Collision Energy Dependence of the Competing Mechanisms of Reaction of Chlorine Atoms with Propene.

Quasi-classical trajectory simulations examine the reaction of Cl with propene across a range of collision energies, from 7 to 28 kJ mol-1. The majority (70% at 7 kJ mol-1, 86% at 14 kJ mol-1, and 93% at 28 kJ mol-1) of reactive trajectories produce HCl by direct abstraction of a hydrogen atom from the methyl group of propene, but the remainder involve a variety of delayed mechanisms. Among these longer-lived trajectories, transient formation of an energized 1-chloropropyl radical intermediate is predominant, with only a minor contribution from the 2-chloropropyl radical and roaming pathways. The branching ratios between these intermediate states are largely invariant to collision energy, although the overall proportion of indirect trajectories increases at lower collision energies. The greater role for longer-lived trajectories is reflected in the computed product scattering angle distributions, which become more isotropic at lower energies. However, the distributions of population over vibrational and rotational states of the product HCl do not change with collision energy because they are controlled by the dynamics late along the reaction path.

Primary vs. secondary H-atom abstraction in the Cl-atom reaction with n-pentane.

Velocity map imaging (VMI) measurements and quasi-classical trajectory (QCT) calculations on a newly developed, global potential energy surface (PES) combine to reveal the detailed mechanisms of reaction of Cl atoms with n-pentane. Images of the HCl (v = 0, J = 1, 2 and 3) products of reaction at a mean collision energy of 33.5 kJ mol-1 determine the centre-of-mass frame angular scattering and kinetic energy release distributions. The HCl products form with relative populations of J = 0-5 levels that fit to a rotational temperature of 138 ± 13 K. Product kinetic energy release distributions agree well with those derived from a previous VMI study of the pentyl radical co-product [Estillore et al., J. Chem. Phys. 2010, 132, 164313], but the angular distributions show more pronounced forward scattering. The QCT calculations reproduce many of the experimental observations, and allow comparison of the site-specific dynamics of abstraction of primary and secondary H-atoms. They also quantify the relative reactivity towards Cl atoms of the three different H-atom environments in n-pentane.

Direct comparison of 3-centre and 4-centre HBr elimination pathways in methyl-substituted vinyl bromides.

Elimination of HBr from UV-photoexcited vinyl bromides can occur through both 3-centre and 4-centre transition states (TSs). The competition between these pathways is examined using velocity map imaging of HBr (v = 0-2, J) photofragments. The three vinyl bromides chosen for study have methyl substituents that block either the 3-centre or the 4-centre TS, or leave both pathways open. The kinetic energy distributions extracted from velocity map images of HBr from 193 nm photolysis of the three vinyl bromide compounds are approximately described by a statistical model of energy disposal among the degrees of freedom of the photoproducts, and are attributed to dissociation on the lowest electronic state of the molecule after internal conversion. Dissociation via the 4-centre TS gives greater average kinetic energy release than for the 3-centre TS pathway. The resonance enhanced multi-photon ionization (REMPI) schemes used to detect HBr restrict measurements to J ≤ 7 for v = 2 and J ≤ 15 for v = 0. Within this spectroscopic range, the HBr rotational temperature is colder for the 4-centre than for the 3-centre elimination pathway. Calculations of the intrinsic reaction coordinates and RRKM calculations of HBr elimination rate coefficients provide mechanistic insights into the competition between the pathways.

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.

Empirical Valence Bond Theory Studies of the CH4 + Cl → CH3 + HCl Reaction.

We report a theoretical investigation of the CH4 + Cl hydrogen abstraction reaction in the framework of empirical valence bond (EVB) theory. The main purpose of this study is to benchmark the EVB method against previous experimental and theoretical work. Analytical potential energy surfaces for the reaction have been developed on which quasi-classical trajectory calculations were carried out. The surfaces agree well with ab initio calculations at stationary points along the reaction path and dynamically relevant regions outside the reaction path. The analysis of dynamical data obtained using the EVB method, such as vibrational, rotational, and angular distribution functions, shows that this method compares well to both experimental measurements and higher-level theoretical calculations, with the additional benefit of low computational cost.

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 addition­elimination 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.

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 under 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 and 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 residue of the catalytic apparatus is positioned near an amylogenic ß-edge, which needs to be protected to prevent aggregation, and we found that different oligopeptidases use different strategies to achieve such an end. We propose that self-assembly within the family results in characteristically different substrate selection mechanisms coupled to different multimerization states.

Dissociative photoionization of X(CH(3))(3) (X = N, P, As, Sb, Bi): mechanism, trends, and accurate energetics.

Threshold photoelectron photoion coincidence spectroscopy is used to study the dissociation of energy-selected X(CH(3))(3)(+) ions (X = As, Sb, Bi) by methyl loss, the only process observed up to 2 eV above the ionization energy. The ion time-of-flight distributions and the breakdown diagrams are analyzed in terms of the statistical RRKM theory to obtain accurate ionic dissociation energies. These experiments complement previous studies on analogous trimethyl compounds of the N group where X = N and P. However, trimethylamine was observed to lose only an H atom, whereas trimethylphosphine was shown to lose methyl radical, H atom, and, to a lesser extent, methane in parallel dissociation reactions. Both kinetic and thermodynamic arguments are needed to explain these trends. The methyl radical loss has two channels: either a H transfer to the central atom, followed by CH(3) loss, or a direct homolytic bond cleavage. However, the H transfer channel is blocked in trimethylamine by an H loss channel with an earlier onset, and, thus, the methyl loss is not observed. Bond energies are defined based on ab initio reaction energies and show that the main thermodynamic reason behind the trends in the energetics is the significantly weakening C=X double bond in the ion in the N --> As direction. The first adiabatic ionization energies of Sb(CH(3))(3) and Bi(CH(3))(3) have also been measured by ultraviolet photoelectron spectroscopy to be 8.02 +/- 0.05 and 8.08 +/- 0.05 eV, respectively.

The acylaminoacyl peptidase from Aeropyrum pernix K1 thought to be an exopeptidase displays endopeptidase activity.

Mammalian acylaminoacyl peptidase, a member of the prolyl oligopeptidase family of serine peptidases, is an exopeptidase, which removes acylated amino acid residues from the N terminus of oligopeptides. We have investigated the kinetics and inhibitor binding of the orthologous acylaminoacyl peptidase from the thermophile Aeropyrum pernix K1 (ApAAP). Complex pH-rate profiles were found with charged substrates, indicating a strong electrostatic effect in the surroundings of the active site. Unexpectedly, we have found that oligopeptides can be hydrolysed beyond the N-terminal peptide bond, demonstrating that ApAAP exhibits endopeptidase activity. It was thought that the enzyme is specific for hydrophobic amino acids, in particular phenylalanine, in accord with the non-polar S1 subsite of ApAAP. However, cleavage after an Ala residue contradicted this notion and demonstrated that P1 residues of different nature may bind to the S1 subsite depending on the remaining peptide residues. The crystal structures of the complexes formed between the enzyme and product-like inhibitors identified the oxyanion-binding site unambiguously and demonstrated that the phenylalanine ring of the P1 peptide residue assumes a position different from that established in a previous study, using 4-nitrophenylphosphate. We have found that the substrate-binding site extends beyond the S2 subsite, being capable of binding peptides with a longer N terminus. The S2 subsite displays a non-polar character, which is unique among the enzymes of this family. The S3 site was identified as a hydrophobic region that does not form hydrogen bonds with the inhibitor P3 residue. The enzyme-inhibitor complexes revealed that, upon ligand-binding, the S1 subsite undergoes significant conformational changes, demonstrating the plasticity of the specificity site.

Translational, rotational and vibrational relaxation dynamics of a solute molecule in a non-interacting solvent.

Spectroscopically observing the translational and rotational motion of solute molecules in liquid solutions is typically impeded by their interactions with the solvent, which conceal spectral detail through linewidth broadening. Here we show that unique insights into solute dynamics can be made with perfluorinated solvents, which interact weakly with solutes and provide a simplified liquid environment that helps to bridge the gap in our understanding of gas- and liquid-phase dynamics. Specifically, we show that in such solvents, the translational and rotational cooling of an energetic CN radical can be observed directly using ultrafast transient absorption spectroscopy. We observe that translational-energy dissipation within these liquids can be modelled through a series of classic collisions, whereas classically simulated rotational-energy dissipation is shown to be distinctly faster than experimentally measured. We also observe the onset of rotational hindering from nearby solvent molecules, which arises as the average rotational energy of the solute falls below the effective barrier to rotation induced by the solvent.

Inelastic Scattering of NO by Kr: Rotational Polarization over a Rainbow.

We use molecular beams and ion imaging to determine quantum state resolved angular distributions of NO radicals after inelastic collision with Kr. We also determine both the sense and the plane of rotation (the rotational orientation and alignment, respectively) of the scattered NO. By full selection and then detection of the quantum parity of the NO molecule, our experiment is uniquely sensitive to quantum interference. For forward-scattered NO, we report hitherto unseen changes in the plane and sense of rotation with scattering angle and show, remarkably, that the rotation of the NO molecule after collision can be near-maximally oriented for certain transitions and scattering angles. These effects are enhanced by the full parity selection in the experiment and result from the interplay between attractive and repulsive forces.