Quantum state-to-state rate constants for the rotationally inelastic collision of CH(B2Sigma(-), nu=0, N-->N') with Ar

We have calculated the state-to-state integral cross sections and rate constants for the rotationally inelastic collision of CH(B (2)Sigma(-), nu=0, N-->N') with Ar using the quantum coupled-state and close-coupling methods on an ab initio potential-energy surface constructed by Alexander et al. [J. Chem. Phys. 101, 4547 (1994)]. Overall the calculated rate constants are in good agreements with the three available experimental results. The rate constants are comparable to the usual gas kinetic and decrease with increasing N and DeltaN. For the multiquantum transition cases, the theory underestimates the experiment. We discuss some possible causes to the discrepancies among the theory and the experiments.     

Cyclosilthianes: II. Stereoisomers of methylethyl— and methylvinycyclo—silthianes

1,3,5-Trimehtyl-1,3,5-triehtylcyclotrisilthiane (I) was prepared by treating methylthyldichlorosilane with hydrogen sulfide in the presence of pyridime. 1,3,5-Trimethyl-1,3,5-trivinylcyclotrisilthiane (II) was prepared in a similar manner from methylethyldichlorosilane.The PMR spectrum of these cyclosilthianes is interpreted in terms of a mixture of conformational isomers. The PMR spectrum of these substances in solution did not allow a distinction among the chair and boat forms possible for the cyclosilthiane ring.Continued refluxing of (I) or (II) resulted in the isolation of a $\text{50}\text{50}$ mixture of cis and trans-1,3-dimethyl-1,3-diethylcyclodisilthiane (III), (IV) and 1,3-dimethyl-1,3-divinylcyclodisilthiane (V), (VI) respectively.When (II) was heated or prepared at higher temperature, the PMR spectrum of the product contained resonances in the methyl region indicating the presence of additional methylvinylcyclosilthianes. Polymeric methylvinylsilthiane was isolated as one of the products formed when (II) is heated.     

Theoretical study of the low-temperature vibrational relaxation of o-H2 in collisions with 4He

Cross sections and rate constants for the vibrational relaxation of H₂(υ = 1, j = 1) in collisions with ⁴He were determined using the coupled states method with a fully-converged channel basis. The interaction potential was taken to be that of Gordon and Secrest with the elastic matrix elements modified to include the spherically-symmetric component of the semi-empirical Shafer-Gordon potential. First-order forbidden transitions play a significant role in the overall relaxation process. The cross sections for the de-excitation of the υ = 1, j = 1 level are slightly larger than those for the υ = 1, j = 0 level. The ratio of the corresponding rate constants for vibrational relaxation varies smoothly from a value of 1.25 at 500 K to 1.63 at 60 K.     

Role of the F spin-orbit excited state in the F+HD reaction: contributions to the dynamical resonance

We report quantum mechanical calculations of excitation functions (relative reaction cross sections) for the F+HD reaction. We include three potential energy surfaces and an accurate treatment of all couplings (non-adiabatic, spin-orbit, and Coriolis). Comparison with experimental results [Dong, Lee, and Liu, J. Chem. Phys., 113, 3633 (2000)] show excellent agreement for the DF product channel and an improved but not perfect agreement for the HF product channel. In the former case, when weighted by the (16%) fractional population of the spin-orbit excited state (F(*)) in the beam, the overall reactivity of the F(*) is small (approximately 5%). For the HF product channel and with the same (16%) fractional weight, F(*) reactivity makes a contribution of approximately 12% in the high-energy tail of the resonance peak. As a result, averaging over the population of F spin-orbit states in the beam changes the shape of the resonance. The greater the fraction of F(*) in the beam, the less pronounced will be the resonance modulation of the reaction excitation function.     

Pattern recognition in the prediction of protein structure. II. Chain conformation from a probability-directed search procedure

A procedure that finds the most probable conformational states of a protein chain is described. Single-residue conformations are represented in terms of four conformational states, α, ?, α*, and ?*. The conformation of the entire chain is represented by a sequence of single-residue conformational states; the distinct conformations in this representation are called “chain-states.” The first article in this series described a procedure that computes tripeptide conformational probabilities from the amino acid sequence using pattern recognition techniques. The procedure described in this article uses the tripeptide probabilities to estimate the probabilities of the chain-states. The chain-state probability estimator is a product of conditional and marginal probabilities (obtained from the tripeptide probabilities), with a penalty factor to eliminate conformations containing α-helices and ?-strands of excessive length. The probability estimator considers short-range conformational information, medium-range sequence information and some simple long-range information (through the restrictions on helix and strand lengths). Energy minimization calculations can be carried out in the region of conformational space corresponding to a particular chain-state. By selecting the most probable chain-states, the search can be focused on the most probable, or “important,” regions of the conformational space. These energy calculations are described in the third article of the series. The complete procedure described by the three articles is called PRISM, for pattern recognition-based importance sampling minimization.     

Cross sections and rate constants for the vibrational relaxation of D2 (υ = 1,j = 0) in collisions with 4He

Fully converged quantum cross sections for ⁴He—D² (υ = 1,j = 0) vibrational relaxation were determined using the coupled-states method and a modified version of the Gordon—Secrest surface. First-order forbidden rotational transitions play a significant role, comparable to that observed previously for the He—H₂ system. At 60 K the υ = 1,j = 0 level of D₂ is predicted to relax ≈4 times slower than the corresponding level of H₂. This difference decreases with increasing temperature.     

High resolution mass spectrometry.—II Some substituted benzothiazoles

The mass spectra of nineteen substituted benzothiazoles have been recorded and the identity of the various ions in the mass spectra has been established by high resulution (accurate) mass measurement. Deuterium labelling has been used to elucidate the fragmentation processes of these compounds. The parent compound of the series, benzothiazole, exhibits the loss of hydrogen cyanide and carbon monosulphide from the parent ion as the most important decomposition pathways. The hydrogen atom concerned in the loss of hydrogen cyanide is shown to originate from the 2-position of benzothiazole, while in 2-substituted benzothiazoles, different mechanisms are apparent for the loss of hydrogen cyanide, and these are clarified by deuterium labelling. Some substituted benzothiazoles can lose sulphur from their molecular ions, a process which does not occur in benzothiazole itself. The substituted benzothiazoles undergo many other types of fragmentations, in some cases retaining the substituent, and in other cases losing it prior to collapse of the thiazole ring.     

Substrate specificity and novel selective inhibitors of TNF-alpha converting enzyme (TACE) from two-dimensional substrate mapping

We report a systematic analysis of the P1' and P2' substrate specificity of TNF-alpha converting enzyme (TACE) using a peptide library and a novel analytical method, and we use the substrate specificity information to design novel reverse hydroxamate inhibitors. Initial truncation studies, using the amino acid sequence around the cleavage site in precursor-TNF-alpha, showed that good turnover was obtained with the peptide DNP-LAQAVRSS-NH2. Based on this result, 1000 different peptide substrates of the form Biotin-LAQA-P1'-P2'-SSK(DNP)-NH2 were prepared, with 50 different natural and unnatural amino acids at P1' in combination with 20 different amino acids at P2'. The peptides were pooled, treated with purified microsomal TACE, and the reaction mixtures were passed over a streptavidin affinity column to remove unreacted substrate and the N-terminal biotinylated product. C-terminal cleavage products not binding to streptavidin were subjected to liquid chromatography/mass spectrometry analysis where individual products were identified and semiquantitated. 25 of the substrates were resynthesized as discrete peptides and assayed with recombinant TACE. The experiments show that recombinant TACE prefers lipophilic amino acids at the P1' position, such as phenylglycine, homophenylalanine, leucine and valine. At the P2' position, TACE can accommodate basic amino acids, such as arginine and lysine, as well as certain non-basic amino acids such as citrulline, methionine sulfoxide and threonine. These substrate preferences were used in the design of novel reverse hydroxamate TACE inhibitors with phenethyl and 5-methyl-thiophene-methyl side-chains at P1', and threonine and nitro-arginine at P2'.