title: Modeling the infrared and circular dichroism spectroscopy of a bridged cyclic diamide.
abstract: Density functional theory based molecular dynamics simulations are used to study the structure, infrared (IR) spectroscopy, circular dichroism (CD) spectroscopy, and coupling between the amide I vibrations of a bridged cyclic diamide in the gas phase and in aqueous solution. IR spectra computed via the dipole moment time correlation function show a large red-shift of 30 cm(-1) in the amide I vibration in solution compared to the gas phase, and are in good agreement with experiment. Conformationally averaged CD spectra computed using the CIS(D) method are highly sensitive to the structures used, and structures sampled in the aqueous phase simulation are required to obtain qualitatively correct CD spectra. Analysis of the coupling between the amide I modes shows that in the aqueous phase there is an increased localization of the vibrations on the individual peptide groups and a reduction in the mode coupling parameter compared to the gas phase. Overall, the results illustrate the significance of incorporating molecular dynamics in the simulation of IR and CD spectra.
authors.affiliation: Université d'Evry Val d'Essonne, LAMBE UMR8587 Laboratoire Analyse et Modélisation pour la Biologie et l'Environment, Blvd F. Mitterrand, Bât. Maupertuis, 91025 Evry, France.
authors.forename: Marie-Pierre
authors.initials: MP
authors.lastname: Gaigeot
authors.forename: Nicholas A
authors.initials: NA
authors.lastname: Besley
authors.forename: Jonathan D
authors.initials: JD
authors.lastname: Hirst
mesh_terms: D002942:Circular Dichroism; D003958:Diamide / Q000737:chemistry*; D005740:Gases / Q000737:chemistry; D056004:Molecular Dynamics Simulation; D013055:Spectrophotometry, Infrared; D013696:Temperature; D014732:Vibration
chemical_list: D005740:Gases; D003958:Diamide