Kinetics of the reactions of the CHBr2 and CHBr2O2 radicals with O2 and NO

When bromoform (CHBr3) is photolyzed at 266 or 303 nm in the presence of O2 and NO, the formation of secondary Br atoms is observed. By following the rate of growth of this secondary Br atom signal as a function of conditions, rate constants have been determined for the reactions CHBr2 + O2, CHBr2 + NO (both pressure-dependent), and CHBr2O2 + NO (k(2a) = (1.74 +/- 0.16) x 10(-11) cm3 molecule(-1) s(-1) at 23 degrees C). By measuring the amplitude of the secondary Br signal compared to the primary Br formed in the initial photolysis, it is established that the CHBr2O radical spontaneously decomposes to form CHBrO + Br at least 90%, and probably 100%, of the time, in agreement with previous work and with recent ab initio calculations. A survey of four other polybrominated methanes, CH2Br2, CHClBr2, CF2Br2, and CBr4, shows that they all generate secondary Br atoms when photolyzed at 266 nm in the presence of O2 and NO, suggesting that their reaction sequences are similar to that of bromoform.     

Diffusion-limited aggregation: A kinetic critical phenomenon?

Diffusion-limited aggregation (DLA) is a model which represents noisy growth limited by diffusion. This process is quite common in nature and the simple algorithm gives a good representation of the large-scale structure of many natural objects. The clusters grown in the computer and the real objects in question are tenuous and approximately self-similar. A good deal is known about the algorithm, but a complete theory is not yet available. I review the current state of knowledge about the model, its applications and theoretical analysis of the results.     

Superspace groups and superstructures: NbS3

The application of superspace groups to short-period superstructures is considered. For niobium tri-sulfide this is worked out in detail. It is shown that in that case the superspace group provides more symmetry then given by the space group of the supercell. Its consequences for the structure, the diffraction pattern and tensor-properties are discussed.     

Heavy-Atom Tunneling in Semibullvalenes: How Driving Force,Substituents, and Environment Influence the Tunneling Rates

The Cope rearrangement of selectively deuterated isotopomers of 1,5-dimethylsemibullvalene 2 a and 3,7-dicyano-1,5-dimethylsemibullvalene 2 b were studied in cryogenic matrices. In both semibullvalenes the Cope rearrangement is governed by heavy-atom tunneling. The driving force for the rearrangements is the small difference in the zero-point vibrational energies of the isotopomers. To evaluate the effect of the driving force on the tunneling probability in 2 a and 2 b , two different pairs of isotopomers were studied for each of the semibullvalenes. The reaction rates for the rearrangement of 2 b in cryogenic matrices were found to be smaller than the ones of 2 a under similar conditions, whereas differences in the driving force do not influence the rates. Small curvature tunneling (SCT) calculations suggest that the reduced tunneling rate of 2 b compared to that of 2 a results from a change in the shape of the potential energy barrier. The tunneling probability of the semibullvalenes strongly depends on the matrix environment; however, for 2 a in a qualitatively different way than for 2 b .     

A Tunable,Fullerene-Based Molecular Amplifier for Vibrational Circular Dichroism

Vibrational circular dichroism (VCD) studies are reported on a chiral compound in which a fullerene C₆₀ moiety is used as an electron acceptor and local VCD amplifier for an alanine-based peptide chain. Four redox states are investigated in this study, of which three are reduced species that possess low-lying electronic states as confirmed by UV/Vis spectroelectrochemistry. VCD measurements in combination with (TD)DFT calculations are used to investigate (i) how the low-lying electronic states of the reduced species modulate the amplification of VCD signals, (ii) how this amplification depends on the distance between oscillator and amplifier, and (iii) how the spatial extent of the amplifier influences amplification. These results pave the way for further development of tailored molecular VCD amplifiers.     

The powder X-band electron paramagnetic resonance spectroscopy of septet pyridyl-2,4,6-trinitrene

The first X-band EPR spectrum containing only non-overlapping signals of septet pyridyl-2,4,6-trinitrene and triplet pyridylnitrenes is reported. This spectrum was recorded after photolysis of 2,4,6-triazidopyridine in solid argon at 5 K. The zero-field splitting (ZFS) parameters of this trinitrene as well as of intermediate triplet mononitrenes and quintet dinitrenes formed at early stages of the photolysis were determined using the combination of modern computer line-shape spectral simulations and density functional theory (DFT) calculations. It was found that septet pyridyl-2,4,6-trinitrene has the record negative parameter D_S = −0.1031 cm⁻¹ among all known to date septet pyridyl-2,4,6-trinitrenes and may be of interest as a model multi-qubit spin system for investigations of quantum computation processing.     

A space–time hybridizable discontinuous Galerkin method for incompressible flows on deforming domains

We present the first space–time hybridizable discontinuous Galerkin (HDG) finite element method for the incompressible Navier–Stokes and Oseen equations. Major advantages of a space–time formulation are its excellent capabilities of dealing with moving and deforming domains and grids and its ability to achieve higher-order accurate approximations in both time and space by simply increasing the order of polynomial approximation in the space–time elements. Our formulation is related to the HDG formulation for incompressible flows introduced recently in, e.g., [N.C. Nguyen, J. Peraire, B. Cockburn, A hybridizable discontinuous Galerkin method for Stokes flow, Comput. Methods Appl. Mech. Eng. 199 (2010) 582–597]. However, ours is inspired in typical DG formulations for compressible flows which allow for a more straightforward implementation. Another difference is the use of polynomials of fixed total degree with space–time hexahedral and quadrilateral elements, instead of simplicial elements. We present numerical experiments in order to assess the quality of the performance of the methods on deforming domains and to experimentally investigate the behavior of the convergence rates of each component of the solution with respect to the polynomial degree of the approximations in both space and time.     

A fast parallel clustering algorithm for molecular simulation trajectories

We implemented a GPU‐powered parallel k‐centers algorithm to perform clustering on the conformations of molecular dynamics (MD) simulations. The algorithm is up to two orders of magnitude faster than the CPU implementation. We tested our algorithm on four protein MD simulation datasets ranging from the small Alanine Dipeptide to a 370‐residue Maltose Binding Protein (MBP). It is capable of grouping 250,000 conformations of the MBP into 4000 clusters within 40 seconds. To achieve this, we effectively parallelized the code on the GPU and utilize the triangle inequality of metric spaces. Furthermore, the algorithm's running time is linear with respect to the number of cluster centers. In addition, we found the triangle inequality to be less effective in higher dimensions and provide a mathematical rationale. Finally, using Alanine Dipeptide as an example, we show a strong correlation between cluster populations resulting from the k‐centers algorithm and the underlying density. © 2012 Wiley Periodicals, Inc.