A density functional theory study of vibrational coupling in the amide I band of beta-sheet models.
We report the first molecular orbital/density functional theory (DFT) calculations on the vibrational frequencies involved in the amide I band of completely geometrically optimized models for beta-sheet peptides based upon (up to 16) glycine residues. These calculations use the B3LYP/D95** level of DFT. The primary means of vibrational coupling occurs through H bond, rather than through space, interactions, which is consistent with a previous report on alpha-helical polyalanines and H-bonding chains of both formamides and 4-pyridones. We decoupled the C=O stretching vibrations using selected 14C substitutions to probe the coupling mechanism and to determine "natural" frequencies for individual 14C=Os. The intermolecular H-bonding interactions affect the geometries of the amide groups. Those near the center of H-bonding chains have long C=O bonds. The C=O bond lengths correlate with these "natural" frequencies, The frequencies obtained from the DFT calculations are generally more coupled, and the most intense are more red shifted than those calculated by transition dipole coupling (TDC). TDC inverts the order of the shifted frequencies compared to DFT in several cases.
Viswanathan
Raji
R
Department of Chemistry, Yeshiva College, 500 West 185th Street, New York, New York 10033, USA.
Dannenberg
J J
JJ
D000577:Amides / Q000737:chemistry*; D002244:Carbon / Q000737:chemistry; D008954:Models, Biological; D008958:Models, Molecular; D010100:Oxygen / Q000737:chemistry; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry*; D014732:Vibration
D000577:Amides; D011506:Proteins; D002244:Carbon; D010100:Oxygen