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At least 991 records · Page 55Linked to original sources
PubMed2004

Computation of the properties of liquid neon, methane, and gas helium at low temperature by the Feynman-Hibbs approach.

The properties of liquid methane, liquid neon, and gas helium are calculated at low temperatures over a large range of pressure from the classical molecular-dynamics simulations. The molecular interactions are represented by the Lennard-Jones pair potentials supplemented by quantum corrections following the Feynman-Hibbs approach. The equations of state, diffusion, and shear viscosity coefficients are determined for neon at 45 K, helium at 80 K, and methane at 110 K. A comparison is made with the existing experimental data and for thermodynamical quantities, with results computed from quantum numerical simulations when they are available. The theoretical variation of the viscosity coefficient with pressure is in good agreement with the experimental data when the quantum corrections are taken into account, thus reducing considerably the 60% discrepancy between the simulations and experiments in the absence of these corrections.

Journal Article↗
PubMed2006

Lower Rydberg series of methane: a combined coupled cluster linear response and molecular quantum defect orbital calculation.

Vertical excitation energies as well as related absolute photoabsorption oscillator strength data are very scarce in the literature for methane. In this study, we have characterized the three existing series of low-lying Rydberg states of CH4 by computing coupled cluster linear response (CCLR) vertical excitation energies together with oscillator strengths in the molecular-adapted quantum defect orbital formalism from a distorted Cs geometry selected on the basis of outer valence green function calculations. The present work provides a wide range of data of excitation energies and absolute oscillator strengths which correspond to the Rydberg series converging to the three lower ionization potential values of the distorted methane molecule, in energy regions for which experimentally measured data appear to be unavailable.

Journal Article↗
PubMed2006

Nonadiabatic response of molecules to strong fields of picosecond, femtosecond, and subfemtosecond duration: an experimental study of the methane dication.

The double ionization of methane has been accomplished using strong optical fields that are generated using moderately intense lasers, and by strong fields that are induced by fast-moving, highly charged ions. In the former case laser intensities in the range 10(14) W cm(-2) generate fields whose durations are of 35 ps and 36 fs while in the latter case equivalent fields last for only 200-300 as. The dynamics of the field-ionized electrons are different in the two temporal regimes, fast (picoseconds), and ultrafast (few tens of femtoseconds and subfemtoseconds). Our experiments show that nonadiabatic effects come into play in the ultrafast regime; we directly monitor such effects by measuring the kinetic energy that is released when a specific bond in the doubly charged methane molecular ion breaks.

Journal Article↗
PubMed2006

Explosive photodissociation of methane induced by ultrafast intense laser.

A new type of molecular fragmentation induced by femtosecond intense laser at the intensity of 2 x 10(14) W/cm2 is reported. For the parent molecule of methane, ethylene, n-butane, and 1-butene, fluorescence from H (n = 3-->2), CH (A 2Delta, B 2Sigma-, and C 2Sigma+-->X 2Pi), or C2 (d 3Pi g-->a 3Pi u) is observed in the spectrum. It shows that the fragmentation is a universal property of neutral molecule in the intense laser field. Unlike breaking only one or two chemical bonds in conventional UV photodissociation, the fragmentation caused by the intense laser undergoes vigorous changes, breaking most of the bonds in the molecule, like an explosion. The fragments are neutral species and cannot be produced through Coulomb explosion of multiply charged ion. The laser power dependence of CH (A-->X) emission of methane on a log-log scale has a slope of 10 +/- 1. The fragmentation is thus explained as multiple channel dissociation of the superexcited state of parent molecule, which is created by multiphoton excitation.

Journal Article↗
PubMed2006

Analysis of methane-to-methanol conversion on clean and defective Rh surfaces.

We investigate by density-functional theory simulations several elementary reactions associated to direct methane-to-methanol conversion on clean Rh(111) surfaces and on Rh adatoms on Rh(111). Energy barriers and reaction paths have been determined by the nudged elastic band method. The rate-limiting step in the process, C-O bond formation, has higher activation energy than the one for complete methane dehydrogenation. Our analysis enables us to understand the effect of defects on the reactivity and rules out Rh as candidate catalyst for methanol synthesis.

Journal Article↗
PubMed2006

Activation of methane by gold cations: guided ion beam and theoretical studies.

The potential energy surface for activation of methane by the third-row transition metal cation, Au+, is studied experimentally by examining the kinetic energy dependence of this reaction using guided ion beam tandem mass spectrometry. A flow tube ion source produces Au+ primarily in its 1S0 (5d10) electronic ground state level but with some 3D (and perhaps higher lying) excited states that can be completely removed by a suitable quenching gas (N2O). Au+ (1S0) reacts with methane by endothermic dehydrogenation to form AuCH2+ as well as C-H bond cleavage to yield AuH+ and AuCH3+. The kinetic energy dependences of the cross sections for these endothermic reactions are analyzed to give 0 K bond dissociation energies (in eV) of D0(Au+ - CH2) = 3.70 +/- 0.07 and D0(Au+ -CH3) = 2.17 +/- 0.24. Ab initio calculations at the B3LYPHW + /6-311++G(3df,3p) level performed here show good agreement with the experimental bond energies and previous theoretical values available. Theory also provides the electronic structures of the product species as well as intermediates and transition states along the reactive potential energy surface. Surprisingly, the dehydrogenation reaction does not appear to involve an oxidative addition mechanism. We also compare this third-row transition metal system with the first-row and second-row congeners, Cu+ and Ag+. Differences in thermochemistry can be explained by the lanthanide contraction and relativistic effects that alter the relative size of the valence s and d orbitals.

Journal Article↗
PubMed1995

Gating effects of component B on oxygen activation by the methane monooxygenase hydroxylase component.

Component B (MMOB) of the soluble methane monooxygenase (MMO) system accelerates the initial velocity of methane oxidation by up to 150-fold by an unknown mechanism. The active site of MMO contains a diferric, hydroxo-bridged diiron cluster located on the hydroxylase component (MMOH). This cluster is reduced by the NAD(P)H-coupled reductase component to the diferrous state, which then reacts with O2 to yield two reaction cycle intermediates sequentially termed compounds P and Q. The rate of compound P formation is shown here to be independent of O2 concentration, suggesting that an MMOH-O2 complex (compound O) is (congruent to irreversibly) formed before compound P. Compound Q is capable of reacting with hydrocarbons to yield the MMOH-product complex, compound T. It is shown here that MMOB accelerates catalysis by increasing congruent to 1000-fold the rate of O2 association and reaction with diferrous MMOH leading to compound P. Modeling of the single turnover reaction in the presence of substoichiometric MMOB suggests that MMOB also accelerates the compound P to Q conversion by congruent to 40-fold. Due to this O2-gating effect of MMOB, either compound Q or T becomes the dominant species during turnover, depending upon the substrate concentration and type. Because these are the species that either react with substrate (Q) or release product (T), their buildup maximizes the turnover rate. This is the first direct role in catalysis to be recognized for MMOB and represents a novel method for oxygenase regulation.

Kinetics↗
PubMed1998

The particulate methane monooxygenase from methylococcus capsulatus (Bath) is a novel copper-containing three-subunit enzyme. Isolation and characterization.

The particulate methane monooxygenase (pMMO) is known to be very difficult to study mainly due to its unusual activity instability in vitro. By cultivating Methylococcus capsulatus (Bath) under methane stress conditions and high copper levels in the growth medium, membranes highly enriched in the pMMO with exceptionally stable activity can be isolated from these cells. Purified and active pMMO can be subsequently obtained from these membrane preparations using protocols in which an excess of reductants and anaerobic conditions were maintained during membrane solubilization by dodecyl beta-D-maltoside and purification by chromatography. The pMMO was found to be the major constituent in these membranes, constituting 60-80% of total membrane proteins. The dominant species of the pMMO was found to consist of three subunits, alpha, beta, and gamma, with an apparent molecular mass of 45, 26, and 23 kDa, respectively. A second species of the pMMO, a proteolytically processed version of the enzyme, was found to be composed of three subunits, alpha', beta, and gamma, with an apparent molecular mass of 35, 26, and 23 kDa, respectively. The alpha and alpha' subunits from these two forms of the pMMO contain identical N-terminal sequences. The gamma subunit, however, exhibits variation in its N-terminal sequence. The pMMO is a copper-containing protein only and shows a requirement for Cu(I) ions. Approximately 12-15 Cu ions per 94-kDa monomeric unit were observed. The pMMO is sensitive to dioxygen tension. On the basis of dioxygen sensitivity, three kinetically distinct forms of the enzyme can be distinguished. A slow but air-stable form, which is converted into a "pulsed" state upon direct exposure to atmospheric oxygen pressure, is considered as type I pMMO. This form was the subject of our pMMO isolation effort. Other forms (types II and III) are deactivated to various extents upon exposure to atmospheric dioxygen pressure. Under inactivating conditions, these unstable forms release protons to the buffer (approximately 10 H+/94-kDa monomeric unit) and eventually become completely inactive.

Amino Acid Sequence↗
PubMed2001

Why OrfY? Characterization of MMOD, a long overlooked component of the soluble methane monooxygenase from Methylococcus capsulatus (Bath).

Soluble methane monooxygenase (sMMO) has been studied intensively to understand the mechanism by which it catalyzes the remarkable oxidation of methane to methanol. The cluster of genes that encode for the three characterized protein components of sMMO (MMOH, MMOB, and MMOR) contains an additional open reading frame (orfY) of unknown function. In the present study, MMOD, the protein encoded by orfY, was overexpressed as a fusion protein in Escherichia coli. Pure MMOD was obtained in high yields after proteolytic cleavage and a two-step purification procedure. Western blot analysis of Methylococcus capsulatus (Bath) soluble cell extracts showed that MMOD is expressed in the native organism although at significantly lower levels than the other sMMO proteins. The cofactorless MMOD protein is a potent inhibitor of sMMO activity and binds to the hydroxylase protein (MMOH) with an affinity similar to that of MMOB and MMOR. The addition of up to 2 MMOD per MMOH results in changes in the optical spectrum of the hydroxylase that suggest the formation of a (micro-oxo)diiron(III) center in a fraction of the MMOH-MMOD complexes. Possible functions for MMOD are discussed, including a role in the assembly of the MMOH diiron center similar to that suggested for DmpK, a protein that shares some properties with MMOD.

Amino Acid Sequence↗
PubMed2003

Structural features of covalently cross-linked hydroxylase and reductase proteins of soluble methane monooxygenase as revealed by mass spectrometric analysis.

Soluble methane monooxygenase requires complexes between its three component proteins for efficient catalysis. The hydroxylase (MMOH) must bind both to the reductase (MMOR) and to the regulatory protein (MMOB) to facilitate oxidation of methane to methanol. Although structures of MMOH, MMOB, and one domain of MMOR have been determined, less geometric information is available for the complexes. To address this deficiency, MMOH and MMOR were cross-linked by a carbodiimide reagent and analyzed by specific proteolysis, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry, and capillary high performance liquid chromatography mass spectrometry. Tandem mass spectra conclusively identified two amine-to-carboxylate cross-linked sites involving the alpha subunit of MMOH and the [2Fe-2S] domain of MMOR (MMOR-Fd). In particular, the N terminus of the MMOH alpha subunit forms cross-links to the side chains of MMOR-Fd residues Glu-56 and Glu-91. These Glu residues are close to one another on the surface of MMOR-Fd and >25 A from the [2Fe-2S] cluster. Because the N terminus of the alpha subunit of MMOH was not located in the crystal structure of MMOH, a detailed structural model of the complex based on the cross-link was precluded; however, a previously proposed binding site for MMOR on MMOH could be ruled out. Based on the cross-linking results, a MMOR E56Q/E91Q double mutant was generated. The mutant retains >80% of MMOR NADH oxidase activity but reduces sMMO activity to approximately 65% of the level supported by the wild type reductase. Cross-linking to MMOH was diminished but not abolished in the double mutant, indicating that other residues of MMOR also form cross-links to MMOH.

Binding Sites↗
PubMed2003

Domain engineering of the reductase component of soluble methane monooxygenase from Methylococcus capsulatus (Bath).

Soluble methane monooxygenase (sMMO) from Methylococcus capsulatus (Bath) is a three-component enzyme system that catalyzes the conversion of methane to methanol. A reductase (MMOR), which contains [2Fe-2S] and FAD cofactors, facilitates electron transfer from NADH to the hydroxylase diiron active sites where dioxygen activation and substrate hydroxylation take place. By separately expressing the ferredoxin (MMORFd, MMOR residues 1-98) and FAD/NADH (MMOR-FAD, MMOR residues 99-348) domains of the reductase, nearly all biochemical properties of full-length MMOR are retained, except for interdomain electron transfer rates. To investigate the extent to which rapid electron transfer between domains might be restored and further to explore the modularity of MMOR, MMOR-Fd and MMOR-FAD were connected in a non-native fashion. Four different linker sequences were employed to create MMOR reversed-domain (MMOR-RD) constructs, MMOR(99-342)-linker-MMOR(2-98), with a domain connectivity observed in other homologous oxidoreductases. The optical, redox, and electron transfer properties of the four MMOR-RD proteins were characterized and compared with those of wild-type MMOR. The linker sequence plays a key role in controlling solvent accessibility to the FAD cofactor, as evidenced by perturbed flavin optical spectra, decreased FADox/FADsq redox potentials, and increased steady-state oxidase activities in three of the constructs. Stopped-flow optical spectroscopy revealed slow interdomain electron transfer (k < 0.04 s(-1) at 4 degrees C, compared with 90 s(-1) for wild-type MMOR) for all three MMOR-RD proteins with 7-residue linkers. A long (14-residue), flexible linker afforded much faster electron transfer between the FAD and [2Fe-2S] cofactors (k = 0.9 s(-1) at 4 degrees C).

Catalysis↗
PubMedDate not supplied

Cardiac damage in rodents after exposure to bis(2-chloroethoxy)methane.

We report that an environmental agent, bis(2-chloroethoxy)methane (CEM), caused cardiac toxicity in male and female F344 rats and B6C3F1 mice exposed to the chemical by dermal administration at doses of 0, 50, 100, 200, 400 or 600 mg/kg 5 days a week for up to 14 weeks. Treatment-related deaths occurred in 10/10 male and 10/10 female rats at 600 mg/kg, in 2/10 female rats at 400 mg/kg, and in 3/10 female mice at 600 mg/kg. The heart lesions were more severe in rats than mice, and more severe in females than males. In rats, the no-observed-adverse-effect level (NOAEL) for the heart lesions was 200 mg/kg for males and 100 mg/kg for females; in mice, it was more than 600 mg/kg for males and 200 mg/kg for females. Multifocal, widespread vacuolization of the myocytes comprised the main morphological feature of the lesions, and only in rats was it accompanied by mononuclear cell infiltration, myocytic necrosis and atrial thrombosis. Hearts from male rats were immunohistochemically stained for troponin T (cTnT) protein. Loss of cytoplasmic cTnT correlated with histopathological damage only in the 600 mg/kg animals. CEM is metabolized to thiodiglycolic acid, a chemical that causes mitochondrial dysfunction. It is hypothesized that mitochondrial damage leads to the heart toxicity from bis(2-chloroethoxy)methane.

Animals↗
PubMed2003

rpoN, mmoR and mmoG, genes involved in regulating the expression of soluble methane monooxygenase in Methylosinus trichosporium OB3b.

The methanotrophic bacterium Methylosinus trichosporium OB3b converts methane to methanol using two distinct forms of methane monooxygenase (MMO) enzyme: a cytoplasmic soluble form (sMMO) and a membrane-bound form (pMMO). The transcription of these two operons is known to proceed in a reciprocal fashion with sMMO expressed at low copper-to-biomass ratios and pMMO at high copper-to-biomass ratios. Transcription of the smmo operon is initiated from a sigma(N) promoter 5' of mmoX. In this study the genes encoding sigma(N) (rpoN) and a typical sigma(N)-dependent transcriptional activator (mmoR) were cloned and sequenced. mmoR, a regulatory gene, and mmoG, a gene encoding a GroEL homologue, lie 5' of the structural genes for the sMMO enzyme. Subsequent mutation of rpoN and mmoR by marker-exchange mutagenesis resulted in strains Gm1 and JS1, which were unable to express functional sMMO or initiate transcription of mmoX. An rpoN mutant was also unable to fix nitrogen or use nitrate as sole nitrogen source, indicating that sigma(N) plays a role in both nitrogen and carbon metabolism in Ms. trichosporium OB3b. The data also indicate that mmoG is transcribed in a sigma(N)- and MmoR-independent manner. Marker-exchange mutagenesis of mmoG revealed that MmoG is necessary for smmo gene transcription and activity and may be an MmoR-specific chaperone required for functional assembly of transcriptionally competent MmoR in vivo. The data presented allow the proposal of a more complete model for copper-mediated regulation of smmo gene expression.

Bacterial Proteins↗
PubMed2005

Interplay of entropic and memory effects in diffusion of methane in silicalite zeolites.

The role of entropic effects in methane distribution and transport in silicalite zeolites is studied using molecular dynamics in the limit of infinite dilution or small loading. Diffusive behavior and its anisotropy is assessed as a function of temperature where we find both an Arrhenius regime above 250 K and deviations thereof below such temperature. Using a previous probabilistic model, geometrical correlations or memory effects are evidenced and are shown to be enhanced as temperature is reduced. Deviations from Arrhenius behavior are concomitant with entropic effects. We find that, the preference of methane towards presence at intersections or channel centers changes at a threshold temperature. A discrete transition is found from a channel-center preferred phase, at low temperatures, versus an intersection preferred phase at high temperatures with evidence of hysteresis effects. Such entropic effects are also reflected, in diffusive transport, as non-Arrhenius-type behavior. A model based on accessible volume as a function of energy agrees with the simulated transition lending new insight into zeolite cavity design.

Journal Article↗
PubMed2003

Hydrogen-bond networks in tris(4-hydroxyphenyl)methane and its 1:1 molecular complex with 4,4'-bipyridine.

In tris(4-hydroxyphenyl)methane (or 4,4',4"-methanetriyltriphenol), C(19)H(16)O(3), molecules are connected by O-H.O hydrogen bonds [O.O = 2.662 (2) and 2.648 (2) A] into two-dimensional square networks that are twofold interpenetrated. In tris(4-hydroxyphenyl)methane-4,4'-bipyridine (1/1), C(19)H(16)O(3).C(10)H(8)N(2), trisphenol molecules form rectangular networks via O-H.O [O.O = 2.694 (3) A] and C-H.O [C.O = 3.384 (3) A] hydrogen bonds. Bipyridine molecules hydrogen bonded to phenol moieties [O.N = 2.622 (3) and 2.764 (3) A] fill the voids to complete the structure.

Journal Article↗
PubMed2006

Bis[4-(salicylideneamino)phenyl]methane.

The crystal structure of the title Schiff base {systematic name: 2,2'-[methylenedi-p-phenylenebis(nitrilomethylidyne)]diphenol}, C27H22N2O2, consists of intramolecularly hydrogen-bonded molecules interlinked by C-H...O hydrogen bonds [C...O = 3.426 (2) A and C-H...O = 152.7 (17) degrees ]. The molecule is in the enol form and is located on a twofold axis. The central methane C atom of the diphenylmethane motif is displaced from the aromatic ring planes. This effect is compared with previous results, which display an inverse correlation between the out-of-plane displacement and the C-C-C angle around the central methane C atom. In the title compound, the displacement is 0.124 (2) A and the C-C-C angle is 110.18 (19) degrees.

Journal Article↗
PubMed1991

Molecular analysis of the methane monooxygenase (MMO) gene cluster of Methylosinus trichosporium OB3b.

The oxidation of methane to methanol in methanotrophic bacteria is catalysed by the enzyme methane monooxygenase (MM0). This multicomponent enzyme catalyses a range of oxidations including that of aliphatic and aromatic compounds and therefore has potential for commercial exploitation. This study details the molecular characterization of the soluble MMO (sMMO) genes from the Type II methanotroph Methylosinus trichosporium OB3b. The structural genes encoding the alpha, beta and gamma subunits of sMMO protein A and the structural gene encoding component B have been isolated and sequenced. These genes have been expressed and their products identified using an in vitro system. A comparative analysis of sMMO predicted sequences of M. trichosporium OB3b and the taxonomically related M. capsulatus (Bath) is also presented.

Amino Acid Sequence↗
PubMed1985

Further characterisation of the FAD and Fe2S2 redox centres of component C, the NADH:acceptor reductase of the soluble methane monooxygenase of Methylococcus capsulatus (Bath).

The absorbance contributions of the FAD and Fe2S2 redox centres of component C of the soluble methane monooxygenase complex have been resolved, using mersalyl to destroy the Fe2S2 centre. The Fe2S2 seems to be very similar to that of spinach ferredoxin, by its absorbance and electron paramagnetic resonance (EPR) spectra, and the FAD semiquinone is a neutral semiquinone. Spectrophotometry near room temperature and EPR spectroscopy near liquid-helium temperature allow the three redox couples of component C to be ordered. Component C can exist in Oe-1 (oxidised), 1e-1 (semiquinone), 2e-1 (mostly semiquinone and reduced Fe2S2), and 3e-1 forms (dihydroquinone and reduced Fe2S2), under equilibrium conditions. The ability of component C to support odd-electron forms is consistent with its proposed role as a 2e-1/1e-1 transformase, splitting electron pairs from NADH for passage to component A in one-electron steps. (The FAD appears to interact with NADH, and transfers single electrons to the Fe2S2, for donation to component A at a constant redox potential.) The mid-point potentials of component C were found using redox dyes and EPR spectroscopy and were: FAD/FAD., Em = -150 mV; Fe2S2/Fe2.S2,Em = -220 mV; FAD./FAD..,Em = -260 mV. the presence of NADH did not alter these mid-point potentials. These mid-point potentials are consistent with the role of component C as the NADH:component A reductase, passing electrons from NADH (Em = -320 mV) onto component A (Em = +150 mV and Em = -150 mV). The reducing power from NADH appears to be required by component A to activate one atom of oxygen, to insert into methane, and the reducing equivalents derived from NADH end up with the other oxygen atom, as water.

Binding Sites↗