Molecular dynamics simulations of CO2 formation in interstellar ices.

CO2 ice is one of the most abundant components in ice-coated interstellar ices besides H2O and CO, but the most favorable path to CO2 ice is still unclear. Molecular dynamics calculations on the ultraviolet photodissociation of different kinds of CO-H2O ice systems have been performed at 10 K in order to demonstrate that the reaction between CO and an OH molecule resulting from H2O photodissociation through the first excited state is a possible route to form CO2 ice. However, our calculations, which take into account different ice surface models, suggest that there is another product with a higher formation probability ((3.00 ± 0.07) × 10(-2)), which is the HOCO complex, whereas the formation of CO2 has a probability of only (3.6 ± 0.7) × 10(-4). The initial location of the CO is key to obtain reaction and form CO2: the CO needs to be located deep into the ice. The HOCO complex becomes trapped in the cold ice surface in the trans-HOCO minimum because it quickly loses its internal energy to the surrounding ice, preventing further reaction to H + CO2. Several laboratory experiments have been carried out recently, and they confirm that CO2 can also be formed through other, different routes. Here we compare our theoretical results with the data available from experiments studying the formation of CO2 through a similar pathway as ours, even though the initial conditions were not exactly the same. Our results also show that the HCO van der Waals complex can be formed through the interaction of CO with the H atom that is formed as a product of H2O photodissociation. Thus, the reaction of the H atom photofragment following H2O photodissociation with CO can be a possible route to form HCO ice.

Hydrogen dissociation on small aluminum clusters.

Transition states and reaction paths for a hydrogen molecule dissociating on small aluminum clusters have been calculated using density functional theory. The two lowest spin states have been taken into account for all the Al(n) clusters considered, with n=2-6. The aluminum dimer, which shows a (3)Π(u) electronic ground state, has also been studied at the coupled cluster and configuration interaction level for comparison and to check the accuracy of single determinant calculations in this special case, where two degenerate configurations should be taken into account. The calculated reaction barriers give an explanation of the experimentally observed reactivity of hydrogen on Al clusters of different size [Cox et al., J. Chem. Phys. 84, 4651 (1986)] and reproduce the high observed reactivity of the Al(6) cluster. The electronic structure of the Al(n)-H(2) systems was also systematically investigated in order to determine the role played by interactions of specific molecular orbitals for different nuclear arrangements. Singlet Al(n) clusters (with n even) exhibit the lowest barriers to H(2) dissociation because their highest doubly occupied molecular orbitals allow for a more favorable interaction with the antibonding σ(u) molecular orbital of H(2).

The photodissociation of the water dimer in the A band: a twelve-dimensional quasiclassical study.

The quasiclassical absorption spectrum of the water dimer in the A band was calculated taking into account motion in all degrees of freedom of the system. The ab initio excited state potentials employed were interpolated by the modified Shepard interpolation method using QMRCI energies and state-averaged MCSCF gradients and Hessians. The ground state vibrational wavefunction was variationally calculated using an adiabatic separation between the high and low frequency normal modes of the system. The calculated spectrum of water dimer shows a clear blueshift with respect to the monomer, but also a small red tail, in agreement with the prediction by Harvey et al. [J. Chem. Phys. 109, 8747 (1998)]. Previous three-dimensional model studies of the photodissociation of the water dimer by Valenzano et al. [J. Chem. Phys. 123, 034303 (2005)] did not show this red tail. A thorough analysis of the dependence of the spectrum on the modes coupled explicitly in the calculation of the spectrum shows that the red tail is due to coupling between the intramolecular stretch vibrations on different monomers.

Two stereoisomers of spheroidene in the Rhodobacter sphaeroides R26 reaction center: a DFT analysis of resonance Raman spectra.

From a theoretical analysis of the resonance Raman spectra of 19 isotopomers of spheroidene reconstituted into the reaction center (RC) of Rhodobacter sphaeroides R26, we conclude that the carotenoid in the RC occurs in two configurations. The normal mode underlying the resonance Raman transition at 1239 cm(-1), characteristic for spheroidene in the RC, has been identified and found to uniquely refer to the cis nature of the 15,15' carbon-carbon double bond. Detailed analysis of the isotope-induced shifts of transitions in the 1500-1550 cm(-1) region proves that, besides the 15,15'-cis configuration, spheroidene in the RC adopts another cis-configuration, most likely the 13,14-cis configuration.

Single rotational product propensity in the photodissociation of HOD.

Photodissociation of HOD from the B state has been studied using the high resolution rydberg "tagging" time-of-flight (TOF) technique. The TOF spectra show an unusually strong population (approximately 50%) for a single rotational state for the OD (A(2)Sigma, upsilon = 0) fragments. Through theoretical studies, this phenomenon, which we have labeled the "single rotational product propensity," is attributed to a dynamically constrained threshold effect in the photodissociation of the HOD molecule on the B state.

An ab initio quantum-chemical study of the blue-copper site of azurin.

The electronic structure of the blue-copper site of Pseudomonas aeruginosa azurin has been investigated by ab initio multireference determinantal configuration interaction (MRD-CI) calculations. A truncated site consisting of copper and its three equatorial ligands has been studied with emphasis on the g tensor and the nitrogen hyperfine tensors of the coordinating histidines. In the ground state the singly occupied molecular orbital (SOMO) involves a copper 3d orbital pi antibonded to the cysteine sulfur and sigma antibonded to the histidine nitrogens. A proper description of the electron-paramagnetic-resonance parameters has been achieved through the use of an effective core potential for copper up to and including the 3s electrons. Both the complete g tensor and the anisotropic hyperfine tensors at the nitrogens are essentially reproduced. Mulliken spin densities of 35 and 59% on copper and sulfur, respectively, and 2.1 and 1.7% on the respective coordinating nitrogens reflect the delocalized character of the SOMO and the inequivalence of the histidines.

Measurement of the conductance of a hydrogen molecule.

Recent years have shown steady progress towards molecular electronics, in which molecules form basic components such as switches, diodes and electronic mixers. Often, a scanning tunnelling microscope is used to address an individual molecule, although this arrangement does not provide long-term stability. Therefore, metal-molecule-metal links using break-junction devices have also been explored; however, it is difficult to establish unambiguously that a single molecule forms the contact. Here we show that a single hydrogen molecule can form a stable bridge between platinum electrodes. In contrast to results for organic molecules, the bridge has a nearly perfect conductance of one quantum unit, carried by a single channel. The hydrogen bridge represents a simple test system in which to understand fundamental transport properties of single-molecule devices.