Normal coordinate analysis and vibrational spectra of adenosine

Abstract

The Fourier transform infrared and Fourier transform Raman spectra of adenosine in the polycrystalline state were recorded in the 4000- to 30-cm−1 spectral region as part of a series of normal coordinate analyses of nucleic acid components and their analogues carried out in our laboratory. The harmonic frequencies and potential energy distributions (PED) of the vibrational modes of adenosine are calculated by two different methods: a classical molecular mechanics method and the semiempirical molecular orbital (MO) method, PM3. The results of both computational methods, based on Wilson's matrix method, are compared with observed spectra, and an assignment of the vibrational modes of adenosine is proposed on the basis of the PED and the results of calculations for the 1,3-15N2, 2-13C, 8-2H, and 1′-2H isotopomers. 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). Infrared intensities calculated by this method did not coincide with the experimental values. Certain out-of-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 the present results and discussed. © 1997 John Wiley & Sons, Inc. Biospect 3: 47–59, 1997