Group contributions for estimating standard gibbs energies of formation of biochemical compounds in aqueous solution

Mavrovouniotis, Michael L.

doi:10.1002/bit.260361013

Cited by 222 publications

(134 citation statements)

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“…[23,24] However, this method could not be applied for the investigated set of reactions, since the group contributions on the substrate and product side are the same, yielding a standard DG 0 a;R ¼ 0, which is physically not reasonable.…”

Section: Obtain K Via Computational Chemistrymentioning

confidence: 98%

Maximise Equilibrium Conversion in Biphasic Catalysed Reactions: How to Obtain Reliable Data for Equilibrium Constants?

et al. 2006

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For the prediction and optimisation of the equilibrium conversion in biphasic catalysed reactions, the equilibrium constant of the desired reaction and the partition coefficients of all reactants have to be known. Within this contribution we have examined the alcohol dehydrogenase-catalysed reduction of several linear and aromatic ketones in biphasic reaction media with respect to equilibrium conversion. In this example, the equilibrium constant can be expressed in terms of differences in oxidation-reduction potentials DE 0 . However, for a large variety of organic compounds, these data are quite rare in the literature. To overcome this lack of data, we have utilised methods of computational chemistry to calculate data for the Gibbs free energy DG R leading to the equilibrium constants of a homologous series of linear ketones. To obtain comparable data for the reduction of substituted acetophenone derivatives, the Hammett relation leads to the necessary equilibrium constants. Furthermore, we compare the equilibrium conversions of a set of cofactor regeneration methods for the alcohol dehydrogenase-catalysed reductions. These results lead to a time-saving experimental design for the enantioselective reduction of 2-octanone to (R)-2-octanol on a preparative scale utilising biphasic reaction conditions.

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Section: Obtain K Via Computational Chemistrymentioning

confidence: 98%

Maximise Equilibrium Conversion in Biphasic Catalysed Reactions: How to Obtain Reliable Data for Equilibrium Constants?

et al. 2006

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“…BADH seems to drastically increase the effect of the E. coli dehydrogenases; the equilibrium of this dehydrogenase reaction seems to lie on the side of the alcohol. In fact, the Gibbs energy change of the dehydrogenation of benzyl alcohol, calculated according to the group contribution method of Mavrovouniotis (32,33), is 5 kcal/mol or, calculated according to the Gibbs energies of formation given by Dean (34), 4 kcal/mol. (The Gibbs energy change of the oxygenation of benzyl alcohol amounts to Ϫ100 kcal/mol.)…”

Section: Xmo Catalyzes the Oxygenation Not Only Of Toluene And Xylenementioning

confidence: 99%

Xylene Monooxygenase Catalyzes the Multistep Oxygenation of Toluene and Pseudocumene to Corresponding Alcohols, Aldehydes, and Acids in Escherichia coli JM101

Bühler¹,

Schmid²,

Hauer³

et al. 2000

Journal of Biological Chemistry

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Xylene monooxygenase of Pseudomonas putida mt-2 catalyzes the methylgroup hydroxylation of toluene and xylenes. To investigate the potential of xylene monooxygenase to catalyze multistep oxidations of one methyl group, we tested recombinant Escherichia coli expressing the monooxygenase genes xylM and xylA under the control of the alk regulatory system of Pseudomonas oleovorans Gpo1. Expression of xylene monooxygenase genes could efficiently be controlled by n-octane and dicyclopropylketone. Xylene monooxygenase was found to catalyze the oxygenation of toluene, pseudocumene, the corresponding alcohols, and the corresponding aldehydes. For all three transformations 18 O incorporation provided stong evidence for a monooxygenation type of reaction, with gem-diols as the most likely reaction intermediates during the oxygenation of benzyl alcohols to benzaldehydes. To investigate the role of benzyl alcohol dehydrogenase (XylB) in the formation of benzaldehydes, xylB was cloned behind and expressed in concert with xylMA. In comparison to E. coli expressing only xylMA, the presence of xylB lowered product formation rates and resulted in back formation of benzyl alcohol from benzaldehyde. In P. putida mt-2 XylB may prevent the formation of high concentrations of the particularly reactive benzaldehydes. In the case of high fluxes through the degradation pathways and low aldehyde concentrations, XylB may contribute to benzaldehyde formation via the energetically favorable dehydrogenation of benzyl alcohols. The results presented here characterize XylMA as an enzyme able to catalyze the multistep oxygenation of toluenes.

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“…The standard free energies (cal/mmol product) for the biosynthesis of each of the 20 protein amino acids, eight nucleotides, and three lipids at 25°C and pH 7 were calculated using the estimation method of Mavrovouniotis (1990Mavrovouniotis ( , 1991 and the energy values of Thauer et al (1977) assuming a water activity of 1.0 (Jencks 1976). The free energies of reactions A, B, and C (in cal/g dry wt.…”

Section: Methodsmentioning

confidence: 99%

“…The organic fermentation reactions were obtained from Gottschalk (1986). The free energy (cal/mmol) of each of these reactions at 25°C and pH 7 was calculated using the estimation method of Mavrovouniotis (1990Mavrovouniotis ( , 1991 and the energy values of Thauer et al (1977) assuming a water activity of 1.0 (Jencks 1976). The energy values were adjusted to 1 mM reactant and product concentrations as described by Jencks (1976) and then divided by the total amount of reactant carbon (mmol) to give the free energy of each process in cal/mmol of carbon.…”

Section: Methodsmentioning

confidence: 99%

“…As shown below for the aldehyde group, the standard reduction potentials in Fig. 3 were determined by first estimating the standard free energy (kcal/mol) of reactions in which each group (molecule) drives hydrogen formation at pH 7 and 25°C using the estimation method of Mavrovouniotis (1990Mavrovouniotis ( , 1991 and the energy values of Thauer et al (1977). The free energy values were then converted to mV units using this relationship-a difference of 100 mV corresponds to a free energy change of −4.6 kcal/mol at pH 7 and 25°C (Zubay 1983b).…”

Section: Redox Disproportionation Calculationsmentioning

confidence: 99%

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Energy from Redox Disproportionation of Sugar Carbon Drives Biotic and Abiotic Synthesis

Weber

1997

J Mol Evol

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To identify the energy source that drives the biosynthesis of amino acids, lipids, and nucleotides from glucose, we calculated the free energy change due to redox disproportionation of the substrate carbon of (1) 26-carbon fermentation reactions and (2) the biosynthesis of amino acids and lipids of E. coli from glucose. The free energy (cal/mmol of carbon) of these reactions was plotted as a function of the degree of redox disproportionation of carbon (disproportionative electron transfers (mmol)/mmol of carbon). The zero intercept and proportionality between energy yield and degree of redox disporportionation exhibited by this plot demonstrate that redox disproportionation is the principal energy source of these redox reactions (slope of linear fit = -10.4 cal/mmol of disproportionative electron transfers). The energy and disproportionation values of E. coli amino acid and lipid biosynthesis from glucose lie near this linear curve fit with redox disproportionation accounting for 84% and 96% (and ATP only 6% and 1%) of the total energy of amino acid and lipid biosynthesis, respectively. These observations establish that redox disproportionation of carbon, and not ATP, is the primary energy source driving amino acid and lipid biosynthesis from glucose. In contrast, we found that nucleotide biosynthesis involves very little redox disproportionation, and consequently depends almost entirely on ATP for energy. The function of sugar redox disproportionation as the major source of free energy for the biosynthesis of amino acids and lipids suggests that sugar disproportionation played a central role in the origin of metabolism, and probably the origin of life.

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Group contributions for estimating standard gibbs energies of formation of biochemical compounds in aqueous solution

Cited by 222 publications

References 8 publications

Maximise Equilibrium Conversion in Biphasic Catalysed Reactions: How to Obtain Reliable Data for Equilibrium Constants?

Maximise Equilibrium Conversion in Biphasic Catalysed Reactions: How to Obtain Reliable Data for Equilibrium Constants?

Xylene Monooxygenase Catalyzes the Multistep Oxygenation of Toluene and Pseudocumene to Corresponding Alcohols, Aldehydes, and Acids in Escherichia coli JM101

Energy from Redox Disproportionation of Sugar Carbon Drives Biotic and Abiotic Synthesis

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