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Effect of inoculum conditioning on hydrogen fermentation and pH effect on bacterial community relevant to hydrogen production.

The effect of conditioning for a variety of inoculums on fermentative hydrogen production was investigated. In addition, the effects of pH condition on hydrogen fermentation and bacterial community were investigated. The effect of conditioning on hydrogen production was different depending on the inoculum types. An appreciable hydrogen production was shown with anaerobic digested sludge and lake sediment without conditioning, however, no hydrogen was produced when refuse compost and kiwi grove soil were used as inoculums without conditioning. The highest hydrogen production was obtained with heat-conditioned anaerobic digested sludge, almost the same production was also obtained with unconditioned digested sludge. The pH condition considerably affected hydrogen fermentation, hydrogen gas was efficiently produced with unconditioned anaerobic sludge when the pH was controlled at 6.0 throughout the culture period and not when only the initial pH was adjusted to 6.0 and 7.0. Hydrogen production decreased when the culture pH was only adjusted at the beginning of each batch in continuous batch culture, and additionally, bacterial community varied with the change in hydrogen production. It was suggested that Clostridium and Coprothermobacter species played important role in hydrogen fermentation, and Lactobacillus species had an adverse effect on hydrogen production.

Anaerobiosis↗

The mechanism of action of ethanolamine ammonia-lyase, an adenosylcobalamin-dependent enzyme. Evidence that the hydrogen transfer mechanism involves a second intermediate hydrogen carrier in addition to the cofactor.

Ethanolamine ammonia-lyase catalyzes the adenosylcobalamin (AdoCbl)-dependent conversion of ethanolamine to acetaldehyde and ammonia. During this reaction, a hydrogen atom migrates from the carbinol carbon of ethanolamine to the methyl carbon of acetaldehyde. Previous studies have shown that this migrating hydrogen equilibrates with the hydrogens on the 5'-(cobalt-linked) carbon of the cofactor. On the basis of those studies, a two-step mechanism for hydrogen transfer has been postulated in which the migrating hydrogen is first transferred from the substrate to the cofactor, then in a subsequent step is returned from the cofactor to the product. We now show that this migrating hydrogen is transferred not only to the cofactor, but also to a second acceptor at the active site. Hydrogens on this acceptor do not exchange with water during the course of the reaction, but are released to water when the enzyme is denatured. The catalytic significance of this second hydrogen acceptor was demonstrated by the findings that the transfer of hydrogen to this acceptor required both AdoCbl and active enzyme and that hydrogen at the second acceptor site could be washed out by unlabeled ethanolamine. On the basis of these results, we propose an expanded hydrogen transfer mechanism in which AdoCbl and the second acceptor site serve as alternative intermediate hydrogen carriers during the course of ethanolamine deamination.

Ammonia-Lyases↗

Simultaneous utilization of acetate and hydrogen by Geobacter sulfurreducens and implications for use of hydrogen as an indicator of redox conditions.

Dissolved hydrogen concentrations, in conjunction with other geochemical indicators, are becoming an accepted means to determine terminal electron acceptor processes (TEAPs) in groundwater aquifers. Aqueous hydrogen concentrations have been found to fall within specific ranges under methanogenic, sulfate-reducing, iron-reducing, and denitrification conditions. Although hydrogen is gaining in acceptance for determining subsurface TEAPs, there is a dearth of data with regards to the kinetic coefficients for hydrogen utilization in the presence or absence of an additional electron donor under different TEAPs. This study expands the kinetic data for hydrogen utilization through a series of batch experiments, which were conducted to study the utilization of acetate and hydrogen by Geobacter sulfurreducens under iron-reducing conditions. The results of these experiments indicate that the kinetic coefficients (cell yield and first-order degradation rate) describing the rate of hydrogen utilization by G. sulfurreducens under iron-reducing conditions correlate energetically with the coefficients found in previous experiments under methanogenic and sulfate-reducing conditions. In addition, with acetate and hydrogen as simultaneous electron donors, there is slight inhibition between the two electron donors for G. sulfurreducens, and this can be modeled through competitive inhibition terms in the classic Monod formulation. Finally, a key result of this study is that the TEAP-dependent hydrogen concentration in aquifers is not related solely to the microbial kinetics of the hydrogen-consuming organisms as previously suggested but is affected by the multi-substrate kinetics of hydrogen being consumed simultaneously with other electron donors as well as the availability of the electron acceptor.

Acetates↗

The orientation of N-H...O=C and N-H...N hydrogen bonds in biological systems: how good is a point charge as a model for a hydrogen bonding atom?

In order to design new ligands for protein-binding sites of unknown structure, it would be useful to predict the likely sites of hydrogen bonding of an unknown protein fragment to a known molecule. The positions of maxima and minima in the electrostatic potential at appropriate distances from the van der Waals surface were calculated for various small molecules, nucleic acid bases, peptide units and amino acid side chains containing groups which can form the biologically important N-H...O=C and N-H...N hydrogen bonds. Their ability to predict the positions of H and O/N in hydrogen bonded complexes, as predicted by optimising the electrostatic interactions of pairs of such molecules constrained by the molecular shapes, was assessed. It is shown that extrema in the electrostatic potential around the isolated molecules give worthwhile predictions for the locations of hydrogen binding partners. For molecules bound by a single N-H...O=C hydrogen bond, the electrostatic maximum associated with the H is usually less than 1 A from an acceptor atom, while a C=O electrostatic minimum is generally less than 1.5 A from the hydrogen bond proton. However, a significant number of hydrogen bonds form to the opposite lone pair from the electrostatic minimum, in which case the separation is up to 3.3 A. This reflects the broad electrostatic potential well around a carbonyl oxygen between the lone pair directions. The model predicts when neighbouring atoms drastically change the hydrogen bonding characteristics of an N-H or C=O group. Although the geometries of hydrogen bonded complexes are influenced by the other van der Waals contacts between the molecules, particularly multiple hydrogen bonds, these influences are constant when considering hydrogen bonding to a specific uncharacterised binding site. Hence, the consideration of sterically accessible electrostatic extrema will be useful in the design of new ligands.

Amides↗

Activation of complement in normal serum by hydrogen peroxide and hydrogen peroxide-related oxygen radicals produced by activated neutrophils.

Neutrophils activated by soluble particulate stimuli generate superoxide anion and subsequently form hydrogen peroxide and other oxygen radicals. The effect of hydrogen peroxide on the complement system in normal serum was investigated. Treatment of normal serum with hydrogen peroxide resulted in a diminution of the haemolytic activity of the total and alternative complement pathways and the haemolytic titres of C3 and C5 but not of C2, in normal serum. These decreases in complement activity depended on the concentration of hydrogen peroxide added to the serum. Immunoelectrophoretic analysis of hydrogen peroxide-treated serum showed that C3 and C5 proteins were activated. Complement degradation products C3a and C5a were produced in normal serum treated with hydrogen peroxide, and 20 mM EDTA abolished C3a and C5a production in hydrogen peroxide-treated serum but 20 mM Mg-EGTA did not. Catalase completely abolished and dimethylsulphoxide and D-mannitol, hydroxyl radical scavengers, partially inhibited the hydrogen peroxide-mediated complement activation. Hypochlorite, incubated with normal serum, significantly inhibited serum haemolytic activity, and sodium thiosulphate, a reducing agent, abolished the effect of hypochlorite. Normal serum incubated with activated neutrophils showed neutrophil chemotactic activity and decreased serum haemolytic activity, and the addition of catalase or methionine (5 mM) completely abolished the effects of activated neutrophils. These results suggest that hydrogen peroxide activates complement via an alternative pathway of complement activation and that hydroxyl radicals and other hydrogen peroxide-related species such as hypochlorite are most likely involved in hydrogen peroxide-mediated complement activation. Complement activation by oxygen radicals produced by activated neutrophils may be one of the mechanisms by which complement is activated in human immune complex diseases.

Complement Activation↗

A theoretical study of the effect of a tetraalkylammonium counterion on the hydrogen bond strength in Z-hydrogen maleate.

High-level ab initio calculations (B3LYP/6-31+G and QCISD(T)/6-311+G**) were carried out to resolve the disagreement between recent experimental and computational estimates of the relative strength of the intramolecular hydrogen bond in Z-hydrogen maleate anion with respect to the normal hydrogen bond in maleic acid. The computational estimates for the strength of the intramolecular hydrogen bond in the gas-phase maleate anion are in a range of 14-28 kcal/mol depending on the choice of the reference structure. Computational data suggest that the electrostatic influence of a counterion such as a tetraalkylammonium cation can considerably weaken the hydrogen bonding interaction (by 1.5-2 times) in the complexed hydrogen maleate anion relative to that in the naked anion. The estimated internal H-bonding energies for a series of Z-maleate/R4N+ salts (R = CH3, C2H5, CH3CH2CH2CH2) range from 8 to 13 kcal/mol. The calculated energy differences between the E- and Z-hydrogen maleates complexed to Me4N+, Et4N+, and Bu4N+ cation are 4.9 (B3LYP/6-31+G(d,p)) and 5.7 and 5.8 kcal/mol (B3LYP/6-31G(d)). It is also demonstrated that the sodium cation exerts a similar electrostatic influence on the hydrogen bond strength in bifluoride anion (FHF-). The present study shows that while low-barrier short hydrogen bonds can exist in the gas phase (the barrier for the hydrogen transfer in maleate anion is only 0.2 kcal/mol at the QCISD(T)/6-311+G//QCISD/6-31+G level), whether they can also be strong in condensed media or not depends on how their interactions with their immediate environment affect their strength.

Enzyme Inhibitors↗

Conjugated linoleic acid isomers in partially hydrogenated soybean oil obtained during nonselective and selective hydrogenation processes.

Partially hydrogenated soybean oil samples were collected during selective and nonselective hydrogenation processes. The formation of conjugated linoleic acids (CLAs) during hydrogenation was greatly dependent on the types and duration of hydrogenation processes. During hydrogenation processes, CLA contents increased initially. After reaching maximum CLA content, the content decreased during hydrogenation. Selective hydrogenation was much more favorable for the formation of conjugated linoleic acids. With nonselective hydrogenation process, the total CLA content was a maximum (9.06 mg total CLA/g oil) at 35 min. However, with the selective hydrogenation process, the total CLA content was a maximum (98.27 mg total CLA/g oil) at 210 min. The CLA contents in some of the tested selectively hydrogenated soybean oils were among the highest ever reported in foods.

Esters↗

Studies on hydrogen bonds. Part IV. Proposed working criteria for assessing qualitative strength of hydrogen bonds.

The data obtained in the earlier parts of this series for the donor and acceptor end parameters of N-H...O and O-H...O hydrogen bonds have been utilised to obtain a qualitative working criterion to classify the hydrogen bonds into three categories: "very good" (VG), "moderately good" (MG) and weak (W). The general distribution curves for all the four parameters are found to be nearly of the Gaussian type. Assuming that the VG hydrogen bonds lie between O and +/- 1 sigma, MG hydrogen bonds between +/- 1 sigma and +/- 2 sigma, W hydrogen bonds beyond +/- 2 sigma (where sigma is the standard deviation), suitable cut-off limits for classifying the hydrogen bonds in the three categories have been derived. These limits are used to get VG and MG ranges for the four parameters 1 and theta (at the donor end) and zeta and xi (at the acceptor end). The qualitative strength of a hydrogen bond is decided by the cumulative application of the criteria to all the four parameters. The criterion has been further applied to some practical examples in conformation studies such as alpha-helix and can be used for obtaining suitable location of hydrogen atoms to form good hydrogen bonds. An empirical approach to the energy of hydrogen bonds in the three categories has also been presented.

Chemical Phenomena↗

Hydrogen-hydrogen bonding in planar biphenyl, predicted by atoms-in-molecules theory, does not exist.

Based on an Atoms-in-Molecules (AIM) analysis, Matta et al. recently claimed evidence for the existence of hydrogen-hydrogen bonding between ortho-hydrogen atoms, pointing towards each other from adjacent phenyl groups in planar biphenyl. This AIM result is opposed to the classical view that nonbonded steric repulsion between the ortho-hydrogen atoms is responsible for the higher energy of the planar as compared to the twisted geometry of biphenyl. In the present work, we address the question if hydrogen-hydrogen bonding in biphenyl exists, as suggested by AIM, or not. To this end, we have analyzed the potential energy surface for internal rotation of biphenyl in terms of two interacting phenyl radicals using density functional theory (DFT) at BP86/TZ2P. A detailed analysis of the bonding mechanism and a quantitative bond energy decomposition in the framework of Kohn-Sham DFT show that Pauli (or overlap) repulsion, mainly between C(ortho)--H(ortho) phenyl MOs, prevents biphenyl from being planar and forces it to adopt a twisted equilibrium geometry. Furthermore, a derivative of biphenyl in which all four ortho-hydrogen atoms have been removed does adopt a planar equilibrium geometry. Thus, our results confirm the classical view of steric repulsion between ortho-hydrogen atoms in biphenyl and they falsify the hypothesis of hydrogen-hydrogen bonding.

Journal Article↗

Hydrogen-bonded adducts of triphenylsilanol with diamines: a finite ten-molecule aggregate, and chain, sheet and framework structures built from O-H...O, O-H...N and C-H...pi(arene) hydrogen bonds.

The structures of five hydrogen-bonded adducts of triphenylsilanol, Ph3SiOH, with diamines have been determined. In the 4:1 adduct formed with 1,4-diazabicyclo[2.2.2]octane, (Ph3SiOH)4.C6H12N2 (I) (triclinic, P1, Z' = 2), there are two independent five-component aggregates built from O-H...N and O-H...O hydrogen bonds, in one of which the diamine exhibits orientational disorder: these two aggregates are linked into a cyclic ten-molecule unit by means of two independent C-H...pi(arene) hydrogen bonds. The 4:1 adduct formed with 1,2-bis(4-pyridyl)ethene, (Ph3SiOH)4.C12H10N2 (II) (triclinic, P1, Z' = 0.5), forms a similar five-component aggregate which lies across a centre of inversion: a single C-H...pi(arene) hydrogen bond links these aggregates into a molecular ladder. With N,N'-dimethylpiperazine, triphenylsilanol forms a 2:1 adduct, (Ph3SiOH)2.C6H14N2 (III) (monoclinic, P2(1)/c, Z' = 0.5), in which a three-component aggregate built from O-H...N hydrogen bonds lies across a centre of inversion: two independent C-H...pi(arene) hydrogen bonds link these aggregates into sheets. In the hydrated 2:1 adduct formed with 1,2-bis(4'-bipyridyl)ethane, (Ph3SiOH)2.C12H12N2.H2O (IV) (triclinic, P1, Z' = 1), a combination of two independent O-H...O and two independent N-H...O hydrogen bonds links the five molecular components into a centrosymmetric eight-molecule aggregate, and six independent C-H...pi(arene) hydrogen bonds link these chains into a continuous three-dimensional framework structure. In the dihydrated 2:1 adduct formed with 4,4'-bipyridyl, (Ph3SiOH)2.C10H8N2.(H2O)2 (V) (triclinic, P1, Z' = 1), a combination of four independent O-H...O and two independent N-H.O hydrogen bonds links the five molecular components into a chain of rings, and four independent C-H...pi(arene) hydrogen bonds link these chains into a continuous three-dimensional framework structure.

Journal Article↗

A method for determining the positions of polar hydrogens added to a protein structure that maximizes protein hydrogen bonding.

An automated method for the optimal placement of polar hydrogens in a protein structure is described. This method treats the polar, side chain hydrogens of lysine, serine, threonine, and tyrosine and the amino terminus of a protein. The program, called NETWORK, divides the potential hydrogen-bonding pairs of a protein into groups of interacting donors and acceptors. A search is conducted on each of the local groups to find an arrangement which forms the most hydrogen bonds. If two or more arrangements have the same number of hydrogen bonds, the arrangement with the shortest set of hydrogen bonds is selected. The polar hydrogens of the histidyl side chain are specifically treated, and the ionization state of this residue is allowed to change, if this change results in additional hydrogen bonds for the local group. The program will accept Protein Data Bank as well as Biosym-format coordinate files. Input and output routines can be easily modified to accept other coordinate file formats. The predictions from this method are compared to known hydrogen positions for bovine pancreatic trypsin inhibitor, insulin, RNase-A, and trypsin for which the neutron diffraction structures have been determined. The usefulness of this program is further demonstrated by a comparison of molecular dynamics simulations for the enzyme cytochrome P-450cam with and without using NETWORK.

Animals↗

Hydrogen production by methanogens under low-hydrogen conditions.

Hydrogen production was studied in four species of methanogens (Methanothermobacter marburgensis, Methanosaeta thermophila, Methanosarcina barkeri, and Methanosaeta concilii) under conditions of low (sub-nanomolar) ambient hydrogen concentration using a specially designed culture apparatus. Transient hydrogen production was observed and quantified for each species studied. Methane was excluded as the electron source, as was all organic material added during growth of the cultures (acetate, yeast extract, peptone). Hydrogen production showed a strong temperature dependence, and production ceased at temperatures below the growth range of the organisms. Addition of polysulfides to the cultures greatly decreased hydrogen production. The addition of bromoethanesulfonic acid had little influence on hydrogen production. These experiments demonstrate that some methanogens produce excess reducing equivalents during growth and convert them to hydrogen when the ambient hydrogen concentration becomes low. The lack of sustained hydrogen production by the cultures in the presence of methane provides evidence against "reverse methanogenesis" as the mechanism for anaerobic methane oxidation.

Alkanesulfonic Acids↗

'Determination' of sugar alcohol and Polydextrose absorption in humans by the breath hydrogen (H2) technique: the stoichiometry of hydrogen production and the interaction between carbohydrates assessed in vivo and in vitro.

The production of hydrogen from substrates and substrate mixture of sugar alcohols and Polydextrose was determined, both in vivo using the breath hydrogen test, and in vitro, using human faecal microorganisms in anaerobic culture. One objective was to test a previous assumption that the stoichiometry of hydrogen production from different alternative carbohydrates is similar. Another objective was to discover whether hydrogen responses from mixtures of substrates were simply additive, or whether interactions occurred. The breath tests were performed in a 10 subject x 10 substrate factorial design with substrates and substrate mixtures (5-11 g) administered in 42 g chocolate confectionery. Incorporation of the alternative carbohydrates lactitol (L), Isomalt (I) and Polydextrose (P) into otherwise conventional confectionery increased breath hydrogen production by approximately 112, 73 and 11%/g respectively. There was no interaction between L and I or between P and I, but a combination of L and P approximately doubled the breath hydrogen anticipated from their individual contributions (P < 0.05). Anaerobic cultures showed a sixfold range in the efficiency of converting individual substrates and mixtures to hydrogen gas (0.003-0.018 kJ H2 per kJ carbohydrate). The positive interaction between L and P, and the lack of interaction between L and I, and between P and I, found in vivo were reproduced in vitro. The work showed that interpretation of the hydrogen breath test is confounded by differing stoichiometries for hydrogen production, by interaction between substrates and by an uncertain extent to which small intestinal hydrolysis yielding species with a fermentation stoichiometry that differs from the parent substrate.

Absorption↗

Assessment of the influence of hydrogen nonexcretion on the usefulness of the hydrogen breath test and lactose tolerance test.

The recognition of hydrogen nonexcretion in up to 20% of tested subjects and the large ethnic differences in the prevalence of lactose malabsorption make it necessary to reassess the diagnostic usefulness of the lactose tolerance test and the hydrogen breath test. Both tests were performed in 83 consecutive patients with suspected lactose malabsorption who ingested 50 g lactose. On a separate day a hydrogen breath test was performed after 25 g lactulose. The prevalence of hydrogen nonexcretion was 18%. The diagnostic usefulness of hydrogen breath test was influenced both by the individual threshold for hydrogen excretion and the amount of malabsorbed lactose. In addition to baseline values, breath samples for hydrogen measurements have to be taken at 30, 60, 90, 180, and 240 minutes after ingestion of lactose. For the lactose tolerance test only one measurement of serum glucose at 30 minutes is needed in addition to the baseline measurement. The combination of both tests excludes the influence of hydrogen nonexcretion, but even if a combined diagnostic approach utilizing the lactose hydrogen breath test and lactose tolerance test is used, 6% of patients presenting with symptoms suggestive of lactose intolerance cannot be classified.

Adolescent↗