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.

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.

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.

Thanks to a considerable modulation of electronic polarizability, six phenylalanine (Phe) vibration modes located at ca. 1606, 1586, 1207, 1031, 1004 and 622 cm−1 appear as intense or medium bands in the Raman spectra of peptides and proteins, as confirmed by the Raman data collected from free amino acid, somatostatin and bovine serum albumin (BSA). To get information on the nature and location of these lines, we resorted to a multiconformational analysis which consists in a systematic investigation of the structural and vibrational features of hydrated Phe in a conformational space depending on four angular variables: φ, ψ, χ1 and χ2. The first two variables correspond to the Phe backbone torsion angles, whereas the latter two refer to its side chain. Based on a protocol described in an accompanying report on glycine and its protonated and deprotonated species, we have prepared an initial set of 123 initial clusters of Phe + 5H2O, including all plausible values of the above mentioned conformational angles. The results of their geometry optimization, by means of the density functional theory using the B3LYP hybrid functional, were first analyzed through the comparison between the E(χ1, χ2) energy maps obtained either by an explicit or by an implicit hydration model. Then, a set of nine doubly minimized clusters corresponding to the deepest local minima were used for further structural and vibrational analysis. Beyond providing a reliable assignment for the above mentioned characteristic Raman lines, the theoretical spectrum allowed us to carry out an overview of the whole observed data of Phe in aqueous solution. Copyright © 2013 John Wiley & Sons, Ltd.

Raman data collected from free amino acid and peptide chains permit assignment of the seven markers located at approximately 1616, 1606, 1210, 1178, 850, 830, and 643 cm À1 to tyrosine. The effects induced by labile hydrogen deuteration, temperature, concentration, and protonation-deprotonation on these Raman markers were analyzed. Following closely a recent multiconformational analysis on phenylalanine, we could confirm the predominance of gauche -/gauche -rotamers with respect to the side chain χ 1 /χ 2 torsion angles in both tyrosine and tyrosinate. Calculated Raman spectra, based on the consideration of both implicit and explicit hydration models, have revealed the effect of hydrogen bonding of water molecules to the phenol ring hydroxyl group of tyrosine. A special attention has been paid to the 850/830 cm À1 tyrosine doublet, for which no intensity ratio inversion could be remarked when the phenol hydroxyl group acts as a hydrogen bond donor or acceptor. On the contrary, this intensity ratio appeared to be strongly dependent on the hydrophobic/hydrophilic balance of the interactions, in which the phenol ring is involved. Based on the present theoretical calculations, the components of the tyrosine doublet might originate from two independent fundamental modes of the phenol ring: one with an in-plane character and the other with an out-ofplane character. As a consequence, the widely spread Fermi resonance-based description of the tyrosine doublet appears to be unjustified. The latter interpretation simply results from the insufficiencies of the simple model compound used at that time for analyzing the vibrational features of a more complex molecular system such as tyrosine.

Raman scattering and Fourier-transform infrared (FT-IR) attenuated transmission reflectance (ATR) spectra of two alpha-amino acids (alpha-AAs), i.e., glycine and leucine, were measured in H2O and D2O (at neutral pH and pD). This series of observed vibrational data gave us the opportunity to analyze vibrational features of both AAs in hydrated media by density functional theory (DFT) calculations at the B3LYP/6-31++G* level. Harmonic vibrational modes calculated after geometry optimization on the clusters containing each AA and 12 surrounding water molecules, which represent primary models for hydration scheme of amino acids, allowed us to assign the main observed peaks.

Ground state energies and geometries have been determined at the DFT/B3LYP level for different model compounds such as ribose, dimethyl phosphate, uridine, cytidine, 3‘-methyl phosphate−uridine, and 5‘-methyl phosphate−uridine as a function of the most prominent conformations adopted by each of them. The counterion used for neutralizing the phosphate negative charge was an ammonium ion (NH4 +). This systematic study allowed us to analyze the stability of a ribonucleotide (base+ribose+phosphate) which is the chemical repeating unit of RNA. In the dimethyl phosphate model, the lowest energy corresponds to the gauche--gauche- conformation, as also predicted by previous calculations on this motif at different theoretical levels. In the ribose model, the C2‘-endo (S-type) conformer has a lower energy than the C3‘-endo (N-type) one. When a pyrimidine base (uracil or cytosine) is added to the ribose to form a ribonucleoside, the electronic energies of the three optimized conformers with the C3‘-endo and C2‘-endo sugar puckers as well as the anti and syn orientations of the base with respect to the sugar are located in the following order:  C3‘-endo/anti < C2‘-endo/anti < C3‘-endo/syn. However, the energy difference between these conformers depends on the type of the pyrimidine base connected to the ribose. The optimization of the ribonucleotides confirms the stability of the conformers containing A- and Z-form conformational angles. The role of the intramolecular O−H···O and C−H···O hydrogen bonds in the overall stability of ribose, nucleosides, and ribonucleotides has been discussed.

Four out of the 20 natural α-amino acids (α-AAs) contain aromatic rings in their side chains. In a recent paper (J. Phys. Chem. B 2010, 114, 9072-9083), we have analyzed the structural and vibrational features of l-histidine, one of the potent elements of this series. Here, we report on the three remaining members of this family, i.e., l-phenylalanine, l-tyrosine, and l-tryptophan. Their solution (H(2)O and D(2)O) Raman scattering and Fourier transform infrared absorption attenuated total reflection (FT-IR ATR) spectra were measured at room temperature from the species corresponding to those existing at physiological conditions. Because of the very low water solubility of tyrosine, special attention was paid to avoid any artifact concerning the report of the vibrational spectra corresponding to nondissolved powder of this AA in aqueous solution. Finally, we could obtain for the first time the Raman and FT-IR spectra of tyrosine at very low concentration (2.3 mM) upon long accumulation time. To clarify this point, those vibrational spectra of tyrosine recorded either in the solid phase or in a heterogeneous state, where dissolved and nondissolved species of this AA coexist in aqueous solution, are also provided as Supporting Information . To carry out a discussion on the general geometrical and vibrational behavior of these AAs, we resorted to quantum mechanical calculations at the DFT/B3LYP/6-31++G* level, allowing (i) determination of potential energy surfaces of these AAs in a continuum solvent as a function of the torsion angles χ(1) and χ(2), defining the conformation of each aromatic side chain around C(α)-C(β) and C(β)-C(γ) bonds, respectively; (ii) analysis of geometrical features of the AAs surrounded by clusters of n explicit (n = 5-7) water molecules interacting with the backbone and aromatic rings; and (iii) assignment of the observed vibrational modes by means of the theoretical data provided by the lowest energy conformers of explicitly hydrated amino acids.