A novel noble-gas compound, HXeOXeH, is identified using IR spectroscopy, and it seems to be the smallest known neutral molecule with two noble-gas atoms’. HXeOXeH is prepared using, for example, UV photolysis of water in solid xenon and subsequent annealing at 40-45 K. The experimental observations are fully supported by extensive quantum chemical calculations. A large energy release of 8.3 eV is computationally predicted for the decomposition of HXeOXeH into the 2Xe + H2O global energy minimum. HXeOXeH may represent a first step toward the possible preparation of (Xe-O)(n) chains and it may be relevant to the terrestrial ‘‘missing xenon’’ problem.

The vibrational spectroscopy of a glycine molecule adsorbed on a silicon surface is studied computationally, using different clusters as models for the surface. Harmonic frequencies are computed using density functional theory (DFT) with the B3LYP functional. Anharmonic frequency calculations are carried out using vibrational self-consistent field (VSCF) algorithms on an improved PM3 potential energy surface. The results are compared with experiments on Glycine@Si(1 00)-2 x 1. The main findings are: (1) Agreement of the computed frequencies with experiment improves with cluster size. (2) The anharmonic calculations are generally in better agreement with experiment than the harmonic ones. The improvements due to anharmonicity are most significant for hydrogenic stretching. (3) An important part of the anharmonic effects is due to anharmonic coupling between different normal modes of the system. (4) The anharmonic coupling between glycine vibrational modes is much larger than the anharmonic coupling between glycine and ‘‘phonon’’ (cluster) modes. Implications of the results for surface vibrational spectroscopy are discussed. (c) 2007 Elsevier B.V. All rights reserved.

The vibrational spectrum of triacetone triperoxide (TATP) is studied by the correlation-corrected vibrational self-consistent field (CC-VSCF) method which incorporates anharmonic effects. Fundamental, overtone, and combination band frequencies are obtained by using a potential based on the PM3 method and yielding the same harmonic frequencies as DFT/cc-pVDZ calculations. Fundamentals and overtones are also studied with anharmonic single-mode (without coupling) DFT/cc-pVDZ calculations. Average deviations from experiment are similar for all methods: 2.1-2.5%. Groups of degenerate vibrations form regions of numerous combination bands with low intensity: the 5600-5800 cm(-1) region contains ca. 70 overtones and combinations of CH stretches. Anharmonic interactions are analyzed. (c) 2008 Elsevier B.V. All rights reserved.

Calculations were performed to determine the structures, energetics, and spectroscopy of the atmospherically relevant complexes (HNO(3))center dot(NO(2)),(HNO(3))center dot(N(2)O(4)),(NO(3)(-))center dot(NO(2)),and(NO(3)(-))center dot(N(2)O(4)). The binding energies indicate that three of the four complexes are quite stable, with the most stable (NO(3)(-))center dot(N(2)O(4)) possessing binding energy of almost -14 kcal mol(-1). Vibrational frequencies were calculated for use in detecting the complexes by infrared and Raman spectroscopy. An ATR-FTIR experiment showed features at 1632 and 1602 cm(-1) that are attributed to NO(2) complexed to NO(3)(-) and HNO(3), respectively. The electronic states of (HNO(3))center dot (N(2)O(4)) and (NO(3)(-))center dot(N(2)O(4)) were investigated using an excited state method and it was determined that both complexes possess one low-lying excited state that is accessible through absorption of visible radiation. Evidence for the existence of (NO(3)(-))center dot(N(2)O(4)) was obtained from UV/vis absorption spectra of N(2)O(4) in concentrated HNO(3), which show a band at 320 nm that is blue shifted by 20 nm relative to what is observed for N(2)O(4) dissolved in organic solvents. Finally, hydrogen transfer reactions within the (HNO(3))center dot(NO(2)) and (HNO(3))center dot(N(2)O(4)) complexes leading to the formation of HONO, were investigated. In both systems the calculated potential profiles rule out a thermal mechanism, but indicate the reaction could take place following the absorption of visible radiation. We propose that these complexes are potentially important in the thermal and photochemical production of HONO observed in previous laboratory and field studies.

Evidence from cross section data indicates that ubiquitin + 13 ions lose their secondary and tertiary structure in mass spectrometric experiments. These transitions from the folded state into the near linear final structure occur at the experimental temperatures on time scales that are far too long for conventional molecular dynamics simulations. In this study, an approach to mass spectrometric unfolding processes is developed and a detailed application to an ubiquitin + 13 ion system is presented. The approach involves a sequence of molecular dynamics simulations at gradually increasing temperatures leading to identification of major intermediate states, and the unfolding pathway. The unfolding rate at any temperature can then be calculated by a Rice-Ramsperger-Kassel (RRK) approach. For ubiquitin + 13, three interesting intermediate states were found and the final near linear geometry was computed. The several relevant energy barriers calculated for the process are in the range of 7 to 15 kcal mol(-1). The unfolding time scale at 300 K was computed to be 2 ms. Cross section calculations using a hard sphere scattering model were carried out for the final structure and found to be in good accord with the results of electrospray experiments supporting the theoretical model used. The approach employed here should be applicable to any other solvent-free protein system.

The photodissociation of F-2 in a lattice model of 255 argon atoms is studied using Tully’s semiclassical ‘surface hopping’ approach. The DIM method is used to model the 36 relevant potential energy surfaces and the nonadiabatic couplings between them. The photoexcitation is modeled by vertical promotion of the F-2 into the (1)Pi(u) state. It is found that early dynamics following excitation leads to rapid build-up of the g states population, and around t approximate to 50 fs the (total) g and u populations are roughly equal. Matrix-induced nonadiabatic transitions between u and g states cause the effect, and are briefly discussed. (C) 2008 Elsevier B.V. All rights reserved.

Recombination events of a proton with NO3- at (H2O)(8) clusters are studied by molecular dynamics, using ‘‘on-the-fly’’ reliable ab initio MP2 potentials. The main findings are: (1) the lifetime of the ions is less than 1.2 picoseconds; (2) the recombination step invariably involves H3O+, not H5O2+; and (3) an essentially unique transition-state structure of H3O+/NO3- for recombination is found in all cases. Proton migration involves both H3O+ and H5O2+ species: Grotthuss and other mechanisms contribute.

The experimental mid- and far-IR spectra of six conformers of phenylalanine in the gas phase are presented. The experimental spectra are compared to spectra calculated at the B3LYP and at the MP2 level. The differences between B3LYP and MP2 IR spectra are found to be small. The agreement between experiment and theory is generally found to be very good, however strong discrepancies exist when -NH2 out-of-plane vibrations are involved. The relative energies of the minima as well as of some transition states connecting the minima are explored at the CCSD(T) level. Most transition states are found to be less than 2000 cm(-1) above the lowest energy structure. A simple model to describe the observed conformer abundances based on quasi-equilibria near the barriers is presented and it appears to describe the experimental observation reasonably well. In addition, the vibrations of one of the conformers are investigated using the correlation-corrected vibrational self-consistent field method.

Raman spectra of HNO(3)center dot NO(2) have been detected on liquid and solid surfaces in the presence of concentrated HNO(3) and NO(2) gas. The Raman spectrum of HNO(3) solutions containing N(2)O(4) has been partly reinterpreted in terms of contributions from HNO(3)center dot N(2)O(4) and N(2)O(4)center dot NO(3)(-) complexes.

Three approaches are combined to study the electronic states’ dynamics in the photodissociation of F-2 and OF in solid argon. These include (a) semiclassical surface-hopping simulations of the nonadiabatic processes involved. These simulations are carried out for the F-2 molecule in a slab of 255 argon atoms with periodic boundary conditions at the ends. The full manifold of 36 electronic states relevant to the process is included. (b) The second approach involves quantum mechanical reduced-dimensionality models for the initial processes induced by a pump laser pulse, which involve wavepacket propagation for the preoriented OF in the frozen argon lattice and incorporate the important electronic states. The focus is on the study of quantum coherence effects. (c) The final approach is femtosecond laser pump-probe experiments for OF in Ar. The combined results for the different systems shed light on general properties of the nonadiabatic processes involved, including the singlet to triplet and intertriplet transition dynamics. The main findings are (1) that the system remains in the initially excited-state only for a very brief, subpicosecond, time period. Thereafter, most of the population is transferred by nonadiabatic transitions to other states, with different time constants depending on the systems. (2) Another finding is that the dynamics is selective with regard to the electronic quantum numbers, including the A and Q quantum numbers, and the spin of the states. (3) The semiclassical simulations show that prior to the first ‘‘collision’’ of the photodissociated F atom with an Ar atom, the argon atoms can be held frozen, without affecting the process. This justifies the rigid-lattice reduced-dimensionality quantum model for a brief initial time interval. (4) Finally, degeneracies between triplets and singlets are fairly localized, but intertriplet degeneracies and near degeneracies can span an extensive range. The importance of quantum effects in photochemistry of matrix-isolated molecules is discussed in light of the results.

The role of different electronic states in cage-exit of F atoms for F-2 photodissociation in solid Ar is investigated by nonadiabatic molecular dynamics simulations, using Tully’s ‘‘Surface-Hopping’’ approach. The 36 potential surfaces involved are treated by the diatomics-in-molecules (DIM) method. A simulation of 255 Ar atoms in an FCC structure with periodic boundary conditions is used. The results are: (I) Direct cage-exit events are not observed. At least two collisions of the F atoms with the Ar cage are necessary for cage-exit. (II) The total singlet to triplet population ratio at the instant of cage-exit is approximately the statistical one. (III) Some cage-exit events occur for the attractive states (1)Sigma(+)(g), (3)pi(u) but their role is much smaller than for the caged species. (IV) The Lambda quantum number distribution at cage-exit is more uniform than for the caged species. Thus, the electronic state distribution for cage-exit differs greatly from that of the caged species. (c) 2007 Elsevier B.V. All rights reserved.

The photodissociation of HF in solid argon is studied by nonadiabatic molecular dynamics simulations, using Tully’s ‘surface hopping’ method. The model includes 12 electronic states, described by DIM method. An extremely fast ‘spin-flip’ transition is found corresponding to a population buildup in the (3)Pi state, already within about 1 fs after a vertical Frank-Condon excitation into the (1)Pi state. The effect is particularly striking in view of the relatively weak spin-orbit coupling in HE. The mechanism of this exceptionally fast spin-flip is discussed and a physical interpretation is provided. Comparison is made to the slower spin-flip computed previously for F-2/Ar, and found both theoretically and experimentally for ClF/Ar. (C) 2007 Elsevier B.V. All rights reserved.

Acceleration of the correlation-corrected Vibrational self-consistent field (CC-VSCF) method for anharmonic calculations of vibrational states of polyatomic molecules is described. The acceleration assumes pairwise additive interactions between different normal modes, and employs orthogonality of the single-mode vibrational wave functions. This greatly reduces the effort in computing correlation effects between different vibrational modes, which is treated by second order perturbation theory in CC-VSCF. The acceleration can improve the scaling of the overall computational effort from N(6) to N(4), where N is the number of vibrational modes. Sample calculation times, using semiempirical potential surfaces (PM3), ire given for a series of glycine peptides. Large Computational acceleration, and significant reduction of the scaling of the effort with system size, is found and discussed.

The role of anharmonic effects in the vibrational spectroscopy of the dark state and two major chromophore intermediates of the photoactive yellow protein (PYP) photocycle is examined via ab initio vibrational self-consistent field (VSCF) calculations and time-resolved resonance Raman spectroscopy. For the first time, anharmonicity is considered explicitly in calculating the vibrational spectra of an ensemble consisting of the PYP chromophore surrounded by model compounds used as mimics of the important active-site residues. Predictions of vibrational frequencies on an ab initio corrected semiempirical potential energy surface show remarkable agreement with experimental frequencies for all three states, thus shedding light on the potential along the reaction path. For example, calculated frequencies for vibrational modes of the red-shifted intermediate, PYPL, exhibit an overall average error of 0.82% from experiment. Upon analysis of anharmonicity patterns in the PYP modes we observe a decrease in anharmonicity in the C-8-C-9 stretching mode nu(29) (trans-cis isomerization marker mode) with the onset of the cis configuration in PYPL. This can be attributed to the loss of the hydrogen-bonding character of the adjacent C-9-O-2 to the methylamine (Cys69 backbone). For several of the modes, the anharmonicity is mostly due to mode-mode coupling, while for others it is mostly intrinsic. This study shows the importance of the inclusion of anharmonicity in theoretical spectroscopic calculations, and the sensitivity of experiments to anharmonicity. The characterization of protein active-site residues by small molecular mimics provides an acceptable chemical structural representation for biomolecular spectroscopy calculations.

The study of evaporation of water from biological macromolecules is important for the understanding of electrospray mass spectrometry experiments. In electrospray ionization (ESI), electrically charged nanoscale droplets are formed from solutions of, for example, proteins. Then evaporation of the solvent leads to dry protein ions that can be analyzed in the mass spectrometer. In this work the dynamics of water evaporation from native cytochrome c covered by a monolayer of water is studied by molecular dynamics (MD) simulations at constant energy. A model of the initial conditions of the process is introduced. The temperature of the protein drops by about 100 K during the 400 picoseconds of the simulations. This sharp drop in temperature causes the water evaporation rate to decrease by about an order of magnitude, leaving the protein with 50% to 90% of the original water molecules, depending on the initial temperature of the simulation. The structural changes of the protein upon desolvation were considered through calculations of the radius of gyration and the root mean square (RMS) of the protein. A variation of 0.4 angstrom in the radius of gyration, together with an RMS value of less than 3 angstrom, indicates only minor changes in the overall shape of the protein structure. The water coordination number of the solvation shell is much smaller than that for bulk water. The mobility of water is high at the beginning of the simulations and drops as the simulation progresses and the temperature decreases. Incomplete desolvation of protein ions was also observed in recent experiments.

Theoretical investigations of the dynamics of the sunlight initiated dehydration of sulfuric acid are performed under atmospheric conditions. The relevant time scales for collisional deactivation and for vibrational fluorescence, which may compete with sulfuric acid dehydration in the upper stratosphere and the mesosphere are evaluated to provide a realistic quantum yield consistent with spectroscopic and theoretical results. The results obtained allow evaluation of the J values for this photochemical reaction in the atmosphere. At the higher altitudes of the upper stratosphere and the mesosphere the J values obtained are sufficiently large to satisfy model requirements and explain field observations of SO2 vertical profiles and the concentration of condensation nuclei in the stratosphere for air of recent polar origin.

Ab initio calculations predict the existence of the dimer and tetramer of HXeCCH. The interaction energies are -6.66 and -19.40 kcal mol(-1) for the dimer and tetramer, respectively. For both complexes, larger blue shifts of the Xe-H stretching mode are found, while the Xe-C stretching modes are slightly redshifted. The stability and structure of HXeCCH crystals is predicted by density functional theory calculations with periodic boundary conditions. Strong electrostatic interactions are found between the monomers in the crystal. The results are first evidence for the existence of crystalline materials made of a novel class of noble gas molecules. (c) 2007 American Institute of Physics.