K1±(892) Production in π−N interactions at 200 GeV/c

K^1±(892) production is studied in the reaction π^?N → K_S⁰K_S⁰ + X where X includes up to five observed charged particles. An excess of K^1? over K¹⁺ is observed for Feynman-x > 0.1. The ratio of K¹⁺ to K^1? decreases with x as predicted by QCD counting rules. K_S⁰ and K¹ production are compared to recent D and D¹ data from other experiments.     

NMR velocimetry and spectroscopy at microscopic resolution in small rheometric devices

We describe several different rheometric devices for use within the nuclear-magnetic-resonance probe of a standard widebore microimaging system. These include both vertical and horizontal Couette cells and the cone- and -plate cell, which produce shearing flows, and the four-roll mill and the opposed-jet (cross-flow junction) cells which produce extensional flow. We demonstrate that velocity images can be obtained for each and that detailed information about local shear and extension rates can be extracted. These systems have considerable potential for use in the study of non-Newtonian viscosity, and of molecular ordering under shear or extension.     

Ranking docking poses by graph matching of protein–ligand interactions: lessons learned from the D3R Grand Challenge 2

A novel docking challenge has been set by the Drug Design Data Resource (D3R) in order to predict the pose and affinity ranking of a set of Farnesoid X receptor (FXR) agonists, prior to the public release of their bound X-ray structures and potencies. In a first phase, 36 agonists were docked to 26 Protein Data Bank (PDB) structures of the FXR receptor, and next rescored using the in-house developed GRIM method. GRIM aligns protein–ligand interaction patterns of docked poses to those of available PDB templates for the target protein, and rescore poses by a graph matching method. In agreement with results obtained during the previous 2015 docking challenge, we clearly show that GRIM rescoring improves the overall quality of top-ranked poses by prioritizing interaction patterns already visited in the PDB. Importantly, this challenge enables us to refine the applicability domain of the method by better defining the conditions of its success. We notably show that rescoring apolar ligands in hydrophobic pockets leads to frequent GRIM failures. In the second phase, 102 FXR agonists were ranked by decreasing affinity according to the Gibbs free energy of the corresponding GRIM-selected poses, computed by the HYDE scoring function. Interestingly, this fast and simple rescoring scheme provided the third most accurate ranking method among 57 contributions. Although the obtained ranking is still unsuitable for hit to lead optimization, the GRIM–HYDE scoring scheme is accurate and fast enough to post-process virtual screening data.     

A slow positron lifetime study of the annealing behaviour of an amorphous silicon layer grown by MBE

We have studied MBE grown amorphous silicon, which was recrystallized at different temperatures for one hour, with a pulsed positron beam. A positron lifetime of 538±10 ps in the as-grown state is attributed to microvoids containing at least 10 vacancies. An incompletely recrystallized sample annealed at 500°C shows an additional long lifetime from ortho-positronium (o-Ps) pick-off annihilation. The o-Ps component disappears for samples, recrystallized at 700°C and above, and the defect lifetime steadily decreases with higher annealing temperature until a value of 310 ps is reached for the layer annealed at 1200°C. This value is explained by positron trapping at dislocations or small vacancy defects stabilized by dislocations or impurities.Paper presented at the 132nd WE-Heraeus-Seminar on Positron Studies of Semiconductor Defects, Halle, Germany, 29 August to 2 September 1994     

Glycoside hydrolase stabilization of transition state charge: new directions for inhibitor design

Carbasugars are structural mimics of naturally occurring carbohydrates that can interact with and inhibit enzymes involved in carbohydrate processing. In particular, carbasugars have attracted attention as inhibitors of glycoside hydrolases (GHs) and as therapeutic leads in several disease areas. However, it is unclear how the carbasugars are recognized and processed by GHs. Here, we report the synthesis of three carbasugar isotopologues and provide a detailed transition state (TS) analysis for the formation of the initial GH-carbasugar covalent intermediate, as well as for hydrolysis of this intermediate, using a combination of experimentally measured kinetic isotope effects and hybrid QM/MM calculations. We find that the α-galactosidase from Thermotoga maritima effectively stabilizes TS charge development on a remote C5-allylic center acting in concert with the reacting carbasugar, and catalysis proceeds via an exploded, or loose, S_N2 transition state with no discrete enzyme-bound cationic intermediate. We conclude that, in complement to what we know about the TS structures of enzyme-natural substrate complexes, knowledge of the TS structures of enzymes reacting with non-natural carbasugar substrates shows that GHs can stabilize a wider range of positively charged TS structures than previously thought. Furthermore, this enhanced understanding will enable the design of new carbasugar GH transition state analogues to be used as, for example, chemical biology tools and pharmaceutical lead compounds.

Positive charge stabilized on remote C5-allylic center with catalysis occurring via a loose S_N2 transition state.     

Solid-state and inclusion properties of hydrogen-bonded 1,3-cyclohexanedione cyclamers

During crystallization 1,3-cyclohexanedione self assembles into either hydrogen-bonded chains or hexameric rings depending on the solvent conditions. The hexameric rings, called cyclamers, are the subject of this paper. These unusual structures occlude benzene as a guest molecule. The structural and crystal chemical properties of these host-guest compounds are explored here with the use of crystal growth studies, X-ray powder patterns, and thermal analysis. The crystal structure of the benzene cyclamer of 5-methyl-1,3-cyclohexanedione is reported (hexagonal,a =b = 19.19(2)Å,c = 10.545(9)Å,R3,Z = 18,V = 3362(6)ų; 717 unique reflections,R = 0.062). An analysis of the stereochemical implications of cyclic directionality in these cyclamers is also discussed.Alfred P. Sloan Foundation Fellow, 1989–1991.