title: Geometry and solvent dependence of the electronic spectra of the amide group and consequences for peptide circular dichroism.
abstract: The influence of geometry variations and solvent environment of N-methylacetamide on its energies and absorption intensities was systematically analyzed with the aid of the time-dependent density functional theory (TD DFT). Selective and often complicated reactions of individual electronic levels on the perturbations were found important for the resultant spectral profile. For example, the n-pi band position varied by tens of nanometers due to the C=O bond length oscillations, while it was rather unaffected by surrounding water. On the contrary, pi-pi type transition energies and intensities were broadly dispersed by the aqueous environment but exhibited a modest coordinate dependence. A simple electrostatic model used previously for absorption in the IR region (J. Chem. Phys. 2005, 122, 144501) explained these changes only partially. Additionally, electronic transfer between the solute and the solvent had to be considered for faithful modeling of the ultraviolet light absorption. The inclusion of the environment and dynamics in the modeling then provided more accurate positions, intensities, and realistic inhomogeneous widths of spectral lines. These factors were found important for absorption and circular dichroism spectra of larger peptides and proteins. This was demonstrated with a combined DFT/coupled oscillator model providing principal features observed in electronic circular dichroism spectra of standard peptide conformations.
authors.affiliation: Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nam. 2, 166 10.
authors.forename: Jirí
authors.initials: J
authors.lastname: Sebek
authors.forename: Zdenek
authors.initials: Z
authors.lastname: Kejík
authors.forename: Petr
authors.initials: P
authors.lastname: Bour
mesh_terms: D000081:Acetamides / Q000737:chemistry*; D000465:Algorithms; D002942:Circular Dichroism; D003198:Computer Simulation; D004583:Electrons; D008956:Models, Chemical; D015394:Molecular Structure; D010455:Peptides / Q000737:chemistry*; D011789:Quantum Theory; D012997:Solvents / Q000737:chemistry*; D014867:Water / Q000737:chemistry
chemical_list: D000081:Acetamides; D010455:Peptides; D012997:Solvents; D014867:Water; C018595:N-methylacetamide