Weir A F, Lowrey A H, Williams R W
Department of Bioinformatics, Uniformed Services University of the Health Sciences, 4301 Jones Bridge Road, Bethesda, MD 20814-4799, USA.
Biopolymers. 2001 May;58(6):577-91. doi: 10.1002/1097-0282(200105)58:6<577::AID-BIP1032>3.0.CO;2-Y.
We have obtained ab initio scale factors and assigned frequencies for the alanine-alanine peptide in water. Calculations were performed on the isolated acidic and basic Ala-Ala structures, two one-water basic Ala-Ala supermolecules, and one two-water acidic and one two-water basic Ala-Ala supermolecules. Force constants were scaled using the experimentally determined Raman and Fourier transform infrared vibrational frequencies of four isotopic species of Ala-Ala in water at pH 13 and pH 1. Most of the 4-31G scale factors were transferable from smaller molecules. All but one scale factor were directly transferable between the pH 1 and pH 13 species for coordinates unchanged by protonation in both the isolated and two-water supermolecule structures. Scale factors for nonpolar coordinates were transferable between all Ala-Ala species with only a few small changes. Good agreement was obtained between the calculated and experimental frequencies for all isotopic species and structures.
