Oxygen- and temperature-dependent kinetic isotope effects in choline oxidase: correlating reversible hydride transfer with environmentally enhanced tunneling

Choline oxidase catalyzes the flavin-linked oxidation of choline to glycine betaine, with betaine aldehyde as intermediate and oxygen as electron acceptor. Here, the effects of oxygen concentration and temperature on the kinetic isotope effects with deuterated choline have been investigated. The D(kcat/Km) and Dkcat values with 1,2-[(2)H4]-choline were pH-independent at saturating oxygen concentrations, whereas they decreased at high pH to limiting values that depended on oxygen concentration at < or = 0.97 mM oxygen. The kcat/Km and kcat pH profiles had similar patterns reaching plateaus at high pH. Both the limiting kcat/Km at high pH and the pKa values were perturbed to lower values with choline and < or = 0.25 mM oxygen. These data suggest that oxygen availability modulates whether the reduced enzyme-betaine aldehyde complex partitions forward to catalysis rather then reverting to the oxidized enzyme-choline alkoxide species. At saturating oxygen concentrations, the D(kcat/Km) was 10.6 +/- 0.6 and temperature independent, and the isotope effect on the preexponential factors (A(H)'/A(D)') was 14 +/- 3, ruling out a classical over-the-barrier behavior for hydride transfer. Similar enthalpies of activation (deltaH(double dagger)) with values of 18 +/- 2 and 18 +/- 5 kJ mol(-1) were determined with choline and 1,2-[(2)H4]-choline. These data suggest that the hydride transfer reaction in which choline is oxidized by choline oxidase occurs quantum mechanically within a preorganized active site, with the reactive configuration for hydride tunneling being minimally affected by environmental vibrations of the reaction coordinate other than those affecting the distance between the donor and acceptor of the hydride.     

Magnesium isotope effects in enzymatic phosphorylation

Recent discovery of magnesium isotope effect in the rate of enzymatic synthesis of adenosine triphosphate (ATP) offers a new insight into the mechanochemistry of enzymes as the molecular machines. The activity of phosphorylating enzymes (ATP-synthase, phosphocreatine, and phosphoglycerate kinases) in which Mg(2+) ion has a magnetic isotopic nucleus 25Mg was found to be 2-3 times higher than that of enzymes in which Mg(2+) ion has spinless, nonmagnetic isotopic nuclei 24Mg or 26Mg. This isotope effect demonstrates unambiguously that the ATP synthesis is a spin-dependent ion-radical process. The reaction schemes, suggested to explain the effect, imply a reversible electron transfer from the terminal phosphate anion of ADP to Mg(2+) ion as a first step, generating ion-radical pair with singlet and triplet spin states. The yields of ATP along the singlet and triplet channels are controlled by hyperfine coupling of unpaired electron in 25Mg+ ion with magnetic nucleus 25Mg. There is no difference in the ATP yield for enzymes with 24Mg and 26Mg; it gives evidence that in this reaction magnetic isotope effect (MIE) operates rather than classical, mass-dependent one. Similar effects have been also found for the pyruvate kinase. Magnetic field dependence of enzymatic phosphorylation is in agreement with suggested ion-radical mechanism.     

Intrinsic isotope effects on benzylic hydroxylation by the aromatic amino acid hydroxylases: evidence for hydrogen tunneling, coupled motion, and similar reactivities

Deuterium kinetic isotope effects for hydroxylation of the methyl group of 4-methylphenylalanine have been used as a probe of the relative reactivities of the hydroxylating intermediates in the aromatic amino acid hydroxylases phenylalanine, tyrosine, and tryptophan hydroxylase. When there are three deuterium atoms in the methyl group, all three enzymes exhibit an intrinsic isotope effect of about 13. The temperature dependence of the isotope effect is consistent with moderate tunneling, with the extent of tunneling identical for all three enzymes. In the case of phenylalanine hydroxylase, the presence of the regulatory domain has no effect on the values. The intrinsic primary and secondary isotope effects were determined using 4-methylphenylalanine containing one or two deuterium atoms in the methyl group. With one deuterium atom, the intrinsic primary and secondary effects have average values of 10 and 1.1, respectively. With two deuterium atoms, the primary effects decrease to 7.4 and the secondary effect increases to 1.3, consistent with coupled motion of the primary and secondary hydrogens. The results with all three enzymes are consistent with a hydrogen abstraction mechanism. The similarities of the isotope effects and extent of tunneling establish that the reactivities of the hydroxylating intermediates in the three enzymes are essentially identical.     

Secondary alpha isotope effects on deuterium tunneling in triplet o-methylanthrones: extraordinary sensitivity to barrier width

The rates of deuterium transfer in the photoenolization of triplet 1,4-dimethyl-10H-anthracen-9-one (1) with varying degrees of deuterium label in their methyl groups (1-d3, 1-d2, and 1-d) have been investigated as a function of temperature between 5 and 77 K. Measurable rate constants in the case of 1-d3 and 1-d2 were used to construct Arrhenius plots which illustrate the expected curvature and leveling off of rate constant versus temperature. The difference in tunneling rate constants of 1-d3 and 1-d2 yields a tunneling isotope effect, TIE = 2.4, which is attributed to the secondary alpha isotopic substitution. Density functional theory (DFT, B3LYP/6-31G*) calculations were carried out to obtain structural and energetic information for the H(D) transfer along the triplet state zero-point energy levels. The temperature dependence of the rate constants for each isotopologue was simulated with a model that considers the frequency of the C-D stretching mode and the quantum mechanical permeability determined from calculated energy parameters. The model suggests that a difference in barrier width of only 0.015 A between 1-d3 and 1-d2 leads to the observed 2-fold difference between tunneling rates.     

Origin of the temperature dependence of isotope effects in enzymatic reactions: the case of dihydrofolate reductase

The origin of the temperature dependence of kinetic isotope effects (KIEs) in enzyme reactions is a problem of general interest and a major challenge for computational chemistry. The present work simulates the nuclear quantum mechanical (NQM) effects and the corresponding KIE in dihydrofolate reductase (DHFR) and two of its mutants by using the empirical valence bond (EVB) and the quantum classical path (QCP) centroid path integral approach. Our simulations reproduce the overall observed trend while using a fully microscopic rather than a phenomenological picture and provide an interesting insight. It appears that the KIE increases when the distance between the donor and acceptor increases, in a somewhat counter intuitive way. The temperature dependence of the KIE appears to reflect mainly the temperature dependence of the distance between the donor and acceptor. This trend is also obtained from a simplified vibronic treatment, but as demonstrated here, the vibronic treatment is not valid at short and medium distances, where it is essential to use the path integral or other approaches capable of moving seamlessly from the adiabatic to the diabatic limits. It is pointed out that although the NQM effects do not contribute to catalysis in DHFR, the observed temperature dependence can be used to refine the potential of mean force for the donor and acceptor distance and its change due to distanced mutations.     

Kinetic isotope effect in hydrogen transfer arising from the effects of rotational excitation and occurrence of hydrogen tunneling in molecular systems

Hydrogen kinetic isotope effect with values of alpha identical with ln(kH/kT)/ln(kD/kT)>3.3 which are generally ascribed to quantum tunneling of hydrogen are shown to arise in O+HCl(DCl,TCl) reactions due to the effects of rotational excitation on the distribution of encounters with the critical dividing surface. At higher rotational excitations these distributions are shifted towards the regions of the critical dividing surface with low barrier energies which can lead to a large enhancement of the barrier crossing. This effect depends strongly on the hydrogen isotope involved in the reaction and, at some temperatures, gives rise to alpha much larger than 3.3. It can be readily seen that the effect should arise also in condensed molecular systems, due to internal rotations or other vibrations "perpendicular" to the reaction coordinate.     

210Po in the environment: insight into the naturally occurring polonium isotope

Journal of Radioanalytical and Nuclear Chemistry - Polonium is rapidly emerging as an international environmental health concern primarily because of the recent rise in hydraulic fracturing...     

On the models for deuterium long-range isotope effects in13C NMR spectroscopy

The long-range deuterium isotope effects on¹³C nuclear shielding are physically not yet completely understood. Two existing models for explaining these effects, vibrational and substituent, are compared here. The vibrational model is based on the Born-Oppenheimer approximation, but it can explain only one-bond deuterium effects. To the contrary, the substituent model may explain many long-range isotope effects, but it is controversial due to the assumption of some distinct electronic properties of isotopes. We explain how long-range deuterium isotope effects may be rationalized by the subtle electronic changes induced by isotope substitution, which does not violate the Born-Oppenheimer approximation.     

Rotational tunneling in CH4 II: disorder effects

Transitions within the tunneling multiplet of CH(4) in phase II have been measured in an experiment at the backscattering instrument BASIS of the Neutron Source SNS. They all involve transitions from or to T-states. A statistical model is put forward which accounts for local departures from tetrahedral symmetry at the sites of ordered molecules. Different from previous work, in which discrete sets of overlap matrix elements have been studied, now large numbers of elements as well as the ensemble of T-states are considered. The observed neutron spectra can be explained rather well, all based on the pocket state formalism of A. Hu?ller [Phys. Rev. B 16, 1844 (1977)]. A completely new result is the observation and simulation of transitions between T-states, which give rise to a double peaked feature close to the elastic position and which reflect the disorder in the system. CH(2)D(2) molecules in the CH(4) matrix are largely responsible for the disorder and an interesting topic for their own sake. The simple model presented may lend itself to a broader application.     

Photo-oxidation of water by molecular oxygen: isotope exchange and isotope effects

Photolysis of (17,18)O-labeled water in the presence of molecular oxygen is accompanied by transfer of (17)O and (18)O isotopes from water to oxygen, demonstrating that photoinduced oxidation of water does occur. The reaction exhibits the following isotope effect: oxidation of H(2)(17)O is faster by 2.6% (in the Earth's magnetic field) and by 6.0% (in the field 0.5 T) than that of H(2)(18)O. The effect is supposed to arise in the two spin-selective, isotope-sorting reactions-recombination and disproportionation-in the pairs of encountering HO(2) radicals. The former is spin allowed from the singlet state; the latter occurs only in the triplet one. Nuclear spin sorting produced by these reactions proceeds in opposite directions with the dominating contribution of recombination, which provides observable (17)O/(18)O isotope fractionation in favor of magnetic isotope (17)O. Neither isotope exchange nor the reaction itself occurs in the dark.     

Metal-catalyzed phosphodiester cleavage: secondary 18O isotope effects as an indicator of mechanism

Information about the transition states of metal-catalyzed hydrolysis reactions of model phosphate compounds has been obtained through determination of isotope effects (IEs) on the hydrolysis reactions. Metal complexation has been found to significantly alter the transition state of the reaction from the alkaline hydrolysis reaction, and the transition state is quite dependent on the particular metal ion used. For the diester, ethyl p-nitrophenyl phosphate, the nonbridge 18O effect for the hydrolysis reactions catalyzed by Co(III) 1,5,9-triazacyclononane and Eu(III) were 1.0006 and 1.0016, respectively, indicative of a slightly associative transition state and little net change in bonding to the nonbridge oxygen. The reaction catalyzed by Zn(II) 1,4,7,10-tetraazacyclododecane had an 18O nonbridge IE of 1.0108, showing the reaction differs significantly from the reaction of the noncomplexed diester and resembles the reactions of triesters. Reaction with Co(III) 1,4,7,10-tetraazacyclododecane showed an inverse effect of 0.9948 reflecting the effects of bonding of the diester to the Co(III). Lanthanide-catalyzed hydrolysis has been observed to have unusually large 15N effects. To further investigate this effect, the 15N effect on the reaction catalyzed by Ce(IV) bis-Tris propane solutions at pH 8 was determined to be 1.0012. The 15N effects were also measured for the reaction of the monoester p-nitrophenyl phosphate by Ce(IV) bis-Tris propane (1.0014) and Eu(III) bis-Tris propane (1.0012). These smaller effects at pH 8 indicate that a smaller negative charge develops on the nitrogen during the hydrolysis reaction.     

An evaluation of non-periodic boundary condition models in molecular dynamics simulations using prion octapeptides as probes

Molecular dynamics simulations have been performed under periodic boundary conditions and using four non-periodic solvation models. The biomolecular probe in these simulations was a single repeat of the copper-binding octapeptide in the human prion protein, PHGGGWGQ. Although the alternative non-periodic solvation models enable a reduction in computational time, the dynamical disadvantages are considerable when using any of these four non-periodic models. For simulations of systems similar to the test system, periodic boundary conditions are a better alternative than any of the four local models.     

"Separated" versus "contact" ion-pair structures in solution from their crystalline states: dynamic effects on dinitrobenzenide as a mixed-valence anion

Qualitative structural concepts about dynamic ion pairs, historically deduced in solution as labile solvent-separated and contact species, are now quantified by the low-temperature isolation of crystalline (reactive) salts suitable for direct X-ray analysis. Thus, dinitrobenzenide anion (DNB(-)) can be prepared in the two basic ion-paired forms by potassium-mirror reduction of p-dinitrobenzene in the presence of macrocyclic polyether ligands: L(C) (cryptand) and L(E) (crown-ethers). The crystalline "separated" ion-pair salt isolated as K(L(C))(+)//DNB(-) is crystallographically differentiated from the "contact" ion-pair salt isolated as K(L(E))(+)DNB(-) by their distinctive interionic separations. Spectral analysis reveals pronounced near-IR absorptions arising from intervalence transitions that characterize dinitrobenzenide to be a prototypical mixed-valence anion. Most importantly, the unique patterns of vibronic (fine-structure) progressions that also distinguish the "separated" from the "contact" ion pair in the crystalline solid state are the same as those dissolved into THF solvent and ensure that the same X-ray structures persist in solution. Moreover, these distinctive NIR patterns are assigned with the aid of Marcus-Hush (two-state) theory to the "separated"ion pair in which the unpaired electron is equally delocalized between both NO(2)-centers in the symmetric ground state of dinitrobenzenide, and by contrast, the asymmetric electron distribution inherent to "contact"ion pairs favors only that single NO(2)-center intimately paired to the counterion. The labilities of these dynamic ion pairs in solution are thoroughly elucidated by temperature-dependent ESR spectral changes that provide intimate details of facile isomerizations, ionic separations, and counterion-mediated exchanges.     

Heat capacity effects associated with urea and tetramethylurea hydration: insight from computer simulation

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Deuterium kinetic isotope effects in microsolvated gas-phase E2 reactions: Methanol and ethanol as solvents

The gas-phase reactions of F(-)(CH(3)OH) and F(-)(C(2)H(5)OH) with t-butyl bromide have been investigated to explore the effect of the solvent on the E2 transition state. Kinetic isotope effects (KIEs) were measured using a flowing afterglow-selected ion flow tube (FA-SIFT) mass spectrometer upon deuteration of both the alkyl halide and the alcohol. Kinetic isotope effects are significantly more pronounced than those previously observed for similar reactions of F(-)(H(2)O) with t-butyl halides. KIEs for the reaction of F(-)(CH(3)OH) with t-butyl bromide are 2.10 upon deuteration of the neutral reagent and 0.74 upon deuteration of the solvent. KIEs for the reaction of F(-)(C(2)H(5)OH) with t-butyl bromide are 3.84 upon deuteration of the neutral reagent and 0.66 upon deuteration of the solvent. The magnitude of these effects is discussed in terms of transition-state looseness. Additionally, deuteration of the neutral regent and deuteration of the solvent do not produce completely separable isotope effects, which is likely due to a crowded transition state. These results are compared to our previous work on S(N)2 and E2 solvated systems.     

The fundamental vibrations of CS2 as probes of matrix effects in matrix isolation spectroscopy

The infrared and Raman spectra of matrix-isolated CS₂ were examined under a variety of experimental conditions. The results are discussed in terms of the physical effects common to matrix isolation spectra in general like site effects, interactions between trapped molecules, effects of matrix materials and of the symmetry at the trapping site, Fermi resonance and the inherent differences between infrared and Raman spectra.     

Matrix effects on the multi-collector inductively coupled plasma mass spectrometric analysis of high-precision cadmium and zinc isotope ratios

Resin-derived contaminants added to samples during column chemistry are shown to cause matrix effects that lead to inaccuracy in multi-collector inductively coupled plasma mass spectrometry measurement of small natural variations in Cd and Zn isotopic compositions. These matrix effects were evaluated by comparing pure Cd and Zn standards and standards doped with bulk column blank from the anion exchange chromatography procedure. Doped standards exhibit signal enhancements (Cd, Ag, Zn and Cu), instrumental mass bias changes and inaccurate isotopic compositions relative to undoped standards, all of which are attributed to the combined presence of resin-derived organics and inorganics. The matrix effect associated with the inorganic component of the column blanks was evaluated separately by doping standards with metals at the trace levels detected in the column blanks. Mass bias effects introduced by the inorganic column blank matrix are smaller than for the bulk column blank matrix but can still lead to significant changes in ion signal intensity, instrumental mass bias and isotopic ratios. Chemical treatment with refluxed HNO₃ or HClO₄/HNO₃ removes resin-derived organic components resulting in matrix effects similar in magnitude to those associated with the inorganic component of the column blank.Mass bias correction using combined external normalization-SSB does not correct for these matrix effects because the instrumental mass biases experienced by Cd and Zn are decoupled from those of Ag and Cu, respectively. Our results demonstrate that ion exchange chromatography and associated resin-derived contaminants can be a source of error in MC-ICP-MS measurement of heavy stable element isotopic compositions.