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.     

Synthesis of (Dicarbonyl)(η5-cyclopentadienyl)Manganese Complex Stabilized Nucleoside Phosphite Esters

Abstract

We have found that stable nucleoside derived phosphite ester manganese complexes can be generated by the reaction of Mn(CO)₂(THF)(η⁵-C₅H₄R) with nucleoside phosphite esters. These complexes appear to be stable towards oxygen and reagents used for DNA synthesis and deprotection. The cyclopentadienyl ligand can be modified by a strong electron withdrawing group and still retain the photochemical and chemical properties necessary to complex readily to phosphite esters.     

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.     

Energy yields for hydrogen cyanide and formaldehyde syntheses: The hcn and amino acid concentrations in the primitive ocean

Prebiotic electric discharge and ultraviolet light experiments are usually reported in terms of carbon yields and involve a large input of energy to maximize yields. Experiments using lower energy inputs are more realistic prebiotic models and give energy yields which can be used to estimate the relative importance of the different energy sources on the primitive earth. Simulated prebiotic atmospheres containing either CH₄, CO or CO₂ with N₂, H₂O and variable amounts of H₂ were subjected to the spark from a high frequency Tesla coil. The energy yields for the synthesis of HCN and H₂CO were estimated. CH₄ mixtures give the highest yields of HCN while H₂CO is most efficiently produced with the CO mixtures. These results are a model for atmospheric corona discharges, which are more abundant than lightning and different in character. Preliminary experiments using artificial lightning are also reported. The energy yields from these experiments combined with the corona discharge available on the earth, allows a yearly production rate to be estimated. These are compared with other experiments and model calculations. From these production rates of HCN (e.g. 100 nmoles cm⁻² yr⁻¹) and the experimental hydrolysis rates, the steady state concentration in the primitive ocean can be calculated (e.g., 4 × 10⁻⁶ M at pH 8 and 0°). A steady state amino acid concentration of 3 × 10⁻⁴ M is estimated from the HCN production rate and the rate of decomposition of the amino acids by passage through the submarine vents.     

Synthesis, characterization of a new open-framework gallium phosphite containing 5,6-fold coordinate gallium atoms

A new open-framework gallium phosphite Ga₅(OH)₂(HPO₃)₈(C₄N₃H₁₆) · 2H₂O (1) is synthesized solvothermally using diethylenetriamine (DETA) as template from a mixed solvent system in which ethylene glycol (EG) was used as the co-solvent. The as-synthesized product is characterized by single crystal X-ray diffraction, powder X-ray diffraction, IR spectroscopy, thermogravimetric analysis (TGA), ICP-AES and elemental analyses. The three-dimensional open-framework of compound 1 is constructed from two novel secondary building units (SBUs), Ga₂O₇(OH)(HPO₃) three-membered ring (3R) and Ga(HPO₃)₆ tooth-wheel type unit. These two novel secondary building units are first found in gallium phosphate/phosphite, which lead to form the one-dimensional 8-membered ring channels along the a-axis. Moreover, it is noted that compound 1 is the first gallium phosphite containing 5-fold coordinate gallium atom.     

Energy Generation from the CO Oxidation-Hydrogen Production Pathway in Rubrivivax gelatinosus

When incubated in the presence of CO gas, Rubrivivax gelatinosus CBS induces a CO oxidation-H₂ production pathway according to the stoichiometry CO + H₂O → CO₂ + H₂. Once induced, this pathway proceeds equally well in both light and darkness. When light is not present, CO can serve as the sole carbon source, supporting cell growth anaerobically with a cell doubling time of nearly 2 days. This observation suggests that the CO oxidation reaction yields energy. Indeed, new ATP synthesis was detected in darkness following CO additions to the gas phase of the culture, in contrast to the case for a control that received an inert gas such as argon. When the CO-to-H₂ activity was determined in the presence of the electron transport uncoupler carbonyl-cyanide m-chlorophenylhydrazone (CCCP), the rate of H₂ production from CO oxidation was enhanced nearly 40% compared to that of the control. Upon the addition of the ATP synthase inhibitor N,N′-dicyclohexylcarbodiimide (DCCD), we observed an inhibition of H₂ production from CO oxidation which could be reversed upon the addition of CCCP. Collectively, these data strongly suggest that the CO-to-H₂ reaction yields ATP driven by a transmembrane proton gradient, but the detailed mechanism of this reaction is not yet known. These findings encourage additional research aimed at long-term H₂ production from gas streams containing CO.     

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.     

Study on the chemical evolution of low molecular weight compounds in a highly oxidized atmosphere using electric discharges

The molecular basis for the chemical evolution of low molecular compounds was studied using electric discharges on a higly oxidized atmosphere comprised of CO₂, N₂ and H₂O. In the gas phase, O₂ and CO were formed by the decomposition of CO₂ and their yields were enhanced by the addition of N₂ to the gas mixture. It was demonstrated that H₂O suppressed the reduction of CO₂ while H₂O also had a role in producing organic compounds such as formic acid and formaldehyde. Infrared analysis of the water soluble products and the inner surface of the reaction vessel indicated the production of compounds more complex than formic acid and formaldehyde. These compounds contained the chemical bonds which were identified to be OH, CO, CN and/or CC.     

Characteristics of the H2 oxidizing system in soybean nodule bacteroids

A derivative of Rhizobium japonicum (strain 122 DES) has been isolated which forms nodules on soybeans that evolve little or no H₂ in air and efficiently fixes N₂. Bacteroids isolated from nodules formed by strain 122 DES took up H₂ with O₂ as the physiological acceptor and appeared to be typical of those R. japonicum strains that possess the H₂ uptake system. The hydrogenase system in soybean nodules is located within the bacteroids and activity in macerated bacteroids is concentrated in a particulate fraction. The pH optimum for the reaction is near 8.0 and apparent K _m values for H₂ and O₂ are 2 M and 1 M, respectively. The H₂ oxidizing activity of a suspension of 122 DES bacteroids was stable at 4°C for at least 4 weeks and was not particularly sensitive to O₂. Neither C₂H₂ nor CO inhibited O₂ dependent H₂ uptake activity.Non-physiological electron acceptors of positive oxidation reduction potential also supported H₂ uptake by bacteroids. The rate of H₂ uptake with phenazine methosulfate as the acceptor was greater than that with O₂. When methylene blue, triphenyltetrazolium, potassium ferricyanide or dichlorophenolindophenol were added to bacteriod suspensions, without preincubation, rates of H₂ uptake were supported that were lower than those in the presence of O₂. Preincubation of the bacteroids with acceptors increased the rates of H₂ uptake. No H₂ evolution was observed from reaction mixtures containing bacteroid suspensions and reduced methyl or benzyl viologens. Of a series of carbon substrates added to bacteroid suspensions only acetate, formate or succinate at concentrations of 50 mM resulted in 20% or greater inhibition of H₂ oxidation.The H₂ uptake capacity of isolated 122 DES bacteroids (expressed on a dry bacteroid basis) was at least 10-fold higher than the rate of the nitrogenase reaction in nodules expressed on a comparable basis. Since about 1 mol of H₂ is evolved for every mol of N₂ reduced during the N₂ fixation reaction, these observations explain why soybean nodules formed by strain 122 DES and other strains with high H₂ uptake activities have a capacity for recycling all the H₂ produced from the nitrogenase reaction.Abbreviations PMS PHenazine methosulfate - MB Methylene blue     

Carbon-13 NMR studies of C2H5N13C binding to various hemoproteins

The addition of an excess of C₂H₅N¹³C to myoglobin and human adult and fetal hemoglobins, gives three characteristic NMR spectra with new ¹³C resonances respectively at δ = ?10,56 ppm, δ = ?7,03 and ?7,95 ppm and δ = ?6,28 and ?7,95 ppm (CH₃CO₂Na as external standard). These signals correspond to the C₂H₅N¹³C bound to the Fe(II) of the different heme units, according to CO exchange experiments. Characteristic resonances can be assigned to C₂H₅N¹³C bound to α, β and γ subunits. C₂H₅N¹³C appears as a more sensitive probe than ¹³CO for hemoprotein NMR studies.     

Carbon Monoxide, Hydrogen, and Formate Metabolism during Methanogenesis from Acetate by Thermophilic Cultures of Methanosarcina and Methanothrix Strains

CO and H₂ have been implicated in methanogenesis from acetate, but it is unclear whether they are directly involved in methanogenesis or electron transfer in acetotrophic methanogens. We compared metabolism of H₂, CO, and formate by cultures of the thermophilic acetotrophic methanogens Methanosarcina thermophila TM-1 and Methanothrix sp. strain CALS-1. M. thermophila accumulated H₂ to partial pressures of 40 to 70 Pa (1 Pa = 0.987 × 10^-5 atm), as has been previously reported for this and other Methanosarcina cultures. In contrast, Methanothrix sp. strain CALS-1 accumulated H₂ to maximum partial pressures near 1 Pa. Growing cultures of Methanothrix sp. strain CALS-1 initially accumulated CO, which reached partial pressures near 0.6 Pa (some CO came from the rubber stopper) during the middle of methanogenesis; this was followed by a decrease in CO partial pressures to less than 0.01 Pa by the end of methanogenesis. Accumulation or consumption of CO by cultures of M. thermophila growing on acetate was not detected. Late-exponential-phase cultures of Methanothrix sp. strain CALS-1, in which the CO partial pressure was decreased by flushing with N₂-CO₂, accumulated CO to 0.16 Pa, whereas cultures to which ca. 0.5 Pa of CO was added consumed CO until it reached this partial pressure. Cyanide (1 mM) blocked CO consumption but not production. High partial pressures of H₂ (40 kPa) inhibited methanogenesis from acetate by M. thermophila but not by Methanothrix sp. strain CALS-1, and 2 kPa of CO was not inhibitory to M. thermophila but was inhibitory to Methanothrix sp. strain CALS-1. Levels of CO dehydrogenase, hydrogenase, and formate dehydrogenase in Methanothrix sp. strain CALS-1 were 9.1, 0.045, and 5.8 μmol of viologen reduced min^-1 mg of protein^-1. These results suggest that CO plays a role in Methanothrix sp. strain CALS-1 similar to that of H₂ in M. thermophila and are consistent with the conclusion that CO is an intermediate in a catabolic or anabolic pathway in Methanothrix sp. strain CALS-1; however, they could also be explained by passive equilibration of CO with a metabolic intermediate.     

Phosphate and phosphite have a differential impact on the proteome and phosphoproteome of Arabidopsis suspension cell cultures

Phosphorus absorbed in the form of phosphate (H₂PO₄⁻) is an essential but limiting macronutrient for plant growth and agricultural productivity. A comprehensive understanding of how plants respond to phosphate starvation is essential for the development of more phosphate-efficient crops. Here we employed label-free proteomics and phosphoproteomics to quantify protein-level responses to 48 h of phosphate versus phosphite (H₂PO₃⁻) resupply to phosphate-deprived Arabidopsis thaliana suspension cells. Phosphite is similarly sensed, taken up and transported by plant cells as phosphate, but cannot be metabolized or used as a nutrient. Phosphite is thus a useful tool for differentiating between non-specific processes related to phosphate sensing and transport and specific responses to phosphorus nutrition. We found that responses to phosphate versus phosphite resupply occurred mainly at the level of protein phosphorylation, complemented by limited changes in protein abundance, primarily in protein translation, phosphate transport and scavenging, and central metabolism proteins. Altered phosphorylation of proteins involved in core processes such as translation, RNA splicing and kinase signaling was especially important. We also found differential phosphorylation in response to phosphate and phosphite in 69 proteins, including splicing factors, translation factors, the PHT1;4 phosphate transporter and the HAT1 histone acetyltransferase – potential phospho-switches signaling changes in phosphorus nutrition. Our study illuminates several new aspects of the phosphate starvation response and identifies important targets for further investigation and potential crop improvement.     

Aerobic hydrogenase activity in Anacystis Nidulans The oxyhydrogen reaction

1. The oxyhydrogen reaction of Anacystis nidulans was studied manometrically and polarographically in whole cells and in cell-free preparations; the activity was found to be associated with the particulate fraction.2. Besides O₂, the isolated membranes reduced artificial electron acceptors of positive redox potential; the reactions were unaffected by O₂ levels <10–15%; aerobically the artificial acceptors were reduced simultaneously with O₂.3. H₂-supported O₂ uptake was inhibited by CO, KCN and 2-n-heptyl-8-hydroxyquinoline-N-oxide. Inhibition by CO was partly reversed by strong light. Uncouplers stimulated the oxyhydrogen reaction.4. The kinetic properties of O₂ uptake by isolated membranes were the same in presence of H₂ and of other respiratory substrates.5. Low rates of H₂ evolution by the membrane preparations were found in presence of dithionite; methyl viologen stimulated the reaction.6. The results indicate that under certain growth conditions Anacystis synthesizes a membrane-bound hydrogenase which appears to be involved in phosphorylative electron flow from H₂ to O₂ through the respiratory chain.     

Ethylenediamine- and propylenediaminediacetic acid derivatives as ligands for the “fac-[M(CO)3]” core (M = Re, Tc)

The reaction of Re(CO)₅Cl with o- or p-N-(nitrophenyl)ethylenediaminediacetic acid (H₂L¹, H₂L²) and o- or p-N-(nitrophenyl)propylenediaminediacetic acid (H₂L³, H₂L⁴) in methanol leads to the formation of stable anionic [Et₃NH][Re(CO)₃(L)] · H₂O complexes 1-4. These compounds have been characterized by means of IR, mass spectrometry, elemental analysis, NMR and conductimetry, as well as X-ray crystallography for 2 and 3. The [Re(CO)₃]⁺ moiety is coordinated via the nitrogen of the iminodiacetic acid unit and two oxygens of monodentate carboxylate groups. In each case, the nitro group of the aromatic ring remains uncoordinated. The analogous technetium-99m complexes 1′ and 3′ were also prepared quantitatively by the reaction of H₂L¹ and H₂L³, respectively, with the fac-[^99mTc(CO)₃(H₂O)₃]⁺ precursor in ethanol. The corresponding Re and ^99mTc compounds were shown to possess the same structure by means of HPLC studies. The high affinity of these ligands for the Tc(I) or Re(I) core, coupled with the easiness of their derivatization (by reduction of the nitro group in amino group), implies that the utilization of this ligand system to develop target-specific radiopharmaceuticals for diagnosis and therapy is promising.     

Overpotentials and Faraday Efficiencies in CO2 Electrocatalysis–the Impact of 1‐Ethyl‐3‐Methylimidazolium Trifluoromethanesulfonate

The mixtures of room temperature ionic liquid 1‐ethyl‐3‐methylimidazolium trifluoromethanesulfonate ([EMIM]TFO) and water as electrolytes for reduction of CO₂ to CO are reported. Linear sweep voltammetry shows overpotentials for CO₂ reduction and the competing hydrogen evolution reaction (HER), both of which vary as a function of [EMIM]TFO concentration in the range from 4 × 10^?3m (0.006 mol%) to 4869 × 10^?3m (50 mol%). A steady lowering of overpotentials up to an optimum for 334 × 10?³m is identified. At 20 mol% and more of [EMIM]TFO, a significant CO₂ reduction plateau and inhibition of HER, which is limited by H₂O diffusion, is noted. Such a plateau in CO₂ reduction correlates to high CO Faraday efficiencies. In case of 50 mol% [EMIM]TFO, a broad plateau spanning over a potential range of 0.58 V evolves. At the same time, the overpotential for HER is increased by 1.20 V when compared to 334 × 10^?3m and, in turn, HER is largely inhibited. The Faraday efficiencies for CO and H₂ formation feature 95.6% ± 6.8% and 0.5% ± 0.3%, respectively, over a period of 3 h in a separator divided cell. Cathodic as well as anodic electrochemical stability of the electrolyte throughout this time period is corroborated in ¹H NMR spectroscopic measurements.     

Reaction of a bulky phosphite with [Ru3(CO)12]: The molecular structure of one of the decomposition products

Mono- and bis-substituted phosphite complexes [Ru₃(CO)_12−x L_x] (L = tris(2,4-di-tert-butylphenyl) phosphite; x = 1, 2) were synthesized by simple substitution reactions, and were characterized by spectroscopic methods. The monosubstituted ruthenium complex disproportionates in acetone producing a mononuclear ruthenium complex as one of the decomposition products. Single crystal X-ray diffraction analysis established the molecular structure of this new compound.     

Computational screening of ZIFs for CO2 separations

Using molecular simulations, we studied a diverse collection of zeolite–imidazolate frameworks (ZIFs) to evaluate their performances in adsorption- and membrane-based gas separations. Molecular simulations were performed for both single-component gases (CH₄, CO₂, H₂ and N₂) and binary gas mixtures (CO₂/CH₄, CO₂/N₂, CO₂/H₂ and CH₄/H₂) to predict the intrinsic and mixture selectivities of ZIFs. These two selectivities were compared to discuss the importance of multi-component mixture effects on making predictions about the separation performance of a material. Gas separation performances of ZIFs were compared with other nanoporous materials and our results showed that several ZIFs can outperform well-known zeolites and metal–organic frameworks in CO₂ separations. Several other properties of ZIFs such as gas permeability, working capacity and sorbent selection parameter were computed to identify the most promising materials in adsorption- and membrane-based separation of CO₂/CH₄, CO₂/N₂, CO₂/H₂ and CH₄/H₂.     

Control of Carbon and Electron Flow in Clostridium acetobutylicum Fermentations: Utilization of Carbon Monoxide to Inhibit Hydrogen Production and to Enhance Butanol Yields

Extracts prepared from non-solvent-producing cells of Clostridium acetobutylicum contained methyl viologen-linked hydrogenase activity (20 U/mg of protein at 37°C) but did not display carbon monoxide dehydrogenase activity. CO addition readily inhibited the hydrogenase activity of cell extracts or of viable metabolizing cells. Increasing the partial pressure of CO (2 to 10%) in unshaken anaerobic culture tube headspaces significantly inhibited (90% inhibition at 10% CO) both growth and hydrogen production by C. acetobutylicum. Growth was not sensitive to low partial pressures of CO (i.e., up to 15%) in pH-controlled fermentors (pH 4.5) that were continuously gassed and mixed. CO addition dramatically altered the glucose fermentation balance of C. acetobutylicum by diverting carbon and electrons away from H₂, CO₂, acetate, and butyrate production and towards production of ethanol and butanol. The butanol concentration was increased from 65 to 106 mM and the butanol productivity (i.e., the ratio of butanol produced/total acids and solvents produced) was increased by 31% when glucose fermentations maintained at pH 4.5 were continuously gassed with 85% N₂-15% CO versus N₂ alone. The results are discussed in terms of metabolic regulation of C. acetobutylicum saccharide fermentations to achieve maximal butanol or solvent yield.     

A simple and rapid GC/MS method for the simultaneous determination of gaseous metabolites

We modified and tuned a commercial model of a gas chromatography/mass spectrometry (GC/MS) instrument to develop a simple and rapid method for the simultaneous quantification of a variety of gas species. Using the developed method with the newly modified instrument, gas species such as H₂, N₂, O₂, CO, NO, CH₄, CO₂, and N₂O, which are common components of microbial metabolism, were accurately identified based on their retention times and/or mass-to-charge ratios (m/z) in less than 2.5 min. By examining the sensitivities and dynamic ranges for the detection of H₂, N₂, O₂, CH₄, CO₂, and N₂O, it was demonstrated that the method developed in this study was sufficient for accurately monitoring the production and the consumption of these gaseous species during microbial metabolism. The utility of the new method was demonstrated by a denitrification study with Pseudomonas aureofaciens ATCC 13985^T. This method will be suitable for a variety of applications requiring the identification of gaseous metabolites in microorganisms, microbial communities, and natural ecosystems.     

Neighbouring metal induced oxidative addition at the iron centre amongst the iron-arylpyridylphosphine complexes

Complexes of the type (η⁴-BuC₅H₅)Fe(CO)₂(P) (P = PPh₂Py 3, PPhPy₂4, PPy₃5; Py = 2-pyridyl) were satisfactorily prepared. Upon treatment of 3 with M(CO)₃(EtCN)₃ (M = Mo, 6a; W, 6b), the pyridyl N-atom could be coordinated to the metal M, which then eliminates a CO ligand from the Fe-centre and induced an oxidative addition of the endo-C-H of (η⁴-BuC₅H₅). This results in a bridged hydrido heterodimetallic complex [(η⁵-BuC₅H₄)Fe(CO)(μ-P,N-PPh₂Py)(μ-H)M(CO)₄] (M = Mo, 7a, 81%; W, 7b, 76%). The reaction of 4 or 5 with 6a,b did not give the induced oxidative addition, although these complexes contain more than one pyridyl N-atom. The reaction of 4 with M(CO)₄(EtCN)₂ (M = Mo, 9a; W, 9b) produced heterodimetallic complexes [(η⁴-BuC₅H₅)Fe(CO)₂(μ-P:N,N′-PPhPy₂)M(CO)₄] (M = Mo, 10a, 81%; W, 10b, 83%). Treatment of 5 with 6a,b gave [(η⁴-BuC₅H₅)Fe(CO)₂(μ-P:N,N′,N″-PPy₃)M(CO)₃] (M = Mo, 12a, 96%; W, 12b, 78%).