Michigan State University Professor Kenneth M. Merz Jr. will give a seminar entitled “In-silico workflows for the elucidation of the structure of metabolites “from 3:05 pm to 3:55 pm on Monday, November 8. Everyone is invited to attend the seminar via Zoom or in person at CHEM 144. The conference is free and open to the public.
Merz is currently the Joseph Zichis Chair in Chemistry and Professor of Biochemistry and Molecular Biology at Michigan State University. He was Director of the Institute for Cyber Enabled Research (iCER) at MSU from 2013 to 2019. Since early 2014, he has been Editor-in-Chief of the Journal of Chemical Information and Modeling, which is part of the journal suite of chemistry from the American Chemical Society. 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. -d. error analysis). In his research, he makes extensive use of the potential functions of quantum and molecular mechanics coupled with a variety of numerical methods, including molecular dynamics and Monte Carlo approaches.
Dr Merz completed postdoctoral training at the University of California at San Francisco (1987-1989, with Peter Kollman) and Cornell University (1986-1987, with Roald Hoffmann). He got his doctorate. in organic chemistry from the University of Texas at Austin in 1985 (with MJS Dewar) and his BS from Washington College, Chestertown, Maryland in 1981. He has received numerous honors including his election in 2013 as President of the COMP Division of ACS, election as an ACS Fellow, the 2010 ACS Prize 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 to obtain a complete and unambiguous identification of the metabolites detected. Ion mobility coupled with mass spectrometry (IM-MS) and NMR spectroscopy are sophisticated, powerful, and generally applicable tools that can be used to infer the identity of newly isolated biogenic molecules. However, interpretation of IMMS data is still a challenge and depends on precise theoretical estimates of the molecular ion collision cross section (CCS) against a buffer gas in a low pressure drift chamber. In addition, the precise prediction of structure using NMR and IM-MS techniques depends on the conformational space of a particular compound. It is inherently difficult to calculate NMR chemical shifts and CCS values using ab initio techniques when the conformational space of a metabolite is large.
Merz will describe two closely related workflows for calculating 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 and open source software (FOSS) where possible.
To virtually attend the seminar, please visit the Zoom link.
Meeting number: 862 5015 5151
Access code: fall @ 2021