Preorganization and reorganization as related factors in enzyme catalysis: the chorismate mutase case

In this paper a deeper insight into the chorismate-to prephenate-rearrangement, catalyzed by Bacillus subtilis chorismate mutase, is provided by means of a combination of statistical quantum mechanics/molecular mechanics simulation methods and hybrid potential energy surface exploration techniques. The main aim of this work is to present an estimation of the preorganization and reorganization terms of the enzyme catalytic rate enhancement. To analyze the first of these, we have studied different conformational equilibria of chorismate in aqueous solution and in the enzyme active site. Our conclusion is that chorismate mutase preferentially binds the reactive conformer of the substrate--that presenting a structure similar to the transition state of the reaction to be catalyzed--with shorter distances between the carbon atoms to be bonded and more diaxial character. With respect to the reorganization effect, an energy decomposition analysis of the potential energies of the reactive reactant and of the reaction transition state in aqueous solution and in the enzyme shows that the enzyme structure is better adapted to the transition structure. This means not only a more negative electrostatic interaction energy with the transition state but also a low enzyme deformation contribution to the energy barrier. Our calculations reveal that the structure of the enzyme is responsible for stabilizing the transition state structure of the reaction, with concomitant selection of the reactive form of the reactants. This is, the same enzymatic pattern that stabilizes the transition structure also promotes those reactant structures closer to the transition structure (i.e., the reactive reactants). In fact, both reorganization and preorganization effects have to be considered as the two faces of the same coin, having a common origin in the effect of the enzyme structure on the energy surface of the substrate.     

In situ sensing of the middle atmosphere with balloonborne near-infrared laser diodes

Since 1997, two near-infrared laser diode sensors have been developed with the support of the CNES, the French space agency, to provide in situ data of H(2)O, CH(4) and CO(2) in the middle atmosphere. The realized instruments were flown from stratospheric balloons within the framework of European campaigns for the study of stratospheric ozone and water vapor and were involved in the validation of the ODIN and ENVISAT satellites. In this paper, we describe the developed laser probing technique, we report atmospheric measurements and finally we discuss future perspectives, particularly the in situ laser sensing of the lower atmosphere of Mars and the implication of the laser hygrometers in balloon campaigns at mid-latitudes and tropical regions to investigate the sources and sinks of stratospheric H(2)O.     

Relativistic molecular wavefunctions: XeF2

A new method is presented to calculate binding energies and eigenfunctions for molecules, using the relativistic Dirac hamiltonian. A numerical basis set of four component wavefunctions is obtained from atom-like Dirac-Slater wavefunctions. A discrete variational method has been developed and applied to the linear XeF₂ molecule.     

Synthesis of benzopyran derivatives,XV Preparation of arylsulfonyloxy-2,2-dimethyl-2H-chromenes

Summary Arylsulfonyloxy-2,2-dimethyl-2H-chromenes (26–35) have been synthesized by reduction of arylsulfonyloxy-2,2-dimethyl-4-chromanones (6–15) followed by dehydration.

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Synthese von Benzopyranderviaten. 15. Mitt.: Darstellung von Arylsulfonyloxy-2,2-dimethyl-2H-chromenen

Zusammenfassung Reduktion von Arylsulfonyloxy-2,2-dimethyl-4-chromanonen (6–15) und anschließende Dehydratisierung liefert Arylsulfonyloxy-2,2-dimethyl-2H-chromene (26–35).

     

Nanofabrication: conventional and nonconventional methods

Nanofabrication is playing an ever increasing role in science and technology on the nanometer scale and will soon allow us to build systems of the same complexity as found in nature. Conventional methods that emerged from microelectronics are now used for the fabrication of structures for integrated circuits, microelectro-mechanical systems, microoptics and microanalytical devices. Nonconventional or alternative approaches have changed the way we pattern very fine structures and have brought about a new appreciation of simple and low-cost techniques. We present an overview of some of these methods, paying particular attention to those which enable large-scale production of lithographic patterns. We preface the review with a brief primer on lithography and pattern transfer concepts. After reviewing the various patterning techniques, we discuss some recent application issues in the fields of microelectronics, optoelectronics, magnetism as well as in biology and biochemistry.     

Strain fields at contacts between small particles

Stress fields between interacting small particles ( approximately 100 nm) have been investigated by transmission electron microscopy. The background for these TEM observations is discussed in terms of adhesion stress fields (due to surface forces), the action of an applied point force, possibly magnetic, and dislocations or misfit strains due to an unfavorable matching of crystal lattices at the grain boundary. A further explanation might be sought along the line "squeezed-in oxide" which can be visualized as a coherent particle or a dislocation loop. Accompanying theoretical calculations have been performed and compared with the experimental results.     

Evaluation of a retention model in comprehensive two-dimensional gas chromatography

Modeling the retention in comprehensive two-dimensional gas chromatography (GC x GC) was achieved using retention indices obtained in conventional GC. Predicted results were compared with experimental data obtained in the two-dimensional separation of a synthetic hydrocarbon mixture. This proved to be helpful in optimizing the operating conditions of GC x GC separation of a complex petroleum sample and in identifying chemical families.     

Machine scheme of additive calculation of physicochemical properties of paraffin hydrocarbons

Summary A machine scheme has been developed for the additive calculation of the physicochemical properties of alkanes necessary for mass calculation of the constants and as a supplementation to the automatic chemical information retrieval system.Translated from Izvestiya Akademii Nauk SSSR, Seriya Khimicheskaya No. 11, pp. 1985–1988, November, 1964     

Deprotonation-electrophile trapping of terminal epoxides

Organolithium-induced deprotonation of terminal epoxides in the presence of appropriate diamine ligands allows trapping with a range of electrophiles, yielding functionalised di- and tri-substituted epoxides in good yields and with control of stereochemistry at the epoxide.     

A Robust and Efficient Method for the Computation of Equilibrium Composition in Gaseous Mixtures

This paper presents in detail a robust, efficient and accurate methodology for the computation of equilibrium composition in gaseous mixtures. The methodology is founded on the concept of the chemical basis, which is defined and formalized using a powerful matricial approach. The method is specially designed to be general, thus providing basic thermodynamic data in several areas, such as combustion, plasma chemistry and, more generally speaking, computational fluid dynamics. The performance of the method is given in terms of CPU usage and the computed results are compared with those in the published literature. The method is shown to yield results of very high quality in terms of accuracy and smoothness.