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The aim of this work is to evaluate the vibrational and structural properties of l-cysteine ethyl ester hydrochloride (CE), and its electronic behavior mainly in relation to the action of the thiol and amine groups at different degrees of solvation. The crystal structure of CE was determined at room temperature by X-ray diffraction methods. Infrared and Raman spectra were collected to compare the behavior of different functional groups in the molecule, both in the solid phase and in aqueous solution. Its UV and circular dichroism spectra were also measured in aqueous solution. The influence of an aqueous environment on the CE spectra was simulated by means of implicit (polarizable continuum model) and explicit (molecular dynamics, solute-solvent clusters) methods. Calculations in explicit and continuous solvent are of interest to explain the behavior of bioavailable sites in this medium. The study was completed by natural bond orbital analysis to determine the presence of hyperconjugative interactions.

Ethyl methanesulfonate, CH3SO2OCH2CH3, is well-known as an alkylating agent in mutagenic and carcinogenic processes. Its electronic structure and that of the methanesulfonate anion (CH3SO3-) were determined using optimization methods based on density functional theory and Moller-Plesset second-order perturbation theory. For CH3SO2OCH2CH3, two conformations with symmetries C(s) and C1 are obtained, the former being more stable than the latter. Natural bond orbital (NBO) calculations show the C(s) conformation provides a more favorable geometry of the lone pairs of the oxygen atom linking the ethyl group. The NBO technique also reveals the characteristics of the methanesulfonate anion as a leaving group due to the rearrangement of the excess electronic charge after alkylation. Furthermore, the infrared spectra of CH3SO2OCH2CH3 are reported for the liquid and solid states as well as the Raman spectrum of the liquid. Comparison to experiment of the conformationally averaged IR spectrum of C(s) and C1 provides evidence of the predicted conformations in the solid IR spectrum. These experimental data along with the calculated theoretical force constants are used to define a scaled quantum mechanical force field for the target molecule, which allowed the measured frequencies to be reproduced with a final root-mean-square deviation of 9 cm(-1) and, thus, a reliable assignment of the vibrational spectrum.