Intrinsic deuterium isotope effects on benzylic hydroxylation by tyrosine hydroxylase

Tyrosine hydroxylase (TyrH) is a mononuclear, non-heme iron monooxygenase that catalyzes the pterin-dependent hydroxylation of tyrosine to dihydroxyphenylalanine. When 4-methylphenylalanine is used as a substrate for TyrH, 4-hydroxymethylphenylalanine is one of the amino acid products. To examine the mechanism of benzylic hydroxylation, the products and their isotopic compositions were determined with 4-methylphenylalanines containing a mono-, di-, or trideuterated methyl group as substrates. Intrinsic primary and secondary deuterium isotope effects for benzylic hydroxylation of 9.6 +/- 0.9 and 1.21 +/- 0.08, respectively, were derived from the data. The magnitudes of these isotope effects are consistent with quantum mechanical tunneling of the hydrogen. The similarity of the effects to those seen for benzylic hydroxylation by other enzymes supports a mechanism where a high valence iron-oxo species, Fe(IV)=O, is the hydroxylating intermediate.     

A common mechanism for branching, cyclopropanation, and cyclobutanation reactions in the isoprenoid biosynthetic pathway

Four reactions--chain elongation, cyclopropanation, branching, and cyclobutanation--are used in nature to join isoprenoid units for construction of the carbon skeletons for over 55,000 naturally occurring isoprenoid compounds. Those molecules produced by chain elongation have head-to-tail (regular) carbon skeletons, while those from cyclopropanation, branching, or cyclobutanation have non-head-to-tail (irregular) skeletons. Although wild type enzymes have not been identified for the branching and cyclobutanation reactions, chimeric proteins constructed from farnesyl diphosphate synthase (chain elongation) and chrysanthemyl diphosphate synthase (cyclopropanation) catalyze all four of the known isoprenoid coupling reactions to give a mixture of geranyl diphosphate (chain elongation), chrysanthemyl diphosphate (cyclopropanation), lavandulyl diphosphate (branching), and maconelliyl and planococcyl diphosphate (cyclobutanation). Replacement of the hydrogen atoms at C1 or C2 or hydrogen atoms in the methyl groups of dimethylallyl diphosphate by deuterium alters the distribution of the cyclopropanation, branching, and cyclobutanation products through primary and secondary kinetic isotope effects on the partitioning steps of common carbocationic intermediates. These experiments establish the sequence in which the intermediates are formed and indicate that enzyme-mediated control of the carbocationic rearrangement and elimination steps determines the distribution of products.     

Secondary kinetic isotope effect on the photoenolization of triplet o-methylanthrones. A microcanonical transition state theory calculation

The energy profile for the tautomerization reaction of 1,4-dimethylanthrone in the first triplet electronic state obtained through electronic calculations (B3LYP/ 6-31G(d)) is used to calculate the rate constants for the process at a wide range of energies using a modified RRKM microcanonical statistical formalism that takes into account tunneling. Through partial or total substitution of the hydrogen atoms of the methyl groups by deuterium atoms, it is possible to evaluate different primary and secondary kinetic isotope effects (KIE). These results can be compared with experimental data for these processes taking place in solid matrix at extremely low temperatures (4-50 K). Such a comparison allows us to conclude that the reaction is taking place at energies just slightly below (around 0.5 kcal/mol) the adiabatic potential energy barrier, a result that was previously found for other related molecules so that this mechanism may be extended to the photoenolization of other o-aryl methyl ketones. Analysis of the different factors contributing to the primary and secondary KIEs discloses that at energies not far below the adiabatic barrier, the tunneling effect is not the only factor that accounts for the large KIE but the differences in the energy level distribution upon isotopic substitution may be the predominant factor at a certain range of negative energies (this is especially so for the case of primary KIE). At positive energies (above the barrier) the levels factor is always the dominant factor in the total KIE.     

13C and (2)H kinetic isotope effects and the mechanism of Lewis acid-catalyzed ene reactions of formaldehyde

13C and (2)H kinetic isotope effects were determined for the ene reaction of formaldehyde with 2-methyl-2-butene at natural abundance catalyzed by diethylaluminum chloride. The reactive methyl group exhibits a k(12)(C)/k(13)(C) of 1.006-1.009 and a k(H)/k(D) of approximately 1.22-1.23. The latter represents a combination of primary and secondary effects and is consistent with a significant primary deuterium isotope effect. A very close correspondence of the other isotope effects with the equilibrium isotope effects predicted for formation of a model intermediate cation is observed. An intermolecular deuterium isotope effect of 2.0-2.5 was observed under several reaction conditions in the Lewis acid-catalyzed reaction of formaldehyde with d(0)/d(12)-tetramethylethylene. The results are interpreted as supporting the reversible formation of an essentially classical open cation followed by rate-limiting proton transfer.     

Large primary kinetic isotope effects in the abstraction of hydrogen from organic compounds by a fluorinated radical in water

Isotope effects have been measured for the abstraction of hydrogen from a series of organic substrates by the perfluoro radical, Na+ -O3SCF2CF2OCF2CF2*, in water. Both primary and secondary deuterium isotope effects were measured, with the primary isotope effects ranging in value from 4.5 for isopropanol to 19.6 for acetic acid. The values for the alpha- and beta-secondary deuterium isotope effects were 1.06 and 1.035, respectively. It was concluded that tunneling contributes significantly to the production of the observed, large primary kinetic isotope effects in these C-H abstraction reactions.     

Investigating Inner-Sphere Reorganization via Secondary Kinetic Isotope Effects in the C-H Cleavage Reaction Catalyzed by Soybean Lipoxygenase: Tunneling in the Substrate Backbone as Well as the Transferred Hydrogen

This work describes the application of NMR to the measurement of secondary deuterium (2° (2)H) and carbon-13 ((13)C) kinetic isotope effects (KIEs) at positions 9-13 within the substrate linoleic acid (LA) of soybean lipoxygenase-1. The KIEs have been measured using LA labeled with either protium (11,11-h2-LA) or deuterium (11,11-d2-LA) at the reactive C11 position, which has been previously shown to yield a primary deuterium isotope effect of ca. 80. The conditions of measurement yield the intrinsic 2° (2)H and (13)C KIEs on k(cat)/K(m) directly for 11,11-d2-LA, whereas the values for the 2° (2)H KIEs for 11,11-h2-LA are obtained after correction for a kinetic commitment. The pattern of the resulting 2° (2)H and (13)C isotope effects reveals values that lie far above those predicted from changes in local force constants. Additionally, many of the experimental values cannot be modeled by electronic effects, torsional strain, or the simple inclusion of a tunneling correction to the rate. Although previous studies have shown the importance of extensive tunneling for cleavage of the primary hydrogen at C11 of LA, the present findings can only be interpreted by extending the conclusion of nonclassical behavior to the secondary hydrogens and carbons that flank the position undergoing C-H bond cleavage. A quantum mechanical method introduced by Buhks et al. [J. Phys. Chem. 1981, 85, 3763] to model the inner-sphere reorganization that accompanies electron transfer has been shown to be able to reproduce the scale of the 2° (2)H KIEs.     

Hydrogen tunneling in peptidylglycine alpha-hydroxylating monooxygenase

The temperature dependence of the primary and secondary intrinsic isotope effects for the C-H bond cleavage catalyzed by peptidylglycine alpha-hydroxylating monooxygenase has been determined. Analysis of the magnitude and Arrhenius behavior of the intrinsic isotope effects provides strong evidence for the use of tunneling as a primary catalytic strategy for this enzyme. Modeling of the isotope effect data allows for a comparison to the hydrogen transfer catalyzed by soybean lipoxygenase in terms of environmental reorganization energy and frequency of the protein vibration that controls the hydrogen transfer.     

Deep tunneling dominates the biologically important hydride transfer reaction from NADH to FMN in morphinone reductase

The temperature dependence of the primary kinetic isotope effect (KIE), combined temperature-pressure studies of the primary KIE, and studies of the alpha-secondary KIE previously led us to infer that hydride transfer from nicotinamide adenine dinucleotide to flavin mononucleotide in morphinone reductase proceeds via environmentally coupled hydride tunneling. We present here a computational analysis of this hydride transfer reaction using QM/MM molecular dynamics simulations and variational transition-state theory calculations. Our calculated primary and secondary KIEs are in good agreement with the corresponding experimental values. Although the experimentally observed KIE lies below the semiclassical limit, our calculations suggest that approximately 99% of the reaction proceeds via tunneling: this is the first "deep tunneling" reaction observed for hydride transfer. We also show that the dominant tunneling mechanism is controlled by the isotope at the primary rather than the secondary position: with protium in the primary position, large-curvature tunneling dominates, whereas with deuterium in this position, small-curvature tunneling dominates. Also, our study is consistent with tunneling being preceded by reorganization: in the reactant, the rings of the nicotinamide and isoalloxazine moieties are stacked roughly parallel to each other, and as the system moves toward a "tunneling-ready" configuration, the nicotinamide ring rotates to become almost perpendicular to the isoalloxazine ring.     

Uncoupled forms of tyrosine hydroxylase unmask kinetic isotope effects on chemical steps

Tyrosine hydroxylase (TyrH) catalyzes the hydroxylation of tyrosine to dihydroxyphenylalanine. In the proposed mechanism, a ferryl-oxo species attacks the aromatic ring of tyrosine, forming a cationic intermediate. However, no significant isotope effect is found for wild-type TyrH when 3,5-2H2-tyrosine is used as a substrate. The isotope effect has now been determined with 3,5-2H2-tyrosine using mutant forms of TyrH in which the oxidation of the pterin is uncoupled from hydroxylation of the amino acid. Three mutant enzymes exhibit significant inverse deuterium isotope effects and inverse solvent isotope effects. A proton inventory for the E326A enzyme is consistent with a normal solvent isotope effect of 2.4 on an unproductive step. The results support the proposed mechanism and demonstrate the utility of using mutant proteins with branched pathways to reveal isotope effects which are masked in the wild-type enzyme.     

Quantum dynamics of hydride transfer catalyzed by bimetallic electrophilic catalysis: synchronous motion of Mg(2+) and H(-) in xylose isomerase

Xylose isomerase exhibits a bridged-bimetallic active-site motif in which the substrate is bound to two metals connected by a glutamate bridge, and X-ray crystallographic studies suggest that metal movement is involved in the hydride transfer rate-controlling catalytic step. Here we report classical/quantal dynamical simulations of this step that provide new insight into the metal motion. The potential energy surface is calculated by treating xylose with semiempirical molecular orbital theory augmented by a simple valence bond potential and the rest of the system by molecular mechanics. The rate constant for the hydride-transfer step was calculated by ensemble-averaged dynamical simulations including both variational transition-state theory for determination of the statistically averaged dynamical bottleneck and optimized multidimensional tunneling calculations. The dynamics calculations include 25 317 atoms, with quantized vibrational free energy in 89 active-site degrees of freedom, and with 32 atoms moving through static secondary zone transition-state configurations in the quantum tunneling simulation. Our simulations show that the average Mg-Mg distance R increases monotonically as a function of the hydride-transfer progress variable z. The range of the average R along the reaction path is consistent with the X-ray structure, thus providing a dynamical demonstration of the postulated role of Mg in catalysis. We also predicted the primary deuterium kinetic isotope effect (KIE) for the chemical step. We calculated a KIE of 3.8 for xylose at 298 K, which is consistent with somewhat smaller experimentally observed KIEs for glucose substrate at higher temperatures. More than half of our KIE is due to tunneling; neglecting quantum effects on the reaction coordinate reduces the calculated KIE to 1.8.     

Investigations of intramolecular hydrogen bonding in three types of Schiff bases by 2H and 3H NMR isotope effects

Hydrogen bonding within the structures of three Schiff bases (1-3), obtained by condensation of 4-methoxy-, 5-methoxy- and 4,6-dimethoxysalicylaldehyde with methylamine, was investigated by measuring deuterium and tritium NMR isotope effects. The primary deuterium and tritium isotope effects (delta(XH)-delta(XD/T)) and secondary one-bond nitrogen deuterium effect appear to be very useful parameters for defining the character of intramolecular hydrogen bonds. The tritium isotope effects were also determined for nitrogen-hydrogen one-bond coupling constants for both 4-methoxy and 4,6-dimethoxy derivatives. These parameters are seen to be highly sensitive to hydrogen bond characteristics and can be used to distinguish localized and tautomeric hydrogen bonds.     

Mechanism of dioxygen cleavage in tetrahydrobiopterin-dependent amino acid hydroxylases

The reaction mechanism for the formation of the hydroxylating intermediate in aromatic amino acid hydroxylases (i.e., phenylalanine hydroxylase, tyrosine hydroxylase, tryptophan hydroxylase) was investigated by means of hybrid density functional theory. These enzymes use molecular oxygen to hydroxylate both the tetrahydrobiopterin cofactor and the aromatic amino acid. A mechanism is proposed in which dioxygen forms a bridging bond between the cofactor and iron. The product is an iron(II)-peroxy-pterin intermediate, and iron was found to be essential for the catalysis of this step. No stable intermediates involving a pterin radical cation and a superoxide ion O(2)(-) were found on the reaction pathway. Heterolysis of the O-O bond in the iron(II)-peroxy-pterin intermediate is promoted by one of the water molecules coordinated to iron and releases hydroxypterin and the high-valent iron oxo species Fe(IV)=O, which can carry out subsequent hydroxylation of aromatic rings. In the proposed mechanism, the formation of the bridging C-O bond is rate-limiting in the formation of Fe(IV)=O.     

Diastereoselectivity in the McLafferty rearrangement of photoionized 3-methyl valeramide

The McLafferty rearrangement of photoionized 3-methyl valeramide proceeds quasi-barrierless and with high regioselectivity. The mass spectra of the stereospecifically labeled syn- and anti-[4-D(1)]-diastereomers reveal a strong preference for activation of the gamma-hydrogen/deuterium in anti-position relative to the methyl group at C(3), which serves as a steric marker. Quantitative analysis of the fragmentation patterns of other photoionized isotopomers permits the determination of primary and secondary kinetic isotope effects (KIEs), the branching ratios of competing McLafferty reactions, and the steric effect (SE) associated with transfer of the diastereotopic H(D) atoms at C(4). While the associated KIEs of the title reaction are negligible, the steric effect (SE = 2.9) is remarkably large for the otherwise flexible, monofunctional compound. The findings can be explained by a preferentially chairlike transition structure for the initial gamma-H atom transfer.     

Boundary conditions for the Swain-Schaad relationship as a criterion for hydrogen tunneling

Hydrogen quantum mechanical tunneling has been suggested to play a role in a wide variety of hydrogen-transfer reactions in chemistry and enzymology. An important experimental criterion for tunneling is based on the breakdown of the semiclassical prediction for the relationship among the rates of the three isotopes of hydrogen (hydrogen -H, deuterium -D, and tritium -T). This is denoted the Swain-Schaad relationship. This study examines the breakdown of the Swain-Schaad relationship as criterion for tunneling. The semiclassical (no tunneling) limit used hereto (e.g., 3.34, for H/T to D/T kinetic isotope effects), was based on simple theoretical considerations of a diatomic cleavage of a stable covalent bond, for example, a C-H bond. Yet, most experimental evidence for a tunneling contribution has come from breakdown of those relationship for a secondary hydrogen, that is, not the hydrogen whose bond is being cleaved but its geminal neighbor. Furthermore, many of the reported experiments have been mixed-labeling experiments, in which a secondary H/T kinetic isotope effect was measured for C-H cleavage, while the D/T secondary effect accompanied C-D cleavage. In experiments of this type, the breakdown of the Swain-Schaad relationship indicates both tunneling and the degree of coupled motion between the primary and secondary hydrogens. We found a new semiclassical limit (e.g., 4.8 for H/T to D/T kinetic isotope effects), whose breakdown can serve as a more reliable experimental evidence for tunneling in this common mixed-labeling experiment. We study the tunneling contribution to C-H bond activation, for which many relevant experimental and theoretical data are available. However, these studies can be applied to any hydrogen-transfer reaction. First, an extension of the original approach was applied, and then vibrational analysis studies were carried out for a model system (the enzyme alcohol dehydrogenase). Finally, the effect of complex kinetics on the observed Swain-Schaad relationship was examined. All three methods yield a new semiclassical limit (4.8), above which tunneling must be considered. Yet, it was found that for many cases the original, localized limit (3.34), holds fairly well. For experimental results that are between the original and new limits (within statistical errors), several methods are suggested that can support or exclude tunneling. These new and clearer criteria provide a basis for future applications of the Swain-Schaad relationship to demonstrate tunneling in complex systems.     

Enzymatic catalysis and transfers in solution. I. Theory and computations, a unified view

The transfer of hydride, proton, or H atom between substrate and cofactor in enzymes has been extensively studied for many systems, both experimentally and computationally. A simple equation for the reaction rate, an analog of an equation obtained earlier for electron transfer rates, is obtained, but now containing an approximate analytic expression for the bond rupture-bond forming feature of these H transfers. A "symmetrization," of the potential energy surfaces is again introduced [R. A. Marcus, J. Chem. Phys. 43, 679 (1965); J. Phys. Chem. 72, 891 (1968)], together with Gaussian fluctuations of the remaining coordinates of the enzyme and solution needed for reaching the transition state. Combining the two expressions for the changes in the difference of the two bond lengths of the substrate-cofactor subsystem and in the fluctuation coordinates of the protein leading to the transition state, an expression is obtained for the free energy barrier. To this end a two-dimensional reaction space (m,n) is used that contains the relative coordinates of the H in the reactants, the heavy atoms to which it is bonded, and the protein/solution reorganization coordinate, all leading to the transition state. The resulting expression may serve to characterize in terms of specific parameters (two "reorganization" terms, thermodynamics, and work terms), experimental and computational data for different enzymes, and different cofactor-substrate systems. A related characterization was used for electron transfers. To isolate these factors from nuclear tunneling, when the H-tunneling effect is large, use of deuterium and tritium transfers is of course helpful, although tunneling has frequently and understandably dominated the discussions. A functional form is suggested for the dependence of the deuterium kinetic isotope effect (KIE) on DeltaG degrees and a different form for the 13C KIE. Pressure effects on deuterium and 13C KIEs are also discussed. Although formulated for a one-step transfer of a light particle in an enzyme, the results would also apply to single-step transfers of other atoms and groups in enzymes and in solution.     

Separation of the primary and secondary kinetic isotope effects at a reactive center using starting material reactivities. Application to the FeCl3-Catalyzed oxidation of CH bonds with tert-butyl hydroperoxide

A method is reported for the determination of both the primary and secondary kinetic isotope effects at a reactive center based on staring material reactivities. This allows the determination of the separate KIEs in reactions for which neither product analysis nor absolute rate measurements are applicable. The methodology is applied to the FeCl₃-catalyzed oxidation of ethylbenzene with tert-butyl hydroperoxide, which exhibits both a primary isotope effect and a substantial secondary isotope effect.     

Enzymatic methyl transfer: role of an active site residue in generating active site compaction that correlates with catalytic efficiency

Human catechol-O-methyltransferase (COMT) catalyzes a methyl transfer from S-adenosylmethionine (AdoMet) to dopamine. Site-specific mutants at three positions (Tyr68, Trp38, and Val108) have been characterized with regard to product distribution, catalytic efficiency, and secondary kinetic isotope effects. The series of mutations at Tyr68 within wild-type protein and the common polymorphic variant (Val108Met) yields a linear correlation between the catalytic efficiency and the size of the secondary kinetic isotope effect. We conclude that active site compaction in COMT is modulated by a proximal side chain residing behind the sulfur-bearing methyl group of AdoMet. These findings are discussed in the context of the active site compression that has been postulated to accompany enzyme-supported hydrogen tunneling.     

Secondary kinetic isotope effects: Deuterium abstraction by chlorine atoms from the CD3 group in CD3CH2Cl,CD3CHDCl,and CD3CD2Cl

The occurrence and magnitude of secondary kinetic isotope effects in the gas phase has been determined for deuterium abstraction from the CD₃ group in CD₃CH₂Cl, CD₃CHDCl, and CD₃CD₂Cl by photochemically generated ground-state chlorine atoms. Over the temperature range 10–94°C a discernible “inverse” kinetic isotope effect is observed. Both the pre-exponential factors and activation energies decrease with deuterium substitution in the vicinal chloromethyl group. The opposing trends result in a net effect close to unity.     

Deuterium and Hydrogen Tunneling in the Hydrogenation of 4‐Oxocyclohexa‐2,5‐dienylidene

4‐Oxocyclohexa‐2,5‐dienylidene is a highly reactive triplet ground state carbene that is hydrogenated in solid H₂, HD, and D₂ at temperatures as low as 3 K. The mechanism of the insertion of the carbene into dihydrogen was investigated by IR and EPR spectroscopy and by kinetic studies. H or D atoms were observed as products of the reaction with H₂ and D₂, respectively, whereas HD produces exclusively D atoms. The hydrogenation shows a very large kinetic isotope effect and remarkable isotope selectivity, as was expected for a tunneling reaction. The experiments, therefore, provide clear evidence for both hydrogen tunneling and the rare deuterium tunneling in an intermolecular reaction.     

The <Emphasis Type="Italic">Saunders-Bell</Emphasis> Analysis of Tunnel Effects in Reactions with Kinetic Isotope Effects

Summary. The primary kinetic isotope effects of deuterium were investigated in 22 hydrogen and deuterium transfer reactions, including enzymatic and nonenzymatic hydride transfer reactions, elimination reactions, and reactions catalyzed by enzymes lipooxygenase, amine dehydrogenase, and methylmalonyl-CoA mutase. In each case, the Saunders-Bell analysis was applied to calculate the tunnel effects and the corresponding thermodynamic parameters. The Saunders-Bell analysis was effective in 14 cases out of 22. A high degree of correlation was found between the barrier factor, the tunnel factor, and the entropy factor among all reactions studied. From this, a general relationship between the three factors was derived, based on the Saunders-Bell analysis of the Bell equation; the Saunders-Bell analysis is valid within certain limits of the barrier factor. This general relationship is universally valid for all hydrogen/deuterium transfer reactions in nature with moderate tunneling, when the Saunders-Bell analysis applies.