Theory of the Kinetics of Chemical Potentials in Heterogeneous Catalysis

Simple and powerful: The reaction kinetics at surfaces of heterogeneous catalysts is reformulated in terms of the involved chemical potentials. Based on this formulism, an approach of searching for good catalysts is proposed without recourse to extensive calculations of reaction barriers and detailed kinetic analyses. (see picture; R=reactant, I=surface intermediate, P=product, and =standard chemical potential).

Divergence of chemical function in the alkaline phosphatase superfamily: Structure and mechanism of the P-C bond cleaving enzyme phosphonoacetate hydrolase

Phosphonates constitute a class of natural products that mimic the properties of the more common organophosphate ester metabolite yet are not readily degraded owing to the direct linkage of the phosphorus atom to the carbon atom. Phosphonate hydrolases have evolved to allow bacteria to utilize environmental phosphonates as a source of carbon and phosphorus. The work reported in this paper examines one such enzyme, phosphonoacetate hydrolase. By using a bioinformatic approach, we circumscribed the biological range of phosphonoacetate hydrolase to a select group of bacterial species from different classes of Proteobacteria. In addition, using gene context, we identified a novel 2-aminoethylphosphonate degradation pathway in which phosphonoacetate hydrolase is a participant. The X-ray structure of phosphonoformate-bound phosphonoacetate hydrolase was determined to reveal that this enzyme is most closely related to nucleotide pyrophosphatase/diesterase, a promiscuous two-zinc ion metalloenzyme of the alkaline phosphatase enzyme superfamily. The X-ray structure and metal ion specificity tests showed that phosphonoacetate hydrolase is also a two-zinc ion metalloenzyme. By using site-directed mutagenesis and P-32-labeling strategies, the catalytic nucleophile was shown to be Thr64. A structure-guided, site-directed mutation-based inquiry of the catalytic contributions of active site residues identified Lys126 and Lys128 as the most likely candidates for stabilization of the aci-carboxylate dianion leaving group. A catalytic mechanism is proposed which combines Lys12/Lys128 leaving group stabilization with zinc ion activation of the Thr64 nucleophile and the substrate phosphoryl group.

Chemical evolution in the circumstellar structure of B5 IRS1

The B5 dark cloud has been identified as a site of low-mass star formation. We report a survey of a selection of the molecular species modelled by the B5 dynamical and chemical model of Charnley et al. at the positions of circumstellar HCN clumps in B5 IRS1. All of the key species observed yield either abundances or upper limits to abundances below both the standard and the predicted values, appearing to show evidence of depletion and/or destruction if the transitions observed are thermalized. Our results are not in good agreement with the model, and they bring into question the interpretation of the structure of B5 IRS1 proposed by Fuller et al. It was expected that HCN clump C might exhibit a higher excitation than HCN clump A, since it appeared to be located within the blueshifted molecular outflow. However, there is no significant difference observed between the two clumps, suggesting that the near-infrared and optical nebulosity is evidence of a reflection nebula rather than shocked material in the outflow. Finally, it is observed that our results are more consistent with gas-grain models than with those models excluding gas-grain interaction.

CHEMICAL PROCESSES IN DARK INTERSTELLAR CLOUDS - THE EFFECTS OF CNO DEPLETION

We have investigated the effects of depletion of the elements C, N and O on the chemical composition of dark clouds, using both isothermal and isochoric cloud models. Our work differs from previous approaches in that we have considered a much larger range of CNO depletions. We have included the chemistry of the ortho-and para-forms of H2 and the exothermic reaction between N+ and ortho-H2, which synthesizes NH3. In the isothermal models, the ortho:para ratio is very small at large depletions, but NH3 formation is still efficient owing to reactions between He+ and CN or HCN. In the isochoric models, the equilibrium temperature of the gas is larger, and a thermal ortho:para ratio, which is large enough to drive NH3 formation, results. In all cases, the fractional abundance of NH3 is close to 10(-8) and this may help to explain the puzzling observation that, in dark clouds, the column density of NH3 is always close to 10(15) cm-2.

Chemical processes in protoplanetary disks. II. On the importance of photochemistry and X-ray ionization

We investigate the impact of photochemistry and X-ray ionization on the molecular composition of, and ionization fraction in, a protoplanetary disk surrounding a typical T Tauri star. We use a sophisticated physical model, which includes a robust treatment of the radiative transfer of UV and X-ray radiation, and calculate the time-dependent chemical structure using a comprehensive chemical network. In previous work, we approximated the photochemistry and X-ray ionization; here, we recalculate the photoreaction rates using the explicit UV wavelength spectrum and wavelength-dependent reaction cross sections. We recalculate the X-ray ionization rate using our explicit elemental composition and X-ray energy spectrum. We find that photochemistry has a larger influence on the molecular composition than X-ray ionization. Observable molecules sensitive to the photorates include OH, HCO+, N2H+, H2O, CO2, and CH3OH. The only molecule significantly affected by the X-ray ionization is N2H+, indicating that it is safe to adopt existing approximations of the X-ray ionization rate in typical T Tauri star-disk systems. The recalculation of the photorates increases the abundances of neutral molecules in the outer disk, highlighting the importance of taking into account the shape of the UV spectrum in protoplanetary disks. A recalculation of the photoreaction rates also affects the gas-phase chemistry due to the adjustment of the H/H2 and C+/C ratios. The disk ionization fraction is not significantly affected by the methods adopted to calculate the photochemistry and X-ray ionization. We determine that there is a probable "dead zone" where accretion is suppressed, present in a layer, Z/R lsim 0.1-0.2, in the disk midplane, within R ˜ 200 AU.

The chemical composition of two supergiants in the dwarf irregular galaxy WLM

The chemical composition of two stars in WLM has been determined from high-quality Ultraviolet-Visual Echelle Spectrograph (UVES) data obtained at the VLT-UT2. The model atmospheres analysis shows that they have the same metallicity, [Fe/H] = - 0.38 +/- 0.20 (+/- 0.29). Reliable magnesium abundances are determined from several lines of two ionization states in both stars resulting in [Mg/Fe] = - 0.24 +/- 0.16 (+/- 0.28). This result suggests that the [alpha(Mg)/Fe] ratio in WLM may be suppressed relative to solar abundances ( also supported by differential abundances relative to similar stars in NGC 6822 and the Small Magellanic Cloud [SMC]). The absolute Mg abundance, [Mg/H] = -0.62, is high relative to what is expected from the nebulae though, where two independent spectroscopic analyses of the H II regions in WLM yield [O/H] = - 0.89. Intriguingly, the oxygen abundance determined from the O I lambda6158 feature in one WLM star is [O/H] = - 0.21 +/- 0.10 (+/- 0.05), corresponding to 5 times higher than the nebular oxygen abundance. This is the first time that a significant difference between stellar and nebular oxygen abundances has been found, and currently, there is no simple explanation for this difference. The two stars are massive supergiants with distances that clearly place them in WLM. They are young ( less than or equal to 10 Myr) and should have a similar composition to the ISM. Additionally, differential abundances suggest that the O/Fe ratio in the WLM star is consistent with similar stars in NGC 6822 and the SMC, galaxies where the average stellar oxygen abundances are in excellent agreement with the nebular results. If the stellar abundances reflect the true composition of WLM, then this galaxy lies well above the metallicity-luminosity relationship for dwarf irregular galaxies. It also suggests that WLM is more chemically evolved than currently interpreted from its color-magnitude diagram. The similarities between the stars in WLM and NGC 6822 suggest that these two galaxies may have had similar star formation histories.

A comparison of the chemical repair rates of free radical precursors of DNA damage and cell killing in Chinese hamster V79 cells.

One of the important temporal stages of radiation action in cellular systems is the chemical phase, where oxygen fixation reactions compete with chemical repair reactions involving reducing agents such as GSH. Using the gas explosion technique it is possible to follow the kinetics of these fast (> 1 ms) reactions in intact cells. We have compared the chemical repair kinetics of the oxygen-dependent free radical precursors leading to DNA single-strand and double-strand breaks, measured using filter elution techniques, with those leading to cell killing in V79 cells. The chemical repair rates for DNA dsb (670s-1 at pH 7.2 and 380s-1 at pH 9.6) and cell killing (530s-1) were similar. This is in agreement with the important role of DNA dsb in radiation induced cell lethality. The rate for DNA ssb precursors was significantly slower (210s-1). The difference in rate between DNA ssb and dsb precursors may be explained on the basis of a dsb free radical precursor consisting of a paired radical, one radical on each strand. The instantaneous probability of one or other of these radicals being chemically repaired and not proceeding to form a dsb will be twice that of a ssb radical precursor. This agrees well with the concept of locally multiply damaged sites (LMDS) produced from clusters of ionizations in DNA (Ward 1985).

The role of non-protein sulphydryls in determining the chemical repair rates of free radical precursors of DNA damage and cell killing in Chinese hamster V79 cells. I

Chinese hamster V79 fibroblasts were irradiated in the gas explosion apparatus and the chemical repair rates of the oxygen-dependent free radical precursors of DNA double-strand breaks (dsb) and lethal lesions measured using filter elution (pH 9.6) and a clonogenic assay. Depletion of cellular GSH levels, from 4.16 fmol/cell to 0.05 fmol/cell, by treatment with buthionine sulphoximine (50 mumol dm-3; 18 h), led to sensitization as regards DNA dsb induction and cell killing. This was evident at all time settings but was particularly pronounced when the oxygen shot was given 1 ms after the irradiation pulse. A detailed analysis of the chemical repair kinetics showed that depletion of GSH led to a reduction in the first-order rate constant for dsb precursors from 385 s-1 to 144 s-1, and for lethal lesion precursors from 533 s-1 to 165 s-1. This is generally consistent with the role of GSH in the repair-fixation model of radiation damage at the critical DNA lesions. However, the reduction in chemical repair rate was not proportional to the severe thiol depletion (down to almost-equal-to 1% for GSH) and a residual repair capacity remained (almost-equal-to 30%). This was found not to be due to compartmentalization of residual GSH in the nucleus, as the repair rate for dsb precursors in isolated nuclei, washed virtually free of GSH, was identical to that found in GSH-depleted cells (144 s-1), also the OER remained substantially above unity. This suggests that other reducing agents may have a role to play in the chemical repair of oxygen-dependent damage. One possible candidate is the significant level of protein sulphydryls present in isolated nuclei.

The activity of a putative polyisoprenol-linked sugar translocase (Wzx) involved in Escherichia coli O antigen assembly is independent of the chemical structure of the O repeat

During O antigen lipopolysaccharide (LPS) synthesis in bacteria, transmembrane migration of undecaprenylpyrophosphate (Und-P-P)-bound O antigen subunits occurs before their polymerization and ligation to the rest of the LPS molecule. Despite the general nature of the translocation process, putative O-antigen translocases display a low level of amino acid sequence similarity. In this work, we investigated whether complete O antigen subunits are required for translocation. We demonstrate that a single sugar, GlcNAc, can be incorporated to LPS of Escherichia coli K-12. This incorporation required the functions of two O antigen synthesis genes, wecA (UDP-GlcNAc:Und-P GlcNAc-1-P transferase) and wzx (O-antigen translocase). Complementation experiments with putative O-antigen translocases from E. coli O7 and Salmonella enterica indicated that translocation of O antigen subunits is independent of the chemical structure of the saccharide moiety. Furthermore, complementation with putative translocases involved in synthesis of exopolysaccharides demonstrated that these proteins could not participate in O antigen assembly. Our data indicate that recognition of a complete Und-P-P-bound O antigen subunit is not required for translocation and suggest a model for O antigen synthesis involving recognition of Und-P-P-linked sugars by a putative complex made of Wzx translocase and other proteins involved in the processing of O antigen.

EMAS and ISO 14001 in the German industry – complements or substitutes?

The two environmental management system (EMS) standards EMAS and ISO 14001 have been available in Europe for the last 15 years. ISO 14001 has been taken up at a much larger scale but many firms in the German automotive and engineering industry have certified their EMSs according to both standards. Two research questions are addressed: (i) What explains why companies adopt both EMAS and ISO 14001? (ii) Are EMAS and ISO 14001 complements or substitutes? Based on 21 interviews with industrial and institutional representatives, this study finds that, first, the two standards are adopted for completely different reasons: while ISO 14001 is often done as a response to external pressure, EMAS tends to be motivated internally. Second, it is argued that EMAS and ISO 14001 are likely in a situation of direct competition at present which may well turn into complementarity in the future.