Structural, Electronic, Topological and Vibrational Properties of Isomers of Thymidine ? A Study Combining Spectroscopic Data with DFT Calculations

Abstract

In this work, the structural, electronic, topological and vibrationalproperties of six Cis and Trans isomers of Thymidine (THY) in gasand aqueous solution phases were studied combining the hybridB3LYP/6-31G* method with the Polarized Continuum Model(PCM) model and the available experimental infrared, Raman, 1HNMR,13C-NMR and UV spectra. Hence, theoretical molecularstructures of two Cis isomers and one Trans isomers of THY weredetermined in the two media for first time. The population analysessuggest the presence in solution of a Trans isomer and of two Cisisomers in accordance with the experimental structures reported byX-ray diffraction by different authors. The study of the charges showclearly the differences between the Cis and Trans isomers where thecharges on the O atoms belonging to the ribose rings in all thestructures, on the N atoms belonging to the glycosidic bond and onthe two chiral C atoms show the higher modifications. TheMolecular Electrostatic Potential (MEP) surface mapped evidenceclearly that the group´s acceptors of H bonds in all the isomers arethe two C=O groups of the pyrimidine rings while the OH groups ofthe ribose rings and the NH group of the pyrimidine rings are donorsof H bonds showing their surfaces colorations red and blue in thosesites, respectively. Natural Bond Orbital (NBO) and QuantumAtoms in Molecules (QAIM) calculations clearly reveal the highstabilities of those three isomers of THY in both media. The frontierorbitals show that in gas phase the decreasing of the gap values aredifferent than those in solution. The vibrational analyses show thepresence of different isomers in both media and confirm that thedifferent positions of the bands are characteristic of their differentstructures. Here, the 1H-NMR, 13C-NMR and UV spectra present areasonable concordance with the corresponding experimental ones.Finally, the spectroscopic studies support the presence of more of anisomer of THY in solution.