title: Nitrogen K-edge x-ray absorption near edge structure of pyrimidine-containing nucleotides in aqueous solution.
abstract: X-ray absorption near edge structure (XANES) was measured at energies around the N K-edge of the pyrimidine-containing nucleotides, cytidine 5'-monophosphate (CMP), 2'-deoxythymidine 5'-monophosphate (dTMP), and uridine 5'-monophosphate (UMP), in aqueous solutions and in dried films under various pH conditions. The features of resonant excitations below the N K-edge in the XANES spectra for CMP, dTMP, and UMP changed depending on the pH of the solutions. The spectral change thus observed is systematically explained by the chemical shift of the core-levels of N atoms in the nucleobase moieties caused by structural changes due to protonation or deprotonation at different proton concentrations. This interpretation is supported by the results of theoretical calculations using density functional theory for the corresponding nucleobases in the neutral and protonated or deprotonated forms.
authors.affiliation: Department of Applied Physics, Tokyo University of Agriculture and Technology, Koganei-shi, Tokyo 184-8588, Japan.
authors.forename: Hiroyuki
authors.initials: H
authors.lastname: Shimada
authors.affiliation: Department of Applied Physics, Tokyo University of Agriculture and Technology, Koganei-shi, Tokyo 184-8588, Japan.
authors.forename: Hirotake
authors.initials: H
authors.lastname: Minami
authors.affiliation: Department of Applied Physics, Tokyo University of Agriculture and Technology, Koganei-shi, Tokyo 184-8588, Japan.
authors.forename: Naoto
authors.initials: N
authors.lastname: Okuizumi
authors.affiliation: Department of Applied Physics, Tokyo University of Agriculture and Technology, Koganei-shi, Tokyo 184-8588, Japan.
authors.forename: Ichiro
authors.initials: I
authors.lastname: Sakuma
authors.affiliation: Department of Applied Physics, Tokyo University of Agriculture and Technology, Koganei-shi, Tokyo 184-8588, Japan.
authors.forename: Masatoshi
authors.initials: M
authors.lastname: Ukai
authors.affiliation: Advanced Science Research Center, Japan Atomic Energy Agency, Tokai-mura, Naka-gun, Ibaraki 319-1195, Japan.
authors.forename: Kentaro
authors.initials: K
authors.lastname: Fujii
authors.affiliation: Advanced Science Research Center, Japan Atomic Energy Agency, Tokai-mura, Naka-gun, Ibaraki 319-1195, Japan.
authors.forename: Akinari
authors.initials: A
authors.lastname: Yokoya
authors.affiliation: Synchrotron Radiation Research Center, Japan Atomic Energy Agency, Sayo-gun, Hyogo 679-5148, Japan.
authors.forename: Yoshihiro
authors.initials: Y
authors.lastname: Fukuda
authors.affiliation: Synchrotron Radiation Research Center, Japan Atomic Energy Agency, Sayo-gun, Hyogo 679-5148, Japan.
authors.forename: Yuji
authors.initials: Y
authors.lastname: Saitoh
mesh_terms: D004583:Electrons; D006863:Hydrogen-Ion Concentration; D017665:Hydroxyl Radical / Q000737:chemistry; D008956:Models, Chemical; D015394:Molecular Structure; D009584:Nitrogen; D011522:Protons; D011742:Pyrimidine Nucleotides / Q000737:chemistry*; D012996:Solutions; D014867:Water / Q000737:chemistry*; D056928:X-Ray Absorption Spectroscopy
chemical_list: D011522:Protons; D011742:Pyrimidine Nucleotides; D012996:Solutions; D014867:Water; D017665:Hydroxyl Radical; D009584:Nitrogen