Primary Deuterium Isotope Effects Research Articles

Kinetics and mechanism of the oxidation of alcohols by ruthenate and perruthenate ions

In addition to being important synthetic reagents, ruthenate and perruthenate are of interest because they are representative of a number of high valent transition metal ions that can be used as oxidants in organic chemistry. In their reactions with alcohols both ions exhibit several striking similarities — concave Hammett plots, primary deuterium isotope effects, small enthalpies of activation, and large negative entropies of activation. The most likely explanation of the concave upward Hammett plots is the involvement of free radical-like transition states that could be formed by the decomposition of organometallic intermediates. Keywords: oxidation, ruthenate, perruthenate, alcohols, mandelic acid.

Rate constants for a mechanism including intermediates in the interconversion of ternary complexes by horse liver alcohol dehydrogenase

Transient kinetic data for partial reactions of alcohol dehydrogenase and simulations of progress curves have led to estimates of rate constants for the following mechanism, at pH 8.0 and 25 degrees C: E in equilibrium E-NAD+ in equilibrium *E-NAD+ in equilibrium E-NAD(+)-RCH2OH in equilibrium E-NAD+-RCH2O- in equilibrium *E-NADH-RCHO in equilibrium E-NADH-RCHO in equilibrium E-NADH in equilibrium E. Previous results show that the E-NAD+ complex isomerizes with a forward rate constant of 620 s-1 [Sekhar, V. C., & Plapp, B. V. (1988) Biochemistry 27, 5082-5088]. The enzyme-NAD(+)-alcohol complex has a pK value of 7.2 and loses a proton rapidly (greater than 1000 s-1). The transient oxidation of ethanol is 2-fold faster in D2O, and proton inventory results suggest that the transition state has a charge of -0.3 on the substrate oxygen. Rate constants for hydride ion transfer in the forward or reverse reactions were similar for short-chain aliphatic substrates (400-600 s-1). A small deuterium isotope effect for transient oxidation of longer chain alcohols is apparently due to the isomerization of the E-NAD+ complex. The transient reduction of aliphatic aldehydes showed no primary deuterium isotope effect; thus, an isomerization of the E-NADH-aldehyde complex is postulated, as isomerization of the E-NADH complex was too fast to be detected. The estimated microscopic rate constants show that the observed transient reactions are controlled by multiple steps.

Labelled compounds of interest as antitumour agents. Part III (1). Synthesis of 2H and 3H isotopomers of etanidazole (SR 2508)

AbstractChemically and radiochemically efficient syntheses of N‐(2‐hydroxy‐2‐[2H]ethyl)‐2‐(2‐nitroimidazol‐l‐yl)acetamide and N‐(2‐hydroxy‐2‐[3H]ethyl)‐2‐(2‐nitroimidazol‐1‐yl)acetamide, isotopomers of the hypoxic cell radiosensitiser etanidazole (SR 2508), have been achieved by reduction of the corresponding aldehyde with isotopically labelled sodium borohydride. The primary kinetic deuterium isotope effect for the process is 1.5.

A radiometric kynurenine monooxygenase assay

Kynurenine 3-monooxygenase is a flavin-dependent monooxygenase that catalyzes the oxidation of l-kynurenine to 3-hydroxyl- l-kynurenine in the kynurenine pathway of tryptophan metabolism. The enzyme requires NADH or NADPH as a cofactor. A discontinuous assay that utilizes l-[ 3H]kynurenine as substrate is described. The assay offers high precision and a wide range of accessible substrate and cofactor concentrations. The assay was used to measure kinetic isotope effects and the stereospecificity of oxidation of the cofactor. Hydride is transferred from the A-side (pro- R) of NADH and NADPH since primary deuterium isotope effects were observed for both cofactors when they were deuterated on the A-side but not on the B-side. The large isotope effect on V max K m for NADH is sensitive to the concentration of kynurenine, which indicates that NADH can bind before kynurenine.

Rate‐limiting deprotonation of (arylsulfonyl)methyl perchlorates in dichloromethane. Evidence for proton tunneling and the high dynamic basicity of HMPA in a nonaqueous solvent

AbstractKinetic data are reported for the water‐catalyzed hydrolysis of several (arylsulfonyl)‐methyl perchlorates in water and for the HMPA‐catalyzed decomposition of the same substrates in dichloromethane. Under both conditions, the reaction exhibits general base catalysis and the covalent perchlorates react via rate‐limiting deprotonation at the α‐sulfonyl methylene moiety. Primary kinetic deuterium isotope effects (KDIE's) in water are indicative for a complete loss of zero‐point energy in the transition state. The high symmetry of the transition state is supported by the Brönsted β value of ca. 0.5.HMPA was found to be an effective general base catalyst in dichloromethane as the solvent. This reaction shows primary KDIE's (kH/kD = 9.3 at 25°C) which are about 1.5 times higher than the (semi)classical limit. In addition, the ratio of the pre‐exponential Arrhenius factors is abnormally small (AH/AD = 0.14). These classically anomalous results are interpreted in terms of a contribution of quantum‐mechanical tunneling to the transition state for HMPA‐induced deprotonation. Possible reasons for the different kinetic characteristics of the deprotonation reaction in the aqueous and nonaqueous medium are given.

Primary kinetic isotope effects on acid-catalysed reduction of p-benzoquinone derivatives by an acid-stable NADH analogue

The primary kinetic deuterium isotope effects on the reduction of a series of p-benzoquinone derivatives (Q) by an acid-stable NADH analogue, 9,10-dihydro-10-methylacridine (AcrH2) in an aqueous solution (H2O–EtOH; 5 : 1 v/v) as well as in acetonitrile have been determined in the absence and presence of various concentrations of perchloric acid at 298 K. Origins of observed variation of the primary kinetic isotope effects depending on the acid concentration and p-benzoquinone derivatives are ascribed to the hydrogen-atom transfer from AcrH+˙2 to QH˙ following the acid-catalysed electron-transfer from AcrH2 to Q, based on the dependence of the primary kinetic isotope effects on the energetics of transfer of hydride ion, proton, and hydrogen atom.

Bovine Liver Formaldehyde Dehydrogenase: Kinetic and molecular properties

The dimeric formaldehyde dehydrogenase from bovine liver has been resolved into three nearly homogeneous enzyme forms by the successive use of ion-exchange, affinity, and ampholine (chromatofocusing) chromatography. The different enzyme species were isolated in the approximate proportions 3:2:1, having pI values of 6.5, 6.2, and 6.0, respectively. The subunit molecular weights of the three forms are all similar (Mr congruent to 41,000), on the basis of sodium dodecyl sulfategel electrophoresis. The enzyme species appear to arise from covalent differences unrelated either to partial proteolysis during isolation or to differential sialization of homodimeric protein. Human liver contains a single major form and two minor forms of formaldehyde dehydrogenase having pI values very similar to those found for the bovine liver enzyme. The macroscopic kinetic constants (V, V/K) for the three forms of the dehydrogenase from bovine liver are all similar in magnitude, using NADH and S-hydroxymethylglutathione as substrates. The isotope-sensitive hydride transfer step is not significantly rate-limiting during catalysis by any of the forms, as evidenced by the near-unity primary deuterium isotope effects on both V and V/KS (for S-hydroxymethylglutathione); catalysis may be limited by the rate of dissociation of at least one (and possibly both) of the product molecules. In support of rate-limiting dissociation of NAD+ in the normal reaction, V increases by approximately 22-fold and isotope effects of approximately 1.4 are observed on both V and V/KS, using the coenzyme analog 3-acetylpyridine adenine dinucleotide. Product dissociation from the active site appears to be accelerated by the presence of dilute denaturing agents, perhaps indicative of a rate-limiting conformational transition associated with product release.

Deuterium Isotope Effects during HMX Combustion: Chemical kinetic burn rate control mechanism verified

AbstractThe appearance of a significant deuterium isotope effect during the combustion of the solid HMX compound verifies that the chemical reaction kinetics is a major contributor in determining the experimentally observed or global burn rate. Burn rate comparison of HMX and its deuterium labeled HMX‐d8 analogue reveals a primary kinetic deuterium isotope effect (1° KDIE) at 500 psig (3.55 MPa) and l000 psig (6.99 MPa) pressures and selectively identifies covalent carbon‐hydrogen bond rupture as the mechanistic step which ultimately controls the HMX bum rate under the static combustion conditions of this experiment. The 1° KDIE value further suggests the rate‐limiting CH bond rupture occurs during the solid state HMX decomposition/deflagration portion of the overall combustion event and is supported by other independently published studies. A possible anomalous KDIE result at 1500 psig (10.4 MPa) is addressed. This condensed phase KDIE approach illustrates a direct link between lower temperature/pressure thermal decomposition and deflagration processes and their potential applicability to the combustion regime. Most importantly, a new general method is demonstrated for mechanistic combustion investigations which selectively permits an in‐situ identification of the compound's burn rate‐controlling step.

Isotope effects on the crotonase reaction.

The primary, alpha-secondary, beta-secondary, and beta'-secondary deuterium and primary 18O kinetic isotope effects on V/K for the dehydration of [(3S)-3-hydroxybutyryl]pantetheine by bovine liver crotonase (enoyl-CoA hydratase, EC 4.2.1.17) have been determined by the equilibrium perturbation method. The primary deuterium and 18O kinetic isotope effects are 1.61 and 1.051, respectively. The secondary deuterium effects at C-2, C-3, and C-4 are 1.12, 1.13, and 1.00 per H, respectively. The large 18O isotope effect suggests C-O bond cleavage is largely rate determining but is consistent with either an E1cb or E2 mechanism with a large amount of carbanion character. The beta-secondary effect is a factor of 1.05 greater than the equilibrium isotope effect, indicating that this C-H bond is less stiff in the affected transition state or that its motion is coupled to the reaction coordinate motion. Analytical solutions to the differential equations describing uni-uni equilibrium perturbations are presented.

Mechanistic studies on the bovine liver mitochondrial dihydroorotate dehydrogenase using kinetic deuterium isotope effects

Dihydroorotates deuteriated at both C5 and C6 have been prepared and used to probe the mechanism of the bovine liver mitochondrial dihydroorotate dehydrogenase. Primary deuterium isotope effects on kcat are observed with both (6RS)-[5(S)-2H]- and (6RS)-[6-2H] dihydroorotates (3 and 6, respectively); these effects are maximal at low pH. At pH 6.6, DV = 3.4 for the C5-deuteriated dihydroorotate (3), and DV = 2.3 for the C6-deuteriated compound (6). The isotope effects approach unity at pH 8.8. Analysis of the pH dependence of the isotope effects on kcat reveals a shift in the rate-determining step of the enzyme mechanism as a function of pH. Dihydroorotate oxidation appears to require general base catalysis (pKB = 8.26); this step is completely rate-determining at low pH and isotopically sensitive. Reduction of the cosubstrate, coenzyme Q6, is rate-limiting at high pH and is isotopically insensitive; this step appears to require general acid catalysis (pKA = 8.42). The results of double isotope substitution studies and analysis for substrate isotope exchange with solvent point toward a concerted mechanism for oxidation of dihydroorotate. This finding serves to distinguish further the mammalian dehydrogenase from its parasitic cognate, which catalyzes a stepwise oxidation reaction [Pascal, R., & Walsh, C.T. (1984) Biochemistry 23, 2745].

Isotopic sensitivity in the microsomal oxidation of the dihydropyridine calcium entry blocker nifedipine

The primary deuterium isotope effect on Vm for the microsomal oxidation of the dihydropyridine calcium entry blocker nifedipine [4-(2-nitrophenyl)-2,6-dimethyl-3,5- bis(methoxycarbonyl)-1,4-dihydropyridine] has been measured. The magnitude of the kinetic isotope effect, 6.7, suggests that the rate-limiting step in the mechanism of microsomal oxidation of nifedipine involves the loss of a hydrogen atom rather than nitrogen oxidation. Thus the microsomal oxidation of nifedipine is mechanistically different from that of other 1,4-dihydropyridines.

Application of natural abundance 2H NMR. Simultaneous measurement of primary and secondary kinetic deuterium isotope effects

AbstractInternal and external reference methods are introduced for the study of kinetic deuterium isotope effects (KDIEs) by natural abundance 2H NMR. These methods take account of both inter‐ and intra‐molecular competive reactions of fully protonated and naturally monodeuteriated molecules of the substrate in the reaction. Specifically deuteriated compounds are not necessary using these methods. These techniques have further advantages over other methods; for example, primary and secondary KDIEs of different types can be measured simultaneously. The methodology is summarized and examples of its application are presented.

2-octynoyl coenzyme A is a mechanism-based inhibitor of pig kidney medium-chain acyl coenzyme A dehydrogenase: isolation of the target peptide.

Pig kidney medium-chain acyl-CoA dehydrogenase (EC 1.3.99.3) is irreversibly and stoichiometrically inactivated by [1-14C]-2-octynoyl coenzyme A. The linkage is stable at pH 2-6, but labile under basic conditions. The inhibitor labels a unique tryptic peptide, Ile-Tyr-Gln-Ile-Tyr-Glu-Gly-Thr-Ala-Gln-Ile-Gln-Arg, close to the C-terminus of the protein. The peptide is labeled at Glu-401 with the acyl moiety of the inhibitor but does not contain detectable coenzyme A. Both the inactivation of the dehydrogenase and the appearance of an absorption band at 800 nm show large primary deuterium isotope effects using 4,4'-dideuterio-2-octynoyl-CoA (7.3 and 6.3, respectively). Thus, 2-octynoyl-CoA is a mechanism-based inactivator of the dehydrogenase and is activated by rate-limiting gamma-proton abstraction. Glutamate-401 may be the base that abstracts the pro-R alpha-proton during the dehydrogenation of normal substrates.

Mechanistic deductions from kinetic isotope effects and pH studies of pyridoxal phosphate dependent carbon-carbon lyases: Erwinia herbicola and Citrobacter freundii tyrosine phenol-lyase.

The pH dependence of the kinetic parameters and primary deuterium isotope effects have been determined for tyrosine phenol-lyase from both Erwinia herbicola and Citrobacter freundii. The primary deuterium isotope effects indicate that proton abstraction from the 2-position of the substrate is partially rate-limiting for both enzymes. The C. freundii enzyme primary deuterium isotope effects [DV = 3.5 and D(V/Ktyr) = 2.5] are pH independent, indicating that tyrosine is not sticky (i.e., does not dissociate slower than it reacts to give products). Since Vmax for both tyrosine and the alternate substrate S-methyl-L-cysteine is also pH independent, substrate binds only to the correctly protonated form of the enzyme. For the E. herbicola enzyme, both Vmax and V/K for tyrosine or S-methyl-L-cysteine are pH dependent, as well as both DV and D(V/Ktyr). Thus, while both the protonated and unprotonated enzyme can bind substrate, and may be interconverted directly, only the unprotonated Michaelis complex is catalytically competent. At pH 9.5, DV = 2.5 and D(V/Ktyr) = 1.5. However, at pH 6.4 the isotope effect on both parameters is equal to 4.1. From these data, the forward commitment factor (cf = 5.2) and catalytic ratio (cvf = 1.1) for tyrosine and S-methyl-L-cysteine (cf = 2.2, cvf = 24) are calculated. Also, the Michaelis complex partition ratio (cf/cvf) for substrate and products is calculated to be 4.7 for tyrosine and 0.1 for S-methyl-L-cysteine.(ABSTRACT TRUNCATED AT 250 WORDS)

Mechanistic deductions from multiple kinetic and solvent deuterium isotope effects and pH studies of pyridoxal phosphate dependent carbon-carbon lyases: Escherichia coli tryptophan indole-lyase

Analysis of the pH dependence of the kinetic parameters and competitive inhibitor Ki values for tryptophan indole-lyase suggests two enzymic groups must be unprotonated in order to facilitate binding and catalysis of tryptophan. The V/K for tryptophan and the pKi for oxindolyl-L-alanine, a putative transition state analogue and competitive inhibitor, decrease below two pK values of 7.6 and 6.0, while the Ki for L-alanine, also a competitive inhibitor, is 3300-fold larger (20 mM) than that for oxindolyl-L-alanine and increases below a single pK of 7.6. A single pK of 7.6 is also observed in the V/K profile for the alternate substrate, S-methyl-L-cysteine. Therefore, the enzymic group with a pK of 7.6 is responsible for proton abstraction at the 2-position of tryptophan, while the enzymic group with a pK of 6.0 interacts with the indole portion of tryptophan and probably catalyzes formation of the indolenine tautomer of tryptophan (in concert with proton transfer to C-3 of indole from the group with pK 7.6) to facilitate carbon-carbon bond cleavage and elimination of indole. The pH variation of the primary deuterium isotope effects for proton abstraction at the 2-position of tryptophan (DV = 2.5 and D(V/Ktrp) = 2.8) are pH independent, while the Vmax for tryptophan or S-methyl-L-cysteine is the same and also pH independent. Thus, substrates bind only to the correctly protonated form of the enzyme. Further, tryptophan is not sticky, and the pK values observed in both V/K profiles are the correct ones.(ABSTRACT TRUNCATED AT 250 WORDS)

ChemInform Abstract: Trajectories of Proton‐Transfer Reactions. Experimental Determination of the Magnitude of Primary Deuterium Isotope Effects for Proton Transfers Occurring at Acute Angles.

ChemInform Abstract: Trajectories of Proton‐Transfer Reactions. Experimental Determination of the Magnitude of Primary Deuterium Isotope Effects for Proton Transfers Occurring at Acute Angles.

Mechanism of the reaction catalyzed by dihydrofolate reductase from Escherichia coli: pH and deuterium isotope effects with NADPH as the variable substrate.

The variations with pH of the kinetic parameters and primary deuterium isotope effects for the reaction of NADPH with dihydrofolate reductase from Escherichia coli have been determined. The aims of the investigations were to elucidate the chemical mechanism of the reaction and to obtain information about the location of the rate-limiting steps. The V and V/KNADPH profiles indicate that a single ionizing group at the active center of the enzyme must be protonated for catalysis, whereas the Ki profiles show that the binding of NADPH to the free enzyme and of ATP-ribose to the enzyme-dihydrofolate complex is pH independent. From the results of deuterium isotope effects on V/KNADPH, it is concluded that NADPH behaves as a sticky substrate. It is this stickiness that raises artificially the intrinsic pK value of 6.4 for the Asp-27 residue of the enzyme-dihydrofolate complex [Howell, E. E., Villafranca, J. E., Warren, M. S., Oatley, S. J., & Kraut, J. (1986) Science (Washington, D.C.) 231, 1123] to an observed value of 8.9. Thus, the binary enzyme complex is largely protonated at neutral pH. The elevation of the intrinsic pK value of 6.4 for the ternary enzyme-NADPH-dihydrofolate complex to 8.5 is not due to the kinetic effects of substrates. Rather, it is the consequence of the lower, pH-independent rate of product release and the faster pH-dependent catalytic step. At neutral pH, the proportion of enzyme present as a protonated ternary enzyme-substrate complex is sufficient to keep catalysis faster than product release.(ABSTRACT TRUNCATED AT 250 WORDS)

Use of primary deuterium and 15N isotope effects to deduce the relative rates of steps in the mechanisms of alanine and glutamate dehydrogenases.

We have used deuterium and 15N isotope effects to study the relative rates of the steps in the mechanisms of alanine and glutamate dehydrogenases. The proposed chemical mechanisms for these enzymes involve carbinolamine formation, imine formation, and reduction of the imine to the amino acid [Grimshaw, C.E., Cook, P.F., & Cleland, W.W. (1981) Biochemistry 20, 5655; Rife, J.E., & Cleland, W.W. (1980) Biochemistry 19, 2328]. These steps are almost equally rate limiting for V/Kammonia with alanine dehydrogenase, while with glutamate dehydrogenase carbinolamine formation, imine formation, and release of glutamate after hydride transfer provide most of the rate limitation of V/Kammonia. Release of oxidized nucleotide is largely rate limiting for Vmax for both enzymes. When beta-hydroxypyruvate replaces pyruvate, or 3-acetylpyridine NADH (Acpyr-NADH) or thio-NADH replaces NADH with alanine dehydrogenase, nucleotide release no longer limits Vmax, and hydride transfer becomes more rate limiting. With glutamate dehydrogenase, replacement of alpha-ketoglutarate by alpha-ketovalerate makes hydride transfer more rate limiting. Use of Acpyr-NADPH has a minimal effect with alpha-ketoglutarate but causes an 8-fold decrease in Vmax with alpha-ketovalerate, with hydride transfer the major rate-limiting step. In contrast, thio-NADPH with either alpha-keto acid causes carbinolamide formation to become almost completely rate limiting. These studies show the power of multiple isotope effects in deducing details of the chemistry and changes in rate-limiting step(s) in complicated reaction mechanisms such as those of alanine and glutamate dehydrogenases.

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

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.

Primary deuterium isotope effects for the 3-methylaspartase-catalyzed deamination of (2S)-aspartic acid, (2S,3S)-3-methylaspartic acid, and (2S,3S)-3-ethylaspartic acid.

3-Methylaspartate ammonia-lyase catalyzes the deamination of (2S)-aspartic acid 137 times more slowly than the deamination of (2S,3S)-3-methylaspartic acid but catalyzes the amination of fumaric acid 1.8 times faster than the amination of mesaconic acid [Botting, N.P., Akhtar, M., Cohen, M. A., & Gani, D. (1988) Biochemistry (preceding paper in this issue)]. In order to understand the mechanistic basis for these observations, the deamination reaction was examined kinetically with (2S)-aspartic acid, (2S,3S)-3-methylaspartic acid, (2S,3S)-3-ethylaspartic acid, and the corresponding C-3-deuteriated isotopomers. Comparison of the double-reciprocal plots of the initial reaction velocities for each of the three pairs of substrates revealed that the magnitude of the primary isotope effect on both Vmax and V/K varied with the substituent at C-3 of the substrate. 3-Methylaspartic acid showed the largest isotope effect (1.7 on Vmax and V/K), 3-ethylaspartic acid showed a smaller isotope effect (1.2 on Vmax and V/K), and aspartic acid showed no primary isotope effect at all. These results, which are inconsistent with earlier reports that there is no primary isotope effect for 3-methylaspartic acid [Bright, H. J. (1964) J. Biol. Chem. 239, 2307], suggest that for both 3-methylaspartic acid and 3-ethylaspartic acid elimination occurs via a predominantly concerted mechanism whereas for aspartic acid an E1cb mechanism prevails.(ABSTRACT TRUNCATED AT 250 WORDS)