Dynamical Effects and Product Distributions in Simulated CN + Methane Reactions

Dynamics of collisions between structured molecular species quickly become complex as molecules become large. Reactions of methane with halogen and oxygen atoms serve as model systems for polyatomic molecule chemical dynamics, and replacing the atomic reagent with a diatomic radical affords further insights. A new, full-dimensional potential energy surface for collisions between CN + CH4 to form HCN + CH3 is developed and then used to perform quasi-classical simulations of the reaction. Coupled-cluster energies serve as input to an empirical valence bonding (EVB) model, which provides an analytical function for the surface. Efficient sampling permits simulation of velocity-map ion images and exploration of dynamics over a range of collision energies. Reaction populates HCN vibration, and energy partitioning changes with collision energy. The reaction cross-section depends on the orientation of the diatomic CN radical. A two-dimensional extension of the cone of acceptance for an atom in the line-of-centers model appropriately describes its reactivity. The simulation results foster future experiments and diatomic extensions to existing atomic models of chemical collisions and reaction dynamics.status: publishe

Computational Study of Competition Between Direct Abstraction and Addition-Elimination in the Reaction of Cl Atoms with Propene

Quasi-classical trajectory calculations on a newly constructed and full-dimensionality potential energy surface (PES) examine the dynamics of the reaction of Cl atoms with propene. The PES is an empirical valence bond (EVB) fit to high-level ab initio energies and incorporates deep potential energy wells for the 1-chloropropyl and 2-chloropropyl radicals, a direct H atom abstraction route to HCl + allyl radical (CH2CHCH2(•)) products (Δ(r)H(298K)(⊖) = −63.1 kJ mol(-1)), and a pathway connecting these regions. In total, 94 000 successful reactive trajectories were used to compute distributions of angular scattering and HCl vibrational and rotational level populations. These measures of the reaction dynamics agree satisfactorily with available experimental data. The dominant reaction pathway is direct abstraction of a hydrogen atom from the methyl group of propene occurring in under 500 fs. Less than 10% of trajectories follow an addition–elimination route via the two isomeric chloropropyl radicals. Large amplitude motions of the Cl about the propene molecular framework couple the addition intermediates to the direct abstraction pathway. The EVB method provides a good description of the complicated PES for the Cl + propene reaction despite fitting to a limited number of ab initio points, with the further advantage that dynamics specific to certain mechanisms can be studied in isolation by switching off coupling terms in the EVB matrix connecting different regions of the PES.status: publishe

A self-compartmentalizing hexamer serine protease from Pyrococcus Horikoshii: Substrate selection achieved through multimerization

Oligopeptidases impose a size limitation on their substrates, the mechanism of which has long been in debate. Here we present the structure of a hexameric serine protease, an oligopeptidase from Pyrococcus horikoshii (PhAAP), revealing a complex, self-compartmentalized inner space, where substrates may access the monomer active sites passing through a double-gated "check-in" system: first passing through a pore on the hexamer surface, then turning to enter through an even smaller opening at the monomers' domain-interface. This substrate screening strategy is unique within the family. We found that among oligopeptidases a member of catalytic apparatus is positioned near an amylogenic beta-edge, which needs to be protected to prevent aggregation and found different strategies applied to such end. We propose that self-assembly within the family results in characteristically different substrate selection mechanisms coupled to different multimerization states

Rotational polarisation effects in the inelastic collisions of NO(X) and Ar

Rotational polarisation effects have been investigated in the rotationally inelastic collisions of NO(X) and Ar by means of theoretical and experimental methods. Rotational polarisation describes the correlation between the k–k'–j' vectors, that is the initial and final relative velocities of the colliding partners and the final rotational angular momentum of the diatom, respectively. The simplest types of polarisation are the rotational orientation, or preferred sense of rotation, and the rotational alignment, or preferred plane of rotation. They are quantised by the renormalised polarisation dependent differential cross sections (PDDCSs) In this thesis the theoretical methods included exact quantum mechanical, quasi- classical trajectory and Monte Carlo classical hard shell calculations. Various features of the interaction potential influence differently the polarisation dynamics. The effects of attraction and soft repulsion were elucidated employing a number of differently modified potentials. The rotational alignment is primarily determined by a classical impulsive, or hard shell mechanism at a collision energy of 66 meV. The attractive and soft repulsive forces only perturb this underlying mechanism. On the other hand, the parity dependent oscillations of the open shell alignment moments are due to differences between the quantum mechanical differential cross sections. It has been shown the bigger the well depth compared to the collision energy, the less applicable becomes the classical hard shell model to describe rotational alignment. The quantum mechanical rotational alignment in the collisions of hard shells was also calculated. The classical and quantum mechanical hard shell models predict different rotational alignment. Nevertheless, the classical alignment is a good approximation to the exact quantum mechanical results. The rotational orientation is much more sensitive to the details of the interaction potential. It does not exist in the classical description of hard shell collisions, if the system exhibits certain symmetry properties. The attraction and finite range repulsion break this symmetry and leads to the molecule having a preferred sense of rotation. In general there is non-vanishing rotational orientation in the collisions of a hard shell in the framework of quantum mechanics. This is due to the finite spatial and temporal interaction of the colliding partners. Quantum mechanical interference effects also play an important role in this phenomenon. The rotational alignment was experimentally determined in the collisions of NO(X) and Ar at collision energy of 66meV with a hexapole state selective ion-imaging apparatus. An algorithm was developed based on the Fourier moment analysis to extract rotational polarisation information from the experimental ion images. It is fast and robust and can also be of used to simulate experimental images. This algorithm was used to retrieve the experimental renormalised PDDCSs ion images. The measurements confirmed that a classical, impulsive dynamics is mainly responsible for the rotational alignment in these collisions.This thesis is not currently available in ORA

Extreme effects of drought on composition of the soil bacterial community and decomposition of plant tissue

The decomposition of soil organic matter, as an essential part of nutrient cycling, has a crucial role in maintaining soil fertility and the regulation of climate. This function of the soil is likely to be affected by extreme weather events that are expected to be more frequent and severe in the future. We conducted an experiment from March 2014 to March 2015 to test the effects of extreme drought on composition of the bacterial community and decomposition of plant tissue with soil microclimate variables such as soil temperature and moisture. Precipitation was excluded for a 5-month period by transparent roofs. To follow organic matter decomposition, we used the tea bag method. Soil samples were taken to determine the effects of extreme drought on the bacterial community 6 months after the dry period (mid-term). Drought plots were drier (P < 0.001) and warmer (P < 0.001) than control plots as a consequence of the extreme drought treatment. The permanova test showed that the dry period altered soil bacterial communities accordingly (Fpermanova = 10.36, P = 0.002). However, there was no significant difference between the control and drought-treated plots 6 months after the dry period in terms of bacterial alpha diversity. Furthermore, rates of organic matter decomposition in the control plots were significantly larger by an average of 93.7% than in the drought plots. The results also indicated that soil temperature and moisture had significant effects on decomposition. Overall, the findings demonstrate clearly the response of soil bacteria and soil function to experimental drought. The strong effect of changes in precipitation and increasing temperature on mass loss suggests that extreme weather events, such as extreme droughts, can markedly change the composition of soil bacterial communities and processes of decomposition. This effect is expected to be more pronounced during dry periods of increasing severity and frequency. Highlights * We studied the effects of extreme drought on plant tissue decay and soil bacterial diversity. * Microbial degradation of organic matter was followed by the novel tea bag method. * Changes in soil microclimate altered bacterial community structure and decomposition. * Microbiota and soil function were markedly affected by extreme weather events like droughts