N-Acetyl-L-alanine N′-methylamide: a density functional analysis of the vibrational absorption and vibrational circular dichroism spectra

Abstract

Abstract Ab initio 6-31G∗ Becke 3LYP DFT optimized geometries, vibrational frequencies, vibrational absorption (VA) intensities and vibrational circular dichroism (VCD) intensities have been calculated for the eight low energy conformers of N-acetyl-L-alanine N′-methylamide (L-AANMA) in the gas phase and one conformer stabilized by the addition of four water molecules. The VA and VCD spectra are calculated with the 6-31G∗ Becke 3LYP force fields (Hessians) and atomic polar tensors (APT); 6-31G∗∗ RHF atomic axial tensors (AAT) for the eight gas phase structures and 6-31G∗/6-31G RHF AAT for the L-AANMA-water complex. The VA and VCD spectra are also calculated using the 6-31G∗ Becke 3LYP Hessians; 6-31G∗∗ RHF APT and AAT for the eight gas phase structures and 6-31G∗/6-31G RHF APT and AAT for the L-AANMA-water complex. The rotational strengths of the amide A, I, II, III, IV, V and VI modes found in proteins as a function of φ and ψ (for various secondary structures) are for the first time reported for an inherently optically active molecule (non-glycine model) using the 6-31G∗∗ and 6-31G∗/6-31G RHF DOG AAT and 6-31G∗ Becke 3LYP Hessians and APT. This is also the first reported VCD calculation of a molecule with the solvent present. The molecule is not completely solvated, but the important hydrogen-bonded interactions are present and the feasibility of the calculation of the Hessian, APT and AAT with solvent molecules present is demonstrated. The VA and VCD spectra are compared to the experimental VA and VCD spectra in the literature and the conformational analysis (CA) and vibrational assignment of L-AANMA are reinvestigated. The rotational strengths of the amide modes for the various conformers are also compared to peptide and protein VCD spectra of molecules with known secondary structures. The agreement between the calculated rotational strengths of the various amide modes for which experimental measurements have been made is very good, in particular, for the right handed α-helical conformation of a poly(L-amino acid) we correctly predict the negative couplet for the amide A band, the positive couplet for the amide I band and the negative monosignate signal for the amide II band as measured by the groups of Nafie and Keiderling. The large change in the amide I region in aqueous solution from this region in carbon tetrachloride or the Ar matrix is also reproduced, documenting that the qualitative features of the vibrational absorption and VCD spectra can reproduced by explicitly adding water molecules to the Hessian and tensor calculations.