In this work, we have studied, by means of Raman spectroscopy, water-additives interactions in the case of alkaline halogenides aqueous solutions. We have obtained some parameters describing the evolution of water structure vs concentration or the nature of the added salts. These parameters show, as previously described, a more important effect of anions than cations. Next, the evolution of the dynamical properties of the solution depends on the size of the ions. Moreover, the development of a new band in the isotropic part of the salts solutions spectra is attributed to water–ions interactions involved in the dynamics of hydration shells.

The band widths in Raman spectra are sensitive to dynamics active on a time scale from 0.1 to 10 ps. The band widths of nucleotide vibrations and their dependence on temperature, concentration, and structure are reported. From the experimental band widths and second moments, it is derived that the adenine vibrations at 725, 1336, 1480, and 1575 cm−1, and the uracil vibration at 787 cm−1, are in the fast modulation limit. The correlation times of the perturbations are faster than 0.4 ps. Thermal melting of the helical structure in polynucleotides results in larger band widths, due to an increase in vibrational dephasing and energy relaxation as a consequence of the increased interaction of the base moieties with the solvent molecules. The band width of the 725 cm−1 adenine vibration is dependent on the type and structure of the backbone. It is found to be perturbed by movements of the sugar‐phosphate moiety relative to the base. The band width of the 1575 cm−1 adenine vibration is found to be sensitive to the base‐pairing interaction. From a comparison of the band widths in polynucleotides with a different base sequence (homopolymer vs alternating purine‐pyrimidine sequence), it is concluded that resonant vibrational energy transfer between the base molecules is not important as a relaxation process for the vibrational band widths of nucleotides. Several theoretical models for the interpretation of band widths are discussed. The theory does not take into account the strong hydrogen‐bonding nature water and hence fails to describe the observations in nucleotide‐water systems. The bands of the carbonyl stretching vibrations are inhomogeneously broadened. The carbonyl groups have a strong dipolar interaction with the polar water molecules and are therefore strongly perturbed by coupling to the heatbath via hydrogen bonds. © 1997 John Wiley & Sons, Inc. Biopoly 41: 751–763, 1997

Isotropic and anisotropic spontaneous Raman spectra were obtained from solutions of polyjrA) and rAh4P in buffer. The temperature dependence of these spectra was measured to elucidate the influence of macromolecular dynamics and solvent dynamics on the bandwidths of base vibrations in the single stranded polynucleotide poly(rA). The temperature dependence of a bandwidth depends upon the particular vibration under study. The bands can for the larger part be described by Lorentz functions. When fitted by Voigt functions, maximally 10% of each bandprofile of the adenine base vibrations can be attributed to a Gaussian component. The second moment has been determined from the spectra for the 725 cm-' band. From the second moment and the bandwidth, we were able to deduce that the vibrational oscillator is in the fast modulation limit. The determined timescale (perturbation correlation time Q 0.13 ps) eliminate perturbations connected to long range diffusion like concentration fluctuations (timescale in the order of 10 ps). The spectra were analyzed by an extensive curve fitting procedure providing accurate bandparameters (position, width and integrated intensity). The 725 cm-' band of adenine has a bandwidth which is dependent upon the degree of polymerization. In rAMP it is 17.6 cm-', in stacked (i.e. low temperature 5OC) poly(rA) it is 11.5 cm-'. The bandwidth of the adenine vibration at 1336 cm-' cm-' has a temperature dependence which is similar to the intensity changes of the Raman and the absorption hypochromic effect as a function of temperature. The melting transition can therefore be followed by the changes in bandwidth of suitable vibrations.

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SYNOPSISPolarized and depolarized Raman spectra are obtained for a number of synthetic polynucleotides containing adenine, uracil, and thymine bases. The depolarization ratios are determined by two methods: (1) by dividing the 1-spectrum by the 11-spectrum and ( 2 ) after curve fitting. Overlapping bands, isotope splitting, reorientational broadening, and noncoincidence splitting affect the magnitude of the depolarization ratios over the bandwidth. For both Lorentz and Gauss curves these influences are simulated. A comparison of the Raman spectra of RNA and DNA molecules shows that the depolarization ratios for a number of similar base vibrations are different. The vibrational modes and the depolarization ratios of sugar vibrations are most sensitive to the structure of the polynucleotide. Base vibrations that have their potential energy distributed over base and sugar atoms also seem to be more sensitive to the structure.

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We have observed a noncoincidence splitting of 1–2 cm−1 for the 1505 cm−1 adenine base vibration in poly(rA), poly(dA), 5rAMP, and 5dAMP. In double stranded polynucleotides, the noncoincidence splitting is smaller than 0.3 cm−1. Noncoincidence splitting is usually associated with a transition dipole–transition dipole coupling between identical vibrational modes on different molecules of the same species, but any angular dependent intermolecular coupling mechanism may cause this effect. It is argued that resonant vibrational coupling of 1505 cm−1 vibrations on different adenine bases cannot be the source of the noncoincidence splitting. As the 1505 cm−1 base vibration does not have a large infrared absorption, it cannot be caused by transition dipole–transition dipole coupling. We propose that a coupling via hydrogen bonding of the 1505 cm−1 adenine base vibration to water vibrations yields the angular dependent intermolecular coupling potential.

Isotropic and Anisotropic Raman spectra of RNA and DNA solutions have been obtained with a scanning monochromator system. The registration of the spectra was optimized for the special purpose of extracting bandwidth information and the non-coincidence effect. The following polynucleotides were selected: poly(rA) poly(rU) , poly(rA) . poly(rU) , poly (rk-rU) . poly(rA-rU) , poly(dA) . poly(dT) and poly(dA-dT) . poly(dA-dT) . The spectra obtained were compared wi th those of rAMP and rUMP. Temperatures were varied for all systems. The transitions from stacked -to unstacked structure (single stranded polynucleotides) and from double strandedto single stranded structure influence the vibratioral bandwidths. Dynamic behaviour of the adenine vibrations at 1334 and 1480 cm follows curves similar to those observed for the Raman hypochromc effect. The totally symmetric stretching vibration in adenine at 725 cm however changes only weakly in bandwidth, while it shows a strong hypochromic effect. The bandwidth even at temperatures above the stacking/unstacking transition is much smaller than for rAMP. Other bandwidth changes will be discussed.The non-coincidence effect, measured as i.S shown to occur in vibrations originating in the aromatic base molecules. The1magnitude of the non-coincidence effect of the adenine vibration at 1505 cm is different in poly(rA) and rAMP.