AUTHOR=Prejanò Mario , Marino Tiziana , Russo Nino TITLE=QM Cluster or QM/MM in Computational Enzymology: The Test Case of LigW-Decarboxylase JOURNAL=Frontiers in Chemistry VOLUME=6 YEAR=2018 URL=https://www.frontiersin.org/journals/chemistry/articles/10.3389/fchem.2018.00249 DOI=10.3389/fchem.2018.00249 ISSN=2296-2646 ABSTRACT=

The catalytic mechanism of the decarboxylation of 5-carboxyvanillate by LigW producing vanillic acid has been studied by using QM cluster and hybrid QM/MM methodologies. In the QM cluster model, the environment of a small QM model is treated with a bulky potential while two QM/MM models studies include partial and full protein with and without explicitly treated water solvent. The studied reaction involves two sequential steps: the protonation of the carbon of the 5-carboxy-vanillate substrate and the decarboxylation of the intermediate from which results deprotonated vanillic acid as product. The structures and energetics obtained by using three structural models and two density functionals are quite consistent to each other. This indicates that the small QM cluster model of the presently considered enzymatic reaction is appropriate enough and the reaction is mainly influenced by the active site.