MD methods in evaluating aromaticity changes by environment
Presented by Dr. Beata SZEFLER
Aromaticity is an important and widely used concept characterizing properties and structure of many organic and inorganic chemical compounds [1–3]. Environmental effects can lead to significant structural alterations of molecules directly exposed to environment. Such changes are of particular interest in molecules important from a biochemical perspective. All nucleobases and four amino acid residues possess aromatic rings that can be affected by the environmental heterogeneity. These influences can be as different as explicit solvent molecules, dense packing in solids, particular molecular surroundings in polymeric neighborhoods and a variety of organic or inorganic ligands directly interact with the solute. Straightforward contacts between molecules in the closest proximity, or chemical modification or indirect influence via intermolecular interactions can lead to sizable alterations of physico-chemical properties including aromaticity. The aim of this study was the quantitative analysis of -electron delocalization in aromatic ring of phenol (as a model system), nucleobases and amino acids in explicit and implicit water solvation. The conformations of these systems were obtained via quenching Molecular Dynamics (MD) method followed by QM/MM  hybrid molecular-mechanics/quantum-chemical geometry optimization using AMBER forcefield [5,6]. 1. Krygowski TM, Cyrański MK (2001) Chem Rev 101:1385–1419 2. Krygowski TM, Cyrański MK, Czarnocki Z, Häfelinger G, Katritzky AR (2000) Tetrahedron 56:1783–1796 3. Chen Z, Wannere CS, Corminboeuf C, Puchta R, Schleyer PvR (2005) Chem Rev 105:3842–3888 4. Svensson M, Humbel S, Morokuma K (1996) J Chem Phys 105:3654–3661 5. B. Mennucci, E. Cancès, J. Tomasi (1997) J. Phys. Chem. B 101: 10506-10517. 6. D.A. Case, T.A. Darden, T.E. III Cheatham, C.L. Simmerling, J. Wang, R.E. Duke, R. Luo, K.M. Merz, B. Wang, D.A. Pearlman, M. Crowley, S. Brozell, V. Tsui, H. Gohlke, J. Mongan, V. Hornak, G. Cui, P. Beroza, C. Schafmeister, J.W. Caldwell, W.S. Ross, P.A. Kollman, AMBER 8, University of California, San Francisco, 2004.
Location: Portorož, Slovenia
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