Sequential C-H and C-Ru bond formation and cleavage during the thermally induced rearrangement of aryl ruthenium(II) complexes with [C6H3(CH2NMe2)(2)-2,6](-) as a bidentate eta(2)-C,N coordinated ligand. The crystal structures of the isomeric pairs [RuCl{eta(6)-C10H14}{eta(2)-C,N-C6H3(CH2NMe2)(2)-2,n}] (n = 4 or 6) and [Ru(eta(5)-C5H5){(eta(2)-C,N-C6H3(CH2NMe2)(2)-2,n} (PPH3)] (n = 4 or 6)

New air-stable ruthenium(II) complexes that contain the aryldiamine ligand [C6H3(CH2-NMe2)(2)-2,6](-) (NCN) are described. These complexes are [RuCl{eta(2)-C,N-C6H3(CH2NMe2)(2)-2,6}(eta(6)-C10H14)] (2; C10H14 = p-cymene = C6H4Me-Pr-i-4), [Ru{eta(2)-C,N-C6H3(CH2NMe2)(2)-2,6}(eta(5)-C5H5)(PPh3)] (5), and their isomeric forms [RuCl{eta(2)-C,N-C6H3(CH2NMe2)(2)-2,4}(eta(6)-C10H14)] (3) and [Ru{eta(2)-C,N-C6H3(CH2NMe2)(2)-2,4}(eta(5)-C5H5)(PPh3)] (6), respectively. Complex 2 has been prepared from the reaction of [Li(NCN)](2) with [RuCl2(eta(6)-C10H14)](2), whereas complex 5 has been prepared by the treatment of [RuCl{eta(3)-N,C,N-C6H3(CH2NMe2)(2)-2,6}(PPh3)] (4) with [Na(C5H5)](n). Both 2 and 5 are formally 18-electron ruthenium(II) complexes in which the monoanionic potentially tridentate coordinating ligand NCN is eta(2)-C,N-bonded, In solution (halocarbon solvent at room temperature or in aromatic solvents at elevated temperature), the intramolecular rearrangements of 2 and 5 afford complexes 3 and 6, respectively. This is a result of a shift of the metal-C-aryl bond from position-1 to position-3 on the aromatic ring of the NCN ligand. The mechanism of the isomerization is proposed to involve a sequence of intramolecular oxidative addition and reductive elimination reactions of both aromatic and aliphatic C-H bonds. This is based on results from deuterium labeling, spectroscopic studies, and some kinetic experiments. The mechanism is proposed to contain fully reversible steps in the case of 5, but a nonreversible step involving oxidative addition of a methyl NCH2-H bond in the case of 2. The solid-state structures of complexes 2, 3, 5, and 6 have been determined by single-crystal X-ray diffraction. A new dinuclear 1,4-phenylene-bridged bisruthenium(II) complex, [1,4-{RuCl(eta(6)-C10H14)}(2){C-6(CH2NMe2)(4)-2,3,5,6-C,N,C',N'}] (9) has also been prepared from the dianionic ligand [C-6(CH2NMe2)(4)-2,3,5,6](2-) (C2N4). The C2N4 ligand is in an eta(2)-C,N-eta(2)-C',N'-bis(bidentate) bonding mode. Compound 9 does not isomerize in solution (halocarbon solvent), presumably because of the absence of an accessible C-aryl-H bond. Complex 9 could not be isolated in an analytically pure form, probably because of its high sensitivity to air and very low solubility, which precludes recrystallization.

An efficient Cu(II)-bis(oxazoline)-based polymer immobilised ionic liquid phase catalyst for asymmetric carbon–carbon bond formation

The asymmetric Diels-Alder reaction between N-acryloyloxazolidinone and cyclopentadiene and the Mukaiyama-aldol reaction between methylpyruvate and 1-phenyl-1-trimethylsilyloxyethene have been catalysed by heterogeneous copper(II)-bis(oxazoline)-based polymer immobilised ionic liquid phase (PIILP) systems generated from a range of linear and cross linked ionic polymers. In both reactions selectivity and ee were strongly influenced by the choice of polymer. A comparison of the performance of a range of Cu(II)-bis(oxazoline)-PIILP catalyst systems against analogous supported ionic liquid phase (SILP) heterogeneous catalysts as well as their homogeneous counterparts has been undertaken and their relative merits evaluated.

General rules for predicting where a catalytic reaction should occur on metal surfaces: A density functional theory study of C-H and C-O bond breaking/making on flat, stepped, and kinked metal surfaces

To predict where a catalytic reaction should occur is a fundamental issue scientifically. Technologically, it is also important because it can facilitate the catalyst's design. However, to date, the understanding of this issue is rather limited. In this work, two types of reactions, CH4 CH3 + H and CO C + 0 on two transition metal surfaces, were chosen as model systems aiming to address in general where a catalytic reaction should occur. The dissociations of CH4 - CH3 + H and CO --> C + O and their reverse reactions on flat, stepped, and kinked Rh and Pd surfaces were studied in detail. We find the following: First, for the CH4 Ch(3) + H reaction, the dissociation barrier is reduced by similar to0.3 eV on steps and kinks as compared to that on flat surfaces. On the other hand, there is essentially no difference in barrier for the association reaction of CH3 + H on the flat surfaces and the defects. Second, for the CO C + 0 reaction, the dissociation barrier decreases dramatically (more than 0.8 eV on Rh and Pd) on steps and kinks as compared to that on flat surfaces. In contrast to the CH3 + H reaction, the C + 0 association reaction also preferentially occurs on steps and kinks. We also present a detailed analysis of the reaction barriers in which each barrier is decomposed quantitatively into a local electronic effect and a geometrical effect. Our DFT calculations show that surface defects such as steps and kinks can largely facilitate bond breaking, while whether the surface defects could promote bond formation depends on the individual reaction as well as the particular metal. The physical origin of these trends is identified and discussed. On the basis of our results, we arrive at some simple rules with respect to where a reaction should occur: (i) defects such as steps are always favored for dissociation reactions as compared to flat surfaces; and (ii) the reaction site of the association reactions is largely related to the magnitude of the bonding competition effect, which is determined by the reactant and metal valency. Reactions with high valency reactants are more likely to occur on defects (more structure-sensitive), as compared to reactions with low valency reactants. Moreover, the reactions on late transition metals are more likely to proceed on defects than those on the early transition metals.

Trends in C-O and C-N bond formations over transition metal surfaces: An insight into kinetic sensitivity in catalytic reactions

Transition metal catalyzed bond formation is a fundamental process in catalysis and is of general interest throughout chemistry. To date, however, the knowledge of association reactions is rather limited, relative to what is known about dissociative processes. For example, surprisingly little is known about how the bond-forming ability of a metal, in general, varies across the Periodic Table. In particular, the effect of reactant valency on such trends is poorly understood. Herein, the authors examine these key issues by using density functional theory calculations to study CO and CN formations over the 4d metals. The calculations reveal that the chemistries differ in a fundamental way. In the case of CO formation, the reaction enthalpies span a much greater range than those of CN formation. Moreover, CO formation is found to be kinetically sensitive to the metal; here the reaction barriers (E-a) are found to be influenced by the reaction enthalpy. CN formation, conversely, is found to be relatively kinetically insensitive to the metal, and there is no correlation found between the reaction barriers and the reaction enthalpy. Analysis has shown that at the final adsorbed state, the interaction between N and the surface is relatively greater than that of O. Furthermore, in comparison with O, relatively less bonding between the surface and N is observed to be lost during transition state formation. These greater interactions between N and the surface, which can be related to the larger valency of N, are found to be responsible for the relatively smaller enthalpy range and limited variation in E-a for CN formation. (C) 2007 American Institute of Physics.

The mechanism of N2O formation via the (NO)(2) dimer: A density functional theory study

Catalytic formation of N2O via a (NO)(2) intermediate was studied employing density functional theory with generalized gradient approximations. Dimer formation was not favored on Pt(111), in agreement with previous reports. On Pt(211) a variety of dimer structures were studied, including trans-(NO)(2) and cis-(NO)(2) configurations. A possible pathway involving (NO)(2) formation at the terrace near to a Pt step is identified as the possible mechanism for low-temperature N2O formation. The dimer is stabilized by bond formation between one O atom of the dimer and two Pt step atoms. The overall mechanism has a low barrier of approximately 0.32 eV. The mechanism is also put into the context of the overall NO+H-2 reaction. A consideration of the step-wise hydrogenation of O-(ads) from the step is also presented. Removal of O-(ads) from the step is significantly different from O-(ads) hydrogenation on Pt(111). The energetically favored structure at the transition state for OH(ads) formation has an activation energy of 0.63 eV. Further hydrogenation of OH(ads) has an activation energy of 0.80 eV. (C) 2004 American Institute of Physics.

N2O and NO2 formation on Pt(111): A density functional theory study

Catalytic formation of N2O and NO2 were studied employing density functional theory with generalized gradient approximations, in order to investigate the microscopic reaction pathways of these catalytic processes on a Pt(111) surface. Transition states and reaction barriers for the addition of chemisorbed N or chemisorbed O to NO(ads) producing N2O and NO2, respectively, were calculated. The N2O transition state involves bond formation across the hcp hollow site with an associated reaction barrier of 1.78 eV. NO2 formation favors a fcc hollow site transition state with a barrier of 1.52 eV. The mechanisms for both reactions are compared to CO oxidation on the same surface. The activation of the chemisorbed NO and the chemisorbed N or O from the energetically stable initial state to the transition state are both significant contributors to the overall reaction barrier E-a, in contrast to CO oxidation in which the activation of the O-(ads) is much greater than CO(ads) activation. (C) 2002 American Institute of Physics.

Subdivision of the bacterioferritin comigratory protein family of bacterial peroxiredoxins based on catalytic activity

Peroxiredoxins are ubiquitous proteins that catalyze the reduction of hydroperoxides, thus conferring resistance to oxidative stress. Using high-resolution mass spectrometry, we recently reclassified one such peroxiredoxin, bacterioferritin comigratory protein (BCP) of Escherichia coli, as an atypical 2-Cys peroxiredoxin that functions through the formation of an intramolecular disulfide bond between the active and resolving cysteine. An engineered E. coli BCP, which lacked the resolving cysteine, retained enzyme activity through a novel catalytic pathway. Unlike the active cysteine, the resolving cysteine of BCP peroxiredoxins is not conserved across all members of the family. To clarify the catalytic mechanism of native BCP enzymes that lack the resolving cysteine, we have investigated the BCP homologue of Burkholderia cenocepacia. We demonstrate that the B. cenocepacia BCP (BcBCP) homologue functions through a 1-Cys catalytic pathway. During catalysis, BcBCP can utilize thioredoxin as a reductant for the sulfenic acid intermediate. However, significantly higher peroxidase activity is observed utilizing glutathione as a resolving cysteine and glutaredoxin as a redox partner. Introduction of a resolving cysteine into BcBCP changes the activity from a 1-Cys pathway to an atypical 2-Cys pathway, analogous to the E. coli enzyme. In contrast to the native B. cenocepacia enzyme, thioredoxin is the preferred redox partner for this atypical 2-Cys variant. BCP-deficient B. cenocepacia exhibit a growth-phase-dependent hypersensitivity to oxidative killing. On the basis of sequence alignments, we believe that BcBCP described herein is representative of the major class of bacterial BCP peroxiredoxins. To our knowledge, this is the first detailed characterization of their catalytic activity. These studies support the subdivision of the BCP family of peroxiredoxins into two classes based on their catalytic activity.

Structure of the adenylation domain of an NAD+-dependent DNA ligase

Background: DNA ligases catalyse phosphodiester bond formation between adjacent bases in nicked DNA, thereby sealing the nick. A key step in the catalytic mechanism is the formation of an adenylated DNA intermediate. The adenyl group is derived from either ATP (in eucaryotes and archaea) or NAD+4 (in bacteria). This difference in cofactor specificity suggests that DNA ligase may be a useful antibiotic target.

Results: The crystal structure of the adenylation domain of the NAD+-dependent DNA ligase from Bacillus stearothermophilus has been determined at 2.8 Å resolution. Despite a complete lack of detectable sequence similarity, the fold of the central core of this domain shares homology with the equivalent region of ATP-dependent DNA ligases, providing strong evidence for the location of the NAD+-binding site.

Conclusions: Comparison of the structure of the NAD+4-dependent DNA ligase with that of ATP-dependent ligases and mRNA-capping enzymes demonstrates the manifold utilisation of a conserved nucleotidyltransferase domain within this family of enzymes. Whilst this conserved core domain retains a common mode of nucleotide binding and activation, it is the additional domains at the N terminus and/or the C terminus that provide the alternative specificities and functionalities in the different members of this enzyme superfamily.

Carboxyl-Functionalized Task-Specific Ionic Liquids for Solubilizing Metal Oxides

Imidazolium, pyridinium, pyrrolidinium, piperidinium, morpholinium, and quaternary ammonium bis(trifluoromethyl-sulfonyl)imide salts were functionalized with a carboxyl group. These ionic liquids are useful for the selective dissolution of metal oxides and hydroxides. Although these hydrophobic ionic liquids are immiscible with water at room temperature, several of them form a single phase with water at elevated temperatures. Phase separation occurs upon cooling. This thermomorphic behavior has been investigated by H-1 NMR, and it was found that it can be attributed to the temperature-dependent hydration and hydrogen-bond formation of the ionic liquid components. The crystal structures of four ionic liquids and five metal complexes have been determined.

Molecular rearrangement reactions in the gas phase triggered by electron attachment

Bond formation and rearrangement reactions in gas phase electron attachment were studied through dissociative electron attachment (DEA) to pentafluorotoluene (PFT), pentafluoroaniline (PFA) and pentafluorophenol (PFP) in the energy range 0-14 eV. In the case of PFA and PFP, the dominant processes involve formation of [M - HF](-) through the loss of neutral HF. This fragmentation channel is most efficient at low incident electron energy and for PFP it is accompanied by a substantial conformational change of the anionic fragment. At higher energy, HF loss is also observed as well as a number of other fragmentation processes. Thermochemical threshold energies have been computed for all the observed fragments and classical trajectories of the electron attachment process were calculated to elucidate the fragmentation mechanisms. For the dominant reaction channel leading to the loss of HF from PFP, the minimum energy path was calculated using the nudged elastic band method.

Thiol isomerases negatively regulate the cellular shedding activity of ADAM17

ADAM17 (where ADAM is 'a disintegrin and metalloproteinase') can rapidly modulate cell-surface signalling events by the proteolytic release of soluble forms of proligands for cellular receptors. Many regulatory pathways affect the ADAM17 sheddase activity, but the mechanisms for the activation are still not clear. We have utilized a cell-based ADAM17 assay to show that thiol isomerases, specifically PDI (protein disulfide isomerase), could be responsible for maintaining ADAM17 in an inactive form. Down-regulation of thiol isomerases, by changes in the redox environment (for instance as elicited by phorbol ester modulation of mitochondrial reactive oxygen species) markedly enhanced ADAM17 activation. On the basis of ELISA binding studies with novel fragment antibodies against ADAM17 we propose that isomerization of the disulfide bonds in ADAM17, and the subsequent conformational changes, form the basis for the modulation of ADAM17 activity. The shuffling of disulfide bond patterns in ADAMs has been suggested by a number of recent adamalysin crystal structures, with distinct disulfide bond patterns altering the relative orientations of the domains. Such a mechanism is rapid and reversible, and the role of thiol isomerases should be investigated further as a potential factor in the redox regulation of ADAM17.

Screened Hybrid Exact Exchange Correction Scheme for Adsorption Energies on Perovskite Oxides

The bond formation between an oxide surface and oxygen, which is of importance for numerous surface reactions including catalytic reactions, is investigated within the framework of hybrid density functional theory that includes nonlocal Fock exchange. We show that there exists a linear correlation between the adsorption energies of oxygen on LaMO3 (M = Sc–Cu) surfaces obtained using a hybrid functional (e.g., Heyd–Scuseria–Ernzerhof) and those obtained using a semilocal density functional (e.g., Perdew–Burke–Ernzerhof) through the magnetic properties of the bulk phase as determined with a hybrid functional. The energetics of the spin-polarized surfaces follows the same trend as corresponding bulk systems, which can be treated at a much lower computational cost. The difference in adsorption energy due to magnetism is linearly correlated to the magnetization energy of bulk, that is, the energy difference between the spin-polarized and the non-spin-polarized solutions. Hence, one can estimate the correction ...

The purification and characterization of phosphonopyruvate hydrolase, a novel carbon-phosphorus bond cleavage enzyme from Variovorax sp. Pal2.

Phosphonopyruvate hydrolase, a novel bacterial carbon-phosphorus bond cleavage enzyme, was purified to homogeneity by a series of chromatographic steps from cell extracts of a newly isolated environmental strain of Variovorax sp. Pal2. The enzyme was inducible in the presence of phosphonoalanine or phosphonopyruvate; unusually, its expression was independent of the phosphate status of the cell. The native enzyme had a molecular mass of 63 kDa with a subunit mass of 31.2 kDa. Activity of purified phosphonopyruvate hydrolase was Co2+-dependent and showed a pH optimum of 6.7–7.0. The enzyme had a Km of 0.53 mM for its sole substrate, phosphonopyruvate, and was inhibited by the analogues phosphonoformic acid, 3-phosphonopropionic acid, and hydroxymethylphosphonic acid. The nucleotide sequence of the phosphonopyruvate hydrolase structural gene indicated that it is a member of the phosphoenolpyruvate phosphomutase/isocitrate lyase superfamily with 41% identity at the amino acid level to the carbon-to-phosphorus bond-forming enzyme phosphoenolpyruvate phosphomutase from Tetrahymena pyriformis. Thus its apparently ancient evolutionary origins differ from those of each of the two carbon-phosphorus hydrolases that have been reported previously; phosphonoacetaldehyde hydrolase is a member of the haloacetate dehalogenase family, whereas phosphonoacetate hydrolase belongs to the alkaline phosphatase superfamily of zinc-dependent hydrolases. Phosphonopyruvate hydrolase is likely to be of considerable significance in global phosphorus cycling, because phosphonopyruvate is known to be a key intermediate in the formation of all naturally occurring compounds that contain the carbon-phosphorus bond.