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

Abstract

The vibrational spectra of a synthetic purine nucleoside with known antiviral activity, 9-fl-D-arabinofuranosyladenine hydrochloride (ara-A.HC1) are reported. The Fourier transform infrared (FT-IR) and Fourier transform Raman (FT-Raman) spectra were recorded in the 4000-30 cm -1 spectral region. The harmonic frequencies and potential energy distributions (PED) of the vibrational modes of ara-A.HC1 were calculated by two different methods: a classical molecular mechanics method and a semiempirical molecular orbital (MO) method, PM3. The results of both computational methods, based on the Wilson GF method, are compared with observed spectra, and an assignment of the vibrational modes of ara-A.HC1 is proposed on the basis of the potential energy distributions (PED). It is found that the wavenumbers can be calculated with remarkable accuracy (=1% deviation in most cases), with the classical mechanics method, by transferring a sufficiently large set of available harmonic force constants, thus permitting a reliable assignment. The semiempirical MO method, PM3, is found to be useful for the assignment of experimental frequencies although it is less accurate (= 10% deviation). IR intensities calculated by this method did not coincide with the experimental values. Certain outof-plane vibrations in the base, not reported in previous studies, have been observed. The performance of both methods was related to the crystallographic and ab initio data available. Previous normal coordinate calculations for the adenine base and the nucleoside 5'-dGMP are compared with our results and discussed, in relation to the crystal structure of Ara-A.HC1.

Vibrational Force Field Calculations of Ara-A. Application to the Analysis of Its Infrared and Raman Spectra

“…The results obtained from all these treatments are compared to evaluate their reliability. They are also compared with previous normal coordinate analyses of related molecules. − …”

Ab initio Hartree–Fock/6‐31G** calculation on 9‐β‐D‐arabinofuranosyladenine‐5′‐monophosphate molecule: Application to the analysis of its IR and Raman spectra

“…16,20,21,24,26,56,57 The scissoring vibration of the amino group appears in this region 16,17,19 -21,24,26,57 and contributes significantly, according to the HF/6-31G** ab initio treatment, to the modes giving rise to the bands at 1696 (very strong in IR and weak in Raman, 35% contribution), 1611 (medium intensity in IR and Raman, 14% contribution), and 1556 cm Ϫ1 (medium intensity in IR and strong in Raman, 11% contribution). In these three cases the scis- Proposed assignment and potential energy distribution (PED) of the vibrational normal modes Types of vibration: , stretching; ␦, in plane bending; , out of plane bending; , torsion.…”

“…Fitting this value, the calculation predicts the antisymmetric stretch, a (NH 2 ), at 3589 cm Ϫ1 . The bands at 3332 (3325 cm Ϫ1 in Raman) and 3278 cm Ϫ1 (3280 cm Ϫ1 , strong in Raman) are assigned to the OЈ 3 OH and OЈ 2 OH stretches (by comparison with other nucleosides and nucleotides 16,37,44,45,55,56 ), while those that appear at 3250 (very strong in IR) and 3225 cm Ϫ1 (resolved by the second derivative) are attributed to the two OOH groups of the phosphate group. Calculations predict that these bands should shift by …”

Phonon dispersion in polycytidilic acid

“…Homopolynucleotides are a class of materials that are used as model compounds for the study of DNAs and RNAs. Several workers have reported preliminary studies on the vibrational spectra of oligonucleotides and polynucleotides 6–25. Their work is mostly confined to zone center frequencies.…”

“…Over the years, a large number of theoretical and experimental studies using techniques such as X‐ray diffraction, ultraviolet, infrared (IR), and Raman spectroscopy have been conducted on the structure of polynucleotides 6–25. These studies also yield information, otherwise difficult to obtain, concerning the specific interactions of base and backbone residues.…”