reaction mechanisms. By choosing small model systems that are relevant to the substrate mechanism of pyruvate formate‐lyase, we are also able to discuss the inhibitory effect of oxamate and the relevance of an alternative H‐abstraction mechanism in that context. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010