title: Conformations of serine in aqueous solutions as revealed by vibrational circular dichroism.
abstract: Vibrational circular dichroism (VCD) spectroscopy is utilized to reveal the detailed conformational distributions of the dominant serine species in aqueous solutions under three representative pH conditions of 1.0, 5.7, and 13.0, together with vibrational absorption (VA) spectroscopy, density functional theory (DFT), and molecular dynamics simulation. The experimental VA and VCD spectra of serine in H(2)O and D(2)O in the fingerprint region under three pH values are obtained. DFT calculations at the B3LYP/6-311++G(d,p) level are carried out for the protonated, zwitterionic, and deprotonated serine species. The lowest-energy conformers of all three species are identified and their corresponding VA and VCD spectra simulated. A comparison between the gas-phase simulations and the experimental VA and VCD spectra suggests that one or two of the most stable conformers of each species contribute predominantly to the observed data, although some discrepancies are noted. To account for the solvent effects, both the polarizable continuum model and the explicit solvation model are considered. Hydrogen-bonded protonated, zwitterionic, and deprotonated serine-(water)(6) clusters are constructed based on radial distribution function analyses and molecular dynamics snapshots. Geometry optimization and VA and VCD simulations are performed for these clusters at the B3LYP/6-311++G(d,p) level. Inclusion of the explicit water molecules is found to improve the agreement between theory and experiment noticeably in all three cases, thus enabling conclusive conformational distribution analyses of serine in aqueous solutions directly.
authors.affiliation: Department of Chemistry, University of Alberta, Edmonton, Alberta, T6G 2G2 Canada.
authors.forename: Peiyang
authors.initials: P
authors.lastname: Zhu
authors.forename: Guochun
authors.initials: G
authors.lastname: Yang
authors.forename: Mohammad Reza
authors.initials: MR
authors.lastname: Poopari
authors.forename: Zhi
authors.initials: Z
authors.lastname: Bie
authors.forename: Yunjie
authors.initials: Y
authors.lastname: Xu
mesh_terms: D002942:Circular Dichroism; D003903:Deuterium / Q000737:chemistry; D006860:Hydrogen Bonding; D006863:Hydrogen-Ion Concentration; D008968:Molecular Conformation; D056004:Molecular Dynamics Simulation; D011522:Protons; D011789:Quantum Theory; D012694:Serine / Q000737:chemistry*; D012996:Solutions; D012997:Solvents / Q000737:chemistry; D013816:Thermodynamics; D014867:Water / Q000737:chemistry*
chemical_list: D011522:Protons; D012996:Solutions; D012997:Solvents; D014867:Water; D012694:Serine; D003903:Deuterium