Structure and kinetics of phosphonopyruvate hydrolase from Variovorax sp. Pal2: New insight into the divergence of catalysis within the PEP mutase/isocitrate lyase superfamily .

Phosphonopyruvate (P-pyr) hydrolase (PPH), a member of the phosphoenolpyruvate (PEP) mutase/isocitrate lyase (PEPM/ICL) superfamily, hydrolyzes P-pyr and shares the highest sequence identity and functional similarity with PEPM. Recombinant PPH from Variovorax sp. Pal2 was expressed in Escherichia coli and purified to homogeneity. Analytical gel filtration indicated that the protein exists in solution predominantly as a tetramer. The PPH pH rate profile indicates maximal activity over a broad pH range.The steady-state kinetic constants determined for a rapid equilibrium ordered kinetic mechanism with Mg+2 binding first (Kd =140 ± 40 M), are kcat = 105 ± 2 s-1 and P-pyr Km = 5 ± 1 M. PEP (slow substrate kcat = 2 × 10-4 s-1), oxalate, and sulfopyruvate are competitive inhibitors with Ki values of 2.0 ± 0.1 mM, 17 ± 1 M, and 210 ± 10 M, respectively. Three PPH crystal structures have been determined, that of a ligand-free enzyme, the enzyme bound to Mg2+ and oxalate (inhibitor), and the enzyme bound to Mg2+ and P-pyr (substrate). The complex with the inhibitor was obtained by cocrystallization, whereas that with the substrate was obtained by briefly soaking crystals of the ligand-free enzyme with P-pyr prior to flash cooling. The PPH structure resembles that of the other members of the PEPM/ICL superfamily and is most similar to the functionally related enzyme, PEPM. Each monomer of the dimer of dimers exhibits an (/)8 barrel fold with the eighth helix swapped between two molecules of the dimer. Both P-pyr and oxalate are anchored to the active site by Mg2+. The loop capping the active site is disordered in all three structures, in contrast to PEPM, where the equivalent loop adopts an open or disordered conformation in the unbound state but sequesters the inhibitor from solvent in the bound state. Crystal packing may have favored the open conformation of PPH even when the enzyme was cocrystallized with the oxalate inhibitor. Structure alignment of PPH with other superfamily members revealed two pairs of invariant or conservatively replaced residues that anchor the flexible gating loop. The proposed PPH catalytic mechanism is analogous to that of PEPM but includes activation of a water nucleophile with the loop Thr118 residue.

The stereoselective coordination chemistry of the helicating ligand N,N '-bis(-2,2 '-dipyridyl-5-yl)carbonyl-(S/R,S/R)-1,2-diphenylethylenediamine

Enantiomerically pure N,N'-bis(-2,2'-dipyridyl-5-yl)carbonyl-(S/R,S/R)-1,2-diphenylethylenediamine has been synthesised by linking two 2,2'-bipyridine units by (R,R)- and (S,S)-1,2-diphenylethylenediamine. The ligands possess a hindered rotation between the bipyridine chromophores, which are held together by intramolecular hydrogen bonds. ES mass spectroscopy confirmed that reaction with Fe(II), Co(III) and Cd(II) afforded dinuclear complexes. CD spectroscopy implied that enantiopure ligands conferred helicity to the metals centre giving a dominant triple helicate diastereoisomer (with the RR isomer giving a P helicate). H-1 NMR spectroscopy of the cadmium complex confirmed the presence of a single diastereoisomer. (C) 2003 Elsevier B.V. All rights reserved.

Stereoselective coordination chemistry of the tetradentate chelating ligand (2R,3R)-bis(2,2 '-dipyridyl-5-methoxyl) butane

The enantiomerically pure ligand L-3RR (2R, 3R)-bis(2,2'-dipyridyl-5-methoxyl) butane has been synthesised by linking two 2,2'-bipyridine units with (2R, 3R)-butandiol. The reaction of L-3RR with Zn(II) afforded a mononuclear species and the H-1 NMR spectroscopy points to a C-1 symmetry, expected for a distorted trigonal bipyramidal coordination environment. These observations were confirmed by MM2 calculations and electrospray mass spectrometry. The reaction of L-3RR with iron(II) indicated the formation of a dinuclear species by mass spectrometry. Solution state CD spectroscopy indicates that both complexes adopt a Lambda-configuration, implying a single stranded dinuclear iron(II) complex is present rather than the anticipated triple helical architecture.

The Effects of Molecular Anions on the Chemistry of Dark Clouds

We have investigated the role of molecular anion chemistry in pseudo-time-dependent chemical models of dark clouds. With oxygen-rich elemental abundances, the addition of anions results in a slight improvement in the overall agreement between model results and observations of molecular abundances in Taurus molecular cloud 1 (TMC-1 (CP)). More importantly, with the inclusion of anions, we see an enhanced production efficiency of unsaturated carbon-chain neutral molecules, especially in the longer members of the families C(n)H, C(n)H(2), and HC(n)N. The use of carbon-rich elemental abundances in models of TMC-1 (CP) with anion chemistry worsens the agreement with observations compared with model results obtained in the absence of anions.

Mechanisms and chemistry of dye adsorption on manganese oxides-modified diatomite

The investigations into structural changes which occur during adsorbent modification and the adsorption mechanisms are essential for an effective design of adsorption systems. Manganese oxides were impregnated onto diatomite to form the type known as delta-birnessite. Initial investigations established the effectiveness of manganese oxides-modified diatomite (MOMD) to remove basic and reactive dyes from aqueous solution. The adsorption capacity of MOMD for methylene blue (MB), hydrolysed reactive black (RB) and hydrolysed reactive yellow (RY) was 320, 419, and 204 mg/g, respectively. Various analytical techniques were used to characterise the structure and the mechanisms of the dye adsorption process onto MOMD such as Fourier transform infrared (FTIR), X-ray diffraction (XRD) and atomic absorption spectrometry (A.A.). A small shift to higher values of the cl-spacing of dye/MOMD was observed indicating that a small amount of the dye molecules were intercalated in the MOMD structure and other molecules were adsorbed on the external surface of MOMD. Two mechanisms of dye adsorption onto MOMD were proposed; intercalation of the dye in the octahedral layers and adsorption of the dye on the MOMD external surface. Moreover, the results demonstrated that the MOMD structure was changed upon insertion of MB and RY with an obvious decrease in the intensity of the second main peak of the MOMD X-ray pattern. (C) 2009 Elsevier Ltd. All rights reserved.

The chemistry of deuterium in hot molecular cores

This paper presents the results of a model of the chemistry of deuterium-bearing molecules in hot molecular cores. It is found that because hydrogen- and deuterium-bearing molecules are destroyed by the same reactions at about the same rates, the initial fractionation present in ice mantles persists for over 10(4) yr. This is the case for a wide range of physical conditions, so it is safe to infer the fractionation on grain surfaces from observations of deuterated molecules in hot cores. The implications of the observed abundances of deuterium-bearing species in Orion are then discussed.

THE CHEMISTRY OF COMPLEX-MOLECULES IN INTERSTELLAR CLOUDS

This paper is concerned with the chemical evolution of large molecules in interstellar clouds. We consider the chemistry and ionisation balance of large polycyclic aromatic hydrocarbon (PAH) type molecules in diffuse clouds and show that certain PAH molecules can be doubly ionised by the interstellar ultraviolet radiation field. If recombination of the dications so produced with electrons is dissociative rather than radiative, then PAHs are rapidly destroyed. PAHs which can only be singly ionised have much smaller recombination energies and can be long lasting in these regions. This type of property may be very important in selecting the PAH species which can populate the general interstellar medium and account for certain of the diffuse bands observed in optical spectra. Destruction of PAH molecules via formation of dications may be responsible for the weakening of the diffuse bands observed in regions of high UV flux.

THE CHEMISTRY OF PHOSPHORUS IN HOT MOLECULAR CORES

Hot molecular cores in star-forming regions are known to have gas-phase chemical compositions determined by the material evaporated from the icy mantles of interstellar grains, followed by subsequent reactions in the gas phase. Current models suggest that the evaporated material is rich in hydrogenated species. In this paper, we consider the chemistry induced in a hot core by the release of phosphine, PH3 from interstellar grains. We find that PH3 is rapidly destroyed by a series of reactions with atomic hydrogen and is converted, within 10(4) yr, into atomic P, and PO and PN, with P atoms being the most abundant species. Other P-bearing molecules can be formed in the hot gas, but on time-scales that are long compared to those of the hot cores.

THE CHEMISTRY OF PAH AND FULLERENE MOLECULES IN INTERSTELLAR CLOUDS

Recent laboratory data on the ion-neutral chemistry of PAH and fullerene ions and molecules have been incorporated into chemical kinetic models of interstellar clouds. The laboratory data show that the-second ionization potentials of many complex molecules are less than the first ionization potential of helium. Thus collisions between He+, generated by cosmic ray ionization, and PAH and fullerene neutrals produce doubly charged cations. I find that these cations, and also protonated neutrals, are abundant in dark clouds. If the recombination of electrons with doubly charged cations, which releases typically 14 eV of energy, is dissociative in nature, then PAH and fullerene species are destroyed m both diffuse and dense clouds on astronomically significant time-scales.