Structure and vibrational spectra of the zwitterion L-alanine in the presence of explicit water molecules: A density functional analysis

Ab initio B3LYP/6-31G* optimized geometries, vibrational frequencies, and absorption intensities have been calculated for the L-alanine zwitterion (ALAZW) structures stabilized by four neighboring water molecules. The ALAZW structures were stabilized by the addition of four neighboring water molecules because at the B3LYP/6-31G* level of theory the ALAZW is not stable in the absence of the water molecules and will be converted to the nonionized species. The ALAZW was not stable at this level of theory within the Onsager continuum model using the recommended cavity radius obtained from the solute volume calculations. Geometry optimization of the ALAZW in the presence of the explicit water molecules resulted in different optimized structures for the amino acid itself. The distributed origin gauge atomic axial tensors and the electric dipole - electric dipole polarizability derivatives calculated at the RHF level of theory were combined with the B3LYP normal modes, frequencies, and atomic polar tensors to calculate the vibrational absorption, the vibrational circular dichroism, and polarized Raman scattering intensities for the ALAZW structures. These calculated vibrational spectra of the solute were found to be very sensitive to the relative arrangement of the neighboring water molecules.