Exploitation of structural and regulatory diversity in glutamate racemases

Glutamate racemase is an enzyme essential to the bacterial cell wall biosynthesis pathway, and has therefore been considered as a target for antibacterial drug discovery. We characterized the glutamate racemases of several pathogenic bacteria using structural and biochemical approaches. Here we describe three distinct mechanisms of regulation for the family of glutamate racemases: allosteric activation by metabolic precursors, kinetic regulation through substrate inhibition, and D-glutamate recycling using a d-amino acid transaminase. In a search for selective inhibitors, we identified a series of uncompetitive inhibitors specifically targeting Helicobacter pylori glutamate racemase that bind to a cryptic allosteric site, and used these inhibitors to probe the mechanistic and dynamic features of the enzyme. These structural, kinetic and mutational studies provide insight into the physiological regulation of these essential enzymes and provide a basis for designing narrow-spectrum antimicrobial agents.     

Biasing reaction pathways with mechanical force

During the course of chemical reactions, reactant molecules need to surmount an energy barrier to allow their transformation into products. The energy needed for this process is usually provided by heat, light, pressure or electrical potential, which act either by changing the distribution of the reactants on their ground-state potential energy surface or by moving them onto an excited-state potential energy surface and thereby facilitate movement over the energy barrier. A fundamentally different way of initiating or accelerating a reaction is the use of force to deform reacting molecules along a specific direction of the reaction coordinate. Mechanical force has indeed been shown to activate covalent bonds in polymers, but the usual result is chain scission. Here we show that mechanically sensitive chemical groups make it possible to harness the mechanical forces generated when exposing polymer solutions to ultrasound, and that this allows us to accelerate rearrangement reactions and bias reaction pathways to yield products not obtainable from purely thermal or light-induced reactions. We find that when placed within long polymer strands, the trans and cis isomers of a 1,2-disubstituted benzocyclobutene undergo an ultrasound-induced electrocyclic ring opening in a formally conrotatory and formally disrotatory process, respectively, that yield identical products. This contrasts with reaction initiation by light or heat alone, in which case the isomers follow mutually exclusive pathways to different products. Mechanical forces associated with ultrasound can thus clearly alter the shape of potential energy surfaces so that otherwise forbidden or slow processes proceed under mild conditions, with the directionally specific nature of mechanical forces providing a reaction control that is fundamentally different from that achieved by adjusting chemical or physical parameters. Because rearrangement in our system occurs before chain scission, the effect we describe might allow the development of materials that are activated by mechanical stress fields.     

Access to Vinyl Ethers and Ketones with Hypervalent Iodine Reagents as Oxy‐Allyl Cation Synthetic Equivalents

We report an Umpolung strategy of enol ethers to generate oxy‐allyl cation equivalents based on the use of hypervalent iodine reagents. Under mild basic conditions, the addition of nucleophiles to aryloxy‐substituted vinylbenziodoxolone (VBX) reagents, easily available in two steps from silyl alkynes, resulted in the stereoselective formation of substituted aryl enol ethers. The reaction was most efficient with phenols as nucleophiles, but preliminary results were also achieved for C‐ and N‐ nucleophiles. In absence of external nucleophiles, the 2‐iodobenzoate group of the reagent was transferred. The obtained aryl enol ethers could then be transformed into α‐difunctionalized ketones by oxidation. The described “allyl cation”‐like reactivity contrast with the well‐established “vinyl‐cation” behavior of alkenyl iodonium salts.     

A closely packed system of low-mass, low-density planets transiting Kepler-11

When an extrasolar planet passes in front of (transits) its star, its radius can be measured from the decrease in starlight and its orbital period from the time between transits. Multiple planets transiting the same star reveal much more: period ratios determine stability and dynamics, mutual gravitational interactions reflect planet masses and orbital shapes, and the fraction of transiting planets observed as multiples has implications for the planarity of planetary systems. But few stars have more than one known transiting planet, and none has more than three. Here we report Kepler spacecraft observations of a single Sun-like star, which we call Kepler-11, that reveal six transiting planets, five with orbital periods between 10 and 47?days and a sixth planet with a longer period. The five inner planets are among the smallest for which mass and size have both been measured, and these measurements imply substantial envelopes of light gases. The degree of coplanarity and proximity of the planetary orbits imply energy dissipation near the end of planet formation.     

Orientational phenomena in comb-shaped liquid crystal polymers induced by laser beam irradiation

Action of the laser illumination on optical properties of liquid crystalline (LC) comb-shaped acrylic and methacrylic copolymers containing cyanobiphenyl mesogenic groups and azo dye fragments has been studied. Under an illumination the cis-trans configurational changes of dye fragments take place and reorientation of the side groups towards a direction perpendicular to the electric vector of the actinic light occurs. As a result the photoinduced optical birefringence (δn = 0.05-0.11) appears. The detailed study of dichrotic and optical properties of polymeric films, kinetics and relaxation of δn, as well as mechanism of orientational transformations during a laser illumination are discussed. The induced optical anisotropy of the films can be changed reversibly by rotating the electric vector of the laser beam in respect to the film that may be used in reversible optical data storage.     

Machine-Learned Free Energy Surfaces for Capillary Condensation and Evaporation in Mesopores

Using molecular simulations, we study the processes of capillary condensation and capillary evaporation in model mesopores. To determine the phase transition pathway, as well as the corresponding free energy profile, we carry out enhanced sampling molecular simulations using entropy as a reaction coordinate to map the onset of order during the condensation process and of disorder during the evaporation process. The structural analysis shows the role played by intermediate states, characterized by the onset of capillary liquid bridges and bubbles. We also analyze the dependence of the free energy barrier on the pore width. Furthermore, we propose a method to build a machine learning model for the prediction of the free energy surfaces underlying capillary phase transition processes in mesopores.     

Evidence for charge Kondo effect in superconducting Tl-doped PbTe

We report results of low-temperature thermodynamic and transport measurements of Pb1-xTlxTe single crystals for Tl concentrations up to the solubility limit of approximately x=1.5%. For all doped samples, we observe a low-temperature resistivity upturn that scales in magnitude with the Tl concentration. The temperature and field dependence of this upturn are consistent with a charge Kondo effect involving degenerate Tl valence states differing by two electrons, with a characteristic Kondo temperature T(K) approximately 6 K. The observation of such an effect supports an electronic pairing mechanism for superconductivity in this material and may account for the anomalously high T(c) values.