Analysis of the catalytic role of water molecules

Dzielendziak, Agnieszka and Sokalski, W. Andrzej (2010) Analysis of the catalytic role of water molecules. Modeling and Design of Molecular Materials 2010, Wroclaw, Poland, Wroclaw University of Science and Technology ­, Wroclaw, Poland. 03 - 07 Jul 2010.

Abstract

Most of water molecules surrounding reacting biological systems in enzyme active sites or DNA bases pairs undergoing chemical reactions may be treated as passive elements of molecular environment. However, some waters are directly involved in the reaction mechanism and have to
e included in QM part of the entire system treated within QMMM approach. To our knowledge there is no clear recipe how to distinguish both kinds of water molecules. The hypothesis put forward by Ken Houk implies that in the enzymes displaying highest catalytic activity transition states are covalently bound to active site. The aim of this work is to determine the specific properties of water molecule indicating covalent character of its interactions with reacting system. As the simple model where the catalytic role of molecular environment can be analysed we selected 4 water molecules consisting first hydration shell of guanine-cytosine base pair undergoing double proton transfer. The role of water molecules in reacting complexes of β-Lactams has been investigated too. The covalent nature of above mentioned systems has
been analysed using variation-perturbation partitioning of interaction energy and AIM tested previously for series of hydrogen bonded complexes.

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Contributors

Author: Agnieszka Dzielendziak

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