A compound QM/MM procedure: comparative performance on a pyruvate formate-lyase model system
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Liquid Chromatography Coupled to Refractive Index or Mass Spectrometric Detection for Metabolite Profiling in Lysate-based Cell-free Systems
Published on: September 23, 2021
Karmen Condic-Jurkic1, Hendrik Zipse, David M Smith
1Centre for Computational Solutions in the Life Sciences, Division of Organic Chemistry and Biochemistry, Ruder Bosković Institute, Bijenicka 54 HR-10002 Zagreb, Croatia.
Abstract:
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.
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