Seminar on 'In-silico Workflows for Metabolite Structure Elucidation' Today

Kenneth M. Merz Jr.
photo submitted

Kenneth M. Merz Jr.

Professor Kenneth M. Merz Jr. of Michigan State University will give a seminar titled "In-silico workflows for metabolite structure elucidation" from 3:05-3:55 p.m. on Monday, Nov. 8. Everyone is welcome to attend the seminar via Zoom or in-person in CHEM 144. The talk is free and open to the public.

Merz is currently the Joseph Zichis Chair in Chemistry and a professor of biochemistry and molecular biology at Michigan State University. He was the director of MSU's Institute for Cyber Enabled Research (iCER) from 2013-2019. Since the start of 2014, he has been the editor-in-chief of the Journal of Chemical Information and Modeling, which is part of the American Chemical Society suite of chemistry journals. His research interest lies in the development of theoretical and computational tools and their application to biological problems including structure and ligand based drug design, mechanistic enzymology and methodological verification and validation (i.e., error analysis). In his research he makes extensive use of quantum and molecular mechanical potential functions coupled with a variety of numerical methods including molecular dynamics and Monte Carlo approaches.

Dr. Merz carried out postdoctoral training at The University of California, San Francisco (1987-1989, with Peter Kollman) and at Cornell University (1986-1987, with Roald Hoffmann). He received his Ph.D. in organic chemistry at the University of Texas at Austin in 1985 (with M. J. S. Dewar) and his B.S. from Washington College, Chestertown, Maryland in 1981. He has received a number of honors including election as the 2013 Chair of the COMP division of the ACS, election as an ACS Fellow, the 2010 ACS Award for Computers in Chemical and Pharmaceutical Research, election as a fellow of the American Association for the Advancement of Science, and a John Simon Guggenheim Fellowship.

A major challenge for metabolomics is obtaining a comprehensive and unambiguous identification of detected metabolites. Ion mobility coupled to mass spectrometry (IM-MS) and NMR spectroscopy are sophisticated, powerful, and generally applicable tools that can be used to deduce the identity of newly isolated biogenic molecules. However, the interpretation of IMMS data is still a challenge and depends on accurate theoretical estimates of the molecular ion collision cross section (CCS) against a buffer gas in a low-pressure drift chamber. Moreover, accurate structure prediction using NMR techniques and IM-MS depends on the conformational space of a particular compound. It is intrinsically challenging to calculate NMR chemical shifts and CCS values using ab initio techniqueswhen the conformational space of a metabolite is extensive.

Merz will describe two closely related workflows to compute NMR and CCS values using modern computational chemistry tools. In particular, he will describe his group's integration strategy using Snakemake and the various software tools used in the integrated workflow. The selection of software tools has emphasized the use of free open-source software (FOSS) when at all possible.

To attend the seminar virtually, please visit the Zoom link.
Meeting ID: 862 5015 5151
Passcode: Fall@2021


Megan Parett, communications specialist
Department of Chemistry and Biochemistry


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