Faculty Publications
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Item Molecular dynamics investigation of dipeptide - Transition metal salts in aqueous solutions(American Chemical Society service@acs.org, 2010) Santosh, M.S.; Lyubartsev, A.; Mirzoev, A.; Bhat, D.K.Molecular dynamics (MD) simulations of glycylglycine dipeptide with transition metal ions (Mn2+, Fe2+, Co2+, Ni2+, Cu2+, and Zn2+) in aqueous solutions have been carried out to get an insight into the solvation structure, intermolecular interactions, and salt effects in these systems. The solvation structure and hydrogen bonding were described in terms of radial distribution function (RDF) and spatial distribution function (SDF). The dynamical properties of the solvation structure were also analyzed in terms of diffusion and residence times. The simulation results show the presence of a well-defined first hydration shell around the dipeptide, with water molecules forming hydrogen bonds to the polar groups of the dipeptide. This shell is, however, affected by the strong electric field of divalent metal ions, which at higher ion concentrations lead to the shift in the dipeptide-water RDFs. Higher salt concentrations lead also to increased residence times and slower diffusion rates. In general, smaller ions (Cu2+, Zn2+) demonstrate stronger binding to dipeptide than the larger ones (Fe2+, Mn 2+). Simulations do not show any stronger association of peptide molecules indicating their dissolution in water. The above results may be of potential interest to future researchers on these molecular interactions. © 2010 American Chemical Society.Item Solute-solvent interactions in aqueous glycylglycine-CuCl2 solutions: Acoustical and molecular dynamics perspective(2011) Santosh, M.S.; Lyubartsev, A.; Mirzoev, A.; Bhat, D.K.Acoustical and molecular dynamics studies were carried out to understand the various interactions present in glycylglycine-CuCl2 aqueous solutions. Amongst these interactions, hydrogen bonding and solute-solvent interactions have been highlighted in this study. The radial distribution function (RDF) was used to investigate solution structure and hydration parameters. Binding of Cu2+ with various polar peptide atoms reveals the nature and degree of binding. The formation of complex clusters between glycylglycine and water molecules increases the relaxation time. The first hydration shell considerably influences the structure of the second shell, facilitating the formation of an ordered hydrogen bonded network. Both experimental and theoretical results have proved to be efficient in analyzing the behavior of molecules and to give a clear idea on molecular interactions in solutions. © 2011 Springer Science+Business Media, LLC.