Ab initio-based exciton model of amide I vibrations in peptides: definition, conformational dependence, and transferability.
Various aspects of the ab initio-based parametrization of an exciton model of amide I vibrations in peptides are discussed. Adopting "glycine dipeptide" (Ac-Gly-NHCH3) as a simple building-block model that describes the vibrational interaction between two peptide units, we perform comprehensive quantum-chemical calculations to investigate the effect and importance of the level of theory, the choice of local coordinates, and the localization method. A solvent continuum model description turns out important to obtain planar CONH peptide units when a full geometry optimization (which is necessary to obtain the correct frequencies) is performed. To study the conformational dependence of the amide I vibrations, we calculate (phi,psi) maps of the local-mode frequencies and couplings. Performing conformational averages of the (phi,psi) maps with respect to the most important peptide conformational states in solution (alpha, beta, P(II), and C5), we discuss the relation between these measurable quantities and the corresponding conformation of the peptide. Finally, the transferability of these maps to dipeptides with hydrophilic and hydrophobic side chains as well as to tripeptides with charged end groups is investigated.
Gorbunov
Roman D
RD
Institute of Physical and Theoretical Chemistry, Johann Wolfgang Goethe University, Marie Curie Str. 11, D-60439 Frankfurt, Germany.
Kosov
Daniil S
DS
Stock
Gerhard
G
D000577:Amides / Q000737:chemistry*; D003198:Computer Simulation; D008954:Models, Biological; D010455:Peptides / Q000737:chemistry*; D011487:Protein Conformation; D012997:Solvents / Q000737:chemistry; D014732:Vibration
D000577:Amides; D010455:Peptides; D012997:Solvents