Raman scattering and Fourier-transform infrared (FT-IR) attenuated transmission reflectance (ATR) spectra of two alpha-amino acids (alpha-AAs), i.e., glycine and leucine, were measured in H2O and D2O (at neutral pH and pD). This series of observed vibrational data gave us the opportunity to analyze vibrational features of both AAs in hydrated media by density functional theory (DFT) calculations at the B3LYP/6-31++G* level. Harmonic vibrational modes calculated after geometry optimization on the clusters containing each AA and 12 surrounding water molecules, which represent primary models for hydration scheme of amino acids, allowed us to assign the main observed peaks.

In two recent reports of the same series (J. Phys. Chem. B 2007, 111, 1470-1477 and J. Phys. Chem. B 2009, 113, 3169-3178), we have described the geometrical and vibrational analysis of glycine and amino acids (AAs) with hydrophobic side chains through the joint use of optical spectroscopy and quantum mechanical calculations. Here, we report Raman scattering and Fourier-Transform Infrared (FT-IR) Attenuated Total Reflectance (ATR) spectra measured from the aqueous solutions (H(2)O and D(2)O) of L-lysine and L-arginine, i.e. two alpha-AAs with positively charged hydrophilic side chains. The discussion on the vibrational features of both AAs could be carried out thanks to the theoretical calculations performed by means of the Density Functional Theory (DFT) approach at the B3LYP/6-31++G* level. We have analyzed the influence of implicit (with a polarizable dielectric continuum) and explicit (by means of an H(2)O cluster interacting with H-donor and H-acceptor sites of AAs) hydration models. In addition, through the calculated geometrical parameters and vibrational wavenumbers, a discussion was performed on the effect of the Cl(-) anion interacting with the positively charged side chains of explicitly hydrated AAs.

Internal rotation is a fundamental motion of methyl groups that provides important insights into the molecular physics of isolated molecules. The barrier heights of such large amplitude motions are highly sensitive to their molecular and electronic environment. To date, it is still not possible to accurately determine these values using quantum chemical calculations. To probe the effect of molecular conformations on the barrier heights of substituted furan rings, the molecular jet Fourier transform microwave spectrum of 5-methyl furfural was recorded in the frequency range from 2.0 to 40.0 GHz. Quantum chemical calculations yielded two conformers with a trans and a cis orientation of the formyl group, which were both observed in the experimental spectrum. Torsional splittings due to the internal rotation of the methyl group were resolved and analyzed. The experimental spectrum is reproduced with standard deviations close to the experimental accuracy, yielding sets of highly accurate rotational and internal rotation parameters. The results, especially the V3 potentials, are compared to quantum chemical calculations and discussed within the scope of the current literature of other methyl substituted furans, where the methyl group is in close proximity of the furan oxygen atom. The present work provides an accurate evaluation of the different case studies and highlights the bottlenecks and future options of the currently available theoretical techniques.