Structural bases of hydrogen tunneling in enzymes: progress and puzzles

Accumulating experimental evidence suggests that the occurrence of hydrogen tunneling is likely to be widespread in enzyme-catalyzed reactions. The realization that hydrogen can transfer via tunneling mechanisms has far-reaching implications for our understanding of enzyme catalysis involving proton, hydride or hydrogen atom transfer reactions. The current status of the field is highlighted by three enzyme systems that have been under intensive study in recent years, including soybean lipoxygenase-1, thermophilic alcohol dehydrogenase and dihydrofolate reductase. Particular attention has been devoted to the issues of whether protein dynamics modulate hydrogen tunneling probability and whether the tunneling process contributes to the catalytic power of enzymes.     

The role of sulphur in chemical evolution

Summary Sulphur may have played an important role, mainly as an energy converter, during the initial steps of Chemical Evolution.In atmospheric processes, sulphur, in the form of H₂S might have been a primary energy acceptor and a source of hot hydrogen atoms. The presence of H₂S in the primeval earth atmosphere with a molar ratio of about 10^–2 could have allowed the formation of several volatile S-containing compounds without inhibiting the synthesis of the reactive products which are formed in the absence of H₂S. An evaluation of the quantity of H₂S which could have been included in the primeval atmosphere suggests that such a molar ratio may have been reached.In the primitive soup, the thiols and sulphides formed in the gaseous phase may have evolved, giving rise to various prebiotic syntheses. Studies on the addition reaction of alkanethiols on malonic nitriles in aqueous solutions show two different condensation processes: the formation of thioethers and the formation of iminothioesters. Taking into account the values of the specific rate constants for the two reactions, it is shown that these reactions may have taken place in the primitive earth conditions. These two compounds may have played an important role in the prebiochemical evolution. In particular, iminothioesters can be considered as the immediate precursors of thioesters.     

Liquid-to-Gas Mass Transfer in Anaerobic Processes: Inevitable Transfer Limitations of Methane and Hydrogen in the Biomethanation Process

Liquid-to-gas mass transfer in anaerobic processes was investigated theoretically and experimentally. By using the classical definition of k(L)a, the global volumetric mass transfer coefficient, theoretical development of mass balances in such processes demonstrates that the mass transfer of highly soluble gases is not limited in the usual conditions occurring in anaerobic fermentors (low-intensity mixing). Conversely, the limitation is important for poorly soluble gases, such as methane and hydrogen. The latter could be overconcentrated to as much as 80 times the value at thermodynamic equilibrium. Such overconcentrations bring into question the biological interpretations that have been deduced solely from gaseous measurements. Experimental results obtained in three different methanogenic reactors for a wide range of conditions of mixing and gas production confirmed the general existence of low mass transfer coefficients and consequently of large overconcentrations of dissolved methane and hydrogen (up to 12 and 70 times the equilibrium values, respectively). Hydrogen mass transfer coefficients were obtained from the direct measurements of dissolved and gaseous concentrations, while carbon dioxide coefficients were calculated from gas phase composition and calculation of related dissolved concentration. Methane transfer coefficients were based on calculations from the carbon dioxide coefficients. From mass balances performed on a gas bubble during its simulated growth and ascent to the surface of the liquid, the methane and carbon dioxide contents in the gas bubble appeared to be controlled by the bubble growth process, while the bubble ascent was largely responsible for a slight enrichment in hydrogen.     

A plausible prebiotic synthesis of pyridoxal phosphate: vitamin B6 - a computational study

A set of chemical reactions is proposed to account for the formation of pyridoxal phosphate, Vitamin B6, from a primeval atmosphere composed of cyanoacetylene, diacetylene, carbon monoxide, hydrogen, water, and a phosphoric acid. The reactions have been shown to be feasible from the overall enthalpy changes in the ZKE approximation at the HF and MP2/6-31G* level.     

Gaseous messengers in the nervous system

Nitric oxide is the first gaseous messenger whose functions were comprehensively studied in different systems of organism. Recently, new data on the physiological role of other endogenous gases: carbon monoxide and hydrogen sulfide, appeared. The role of gases in gastrointestinal tract and cardiovascular system have been established; however, data on their function and mechanisms of action in nervous system are insufficient. This article highlights the current information on the role of gaseous messengers in central and peripheral nervous system.     

Investigation of the selectivity of hydrogen abstraction in the nonenzymatic formation of hydroxyeicosatetraenoic acids and leukotrienes by autoxidation

The biosynthetic conversions of arachidonic acid to hydroperoxyeicosatetraenoic acids (HPETEs) and the further conversion of leukotriene epoxides are accompanied by stereoselective hydrogen abstraction from the reaction substrate. Furthermore, this hydrogen removal has always been found to occur in fixed stereochemical relationship to carbon-oxygen chiral center(s) in the substrate or product. We have used stereospecifically labeled 10-3H-substrates with 14C internal standard to investigate whether the same relationships bear in HPETE and leukotriene formation during autoxidation. After autoxidation of labeled arachidonate, both the 8(R)- and 8(S)-HPETE enantiomers (resolved as diastereomer derivatives) and the 12(RS)-HPETE were observed to retain 41-47% 3H relative to the starting material. In autoxidative formation of leukotrienes from labeled 15(S)-HPETE the four main leukotrienes, including two derived from 14,15-leukotriene A4 hydrolysis, were observed to have retained an average of 45% 3H. Primary and secondary isotope effects were found to accompany these reactions. The results prove that stereorandom hydrogen abstraction occurs in autoxidation and that the hydrogen loss bears no stereochemical relationship to chiral oxygen center(s) in the HPETE product, (8(R) or 8(S], or the 15(S)-hydroperoxy substrate. We conclude that the chiral features of the biosynthetic reactions are a reflection of enzymatic control of stereochemistry. Nonetheless, the findings of primary and secondary isotope effects in autoxidation which are similar to those observed in the analogous biosynthetic reactions suggests that, except for stereochemical control, the autoxidative and enzymatic reactions may be mechanistically similar.     

Radical mechanisms in adenosylcobalamin-dependent enzymes

Adenolsylcobalamin-dependent enzymes catalyze free radical mediated reactions of their substrates. Stereochemical methods have been used to establish the nature of the primary radical initiation step in ribonucleoside triphosphate reductase. Kinetic isotope effects have been used to establish a kinetic coupling between cobalt-carbon bond cleavage and hydrogen atom abstraction from the substrate. Isotope effects have also been used to identify rate-limiting steps with wild type and mutant forms of the enzymes and in model reactions to assess tunneling contributions to hydrogen atom transfer steps. Computational methods have been employed to explore the pathways for functional group migration in the radical pathways. Analogs of substrates and of adenosylcobalamin have been used to explore the fidelity of the enzyme active sites and the radical pathways.     

Solar‐to‐Hydrogen Energy Conversion Based on Water Splitting

Artificial photosynthesis provides a blueprint to harvest solar energy to sustain the future energy demands. Solar‐driven water splitting, converting solar energy into hydrogen energy, is the prototype of photosynthesis. Various systems have been designed and evaluated to understand the reaction pathways and/or to meet the requirements of potential applications. In solar‐to‐hydrogen conversion, electrocatalytic hydrogen and oxygen evolution reactions are key research areas that are meaningful both theoretically and practically. To utilize hydrogen energy, fuel cell technology has been extensively investigated because of its high efficiency in releasing chemical energy. In this review, general concepts of the photosynthesis in green plants are discussed, different strategies for the light‐driven water splitting proposed in laboratories are introduced, the progress of electrocatalytic hydrogen and oxygen evolution reactions are reviewed, and finally, the reactions in hydrogen fuel cells are briefly discussed. Overall, the mass and energy circulation in the solar‐hydrogen‐electricity circle are delineated. The authors conclude that attention from scientists and engineers of relevant research areas is still highly needed to eliminate the wide disparity between the aspirations and realities of artificial photosynthesis.     

Hydrogen abstraction ability of different aromatic nitroxides

Indolinonic aromatic nitroxides have been shown to efficiently inhibit free radical mediated oxidation reactions in biological systems. Since all antioxidants also possess pro-oxidant activity, possibly through a hydrogen abstraction process from suitable substrates, the relative hydrogen abstraction abilities of these compounds were evaluated. Different hydrogen donors were reacted with an indolinic and two indolinonic nitroxides and the rates of hydrogen abstraction were determined using UV-Vis spectroscopy. From the data obtained, a structure-activity relationship was found. In addition, the hydrogen abstraction ability of these compounds was found to be much greater than that of the aliphatic nitroxide TEMPO, despite existing reports indicating that these two classes of compounds show similar antioxidant activities in biological systems.     

Reactions of agostic manganese complexes with molecular hydrogen

Reactions between manganese agostic species having (Mn---C---H) interactions and molecular hydrogen have been investigated. Treatment of the bridging agostic cyclooctenylmanganese tricarbonyl, 3, and butenylmanganese tricarbonyl, 5, with hydrogen in benzene results in the formation of the cyclohexadienylmanganese tricarbonyl compound 4. This suggests that the hydrogen molecule is highly reactive toward organometallic manganese complexes containing an agostic C---H bond. In these reactions (η²-H₂) bonded species are plausible intermediates but these are not detected by NMR. The results indicate that the suggested intermediates in the reactions may be useful as hydrogenation catalysts and as precursors to prepare new manganese compounds which may not be accessible by other pathways.     

Changes in binding of hydrogen ions in enzyme-catalyzed reactions

Most enzyme-catalyzed reactions produce or consume hydrogen ions, and this is expressed by the change in the binding of hydrogen ions in the biochemical reaction, as written in terms of reactants (sums of species). This property of a biochemical reaction is important because it determines the change in the apparent equilibrium constant K' with pH. This property is also important because it is the number of moles of hydrogen ions that can be produced by a biochemical reaction for passage through a membrane, or can be accepted from a transfer through a membrane. There are two ways to calculate the change in binding of hydrogen ions for an enzyme-catalyzed reaction. The first, which has been used for a long time, involves calculating the partial derivative of the standard transformed Gibbs energy of reaction with respect to pH. The second involves calculating the average numbers of hydrogen ions in each reactant and adding and subtracting these average numbers. The changes in binding of hydrogen ions calculated by the second method at pHs 5, 6, 7, 8, and 9 are given for 23 enzyme-catalyzed reactions. Values are given for 206 more reactions on the web. This database can be extended to include more reactions for which pKs of reactants are known or can be estimated.     

Growth of Seliberia carboxydohydrogena carboxy bacteria with an altered composition of the gas mixture

The growth and gas exchange of Seliberia carboxydohydrogena Z-1062 were studied in the regime of turbidostat when the conditions of gaseous nutrition were changed: a decrease in hydrogen concentration and an increase in carbon monoxide concentration, growth on two carbon sources (CO+CO2) and on two energy sources (H2+CO). The inhibition of the bacterial growth by CO was expressed in a decrease of the specific growth rate and in the reduced effectiveness of using a gaseous substrate. When the concentration of carbon monoxide was elevated from 0 to 40% and that of hydrogen was reduced from 80 to 40%, the specific growth rate of the cells was decreased from 0.4 to 0.04 h-1; here, the economic coefficient in terms of hydrogen fell from 3.6 to 0.62 g/g. The CO-oxidizing system of the bacterium was shown to be resistant. The rate of CO oxidation by the culture was from 0.6 to 0.8 L/h per 1 g of the synthesized biomass at the following concentration of gases in the medium (%); H2, 80-40; CO2, 5; O2, 15; CO, 10-40. The rate of CO oxidation by the culture rose when hydrogen concentration was decreased and CO concentration was increased.     

Biomass Pyrolysis in an Argon/Hydrogen Plasma Reactor

This paper presents the experimental results of biomass pyrolysis in a laboratory argon/hydrogen plasma reactor. The samples tested were wood and rice husk. The gaseous product was found to contain mainly H₂, CO, C₂H₂ and CH₄. The conversion of carbon and oxygen from the biomass feed to gaseous product can reach up to 79 % and 72 %, respectively. The results indicate that plasma pyrolysis of biomass may be a useful way for gaseous fuel production.     

Advances in thermochemical conversion of woody biomass to energy,fuels and chemicals

Biomass has been recognised as a promising resource for future energy and fuels. The biomass, originated from plants, is renewable and application of its derived energy and fuels is close to carbon-neutral by considering that the growing plants absorb CO₂ for photosynthesis. However, the complex physical structure and chemical composition of the biomass significantly hinder its conversion to gaseous and liquid fuels.This paper reviews recent advances in biomass thermochemical conversion technologies for energy, liquid fuels and chemicals. Combustion process produces heat or heat and power from the biomass through oxidation reactions; however, this is a mature technology and has been successfully applied in industry. Therefore, this review will focus on the remaining three thermochemical processes, namely biomass pyrolysis, biomass thermal liquefaction and biomass gasification. For biomass pyrolysis, biomass pretreatment and application of catalysts can simplify the bio-oil composition and retain high yield. In biomass liquefaction, application of appropriate solvents and catalysts improves the liquid product quality and yield. Gaseous product from biomass gasification is relatively simple and can be further processed for useful products. Dual fluidised bed (DFB) gasification technology using steam as gasification agent provides an opportunity for achieving high hydrogen content and CO₂ capture with application of appropriate catalytic bed materials. In addition, multi-staged gasification technology, and integrated biomass pyrolysis and gasification as well as gasification for poly-generation have attracted increasing attention.     

New assay method based on Raman spectroscopy for enzymes reacting with gaseous substrates

Enzyme activity is typically assayed by quantitatively measuring the initial and final concentrations of the substrates and/or products over a defined time period. For enzymatic reactions involving gaseous substrates, the substrate concentrations can be estimated either directly by gas chromatography or mass spectrometry, or indirectly by absorption spectroscopy, if the catalytic reactions involve electron transfer with electron mediators that exhibit redox‐dependent spectral changes. We have developed a new assay system for measuring the time course of enzymatic reactions involving gaseous substrates based on Raman spectroscopy. This system permits continuous monitoring of the gas composition in the reaction cuvette in a non‐invasive manner over a prolonged time period. We have applied this system to the kinetic study of the [NiFe] hydrogenase from Desulfovibrio vulgaris Miyazaki F. This enzyme physiologically catalyzes the reversible oxidation of H₂ and also possesses the nonphysiological functions of H/D exchange and nuclear spin isomer conversion reactions. The proposed system has the additional advantage of enabling us to measure all of the hydrogenase‐mediated reactions simultaneously. Using the proposed system, we confirmed that H₂ (the fully exchanged product) is concomitantly produced alongside HD by the H/D exchange reaction in the D₂/H₂O system. Based on a kinetic model, the ratio of the rate constants of the H/D exchange reaction (k) at the active site and product release rate (k_out) was estimated to be 1.9 ± 0.2. The proposed assay method based on Raman spectroscopy can be applied to the investigation of other enzymes involving gaseous substrates.     

Haloperoxidases: Enzymatic Synthesis of alpha,beta-Halohydrins from Gaseous Alkenes

The enzymatic synthesis of alpha,beta-halohydrins from gaseous alkenes is described. The enzymatic reaction required an alkene, a halide ion, dilute hydrogen peroxide, and a haloperoxidase enzyme. A wide range of gaseous alkenes were suitable for this reaction, including those containing isolated, conjugated, and cumulative carbon-carbon double bonds. Chlorohydrins, bromohydrins, and iodohydrins could be formed. The combining of this enzymatic synthesis with a previously described enzymatic synthesis of epoxides from alpha,beta-halohydrins provides an alternate pathway, other than the well-known enzymatic direct epoxidation pathway, from alkene to an epoxide.     

Die vielen Seiten des Sulfids. Tödlich und doch lebensnotwendig

Hydrogen sulfide is highly toxic, but nevertheless it has several physiological functions. Animals from sulfide containing habitats are able to protect themselves from sulfide poisoning and furthermore use this reduced sulfur compound for ATP production. Life at the deep‐sea hydrothermal vents entirely depends on the oxidation of inorganic substrates, mainly sulfide. In humans sulfide acts as a gaseous signalling molecule. It is produced in many tissues and takes part in a number of important metabolic processes such as the regulation of blood pressure and insulin secretion. Several severe diseases are caused by dysfunctions in sulfur metabolism. Thus, a detailed knowledge of the reactions and effects of hydrogen sulfide is of considerable clinical relevance.     

Oxidation of dihydronicotinamide adenine dinucleotide by a flavin derivative of polyethylenimine

A modified Polyethylenimine has been prepared that has riboflavin attached to it, as well as hydrophobic groups. The catalytic efficiency toward oxidation of6 dihydronicotinamide adenine dinucleotide (NADH) by this flavopolymer is more than 100-fold greater than observed with small-molecular riboflavin. The products of the reaction in aerobic solution have been established to be the oxidized nicotinamide NAD⁺ and hydrogen peroxide. The kinetics fit a Michaelis-Menten mechanism. Thus, the versatility of modified polyethylenimines as catalysts has been extended from hydrolyses and decarboxylations to oxidation-reduction reactions also.     

Compounds of the organogenic elements in Apollo 11 and 12 lunar samples: A review

Investigations of low molecular weight compounds of the organogenic elements on lunar samples are reviewed. The three general techniques of vacuum pyrolysis, acid hydrolysis, and crushing have been employed by most investigators. Vacuum pyrolysis of lunar fines produce a variety of gaseous species which are either: (1) indigenous, (2) solar wind products and/or (3) chemical reaction products of mineral phases found in the lunar samples. Acid hydrolysis of lunar fines using deuteriumlabeled acids yields evidence for indigenous methane and ethane. Methane and ethane found in the lunar fines are largely derived from the solar wind with only trace amounts indigenous to the samples. Crushing experiments with lunar fines and breccias produce methane, ethane, hydrogen, nitrogen, hydrogen sulfide and the rare gases.     

Metabolic flux network and analysis of fermentative hydrogen production

Fermentative hydrogen production (FHP) has received a great R & D interest in recent decades, as it offers a potential means of producing H₂ from a variety of renewable resources, even wastewater via a low energy continuous process. Various extracellular metabolites including ethanol, acetate, butyrate and lactate can be produced during the fermentation, building a complex metabolic network of the FHP. Except for the recognition of its complexity, the metabolic flux network has not been well understood. Studies on biochemical reactions and metabolic flux network associated with the FHP in anaerobic fermentation system have only been drawn attention in recent years. This review summarizes the biochemical reactions taking place in the metabolic network of FHP. We discuss how the key operation factors influence metabolism in the FHP process. Recently developed and applied technologies for metabolic flux analysis have been described. Future studies on the metabolic network to enhance fermentative hydrogen production by strict anaerobes are recommended. It is expected that this review can provide useful information in terms of fundamental knowledge and update technology for scientists and research engineers in the field of biological hydrogen production.