title: Microsolvation and hydrogen bond interactions in Glycine Dipeptide: molecular dynamics and density functional theory studies.
abstract: Molecular dynamics (MD) simulations were carried out to study the conformational characteristics of Glycine Dipeptide (GD) in the presence of explicit water molecules for over 10 ns with a MD time step of 2 fs. The density functional theory (DFT) methods with 6-311G** basis set have been employed to study the effects of microsolvation on the conformations of GD with 5-10 water molecules. The interaction energy with BSSE corrections and the strength of the intermolecular hydrogen bond interactions have been analyzed. The Bader's Atoms in Molecules (AIM) theory has been employed to investigate H-bonding patterns in water interacting complexes. The natural bond orbital (NBO) analysis has been carried out to analyze the charge transfer between proton acceptor to the antibonding orbital of the XH bond in the hydrated complexes. NMR calculations have been carried out at B3LYP/6-311G (2d, 2p) level of theory to analyse the changes in structure and hydrogen bonding environment that occur upon solvation.
authors.affiliation: Department of Physics, NGM College, Pollachi 642 001, India.
authors.forename: Balasubramaniam
authors.initials: B
authors.lastname: Yogeswari
authors.forename: Ramasamy
authors.initials: R
authors.lastname: Kanakaraju
authors.forename: Subramaniam
authors.initials: S
authors.lastname: Boopathi
authors.forename: Ponmalai
authors.initials: P
authors.lastname: Kolandaivel
mesh_terms: D000465:Algorithms; D020816:Amino Acid Motifs; D004151:Dipeptides / Q000737:chemistry*; D005998:Glycine / Q000737:chemistry*; D006860:Hydrogen Bonding; D056004:Molecular Dynamics Simulation; D011789:Quantum Theory; D012997:Solvents / Q000737:chemistry*; D013816:Thermodynamics; D014867:Water / Q000737:chemistry*
chemical_list: D004151:Dipeptides; D012997:Solvents; D014867:Water; D005998:Glycine