Volume 138, Issue 7, 21 February 2013
Index of content:
Communication: Structure, formation, and equilibration of ensembles of Ag-S complexes on an Ag surface138(2013); http://dx.doi.org/10.1063/1.4790571View Description Hide Description
We have utilized conditions of very low temperature (4.7 K) and very low sulfur coverage to isolate and identify Ag-S complexes that exist on the Ag(111) surface. The experimental conditions are such that the complexes form at temperatures above the temperature of observation. These complexes can be regarded as polymeric chains of varying length, with an Ag 4S pyramid at the core of each monomeric unit. Steps may catalyze the formation of the chains and this mechanism may be reflected in the chain length distribution.
138(2013); http://dx.doi.org/10.1063/1.4793220View Description Hide Description
A high-resolution spectrum in the region of 2144 cm−1 is assigned to the previously elusive CO trimer. In spite of interference from the CO dimer and some remaining unexplained details, there is strong evidence for a planar, cyclic, C-bonded trimer structure, with C 3h symmetry and 4.42 Å intermolecular separation, in agreement with theoretical calculations. A modest vibrational blueshift of +0.85 cm−1 is observed for the CO trimer, as compared to +0.71 cm−1 for the C-bonded form of the dimer.
138(2013); http://dx.doi.org/10.1063/1.4791708View Description Hide Description
Cryo electron microscopy (cryo-EM) data of the interior of phages show ordering of the interior DNA that has been interpreted as a nearly perfectly ordered polymer. We show surface-induced correlations, excluded volume, and electrostatic forces are sufficient to predict most of the major features of the current structural data for DNA packaged within viral capsids without additional ordering due to elastic bending forces for the polymer. Current models assume highly-ordered, even spooled, hexagonally packed conformations based on interpretation of cryo-EM density maps. We show herein that the surface induced packing of short (6mer), unconnected DNA polymer segments is the only necessary ingredient in creating ringed densities consistent with experimental density maps. This implies the ensemble of possible conformations of polymeric DNA within the capsid that are consistent with cryo-EM data may be much larger than implied by traditional interpretations where such rings can only result from highly-ordered spool-like conformations. This opens the possibility of a more disordered, entropically-driven view of phage packaging thermodynamics. We also show the electrostatics of the DNA contributes a large portion of the internal hydrostatic and osmotic pressures of a phage virion, suggesting that nonlinear elastic anomalies might reduce the overall elastic bending enthalpy of more disordered conformations to have allowable free energies.
138(2013); http://dx.doi.org/10.1063/1.4792834View Description Hide Description
We computationally demonstrate the one-photon phase control of retinal isomerization under conditions of low laser intensity. The calculations, utilizing the multiconfigurational time dependent Hartree method, include coupling between the two modes that are active in isomerization and the background molecular vibrational environment. Noting previously unsuccessful computations highlights the significance of this result.
138(2013); http://dx.doi.org/10.1063/1.4792371View Description Hide Description
The Joule–Thomson coefficient μ H (P, T) is computed from the virial equation of state up to seventh-order for argon obtained from accurate ab initio data. Higher-order corrections become increasingly more important to fit the low-temperature and low-pressure regime and to avoid the early onset of divergence in the Joule–Thomson inversion curve. Good agreement with experiment is obtained for temperatures T > 250 K. The results also illustrate the limitations of the virial equation in regions close to the critical temperature.