Thermodynamics of the Hydroxyl Radical Addition to Isoprene

Oxidation of isoprene by the hydroxyl radical leads to tropospheric ozone formation. Consequently, a more complete understanding of this reaction could lead to better models of regional air quality, a better understanding of aerosol formation, and a better understanding of reaction kinetics and dynamics. The most common first step in the oxidation of isoprene is the formation of an adduct, with the hydroxyl radical adding to one of four unsaturated carbon atoms in isoprene. In this paper, we discuss how the initial conformations of isoprene, s-trans and s-gauche, influences the pathways to adduct formation. We explore the formation of pre-reactive complexes at low and high temperatures, which are often invoked to explain the negative temperature dependence of this reaction’s kinetics. We show that at higher temperatures the free energy surface indicates that a pre-reactive complex is unlikely, while at low temperatures the complex exists on two reaction pathways. The theoretical results show that at low temperatures all eight pathways possess negative reaction barriers, and reaction energies that range from −36.7 to −23.0 kcal·mol−1. At temperatures in the lower atmosphere, all eight pathways possess positive reaction barriers that range from 3.8 to 6.0 kcal·mol−1 and reaction energies that range from −28.8 to −14.4 kcal·mol−1.

Bulk Metallic Glasses Deform via Slip Avalanches

For the first time in metallic glasses, we extract both the exponents and scaling functions that describe the nature, statistics, and dynamics of slip events during slow deformation, according to a simple mean field model. We model the slips as avalanches of rearrangements of atoms in coupled shear transformation zones (STZs). Using high temporal resolution measurements, we find the predicted, different statistics and dynamics for small and large slips thereby excluding self-organized criticality. The agreement between model and data across numerous independent measures provides evidence for slip avalanches of STZs as the elementary mechanism of inhomogeneous deformation in metallic glasses.

Molecular Dynamics Simulation of a PNA·DNA·PNA Triple Helix in Aqueous Solution

Molecular dynamics simulations have been used to explore the conformational flexibility of a PNA·DNA·PNA triple helix in aqueous solution. Three 1.05 ns trajectories starting from different but reasonable conformations have been generated and analyzed in detail. All three trajectories converge within about 300 ps to produce stable and very similar conformational ensembles, which resemble the crystal structure conformation in many details. However, in contrast to the crystal structure, there is a tendency for the direct hydrogen-bonds observed between the amide hydrogens of the Hoogsteen-binding PNA strand and the phosphate oxygens of the DNA strand to be replaced by water-mediated hydrogen bonds, which also involve pyrimidine O2 atoms. This structural transition does not appear to weaken the triplex structure but alters groove widths and so may relate to the potential for recognition of such structures by other ligands (small molecules or proteins). Energetic analysis leads us to conclude that the reason that the hybrid PNA/DNA triplex has quite different helical characteristics from the all-DNA triplex is not because the additional flexibility imparted by the replacement of sugar−phosphate by PNA backbones allows motions to improve base-stacking but rather that base-stacking interactions are very similar in both types of triplex and the driving force comes from weak but definate conformational preferences of the PNA strands.

Hydration of OCS with One to Four Water Molecules in Atmospheric and Laboratory Conditions

Carbonyl sulfide is the most abundant sulfur gas in the atmosphere. We have used MP2 and CCSD(T) theory to study the structures and thermochemistries of carbonyl sulfide interacting with one to four water molecules. We have completed an extensive search for clusters of OCS(H2O)n, where n = 1−4. We located three dimers, two trimers, five tetramers, and four pentamers with the MP2/aug-cc-pVDZ method. In each of the complexes with two or more waters, OCS preferentially interacts with low-energy water clusters. Our results match current theoretical and experimental literature, showing correlation with available geometries and frequencies for the OCS(H2O) species. The CCSD(T)/aug-cc-pVTZ thermochemical values combined with the average amount of OCS and the saturated concentration of H2O in the troposphere, lead to the prediction of 106 OCS(H2O) clusters·cm−3 and 102 OCS(H2O)2 clusters·cm−3 at 298 K. We predict the structures of OCS(H2O)n, n = 1−4 that should predominate in a low-temperature molecular beam and identify specific infrared vibrations that can be used to identify these different clusters.

Competition between single and double electron transfer in collisions of doubly charged molecular pyrrole ions with neutral pyrrole molecules

Cross-sections have been determined for one- and two-electron transfer channels in the collisions of keV gas-phase doubly charged pyrrole ions with pyrrole molecules. Measured single and double electron transfer total cross-sections approximate 45 Å2 and 15 Å2, respectively. A combination of symmetric resonance charge exchange and multistate curve-crossing models has been invoked to describe these reactions.