Search for a reliable nucleic acid force field using neutron inelastic scattering and quantum mechanical calculations: Bases, nucleosides and nucleotides
- Laboratoire de Physicochimie Biomoleculaire et Cellulaire, UPRESA 7033, Universite P. and M. Curie, Case Courrier 138, 75252 Paris Cedex 05 (France)
- Institut de Recherche sur la Catalyse, 2 avenue A. Einstein, 69626 Villeurbanne (France)
Neutron inelastic scattering (NIS), IR and Raman spectra of the RNA constituents: bases, nucleosides and nucleotides have been analyzed. The complementary aspects of these different experimental techniques makes them especially powerful for assigning the vibrational modes of the molecules of interest. Geometry optimization and harmonic force field calculations of these molecules have been undertaken by quantum mechanical calculations at several theoretical levels: Hartree-Fock (HF), Moller-plesset second-order perturbation (MP2) and Density Functional Theory (DFT). In all cases, it has been shown that HF calculations lead to insufficient results for assigning accurately the intramolecular vibrational modes. In the case of the nucleic bases, these discrepancies could be satisfactorily removed by introducing the correlation effects at MP2 level. However, the application of the MP2 procedure to the large size molecules such as nucleosides and nucleotides is absolutely impossible, taking into account the prohibitive computational time needed. On the basis of our results, the calculations at DFT levels using B3LYP exchange and correlation functional appear to be a cost-effective alternative in obtaining a reliable force field for the whole set of nucleic acid constituents.
- OSTI ID:
- 21208173
- Journal Information:
- AIP Conference Proceedings, Vol. 479, Issue 1; Conference: Workshop on neutrons and numerical methods, Grenoble (France), 9-12 Dec 1998; Other Information: DOI: 10.1063/1.59464; (c) 1999 American Institute of Physics; Country of input: International Atomic Energy Agency (IAEA); ISSN 0094-243X
- Country of Publication:
- United States
- Language:
- English
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