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J. Phys. Chem. 1993,97, 10890
Reply to Comments on “Vibrational Motions of Nucleic Acids As Revealed by Neutron Inelastic Scattering and Resonance Raman Spectroscopy. 1. Adenine and Its Deuterated Species” M. Ghomi Physique Thborique des Macromolbcules Biologiques, UFR de Santb- Mbdecine-Biologie Humaine, 74, Rue Marcel Cachin, 93012 Bobigny Cedex, France Received: March 18, 1993; In Final Form: July 12, 1993 This paper aims to illustrate the complementary aspects of the NIS and RRS spectroscopies in order to study the vibrational modes of nucleic acid bases. We have extensively discussed the fact that the in-plane modes of adenine can be analyzed from RRS data, while NIS data mainly deal with the out-of-plane vibrations. The use of N I S to investigate nucleic acids is completely new. We had mentioned the capabilities of this technique in a short paper devoted to guanine.’ It is known that off-resonance Raman scattering, as well as infrared absorption, does not allow the out-of-plane of these molecules to be completely analyzed.2J As far as the assignment of the vibrational modes of the purine bases is concerned, we think that the work of M a j ~ u b eon ~ ,the ~ in-plane vibrational modes, based on an empirical force field, seems to be the most serious. Majoube took advantage of a complete series of experimental data (IR and Raman of polycrystalline samples) derived from the pure moleculear species as well as from deuterated and ISN-substituted derivatives of purine bases. These force fields were successfully transferred to the base residues435 and helped a number of authors to study with success the DNA conformation vibrational markers6,’ These investigations have been later completed by an out-of-plane vibrational mode analysis based on another empirical valence force field,* which accurately assigned the limited number of experimental data available from Majoube’s spectra. In the present numerical calculations, we attempted to improve the empirical force fields mentioned above by using new results available from both the RRS and NIS data, not only from the native species but also from selectively deuterated species. We have shown that, keeping Majoube’s diagonal force constants, a good agreement between the experimental and calculated results can be obtained by only refining the interaction (off-diagonal) force constants. In our potential field expansion, attention was given to taking into account only the interaction force constants due to the coupling between adjacent internal coordinates. The number of available experimental wavenumbers was larger than that of the refined force constants. Indeed, the whole set of the force constant values (in-plane and out-of-plane) have been reported in our paper. Up to now, most authors only attempted to compare the calculated wavenumbers to the experimental ones. In contrast, here we simulated the NIS and RRS wavenumbers and intensities by using the theoretical procedures which are available to date. The NIS intensity simulation is quite simple and is perhaps the best way to test the reliability of the atomic displacement amplitudes derived from an empirical or quantum chemical normal-mode calculation. Now the NIS intensities from both the purine nucleic bases (guanine and adenine) and their deuterated species are available: consequently, we can suggest that other authors use them to test the atomic displacements that they determined by quantum chemistry calculations. This trial procedure should help them to discuss the ability of a different wave function basis to reproduce the experimental results, which finally make the law. As far as the RRS intensity simulation is concerned, we have used Peticola’s theory9J0 which constitutes a simple model 0022-3654/93/2097- 10890$04.00/0
especially built for the nucleic acid bases. Only Albrecht’s A term is considered in the expansion of the electronic polarizability. Peticolas’o was the first one to use this theory of his own to refine the molecular force field of uracil. In this model, based on the well-known ”small shift approximation” and applicable only to the in-plane stretching modes, one estimates the excited-state geometries via the changes occurring in the molecular bond orders in coming from the ground-state geometry. We adopted and recalled the different approximations considered by Peticolas et al.9J0 for obtaining the simplified and final formulas allowing the RRS intensities to be calculated. Before us, other authors” also used the RRS intensities to test their molecular force fields of nucleic acid bases. We have discussed the domain of application of this model in our paper and explained how it can only be applied to the modes above 1000 cm-I, associated (mainly) with the ring stretching vibrations. Of course, the bond order changes which we used in the present paper are not recent, and we think that one can now obtain better values for these parameters by new theoretical procedures. However, our RRS simulated intensities speak of themselves (see Figure 6 of the paper), and the agreement with the experimental intensities of 10 bands (and not only two, as Dr. Florian puts it) shows that Peticolas’ model, although quite simple, is very efficient for this purpose. As Dr. Florian mentioned, one could improve this preliminary simulation by a more sophisticated model, allowing the exact geometry of the excited states to be estimated. However, wedo not understand how Dr. Florian might evaluate the excited-state geometry by considering only the two most intense RRS bands. How can one be confident of the normal-mode assignments if the RRS intensities are not calculated accurately? As far as the quantum chemistry calculations are concerned, the recent progress in supercomputor development and the existence of optimized versions of ab initio codes allow quite heavy computations on large molecules like purine bases to be undertaken. Recent results of quantum mechanical calculations on purine basesl2Jj using STO-3G basis mainly discuss the molecular in-plane modes for which the theoretical wavenumbers have been compared with the infrared and off-resonance spectra of the native polycrystalline samples. It would be interesting to test the reliability of the obtained scaling factors in reproducing the wavenumber shifts observed by us upon selective deuterations. The correct simulation of isotopic shifts was the key point of our theoretical study. In conclusion, empirical force field calculations allow significant assignments of the vibrational modes to be made, thus helping other authors to select the best basis in the ab initio calculations. However, a theoretical treatment, whatever its origin, must remain a tool to analyze complete and well-defined experimental results. Our paper should be considered as an example (and not the only possible one) of theoretical interpretation of vibrational modes of nucleic acids fragments. References and Notes (1) Coulombeau, C.;Dhaouadi, 2.;Ghomi, M.; Jobic, H.; Tomkinson, J. Eur. Biophys. J . 1991, 19,323. (2) Majoube, M. J . Chim. Phys. (Paris) 1984, 81, 303. (3) Majoube, M. J . Raman Spectrosc. 1985, 16,98. (4) Majoube, M. Biopolymers 1985, 24, 1075. (5) Majoube, M. Biopolymers 1985, 24, 2357. (6) Ghomi, M.; Letellier, R.; Taillandier, E. Biopolymers 1988,27,605. (7) Vergoten, G.; Lagant, Ph.; Peticolas, W. L.; Moschetto, Y.; Morize, I.; Vaney, M. C.; Mornon, J. P. J . Mol. Graphics 1986, 4, 187. (8) Letellier, R.; Ghomi, M.; Taillandier, E. Eur. Biophys. J . 1987, 14, 243. (9) Peticolas, W. L.; Blazej, D. C. Chem. Phys. Lett. 1979, 63,604. (10) Peticolas, W.L.;Strommen, D. P.; Lakshminarayanan, V. J . Chem. Phys. 1980, 73, 4185. ( 1 1 ) Lagant, Ph.; Derreumaux, Ph.; Vergoten, G.; Peticolas, W. L. J . Comput. Chem. 1991, 12, 731. (12)Florian, J.; Mojzes, P.; Stepanek, J . J . Phys. Chem. 1992, 96,9278. (13) Florian, J.; Baumruk, V. J . Phys. Chem. 1992, 96,9283.
0 1993 American Chemical Society
