This paper reports an analysis using molecular dynamics simulations of the effect of urea on the structure of water. Two definitions of the tetrahedral distributions are used to quantify this effect. The first one is sensitive to the mutual orientation between a reference water molecule and the water molecules forming the tetrahedron, and the second is sensitive to their radial distribution. The analysis shows that increasing urea mole fraction results in a reduction of the structured tetrahedral arrangement contribution in favor of an unstructured one. In order to understand this behavior, we used the nearest neighbor approach which allows us to get unambiguous information on the radial and orientation distributions of the water molecules around a probe one. The results indicate that the decrease of the tetrahedral arrangement of the nearest neighbors around a probe water molecule is associated with both the increase of the fluctuation in their radial distances as well as with the loss of their mutual orientations with respect to those observed in pure water. The tetrahedral distribution of water in the hydration shell of urea as well as that around its carbonyl and amine groups is also discussed.

In the present work, the SPASIBA spectroscopic force field has been introduced into the CHARMM program. The SPASIBA force field combines the van der Waals and electrostatic interactions as originally found into CHARMM with Urey-Bradley-Shimanouchi terms for bond stretching, valence angle bending, torsional and improper torsional internal coordinates. SPASIBA has a vibrational spectroscopic origin, and it has largely proven its efficiency in reproducing experimental data such as vibrational wavenumbers, dipole moments, rotational barriers, conformational energy differences, and moments of inertia. The SPASIBA parameters have been included into CHARMM by way of a particular library which directly activates calculations of the specific energetic terms.

Reliable assignments for normal modes of adenine, 9-methyladenine, guanine and 9-methylguanine were obtained from ab initio 3-216 force fields and optimized geometries. In addition, relative itensities were calculated at resonance with the excited states corresponding to the lowest energy x-x* orbital excitations from the change in bond order and the L-' matrix. Wavenumbers and relative intensities for resonance Raman active modes were compared with those previously observed for resonance Raman enhanced bands of AMP and GMP in aqueous solutions obtained with excitation near the absorption band at 260 nm and below. There is satisfactory agreement between observed and calculated relative intensities for the guanine residue. In particular, the large increase in intensity observed for the CO stretching band at 1670 cm-' with excitation below 220 nm is correctly reproduced. On the other hand, there is less agreement for the adenine residue where the distribution of intensity at resonance according to the A term of the resonance Raman theory is probably altered by the presence of vibronic coupling.