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.

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.

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 1π g * orbital <10 GPa. Enhanced intermolecular interactions develop because of increasing overlap of the 1π g * orbital in the low-pressure phases, leading to electron delocalization and ultimately intermolecular bonding between O 2 molecules at the transition to the ε-phase. The ε-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 ε-phase, and provide a potential mechanism for intercluster bonding in still higher-pressure phases.

High resolution X-ray Photoelectron Spectroscopy ͑XPS͒ core-level Si 2p and O 1s spectra of the nonconductors ␣-SiO 2 ͑quartz͒ at 120 and 300 K and vitreous SiO 2 at 300 K were obtained with a Kratos Axis Ultra XPS instrument ͑instrumental resolution of Ͻ0.4 eV͒ which incorporates a unique charge compensation system that minimizes differential charge broadening on nonconductors. The Si 2p and O 1s linewidths at 300 K ͑ϳ1.1 and ϳ1.2 eV, respectively͒ are similar for all silicates ͑and similar to previous thin film SiO 2 spectra obtained previously͒, showing that differential charging does not contribute significantly to our spectra. At 120 K, there is a small decrease ͑0.04 eV͒ in the Si 2p linewidth of ␣-SiO 2 , but no measurable decrease in O 1s linewidth. The O 1s lines are generally and distinctly asymmetric. We consider all possible sources of line broadening and show that final state vibrational broadening ͑FSVB͒ and phonon broadening are the major causes of the broad and asymmetric lines. Previous high resolution gas phase XPS studies have identified large FSVB contributions to the Si 2p spectra of SiCl 4 , SiF 4 , and Si͑OCH 3 ͒ 4 molecules, and this vibrational structure leads total Si 2p 3/2 linewidths of up to ϳ0.5 eV, even with individual peak linewidths of Ͻ0.1 eV. The Si atom of Si͑OCH 3 ͒ 4 is an excellent analog for Si in crystalline SiO 2 because the Si-O bond lengths and symmetric stretch frequencies are similar in both compounds. Similar vibrational contributions to the Si 2p and O 1s spectra of solid silicates are anticipated if the Si 2p and O 1s core-hole states produce similar changes to the Si-O bond length in both phases. To investigate the possibility, Car-Parrinello molecular dynamics calculations were performed and show that changes to Si-O bond lengths between ion and ground states ͑⌬r͒ for both Si 2p and O 1s hole states are similar for both crystalline SiO 2 and gaseous Si͑OCH 3 ͒ 4 . ⌬r are −0.04 Å for Si 2p and ϳ+0.05 Å for O 1s in both compounds. Indeed, the vibrational envelope from the Si 2p spectrum of Si͑OCH 3 ͒ 4 , broadened to our instrumental linewidth of 0.4 eV, accounts for the majority ͑ϳ0.8 eV͒ of the Si 2p 3/2 linewidth for crystalline SiO 2 ͑ϳ1.1 eV͒ with phonon broadening accounting for the remainder. The results provide excellent support for the tenet that final state vibrational splitting, as seen in the gas phase molecules, similarly affects the solid-state spectra. The calculations also indicate that the O 1s linewidths should be larger than the Si 2p linewidths, as observed in our spectra. FSVB should also lead to small peak asymmetries, as seen in the O 1s spectra. The contribution of phonon broadening to the linewidth is also evaluated and shown to be comparable to the FSVB contribution at 120 and 300 K but considerably smaller at very low temperatures.

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