Normal coordinate analysis and vibrational spectra of 9-?-D-arabinofuranosyladenine hydrochloride (ara-A.HCl)

Ab initio Hartree-Fock/6-31G** calculation on 9-beta-D-arabinofuranosyladenine-5'-monophosphate molecule: application to the analysis of its IR and Raman spectra

9-beta-D-arabinofuranosyaldenine-5'-monophosphate (5'-ara-AMP) is an arabinonucleotide that has antiviral and antitumor activity. The accurate knowledge of the nature of its vibrational modes is a valuable step for the forthcoming elucidation of drug-nucleotide and drug-enzyme interactions. The FTIR and FT Raman spectra (4000-30 cm(-1)) of 5'ara-AMP and two deuterated derivatives ara-AMP-d(C8) (deuteration in C8) and ara-AMP-d7 (deuteration in C8, amino and hydroxyl groups) are reported. Theoretical vibrational calculations were performed using the Hartree-Fock/6-31G** method. An assignment of the observed spectra is proposed considering the scaled potential energy distribution of the vibrational modes of the 5'ara-AMP molecule and the observed band shifts by deuteration. The scaled ab initio frequencies are in good agreement with the experimental data (<3 cm(-1) SD).

Vibrational analysis and spectra of orotic acid

The IR and Raman spectra of polycrystalline anhydrous orotic acid and its N1, N3, and O12 trideuterated isotopomer are recorded in the 4000-40 cm(-1) spectral interval as part of a series of vibrational analyses of nucleosides, nucleotides, and related compounds carried out in our laboratory. The frequencies of the fundamental transitions and the potential energy distributions of the 39 normal modes of orotic acid and its isotopomer are calculated by an ab initio density functional theory Becke3P86/6-311G** treatment. Assignments of the vibrational modes are proposed that consider the results of these calculations and the observed spectra. The results of the ab initio treatment are related to crystallographic and spectral data, and they are compared with previous assignments for similar molecules.