title: Study on the conformational equilibrium of the alanine dipeptide in water solution by using the averaged solvent electrostatic potential from molecular dynamics methodology.
abstract: The ASEP/MD method has been employed for studying the solvent effect on the conformational equilibrium of the alanine dipeptide in water solution. MP2 and density functional theory (DFT) levels of theory were used and results were compared. While in gas phase cyclic structures showing intramolecular hydrogen bonds were found to be the most stable, the stability order is reversed in water solution. Intermolecular interaction with the solvent causes the predominance of extended structures as the stabilizing contacts dipeptide-water are favoured. Free-energy differences in solution were calculated and PPII, α(R), and C5 conformers were identified as the most stable at MP2 level. Experimental data from Raman and IR techniques show discrepancies about the relative abundance of α(R) y C5, our results support the Raman data. The DFT level of theory agrees with MP2 in the location and stability of PPII and α(R) forms but fails in the location of C5. MP2 results suggest the possibility of finding traces of C7eq conformer in water solution, in agreement with recent experiments.
authors: Química Física, Edif. José María Viguera Lobo, Universidad de Extremadura, Avda. de Elvas s/n, 06071 Badajoz, Spain.
authors: Francisco F
authors: FF
authors: García-Prieto
authors: Ignacio
authors: I
authors: Fdez Galván
authors: Manuel A
authors: MA
authors: Aguilar
authors: M Elena
authors: ME
authors: Martín
mesh_terms: D000409:Alanine / Q000737:chemistry*; D004151:Dipeptides / Q000737:chemistry*; D056004:Molecular Dynamics Simulation; D011487:Protein Conformation; D012996:Solutions; D012997:Solvents / Q000737:chemistry; D055672:Static Electricity; D014867:Water / Q000737:chemistry
chemical_list: D004151:Dipeptides; D012996:Solutions; D012997:Solvents; D014867:Water; D000409:Alanine