Amino acid chemistry in solution: structural properties and vibrational dynamics of serine using density functional theory and a continuum solvent model

Abstract

A structural and vibrational study of amino acid serine in aqueous solution has been carried out using Fourier transform spectroscopies and quantum mechanical calculations. FT-IR and FT-Raman spectra of serine in H2O and D2O solutions were recorded and a general assignment of the observed bands was proposed on the basis of a zwitterionic structure for serine. Main criteria were the observed wavenumber shifts upon deuteration and previous assignments for other amino acids. A quadratic force field was computed using ab initio methodology at the 6-31+G** level and the hybrid functional B3LYP. The solvent effect was simulated by placing the serine molecule into an ellipsoidal cavity surrounded by a continuum solvent characterized by its dielectric constant. The solute–solvent electrostatic interaction was evaluated by means a multipolar moment expansion introduced in the Hamiltonian. The ab initio force field was obtained from the analytical second derivatives of the molecular geometry evaluated in a point of minimal energy, which was reached under the same calculation methodology. The optimized structural parameters were compared to those reported for l-serine crystal, which confirmed the zwitterionic structure for this molecule in aqueous solution. Ab initio force constants in cartesian coordinates were transformed into a set of locally symmetrized internal coordinates, thus allowing for a scaling procedure using two generic factors. Normal mode description was obtained as the potential energy distribution. The scaled wavenumbers were compared with those experimental in order to check the previous assignments. It also allowed us to add new data to the sets of experimental wavenumbers. Infrared intensities were calculated for both, H2O and D2O solutions, and compared to the experimental intensities.