A combined QM/MM study of the nucleophilic addition reaction of methanethiolate and N-methylacetamide

Kyoungrim Byun, Jiali Gao

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16 Scopus citations


A combined quantum mechanical (QM) and molecular mechanical (MM) method was used to study the nucleophilic addition reaction of methanethiolate to N-methylacetamide (NMA) in the gas phase and aqueous solution. At the B3LYP/aug-cc-pVDZ//HF/6-31+G(d) level, the ion-dipole complex was found to be the global minimum on the potential energy surface in the gas phase with a binding energy of 21.2 kcal/mol. The complex has a C-S distance of 4.33 Å, and no stabilized tetrahedral intermediate was located. The computed potential of mean force in water shows that solvent effects stabilize the reactants over the tetrahedral adduct by 36.5 kcal/mol, and that the tetrahedral intermediate does not exist for the present reaction in water. The present study provides an initial step for modeling the cysteine protease hydrolysis reactions in enzymes.

Original languageEnglish (US)
Pages (from-to)50-55
Number of pages6
JournalJournal of Molecular Graphics and Modelling
Issue number1
StatePublished - 2000

Bibliographical note

Funding Information:
This research was generously supported by the National Institutes of Health and the National Science Foundation.

Copyright 2007 Elsevier B.V., All rights reserved.


  • Combined QM/MM simulations
  • Monte Carlo simulation
  • Nucleophilic addition reaction
  • Potential of mean force
  • Solvent effects


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