title: Effect of intermolecular hydrogen bonding, vibrational analysis and molecular structure of a biomolecule: 5-Hydroxymethyluracil.
abstract: In the present work, the experimental and theoretical vibrational spectra of 5-hydroxymethyluracil were investigated. The FT-IR (4000-400cm(-1)) spectrum of the molecule in the solid phase was recorded. The geometric parameters (bond lengths and bond angles), vibrational frequencies, Infrared intensities of the title molecule in the ground state were calculated using density functional B3LYP and M06-2X methods with the 6-311++G(d,p) basis set for the first time. The optimized geometric parameters and theoretical vibrational frequencies were found to be in good agreement with the corresponding experimental data, and with the results found in the literature. The vibrational frequencies were assigned based on the potential energy distribution using the VEDA 4 program. The dimeric form of 5-hydroxymethyluracil molecule was also simulated to evaluate the effect of intermolecular hydrogen bonding on its vibrational frequencies. It was observed that the NH stretching modes shifted to lower frequencies, while its in-plane and out-of-plane bending modes shifted to higher frequencies due to the intermolecular NH⋯O hydrogen bond. Also, the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) energies and diagrams were presented.
authors.affiliation: Department of Physics, Faculty of Art & Sciences, Erzincan University, Erzincan, Turkey. Electronic address: ccirak@erzincan.edu.tr.
authors.forename: Çağrı
authors.initials: Ç
authors.lastname: Çırak
authors.affiliation: Department of Physics, Faculty of Art & Sciences, Bozok University, Yozgat, Turkey; Sorgun Vocational School, Bozok University, Yozgat 66100, Turkey.
authors.forename: Yusuf
authors.initials: Y
authors.lastname: Sert
authors.affiliation: Department of Physics, Faculty of Art & Sciences, Süleyman Demirel University, Isparta, Turkey.
authors.forename: Fatih
authors.initials: F
authors.lastname: Ucun
mesh_terms: D003198:Computer Simulation; D006860:Hydrogen Bonding; D008956:Models, Chemical; D056004:Molecular Dynamics Simulation; D010432:Pentoxyl / Q000031:analogs & derivatives* / Q000737:chemistry; D017550:Spectroscopy, Fourier Transform Infrared
chemical_list: C008055:5-hydroxymethyluracil; D010432:Pentoxyl
keywords: 5-Hydroxymethyluracil; 5hmU; B3LYP; FT-IR; Hydrogen bonding; M06-2X