title: Car-Parrinello simulation of the vibrational spectrum of a medium strong hydrogen bond by two-dimensional quantization of the nuclear motion: application to 2-hydroxy-5-nitrobenzamide.
abstract: The nature of medium strong intra- and intermolecular hydrogen bonding in 2-hydroxy-5-nitrobenzamide in the crystal phase was examined by infrared spectroscopy and Car-Parrinello molecular dynamics simulation. The focal point of our study was the part of the infrared spectra associated with the O-H and N-H stretching modes that are very sensitive to the strength of hydrogen bonding. For spectra calculations we used an isolated dimer and the fully periodic crystal environment. We calculated the spectra by using harmonic approximation, the time course of the dipole moment function as obtained from the Car-Parrinello simulation, and the quantization of the nuclear motion of the proton for an instantaneous snapshot of the structures in one and two dimensions. Although quantitative assessment of the agreement between the computed and experimental band contour is difficult due to the fact that the experimental band is very broad, we feel that the most reasonable qualitative agreement with the experiment is obtained from snapshot structures and two-dimensional quantization of the proton motion. We have also critically examined the methods of constructing the one-dimensional proton potential. Perspectives are given for the treatment of nuclear quantum effects in biocatalysis.
authors.affiliation: Laboratory for Biocomputing and Bioinformatics, National Institute of Chemistry, Ljubljana, Slovenia.
authors.forename: Mateusz
authors.initials: M
authors.lastname: Brela
authors.forename: Jernej
authors.initials: J
authors.lastname: Stare
authors.forename: Gordana
authors.initials: G
authors.lastname: Pirc
authors.forename: Marija
authors.initials: M
authors.lastname: Sollner-Dolenc
authors.forename: Marek
authors.initials: M
authors.lastname: Boczar
authors.forename: Marek J
authors.initials: MJ
authors.lastname: Wójcik
authors.forename: Janez
authors.initials: J
authors.lastname: Mavri
mesh_terms: D001549:Benzamides / Q000737:chemistry*; D055162:Biocatalysis; D003198:Computer Simulation; D006860:Hydrogen Bonding; D006900:Hydroxylation; D008958:Models, Molecular; D011522:Protons; D017550:Spectroscopy, Fourier Transform Infrared; D014732:Vibration
chemical_list: D001549:Benzamides; D011522:Protons