Intramolecular Isotope Effects for Benzylic Hydroxylation of Isomeric Xylenes and 4,4‘-Dimethylbiphenyl by Cytochrome P450:  Relationship between Distance of Methyl Groups and Masking of the Intrinsic Isotope Effect†

Biochemistry ◽  
1997 ◽  
Vol 36 (23) ◽  
pp. 7136-7143 ◽  
Author(s):  
Krishna R. Iyer ◽  
Jeffrey P. Jones ◽  
John F. Darbyshire ◽  
William F. Trager
Keyword(s):  
Cytochrome P450 ◽  
Isotope Effect ◽  
Isotope Effects ◽  
Methyl Groups ◽  
Benzylic Hydroxylation

scholarly journals Insights Into the Known 13C Depletion of Methane—Contribution of the Kinetic Isotope Effects on the Serine Hydroxymethyltransferase Reaction

2022 ◽  
Vol 9 ◽  
Author(s):  
Gerd Gleixner
Keyword(s):  
Isotope Effect ◽  
Kinetic Isotope Effect ◽  
Isotope Effects ◽  
Serine Hydroxymethyltransferase ◽  
Chemical Degradation ◽  
Methyl Groups ◽  
Kinetic Isotope ◽  
Isotopic Pattern ◽  
Before And After ◽  
Metal Organic

We determined the kinetic isotope effect on the serine hydroxymethyltransferase reaction (SHMT), which provides important C1 metabolites that are essential for the biosynthesis of DNA bases, O-methyl groups of lignin and methane. An isotope effect on the SHMT reaction was suggested being responsible for the well-known isotopic depletion of methane. Using the cytosolic SHMT from pig liver, we measured the natural carbon isotope ratios of both atoms involved in the bond splitting by chemical degradation of the remaining serine before and after partial turnover. The kinetic isotope effect 13(VMax/Km) was 0.994 0.006 and 0.995 0.007 on position C-3 and C-2, respectively. The results indicated that the SHMT reaction does not contribute to the 13C depletion observed for methyl groups in natural products and methane. However, from the isotopic pattern of caffeine, isotope effects on the methionine synthetase reaction and on reactions forming Grignard compounds, the involved formation and fission of metal organic bonds are likely responsible for the observed general depletion of “activated” methyl groups. As metal organic bond formations in methyl transferases are also rate limiting in the formation of methane, they may likely be the origin of the known 13C depletion in methane.

DEUTERIUM KINETIC ISOTOPE EFFECTS: V TEMPERATURE DEPENDENCE OF β-DEUTERIUM EFFECTS IN WATER SOLVOLYSIS OF ISOPROPYL COMPOUNDS

1961 ◽  
Vol 39 (10) ◽  
pp. 1989-1994 ◽  
Author(s):  
K. T. Leffek ◽  
R. E. Robertson ◽  
S. E. Sugamori
Keyword(s):  
Temperature Dependence ◽  
Isotope Effect ◽  
Isotope Effects ◽  
Zero Point ◽  
Kinetic Isotope Effects ◽  
Methyl Groups ◽  
Deuterium Isotope Effect ◽  
Point Energy ◽  
Kinetic Isotope ◽  
Enthalpy Of Activation

The secondary β-deuterium isotope effect (kH/kD) has been measured over a range of temperature for the water solvolysis reactions of isopropyl methanesulphonate, p-toluenesulphonate, and bromide. In these cases the isotope effect is due to a difference in entropies of activation of the isotopic analogues rather than a difference in the enthalpies of activation. It is suggested that the observed isotope effect is due to internal rotational effects of the methyl groups in the isopropyl radical, and the lack of an isotope effect on the enthalpy of activation is accounted for by a cancellation of an effect from this source and one from zero-point energy.

Proton transfer reactions between ortho-methyl substituted derivatives of 4-nitrophenylphenylcyanomethane and nitrogen bases in acetonitrile solvent

1988 ◽  
Vol 66 (6) ◽  
pp. 1454-1458 ◽  
Author(s):  
Kenneth T. Leffek ◽  
Przemyslaw Pruszynski
Keyword(s):  
Proton Transfer ◽  
Isotope Effect ◽  
Rate Constants ◽  
Isotope Effects ◽  
Equilibrium Constants ◽  
Activation Parameters ◽  
Transfer Reactions ◽  
Methyl Groups ◽  
Methyl Group ◽  
Proton Transfer Reactions

Equilibrium constants, rate constants, primary deuterium isotope effects, and activation parameters have been measured for the proton transfer reactions in acetonitrile solvent of 4-nitrophenylphenylcyanomethane and 2-methyl-4-nitrophenylphenyl-cyanomethane with tetramethylguanidine base and for the reactions of 2-methyl-4-nitrophenylphenylcyanomethane and 2,6-di-methyl-4-nitrophenylphenylcyanomethane with 1,5-diazabicyclo[5.4.0]undec-7-ene base. Introduction of the ortho-methyl groups in the substrate molecule caused significant reductions in the equilibrium and rate constants. The expected rise in the kinetic primary deuterium isotope effect was not observed when the first ortho-methyl group was introduced, but a 20% increase did accompany the introduction of the second ortho-methyl group. Enthalpy of activation measurements indicated that there was no increase in the proton tunnelling contribution to the isotope effect when the amount of steric hindrance is increased with ortho-methyl groups.

Secondary Isotope Effects on the Ionization of 2-Nitropropane

1974 ◽  
Vol 52 (10) ◽  
pp. 1889-1896 ◽  
Author(s):  
A. J. Kresge ◽  
D. A. Drake ◽  
Y. Chiang
Keyword(s):  
Aqueous Solution ◽  
Isotope Effect ◽  
Kinetic Isotope Effect ◽  
Isotope Effects ◽  
Kinetic Isotope Effects ◽  
Acid Dissociation ◽  
Methyl Groups ◽  
Anomalous Effect ◽  
Hydroxide Ion ◽  
Kinetic Isotope

The equilibrium isotope effect on the acid dissociation of 2-nitropropane in wholly aqueous solution at 25° was found to be KH/KD = 1.23 ± 0.03 for complete deuteration of both methyl groups; the kinetic isotope effect for reaction of the same substrate with hydroxide ion, kH/kD = 1.09 ± 0.01; and the kinetic isotope effect for reaction with tris-(hydroxymethyl)-methylamine, kH/kD = 1.10 ± 0.01; both of the latter also refer to wholly aqueous solution at 25° and are for complete deuteration of both methyl groups. It is shown that the equilibrium isotope effect is largely, and the kinetic isotope effects probably partly, hyper conjugative in origin, thus supporting a hyper conjugative explanation of the anomalous effect of methyl groups on nitroalkane ionization.

scholarly journals Nitrogen isotope effects can be used to diagnose N transformations in wastewater anammox systems

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Paul M. Magyar ◽  
Damian Hausherr ◽  
Robert Niederdorfer ◽  
Nicolas Stöcklin ◽  
Jing Wei ◽  
...  
Keyword(s):  
Isotope Effect ◽  
Isotope Composition ◽  
Isotope Effects ◽  
Nitrogen Isotope ◽  
Anammox Bacteria ◽  
Ammonium Oxidation ◽  
Experimental Conditions ◽  
N Transformations ◽  
Natural Systems ◽  
Inverse Isotope Effect

AbstractAnaerobic ammonium oxidation (anammox) plays an important role in aquatic systems as a sink of bioavailable nitrogen (N), and in engineered processes by removing ammonium from wastewater. The isotope effects anammox imparts in the N isotope signatures (15N/14N) of ammonium, nitrite, and nitrate can be used to estimate its role in environmental settings, to describe physiological and ecological variations in the anammox process, and possibly to optimize anammox-based wastewater treatment. We measured the stable N-isotope composition of ammonium, nitrite, and nitrate in wastewater cultivations of anammox bacteria. We find that the N isotope enrichment factor 15ε for the reduction of nitrite to N2 is consistent across all experimental conditions (13.5‰ ± 3.7‰), suggesting it reflects the composition of the anammox bacteria community. Values of 15ε for the oxidation of nitrite to nitrate (inverse isotope effect, − 16 to − 43‰) and for the reduction of ammonium to N2 (normal isotope effect, 19–32‰) are more variable, and likely controlled by experimental conditions. We argue that the variations in the isotope effects can be tied to the metabolism and physiology of anammox bacteria, and that the broad range of isotope effects observed for anammox introduces complications for analyzing N-isotope mass balances in natural systems.

A New Mechanistic Probe for Cytochrome P450:  An Application of Isotope Effect Profiles

1997 ◽  
Vol 119 (21) ◽  
pp. 5069-5070 ◽  
Author(s):  
John I. Manchester ◽  
Joseph P. Dinnocenzo ◽  
Higgins ◽  
Jeffrey P. Jones
Keyword(s):  
Cytochrome P450 ◽  
Isotope Effect ◽  
Mechanistic Probe

scholarly journals Deuterium isotope effects in drug pharmacokinetics II: Substrate-dependence of the reaction mechanism influences outcome for cytochrome P450 cleared drugs

PLoS ONE ◽  
2018 ◽  
Vol 13 (11) ◽  
pp. e0206279 ◽  
Author(s):  
Hao Sun ◽  
David W. Piotrowski ◽  
Suvi T. M. Orr ◽  
Joseph S. Warmus ◽  
Angela C. Wolford ◽  
...  
Keyword(s):  
Cytochrome P450 ◽  
Reaction Mechanism ◽  
Isotope Effects ◽  
Substrate Dependence ◽  
Deuterium Isotope Effects ◽  
Drug Pharmacokinetics

scholarly journals Oxygen isotope fractionation during N<sub>2</sub>O production by soil denitrification

2016 ◽  
Vol 13 (4) ◽  
pp. 1129-1144 ◽  
Author(s):  
Dominika Lewicka-Szczebak ◽  
Jens Dyckmans ◽  
Jan Kaiser ◽  
Alina Marca ◽  
Jürgen Augustin ◽  
...  
Keyword(s):  
Oxygen Isotope ◽  
Soil Water ◽  
Isotope Effect ◽  
Isotope Exchange ◽  
Isotope Fractionation ◽  
Isotope Effects ◽  
N2o Production ◽  
Oxygen Isotope Fractionation ◽  
Oxygen Isotope Exchange ◽  
Incubation Experiments

Abstract. The isotopic composition of soil-derived N2O can help differentiate between N2O production pathways and estimate the fraction of N2O reduced to N2. Until now, δ18O of N2O has been rarely used in the interpretation of N2O isotopic signatures because of the rather complex oxygen isotope fractionations during N2O production by denitrification. The latter process involves nitrate reduction mediated through the following three enzymes: nitrate reductase (NAR), nitrite reductase (NIR) and nitric oxide reductase (NOR). Each step removes one oxygen atom as water (H2O), which gives rise to a branching isotope effect. Moreover, denitrification intermediates may partially or fully exchange oxygen isotopes with ambient water, which is associated with an exchange isotope effect. The main objective of this study was to decipher the mechanism of oxygen isotope fractionation during N2O production by soil denitrification and, in particular, to investigate the relationship between the extent of oxygen isotope exchange with soil water and the δ18O values of the produced N2O. In our soil incubation experiments Δ17O isotope tracing was applied for the first time to simultaneously determine the extent of oxygen isotope exchange and any associated oxygen isotope effect. We found that N2O formation in static anoxic incubation experiments was typically associated with oxygen isotope exchange close to 100 % and a stable difference between the 18O ∕ 16O ratio of soil water and the N2O product of δ18O(N2O ∕ H2O)  =  (17.5 ± 1.2) ‰. However, flow-through experiments gave lower oxygen isotope exchange down to 56 % and a higher δ18O(N2O ∕ H2O) of up to 37 ‰. The extent of isotope exchange and δ18O(N2O ∕ H2O) showed a significant correlation (R2 = 0.70, p <  0.00001). We hypothesize that this observation was due to the contribution of N2O from another production process, most probably fungal denitrification. An oxygen isotope fractionation model was used to test various scenarios with different magnitudes of branching isotope effects at different steps in the reduction process. The results suggest that during denitrification, isotope exchange occurs prior to isotope branching and that this exchange is mostly associated with the enzymatic nitrite reduction mediated by NIR. For bacterial denitrification, the branching isotope effect can be surprisingly low, about (0.0 ± 0.9) ‰, in contrast to fungal denitrification where higher values of up to 30 ‰ have been reported previously. This suggests that δ18O might be used as a tracer for differentiation between bacterial and fungal denitrification, due to their different magnitudes of branching isotope effects.

scholarly journals Continuous measurements of nitrous oxide isotopomers during incubation experiments

2016 ◽  
Author(s):  
Malte Winther ◽  
David Balslev-Harder ◽  
Søren Christensen ◽  
Anders Priemé ◽  
Bo Elberling ◽  
...  
Keyword(s):  
Nitrous Oxide ◽  
Greenhouse Gas ◽  
Isotope Effect ◽  
Atmospheric Chemistry ◽  
Isotope Effects ◽  
Denitrifying Bacteria ◽  
Central Position ◽  
Site Preference ◽  
Continuous Measurements ◽  
Incubation Experiments

Abstract. Nitrous oxide (N2O) is an important and strong greenhouse gas in the atmosphere and part of a feed-back loop with climate. N2O is produced by microbes during nitrification and denitrification in terrestrial and aquatic ecosystems. The main sinks for N2O are turnover by denitrification and photolysis and photo-oxidation in the stratosphere. The position of the isotope 15N in the linear N = N = O molecule can be distinguished between the central or terminal position (isotopomers of N2O). It has been demonstrated that nitrifying and denitrifying microbes have a different relative preference for the terminal and central position. Therefore, measurements of the site preference in N2O can be used to determine the source of N2O i.e. nitrification or denitrification. Recent instrument development allows for continuous (on the order of days) position dependent δ15N measurements at N2O concentrations relevant for studies of atmospheric chemistry. We present results from continuous incubation experiments with denitrifying bacteria, Pseudomonas fluorescens (producing and reducing N2O) and P. chlororaphis (only producing N2O). The continuous position dependent measurements reveal the transient pattern (KNO3 to N2O and N2, respectively), which can be compared to previous reported site preference (SP) values. We find bulk isotope effects of −5.5 ‰ ± 0.9 for P. chlororaphis. For P. fluorescens, the bulk isotope effect during production of N2O is −50.4 ‰ ± 9.3 and 8.5 ‰ ± 3.7 during N2O reduction. The values for P. fluorescens are in line with earlier findings, whereas the values for P. chlororaphis are larger than previously published δ15Nbulk measurements from production. The calculations of the SP isotope effect from the measurements of P. chlororaphis result in values of −6.6 ‰ ± 1.8. For P. fluorescens, the calculations results in SP values of −5.7 ‰ ± 5.6 during production of N2O and 2.3 ‰ ± 3.2 during reduction of N2O. In summary, we implemented continuous measurements of N2O isotopomers during incubation of denitrifying bacteria and believe that similar experiments will lead to a better understanding of denitrifying bacteria and N2O turnover in soils and sediments and ultimately hands-on knowledge on the biotic mechanisms behind greenhouse gas exchange of the Globe.

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