title: Simulations of the temperature dependence of amide I vibration.
abstract: For spectroscopic studies of peptide and protein thermal denaturation it is important to single out the contribution of the solvent to the spectral changes from those originated in the molecular structure. To obtain insights into the origin and size of the temperature solvent effects on the amide I spectra, combined molecular dynamics and density functional simulations were performed with the model N-methylacetamide molecule (NMA). The computations well reproduced frequency and intensity changes previously observed in aqueous NMA solutions. An empirical correction of vacuum frequencies in single NMA molecule based on the electrostatic potential of the water molecules provided superior results to a direct density functional average obtained for a limited number of solute-solvent clusters. The results thus confirm that the all-atom quantum and molecular mechanics approach captures the overall influence of the temperature dependent solvent properties on the amide I spectra and can improve the accuracy and reliability of molecular structural studies.
authors.affiliation: University of Wyoming, 1000 East University Avenue, Laramie, Wyoming 82071, USA. kaminskj@gmail.com
authors.forename: Jakub
authors.initials: J
authors.lastname: Kaminský
authors.forename: Petr
authors.initials: P
authors.lastname: Bouř
authors.forename: Jan
authors.initials: J
authors.lastname: Kubelka
mesh_terms: D000081:Acetamides / Q000737:chemistry; D000577:Amides / Q000737:chemistry*; D017097:Electric Impedance; D008968:Molecular Conformation; D056004:Molecular Dynamics Simulation; D011789:Quantum Theory; D012997:Solvents / Q000737:chemistry; D013055:Spectrophotometry, Infrared; D013696:Temperature; D014732:Vibration
chemical_list: D000081:Acetamides; D000577:Amides; D012997:Solvents; C018595:N-methylacetamide