Mechanistic study of the deamination reaction of guanine: a computational study.

The mechanism for the deamination of guanine with H(2)O, OH(-), H(2)O/OH(-) and for GuaH(+) with H(2)O has been investigated using ab initio calculations. Optimized geometries of the reactants, transition states, intermediates, and products were determined at RHF/6-31G(d), MP2/6-31G(d), B3LYP/6-31G(d), and B3LYP/6-31+G(d) levels of theory. Energies were also determined at G3MP2, G3MP2B3, G4MP2, and CBS-QB3 levels of theory. Intrinsic reaction coordinate (IRC) calculations were performed to characterize the transition states on the potential energy surface. Thermodynamic properties (ΔE, ΔH, and ΔG), activation energies, enthalpies, and Gibbs free energies of activation were also calculated for each reaction investigated. All pathways yield an initial tetrahedral intermediate and an intermediate in the last step that dissociates to products via a 1,3-proton shift. At the G3MP2 level of theory, deamination with OH(-) was found to have an activation energy barrier of 155 kJ mol(-1) compared to 187 kJ mol(-1) for the reaction with H(2)O and 243 kJ mol(-1) for GuaH(+) with H(2)O. The lowest overall activation energy, 144 kJ mol(-1) at the G3MP2 level, was obtained for the deamination of guanine with H(2)O/OH(-). Due to a lack of experimental results for guanine deamination, a comparison is made with those of cytosine, whose deamination reaction parallels that of guanine.

Inelastic x-ray scattering of dense solid oxygen: evidence for intermolecular bonding.

The detailing of the intermolecular interactions in dense solid oxygen is essential for an understanding of the rich polymorphism and remarkable properties of this element at high pressure. Synchrotron inelastic x-ray scattering measurements of oxygen K-edge excitations to 38 GPa reveal changes in electronic structure and bonding on compression of the molecular solid. The measurements show that O(2) molecules interact predominantly through the half-filled 1pi(g)* orbital <10 GPa. Enhanced intermolecular interactions develop because of increasing overlap of the 1pi(g)* orbital in the low-pressure phases, leading to electron delocalization and ultimately intermolecular bonding between O(2) molecules at the transition to the epsilon-phase. The epsilon-phase, which consists of (O(2))(4) clusters, displays the bonding characteristics of a closed-shell system. Increasing interactions between (O(2))(4) clusters develop upon compression of the epsilon-phase, and provide a potential mechanism for intercluster bonding in still higher-pressure phases.

X-ray Raman spectroscopic study of water in the condensed phases.

Oxygen K-edge x-ray absorption spectra of high-density amorphous (HDA) ice, low-density amorphous ice Ic, ice Ih, normal and deuterated liquid water were measured with the synchrotron x-ray Raman scattering method under almost identical experimental conditions by in situ heating of an HDA ice sample. The distinct preedge structure previously reported in water was observed in all the spectra. The results show that core-hole excitations are localized and not strongly affected by the local environment. Therefore, the existence of the preedge feature is not a concise indicator of the magnitude of local disorder within the hydrogen bonded network. The intensity of the near-edge absorption shifts into the postedge region when the hydrogen bond network becomes more ordered. This observation is interpreted as an enhancement of Wannier over Frenkel excitations in an ordered crystal.