In the present paper, we have analyzed the conformational energy and geometrical parameters of the isolated 2′-deoxyribonucleosides and ribonucleosides. Geometry optimization of these nucleic acid constituents has been undertaken by means of density functional theory with the Becke-Lee-Yang-Parr exchange and correlation functional and split valence basis sets, 6-31G (/) , including nonstandard polarization functions on carbon, nitrogen, and oxygen atoms. For each nucleoside, three major conformers, i.e., C2′-endo/anti, C3′endo/anti, and C3′-endo/syn, have been taken into consideration, where C3′-endo and C2′-endo refer to the north (N)-type and south (S)-type sugar puckering, respectively, and anti and syn designate the orientation of the base with respect to the sugar. In both families (2′-deoxyribonucleosides and ribonucleosides) the anti orientation of the base stabilized by an intramolecular C-H‚‚‚O hydrogen bond formed between the base and the O5′ atom of the sugar moiety corresponds to the lowest energy states. In the 2′-deoxyribonucleosides including uracil, guanine, and adenine bases the lowest energy conformer is C2′-endo/anti, whereas in 2′deoxycytidine the most stable conformer is C3′-endo/anti. In ribonucleosides, the C3′-endo/anti and C2′endo/anti conformers nearly have the same energy, except in cytidine, where the most stable conformer is C3′-endo/anti. Therefore, a general discussion has been devoted to the exceptional cases of 2′-deoxycytidine and cytidine compared to the other nucleosides. The present calculated results have also been compared with those recently reported at the MP2 level by other authors on the 2′-deoxyribonucleosides or smaller model compounds on one hand, and with the experimental results based on a statistical survey of nucleoside crystal structures on the other hand.

A complete set of vibrational spectra obtained from several spectroscopic techniques, i.e., neutron inelastic scattering (NIS), Raman scattering, and infrared absorption (IR), has been used in order to assign the vibrational modes of uracil on the basis of an ab initio scaled quantum mechanical (SQM) force field. NIS, Raman, and IR spectra of polycrystalline uracil recorded at T ) 15 K from native and N-deuterated species provide complementary data for analysing different groups of molecular vibrational modes. Solid-state spectra have been completed with various Raman (λ exc ) 257 nm, 514.5 nm, and 1.06 µm, and IR spectra in aqueous solutions. Both phases allowed effects of the environment on the vibrational modes, related to either strong (crystal) or weak (solution) hydrogen bondings, to be shown. In addition, the various laser excitations allowed the wavelength dependence of the Raman cross sections of in-plane characteristic modes to be observed. Due to the large NIS incoherent cross section of protons, the intense NIS bands are those arising from the vibrational modes containing hydrogen motions. The molecular fundamental wavenumbers calculated at the SCF+MP2 level, by using different types of molecular orbitals, have first been compared with the experimental wavenumbers taken from gas phase or Ar-matrix isolated uracil. Then the force field has been scaled in order to improve the agreement with experimental data from solid and aqueous phases. In the scaling procedure, the standard Pulay method was reliable for the in-plane vibrational modes, whereas it failed to scale successfully the out-of-plane vibrational modes. Consequently another scaling method, which consists of refining the nondiagonal elements of the internal force field matrix, has been used. On the basis of this procedure for out-of-plane modes, the simulation of the NIS intensity related to the C-H wagging motions could be performed without any particular difficulty. However some difficulties still exist for the N-H wagging motions which are largely perturbed by hydrogen bonding and packing effects in solid phase.

In relation with the difficulties encountered in previous works concerning the preservation of the S–S linkage in cystine (Cys-Cys dimer) on Ag nanoparticles (NPs), we present here a systematic investigation on both cysteine and cystine as a function of various parameters governing the preparation of metal substrates. Surface-enhanced Raman scattering (SERS) was used as a probe for analyzing (i) the integrity of the disulfide bonds of the adsorbed dimers, (ii) the influence of the metal nature, the reduction protocol as well as the Cys-Cys concentration on the adsorption, (iii) the terminal groups through which the interaction with metal surfaces take place, and (iv) the side chain conformation of the adsorbed molecules. From the whole set of experimental data collected in this work, it appears that large size Au NPs, prepared at low citrate concentration, can be considered as the most appropriate substrates for ensuring the integrity of disulfide linkages. Although Ag NPs prepared with hydroxylamine lead to the cleavage of dimers at low concentration, they have shown their adequacy to keep intact S–S bonds beyond a concentration threshold of ∼200 μM. Based on the examination of the SERS data recorded as a function of dimer concentration, we can now assume that this effect is mainly due to the bidentate and monodentate binding of Cys-Cys dimers at low and high concentrations, respectively, facilitating or not their cleavage on Ag surfaces.