A theoretical study on the reaction mechanism of O<Subscript>2</Subscript> with C<Subscript>4</Subscript>H<Subscript>9</Subscript>• radical

Ab initio calculations have been performed using the complete basis set model (CBS-QB3) to study the reaction mechanism of butane radical (C₄H₉•) with oxygen (O₂). On the calculated potential energy surface, the addition of O₂ to C₄H₉• forms three intermediates barrierlessly, which can undergo subsequent isomerization or decomposition reaction leading to various products: HOO• + C₄H₈, C₂H₅• + CH₂CHOOH, OH• + C₃H₇CHO, OH• + cycle-C₄H₈O, CH₃• + CH₃CHCHOOH, CH₂OOH• + C₃H₆. Five pathways are supposed in this study. After taking into account the reaction barrier and enthalpy, the most possible reaction pathway is C₄H₉• + O₂ → IM1 → TS5 → IM3 → TS6 → IM4 → TS7 → OH• + cycle-C₄H₈O.     

Carbon and energy yields in prebiotic syntheses using atmospheres containing CH4, CO and CO2

Yields based on carbon are usually reported in prebiotic experiments, while energy yields (moles cal^–1) are more useful in estimating the yields of products that would have been obtained from the primitive atmosphere of the earth. Energy yields for the synthesis of HCN and H₂CO from a spark discharge were determined for various mixtures of CH₄, CO, CO₂, H₂, H₂O, N₂ and NH₃. The maximum yields of HCN and H₂CO from CH₄, CO, and CO₂ as carbon sources are about 4×10^–8 moles cal^–1.     

Quantum chemical study of the thermodynamics,kinetics of formation and bonding of H2CN relevance to prebiotic chemistry

Using the Iterative Extended Huckel Theory (IEHT), energy-conformation studies have been carried out for H₂CN (I),trans-HCNH (IIA), andcis-HCNH (IIB), three possible isomers formed by addition of a hydrogen atom to hydrogen cyanide. Calculations show that the order of decreasing thermodynamic stability is I≫IIA>IIB. Additionally, from calculated energies along simulated reaction pathways, the formation of I from HCN+H appears to be kinetically favored over IIA. Calculated properties of the minimum energy conformers of I and IIA are described and the potential role of H₂CN (I) as a reactive intermediate in prebiotic organic synthesis and its possible relevance to interstellar organic chemistry are discussed.     

Shape‐Controlled CO2 Electrochemical Reduction on Nanosized Pd Hydride Cubes and Octahedra

Electrochemical CO₂ reduction reaction (CO₂RR) provides a potential pathway to mitigate challenges related to CO₂ emissions. Pd nanoparticles have shown interesting properties as CO₂RR electrocatalysts, while how different facets of Pd affect its performance in CO₂ reduction to synthesis gas with controlled H₂ to CO ratios has not been understood. Herein, nanosized Pd cubes and octahedra particles dominated by Pd(100) and Pd(111) facets are, respectively, synthesized. The Pd octahedra particles show higher CO selectivity (up to 95%) and better activity than Pd cubes and commercial particles. For both Pd octahedra and cubes, the ratio of H₂/CO products is tunable between 1 and 2, a desirable ratio for methanol synthesis and the Fischer–Tropsch processes. Further studies of Pd octahedra in a 25 cm² flow cell show that a total CO current of 5.47 A is achieved at a potential of 3.4 V, corresponding to a CO partial current density of 220 mA cm^?2. In situ X‐ray absorption spectroscopy studies show that regardless of facet Pd is transformed into Pd hydride (PdH) under reaction conditions. Density functional theory calculations show that the reduced binding energies of CO and HOCO intermediates on PdH(111) are key parameters to the high current density and Faradaic efficiency in CO₂ to CO conversion.     

Reaction mechanism of CH3M≡MCH3 (M=C, Si, Ge) with C2H4: [2+1] or [2+2] cycloaddition?

The mechanism of the cycloaddition reaction CH₃M≡MCH₃ (M=C, Si, Ge) with C₂H₄ has been studied at the CCSD(T)/6-311++G(d,p)//MP2/6-311++G(d,p) level. Vibrational analysis and intrinsic reaction coordinate (IRC), calculated at the same level, have been applied to validate the connection of the stationary points. The breakage and formation of the chemical bonds of the titled reactions are discussed by the topological analysis of electron density. The calculated results show that, of the three titled reactions, the CH₃Si≡SiCH₃+C₂H₄ reaction has the highest reaction activity because it has the lowest energy barriers and the products with the lowest energy. The CH₃C≡CCH₃+C₂H₄ reaction occurs only with difficulty since it has the highest energy barriers. The reaction mechanisms of the title reactions are similar. A three-membered-ring is initially formed, and then it changed to a four-membered-ring structure. This means that these reactions involve a [2+1] cycloaddition as the initial step, instead of a direct [2+2] cycloaddition.     

Interstellar Ices as a Source of CN-Bearing Molecules in Protoplanetary Disks

A reliable model for the composition and evolution of interstellar ices inregions of active star formation is fundamental to our quest to determinethe organic inventory of planetesimals in the early Solar System. This hasbecome a realistic goal since the launch of the Infrared Space Observatory,which provides a facility for infrared spectroscopy unhindered by telluricabsorption over the entire spectral range of vibrational modes in solids ofexobiological interest. Interstellar molecules detected in the solid phaseto date include H_{_2O}, NH₃, CO, CO₂,CH₃OH, CH₄, H₂CO, OCS andHCOOH, together with a CN-bonded absorber generically termed`XCN'. In this article, we focus on cosmic synthesis of CN-bearing species,as this important class of prebiotic molecules may not have formedendogenously in significant quantities on early Earth if conditions were nothighly reducing. Experiments in which interstellar ice analogs are subjectto UV photolysis or energetic ion bombardment yield CN-rich residues with aspectral signature that matches a corresponding feature observed in youngprotostars enshrouded in dust and gas. CN-bearing species are also presentin cometary ices, with a combined abundance comparable to the lower end of therange observed in protostars. Energetic processing of interstellar ices isthus a viable and potentially significant source of CN compounds inprotoplanetary disks.     

Synthesis,structure and properties of syn-bis(μ-N-methylpiperidine-4-thiolate tricarbonyl iron)

The reaction of Fe₃(CO)₁₂ with N-methyl-4- mercaptopiperidine gives the title compound. Crystals are monoclinic, space group P2₁/c with a = 12.922(2), b = 14.784(5), c = 13.607(2) Å, β = 112.41(1)°. With Z = 4 the calculated density is 1.49 g cm⁻³. Solution of the structure by direct methods led to a final weighted R factor of 0.029 for 2270 independent reflections. The FeFe bond length is 2.534(1) Å and the S···S distance of 2.940(1) suggests bonding interactions. By heating upon reflux in toluene during 10 h, the IR spectrum of the chromatographed solution indicates the syn isomer formation. The reaction with CH₃I and HClO₄ produces the methylation and protonation, respectively, of the nitrogen atoms of the piporidine rings giving rise to the formation of the [Fe(μ-(CH₃)₂NC₅H₉S)(CO)₃]₂I₂·2H₂O and [Fe(μ-HCH₃NC₅H₉S)(CO)₃]₂·H₂O·CH₃OH compounds.     

Effect of H2S on the formation of organic compounds from C,N, H,S model atmospheres submitted to a glow discharge

H₂S has been often invoked as the initial source of sulfur in prebiotic evolution, and several sulfur-containing compounds has been proposed as intermediates in the primordial synthesis of biologically relevant sulfur-containing chemicals. The possibilities of synthesis of the principal key intermediates by glow discharges in CH₄−N₂−H₂S mixtures is studied. It is shown that synthesis of important intermediates such as HCN, (CN)₂, CHCCN and CH₃SH is possible from such mixtures if the amount of H₂S is not more than 10%. For higher amounts of H₂S, the syntheses are strongly inhibited.     

Atomistic simulations of materials for optical chemical sensors: DFT-D calculations of molecular interactions between gas-phase analyte molecules and simple substrate models

The structures of complexes of some small molecules (formaldehyde, acetaldehyde, ammonia, methylamine, methanol, ethanol, acetone, benzene, acetonitrile, ethyl acetate, chloroform, and tetrahydrofuran, considered as possible analytes) with ethylbenzene and silanol (C₆H₅C₂H₅ and SiH₃OH, considered as models of polystyrene and silica gel substrates) and with acridine (C₁₃H₉N, considered as a model of an indicator dye molecule of the acridine series) and the corresponding interaction energies have been calculated using the DFT-D approximation. The PBE exchange-correlation potential was used in the calculations. The structures of complexes between the analyte and the substrate were determined by optimizing their ground-state geometry using the SVP split-valence double-zeta plus polarization basis set. The complex formation energies were refined by single-point calculations at the calculated equilibrium geometries using the sufficiently large triple-zeta TZVPP basis set. The calculated interaction energies are used to assess the possibility of using dyes of the acridine series adsorbed on a polystyrene or silica substrate for detecting the small molecules listed above.     

Application of dimeric orthopalladated complex in Suzuki-Miyaura cross coupling reaction under microwave irradiation and conventional heating

The Suzuki-Miyaura reaction of various aryl halides using [Pd{C₆H₂(CH₂CH₂NH₂)-(OMe)₂,3,4} (μ-Br)]₂ have been investigated. This orthopalladated complex is an efficient, stable and non-sensitive to air and moisture catalyst for the hetrocoupling reaction in DMF as the reaction solvent at 130 °C. The combination of dimeric complex as homogenous catalyst and microwave irradiation can be very useful and efficient methods in organic synthesis, so the application of microwave irradiation have been investigated using homogenous dimeric complex [Pd{C₆H₂(CH₂CH₂NH₂)-(OMe)₂,3,4} (μ-Br)]₂. Application of dimeric complex as catalyst caused to produce the desired coupling products and the using of microwave irradiation improving the yields of the reactions and shortening the reaction times.     

Biochemistry of Methanogenesis

Abstract

Methane is a product of the energy-yielding pathways of the largest and most phylogenetically diverse group in the Archaea. These organisms have evolved three pathways that entail a novel and remarkable biochemistry. All of the pathways have in common a reduction of the methyl group of methyl-coenzyme M (CH₃-S-CoM) to CH₄. Seminal studies on the CO₂-reduction pathway have revealed new cofactors and enzymes that catalyze the reduction of CO₂ to the methyl level (CH₃-S-CoM) with electrons from H₂ or formate. Most of the methane produced in nature originates from the methyl group of acetate. CO dehydrogenase is a key enzyme catalyzing the decarbonylation of acetyl-CoA; the resulting methyl group is transferred to CH₃-S-CoM, followed by reduction to methane using electrons derived from oxidation of the carbonyl group to CO₂ by the CO dehydrogenase. Some organisms transfer the methyl group of methanol and methylamines to CH₃-S-CoM; electrons for reduction of CH₃-S-CoM to CH₄ are provided by the oxidation of methyl groups to CO₂.     

Nitric oxide and hydrogen sulfide crosstalk during heavy metal stress in plants

Gases such as ethylene, hydrogen peroxide (H₂O₂), nitric oxide (NO), carbon monoxide (CO) and hydrogen sulfide (H₂S) have been recognized as vital signaling molecules in plants and animals. Of these gasotransmitters, NO and H₂S have recently gained momentum mainly because of their involvement in numerous cellular processes. It is therefore important to study their various attributes including their biosynthetic and signaling pathways. The present review provides an insight into various routes for the biosynthesis of NO and H₂S as well as their signaling role in plant cells under different conditions, more particularly under heavy metal stress. Their beneficial roles in the plant's protection against abiotic and biotic stresses as well as their adverse effects have been addressed. This review describes how H₂S and NO, being very small-sized molecules, can quickly pass through the cell membranes and trigger a multitude of responses to various factors, notably to various stress conditions such as drought, heat, osmotic, heavy metal and multiple biotic stresses. The versatile interactions between H₂S and NO involved in the different molecular pathways have been discussed. In addition to the signaling role of H₂S and NO, their direct role in posttranslational modifications is also considered. The information provided here will be helpful to better understand the multifaceted roles of H₂S and NO in plants, particularly under stress conditions.     

The addition reactions of germylenoid H<Subscript>2</Subscript>GeAlCl<Subscript>3</Subscript> with ethylene: a theoretical investigation

Theoretical calculations using the M062X and QCISD methods were performed on the addition reactions of the aluminum germylenoid H₂GeAlCl₃ with ethylene. The most two stable structures of germylenoid H₂GeAlCl₃, i.e., the p-complex and three-membered ring structures, respectively, were employed as reactants. The calculated results indicate that, for the p-complex, H₂GeAlCl₃ there are two pathways, I and II, of which path I involves just one transition state, while path II involves two transition states between reactants and products. Comparing the reaction barrier heights of path I (44.6 kJ mol^?1) and II (37.6 kJ mol^?1), the two pathways are competitive, with similar barriers under the same conditions, while for the three-membered ring structure, another two pathways, III and IV, also exist. Path III has one transition state; however, in path IV, two transition states exist. By comparing their barrier heights, path III (barrier height 39.2 kJ mol^?1) could occur more easily than path IV (barrier height 92.8 kJ mol^?1). Considering solvent effects on these addition reactions, the PCM model and CH₂Cl₂ solvent were used in calculations, and the calculated results demonstrate that CH₂Cl₂ solvent is unfavorable for the reactions, except for path II. In CH₂Cl₂ solvent, paths II and III are more favorable than paths I and IV.     

Reductive Coupling of Aldehydes by H2S in Aqueous Solutions,a C?C Bond Forming Reaction of Prebiotic Interest

We report here a novel reductive coupling reaction of conjugated, non‐ or poorly enolizable aldehydes induced by H₂S and operative in aqueous solutions under prebiotically relevant conditions. This reaction leads from retinal to β‐carotene, and from benzylic aldehydes to the corresponding diarylethylenes. This novel reaction also opens a new potentially prebiotic pathway leading from glyoxylic acid to various compounds that are involved in the reductive tricarboxylic acid cycle. This C? C bond forming reaction of prebiotic interest might have been operative, notably, in the sulfide‐rich environments of hydrothermal vents, which have been postulated as possible sites for the first steps of organic chemical evolution.     

A coupled atmosphere–ecosystem model of the early Archean Earth

A coupled photochemical‐ecosystem model has been developed to simulate the early Archean biosphere. The model incorporates kinetic and nutrient limitations on biological productivity, along with constraints imposed by metabolic thermodynamics. We have used this model to predict the biogenic CH₄ flux and net primary productivity (NPP) of the marine biosphere prior to the advent of oxygenic photosynthesis. Organisms considered include chemotrophic and organotrophic methanogens, H₂‐, H₂S‐, and Fe‐using anoxygenic phototrophs, S‐reducing bacteria, CO‐using acetogens, and fermentative bacteria. CH₄ production and NPP in our model are limited by the downward flux of H₂, CO, S₈, and H₂S through the atmosphere–ocean interface and by the upwelling rate of Fe²⁺ from the deep oceans. For reasonable estimates of the supply rates of these compounds, we find that the biogenic CH₄ flux should have ranged from approximately ¹/₃ to 2.5 times the modern CH₄ flux. In the anoxic Archean atmosphere, this would have produced CH₄ concentrations of 100 ppmv to as much as 35 000 ppmv (3.5%), depending on the rate at which hydrogen escaped to space. Recent calculations indicating that hydrogen escape was slow favour the higher CH₄ concentrations. Calculated NPP is lower than in the modern oceans by a factor of at least 40. In our model, H₂‐based metabolism is moderately more productive than Fe²⁺‐based metabolism, with S‐based metabolism being considerably less productive. Internal recycling of sulphur within the surface ocean could conceivably raise rates of sulphur metabolism by a factor of 10 higher than the values predicted by our model. Although explicit climate calculations have not been performed here, our results are consistent with the idea that the Archean climate was warm, and possibly very hot. Some or most of our ecosystem scenarios are consistent with the carbon isotope record, depending on how that record is interpreted. If the conventional view is correct and organic carbon burial accounted for approximately 20% of total carbon burial during the Archean, then only two of our phototroph‐based model ecosystems are plausible. However, if a recent alternative analysis is correct and only approximately 0–10% of total buried carbon was organic, then essentially all of our anaerobic ecosystems are plausible. A better understanding of both the geochemical and the biological records is needed to better constrain our models.     

Kinetics and mechanism of alkali-induced decomposition of 2-alkoxyethylcobaloximes

Kinetics of the base-induced decomposition of five 2-alkoxyethyl(aquo)cobaloximes, ROCH₂CH₂- Co(D₂H₂)OH₂ (R = C₆H₅, CF₃CH₂, CH₃, CH₃CH₂, (CH₃)₂CH), have been studied manometrically in aqueous base, ionic strength 1.0 M (KC1) at 25.0± 0.1 °C under an argon atmosphere. For the complexes with good leaving group alkoxide substituents (R = C₆H₅ and CF₃CH₂) the reactions are first- order in cobaloxime and first-order in hydroxide ion and produce stoichiometric amounts of ethylene and leaving group alcohol (ROH). NMR observation of decomposing solutions and workup of cobalt chelate products show that the reaction is initiated by hydroxide ion attack on an equatorial quaternary carbon leading to formation of an altered cobal- oxime product in which one of the Schiff's base linkages has become hydrated. For the remainer of the complexes the yield of ethylene is less than stoichiometric and pH-dependent, and the ethylene evolving reaction is second-order in hydroxide ion activity. The yield-limiting side reaction is shown to be base-catalyzed formation of a base-stable but photolabile alkoxyethylcobaloxime analog in which a Schiff's base linkage of the chelate has become hydrated, β-Elimination to form alkyl vinyl ethers was not observed for any of the alkoxyethylcobal- oximes. The second-order dependence of ethylene formation on hydroxide ion activity for R = CH₃, CH₂CH₃, and CH(CH₃)₂ is discussed at some length, but is not well understood at present.     

Kinetic studies on partial oxidation of methane over samarium oxides

Kinetic studies on the oxidative coupling of methane over Sm₂O₃ have been carried out. The experimental rate equation observed could be well explained in terms of the reaction mechanism proposed. The reaction is initiated by abstracting hydrogen atom from the methane adsorbed by the diatomic oxygen on the surface. The coupling of two CH₃· radicals leads to C₂H₆. Deep oxidation of CH₃· produces CO and CO₂. The large activation energy (149 kJ mol⁻¹) needed for the formation of CH₃· explains the sharp increase in the selectivity to C₂-compounds (C₂H₆ + C₂H₄) as raising temperatures. The oxygen species responsible for initiating the reaction was suggested to be O₂²⁻ or O₂⁻ on the surface.     

Comments on the Role of H2S in the Chemistry of Earth's Early Atmosphere and in Prebiotic Synthesis

Free energy calculations and experimental measurements have been used to show that H₂S/CO₂ mixtures outgassing from a prebiotic Earth's crust would have produced a reducing gas mixture containing CO, H₂, H₂O, and S _x as principal components. Due to rapid recombination of H₂, CO, and S _x to H₂S and CO₂ on cooling from a high temperature to ambient conditions, reducing components would have been retained only if efficient quenching of the reduced gas mixture had been possible. Consequently, subsea vents or vents with efficient infusion of water would have been ideal sites for retention of reduced species and for prebiotic organic synthesis. It is suggested that C/H/O/S ratios are important factors in controlling the degree of prebiotic organic synthesis and, hence, the emergence of life, since if oxygen is abundant, CO₂ and SO₂ would have been dominant species. Received: 5 March 1997 / Accepted: 15 December 1997     

Kinetics of CH4 production from H2 and CO2 in a hollow fiber reactor by plug flow reaction model

For microbial production of CH₄ from H₂ and CO₂, a hollow fiber reactor had been developed to increase an interfacial area between liquid and gas phases. The CH₄ production with the hollow fiber reactor was analyzed by applying a plug flow reaction model of a tubular reactor. It was possible to apply the model to the reaction of CH₄ production. The relationships between influent gas velocity, length of reactor and reaction yield were simulated by the reaction model. The plug flow reaction model was useful to design a hollow fiber bioreactor for the biomethanation of H₂ and CO₂.     

Biomass fast pyrolysis in a fluidized bed reactor under N2, CO2, CO, CH4 and H2 atmospheres

Biomass fast pyrolysis is one of the most promising technologies for biomass utilization. In order to increase its economic potential, pyrolysis gas is usually recycled to serve as carrier gas. In this study, biomass fast pyrolysis was carried out in a fluidized bed reactor using various main pyrolysis gas components, namely N₂, CO₂, CO, CH₄ and H₂, as carrier gases. The atmosphere effects on product yields and oil fraction compositions were investigated. Results show that CO atmosphere gave the lowest liquid yield (49.6%) compared to highest 58.7% obtained with CH₄. CO and H₂ atmospheres converted more oxygen into CO₂ and H₂O, respectively. GC/MS analysis of the liquid products shows that CO and CO₂ atmospheres produced less methoxy-containing compounds and more monofunctional phenols. The higher heating value of the obtained bio-oil under N₂ atmosphere is only 17.8 MJ/kg, while that under CO and H₂ atmospheres increased to 23.7 and 24.4 MJ/kg, respectively.