A scaled quantum mechanical force field for the alanine–alanine zwitterions in water based on scale factors for alanine, glycine, N-methylacetamide, acetate, formate, and methylamine

We present ab initio scale factors and force constants, and vibrational modes assigned to experimental Raman and FTIR spectra of eight isotopomers of the alanine–alanine zwitterion peptide in water, at neutral pH, in extended and helical f/c conformations. Results are shown for the HF/4-31G and density functional theory B3LYP/6-31 þ G* levels. The HF/4-31G scale factors are for the most part based on previously published scale factors for smaller molecules and from alanine–alanine at pH 1 and 13 (Biopolymers, 58 (2001) 577). Similar results at the B3LYP/6-31 þ G* level are shown here for smaller molecules: alanine, glycine, N-methylacetamide, acetate, formate, and methylamine, from which the B3LYP/6-31 þ G* scale factors for alanine–alanine are derived. The helical conformation yields calculated frequencies that are in better agreement with the experiment than are those from the extended conformation. Scale factors are used here as an index of how well each calculated model for the average geometry of alanine–alanine in water corresponds to the experimental data, or to what extent the ‘same’ functional group is different in differently charged molecules. Scale factors for the helical conformation of ala–ala tend to be closer to those from the smaller molecules than are those for the extended geometry. We think this suggests that the helical conformation of this small peptide is preferred in water. As expected, scale factors for several important internal coordinates, the amide C–N stretch (CNs), the in-plane amide N–H in-plane bend (NHib), and others were significantly different from those for ala–ala in acid and base. q 2004 Elsevier B.V. All rights reserved.