Observed Isotope Effect Research Articles

Molecular Orbital Studies of the Structures and Reactions of a Singly Charged Calcium Ion with Water Clusters, Ca+(H2O)n

Structures of hydrated singly positive charged calcium−water clusters Ca+(H2O)n and their hydrogen-eliminated products (CaOH)+(H2O)n-1 were optimized using the ab initio molecular orbital methods and are compared with cationic magnesium−water clusters which have been investigated previously. For n ≥ 2, the structures of Ca+(H2O)n are different from those of Mg+(H2O)n. In the Mg+(H2O)n clusters, a pyramidical Mg+(H2O)3 forms the first shell. In contrast, a quasi-square-planar Ca+(H2O)4 is the first shell. The structures of (CaOH)+(H2O)n-1 are also different from structures (MgOH)+(H2O)n-1. The structural difference is attributed to the participation of the d orbitals of Ca atom in the bonding. Despite these structural differences, the core molecular ion (CaOH)+ in the hydrogen-eliminated products (CaOH)+(H2O)n-1 is very similar to the corresponding core ion (MgOH)+. Both ions, CaOH+ and MgOH+, are strongly polarized to Ca2+O-H and Mg2+O-H. Consequently, the hydration energies of the (CaOH)+(H2O)n are much larger than those of the corresponding Ca+(H2O)n. The internal energy change of the hydrogen-elimination reactions of the Ca+(H2O)n is positive for n = 1−4 but becomes negative for n ≥ 5, which is consistent with the product switch in the time-of-flight mass spectrum reported by Fuke's group. The equilibrium constants of the hydrogen elimination reaction are also consistent with the experimental observed isotope effects and the determined metal dependencies.

CH4/CD4 isotope effect on the reaction of adsorbed hydrocarbon species in CO2-reforming over Ni/Al2O3 catalyst

By replacing CH4 with CD4, the isotope effect on the reaction of adsorbed hydrocarbon species with CO2 over Ni/Al2O3 catalyst was studied using pulse surface reaction rate analysis (PSRA). The first-order rate constant for this step was 1.45 times larger for CH4 than for CD4. The observed isotope effect suggests that the reaction of adsorbed hydrocarbon species with CO2 (or adsorbed oxygen) is rate-controlling for the reforming of CH4.

EPR Evidence of Jahn-Teller Polaron Formation in La1-xCaxMnO3+y.

The electron paramagnetic resonance (EPR) signal in the mixed valence perovskite ${\mathrm{La}}_{1\ensuremath{-}x}{\mathrm{Ca}}_{x}{\mathrm{MnO}}_{3+y}$ was investigated in the paramagnetic regime for ${}^{16}$O and ${}^{18}$O isotope substituted compounds. The characteristic differences observed in EPR intensity and linewidth for the two isotope samples can be explained by a model in which a bottlenecked spin relaxation takes place from the exchange-coupled constituent ${\mathrm{Mn}}^{4+}$ ions via the ${\mathrm{Mn}}^{3+}$ Jahn-Teller ions to the lattice. For $x\phantom{\rule{0ex}{0ex}}=\phantom{\rule{0ex}{0ex}}0.2$ the ferromagnetic exchange energy $J$ exhibits a ${}^{16}\mathrm{O}{/}^{18}\mathrm{O}$ oxygen isotope effect of $\ensuremath{\sim}\ensuremath{-}10%$. The observed isotope effects suggest the presence of Jahn-Teller polarons in these materials.

Empirical model of the state-to-state dynamics in near-resonant hyperthermal X + + H 2O charge-transfer reactions

H 2O + Ã-X luminescence studies involving X + + H 2O (X = Ar, N, Kr, N 2) charge-transfer systems are consolidated into an empirical model for the charge-transfer product state distributions associated with hyperthermal collisions of ground-state reactants. The model predicts that Franck-Condon active states are populated with a Gaussian vibrational energy distribution that is shifted by approximately − 0.18 eV with respect to energy resonance. The model is applied to hyperthermal O +( 4S) + H 2O charge-transfer collisions for which luminescence experiments are too insensitive because weakly emitting vibrationally excited states of the H 2O + X 2 B 1 state are populated. Isotope effects in the O +( 4S) + H 2O/D 2O charge-transfer cross sections are measured using guided-ion beams to test the model. The model correctly predicts the observed isotope effect within the hyperthermal collision energy range of 2 and 8 eV.

Ultra-fast excited state dynamics in green fluorescent protein: multiple states and proton transfer.

The green fluorescent protein (GFP) of the jellyfish Aequorea Victoria has attracted widespread interest since the discovery that its chromophore is generated by the autocatalytic, posttranslational cyclization and oxidation of a hexapeptide unit. This permits fusion of the DNA sequence of GFP with that of any protein whose expression or transport can then be readily monitored by sensitive fluorescence methods without the need to add exogenous fluorescent dyes. The excited state dynamics of GFP were studied following photo-excitation of each of its two strong absorption bands in the visible using fluorescence upconversion spectroscopy (about 100 fs time resolution). It is shown that excitation of the higher energy feature leads very rapidly to a form of the lower energy species, and that the excited state interconversion rate can be markedly slowed by replacing exchangeable protons with deuterons. This observation and others lead to a model in which the two visible absorption bands correspond to GFP in two ground-state conformations. These conformations can be slowly interconverted in the ground state, but the process is much faster in the excited state. The observed isotope effect suggests that the initial excited state process involves a proton transfer reaction that is followed by additional structural changes. These observations may help to rationalize and motivate mutations that alter the absorption properties and improve the photo stability of GFP.

Quantum decoherence and the isotope effect in condensed phase nonadiabatic molecular dynamics simulations

In this paper, we explore in detail the way in which quantum decoherence is treated in different mixed quantum-classical molecular dynamics algorithms. The quantum decoherence time proves to be a key ingredient in the production of accurate nonadiabatic dynamics from computer simulations. Based on a short time expansion to a semiclassical golden rule expression due to Neria and Nitzan [J. Chem. Phys. 99, 1109 (1993)], we develop a new computationally efficient method for estimating the decay of quantum coherence in condensed phase molecular simulations. Using the hydrated electron as an example, application of this method finds that quantum decoherence times are on the order of a few femtoseconds for condensed phase chemical systems and that they play a direct role in determining nonadiabatic transition rates. The decay of quantum coherence for the solvated electron is found to take ≊50% longer in D2O than in H2O, providing a rationalization for a long standing puzzle concerning the lack of experimentally observed isotope effect on the nonadiabatic transition rate: Although the nonadiabatic coupling is smaller in D2O due to smaller nuclear velocities, the smaller coupling in D2O adds coherently for a longer time than in H2O, leading to nearly identical nonadiabatic transition rates. The implications of this isotope dependence of the nonadiabatic transition rate on changes in the quantum decoherence time for electron transfer and other important chemical reactions are discussed.

Ferromagnetic Spin Ordering Along Intermolecular Hydrogen Bonds of a Hydroquinone Derivative Carrying a Nitronyl Nitroxide

Abstract The crystal structure of an organic ferromagnet, α-HQNN, was characterized by one-dimensional chains constructed through intermolecular hydrogen bonds. Furthermore two parallel hydrogen-bonded chains are connected by bifurcated hydrogen bonds. The analysis of heat capacity data indicates the three-dimensional ferromagnetic intermolecular interaction in this crystal. The results confirm the presence of the ferromagnetic intermolecular interaction along hydrogen bond. The observed isotope effect in the α-HQNN-d2 crystal is consistent with the above interpretation.

How Important Are Quantum Mechanical Nuclear Motions in Enzyme Catalysis?

The role of quantum mechanical nuclear motions in enzymatic reactions is examined by realistic simulations that take into account the fluctuations of an entire enzyme−substrate complex. This is done by using the quantized classical path (QCP) approach which is based on Feynman's path integral formulation. The calculations evaluate the quantum mechanical activation free energy and deuterium isotope effect for the proton transfer step in the catalytic reaction of carbonic anhydrase. The calculated and observed isotope effects are in very good agreement, thus demonstrating the potential of our approach in extracting mechanistic information. Furthermore, the value of the calculated quantum mechanical rate constant is in a good agreement with the corresponding observed value. This is significant since the evaluation of the ratio between the quantum mechanical rate constants of the reaction in the protein and in aqueous solution does not involve any adjustable parameter. The reliability of our calculations is b...

Probing the mechanism of nitrogen transfer in Escherichia coli asparagine synthetase by using heavy atom isotope effects.

In experiments aimed at determining the mechanism of nitrogen transfer in purF amidotransferase enzymes, 13C and 15N kinetic isotope effects have been measured for both of the glutamine-dependent activities of Escherichia coli asparagine synthetase B (AS-B). For the glutaminase reaction catalyzed by AS-B at pH 8.0, substitution heavy atom labels in the side chain amide of the substrate yields observed values of 1.0245 and 1.0095 for the amide carbon and amide nitrogen isotope effects, respectively. In the glutamine-dependent synthesis of asparagine at pH 8.0, the amide carbon and amide nitrogen isotope effects have values of 1.0231 and 1.0222, respectively. We interpret these results to mean that nitrogen transfer does not proceed by the formation of free ammonia in the active site of the enzyme and probably involves a series of intermediates in which glutamine becomes covalently attached to aspartate. While a number of mechanisms are consistent with the observed isotope effects, a likely reaction pathway involves reaction of an oxyanion with beta-aspartyl-AMP. This yields an intermediate in which C-N bond cleavage gives an acylthioenzyme and a second tetrahedral intermediate. Loss of AMP from the latter gives asparagine. An alternate reaction mechanism in which asparagine is generated from an imide intermediate also appears consistent with the observed kinetic isotope effects.

Isotope effect in d-wave superconductors.

Based on recently proposed anti-ferromagnetic spin fluctuation exchange models for $d_{x^2-y^2}$-superconductors, we show that coupling to harmonic phonons {\it{cannot}} account for the observed isotope effect in the cuprate high-$T_c$ materials, whereas coupling to strongly anharmonic multiple-well lattice tunneling modes {\it{can}}. Our results thus point towards a strongly enhanced {\it{effective}} electron-phonon coupling and a possible break-down of Migdal-Eliashberg theory in the cuprates.

13] Isotope effects: Determination of enzyme transition state structure

Publisher Summary Enzymologists wish to determine the transition state structures for enzymatic reactions for several reasons: (1) to compare the mechanisms of enzymatic and nonenzymatic reactions in order to understand better the factors involved in enzymatic catalysis and (2) “transition state analogs” being used for drugs, to know what structure should be mimicked. Isotope effects have been used for many years to study the nonenzymatic reactions. For many enzymatic reactions, the observed isotope effects can be reasonably interpreted once the intrinsic values are known on the chemical steps. The problem is that the chemical step (or steps) of an enzymatic reaction is often not totally rate limiting, so that one has to either find a way to make this step rate limiting (by changing substrate, changing pH, or mutating the enzyme) or find a way to calculate the intrinsic isotope effect. This chapter discusses some basic definitions, and then describes the more modern methods of measuring isotope effects and determining intrinsic isotope effects. After that, it gives examples of the determination of transition state structure and what these studies tell about enzymatic mechanisms.

A Time Resolved IR Laser Photolysis‐Laser Induced Fluorescence Study of theOH/Methanol Reaction

The reaction of hydroxyl radicals (OH and OD) generated by infrared multiphoton dissociation of different isotopomers of methanol were studied in the presence of variable amounts of Ar buffer gas. The disappearance of the OH, or OD, radicals in the presence of the parent methanol was followed by laser induced fluorescence at 310 nm. Comparison of the rate constants obtained from these experiments reveal good agreement with observed isotope effects observed by other authors but suggest that the reactions occurs at higher temperatures than the macroscopic bulk temperature of the sample.

Direct reaction of gas-phase atomic hydrogen with chemisorbed hydrogen on Ru(001)

The adsorption of gas-phase atomic hydrogen on the Ru(001) surface results in a saturation coverage of 1.42 hydrogen adatoms per primitive surface unit cell, which may be compared with a saturation coverage of one hydrogen adatom per primitive surface unit cell in the case of dissociative chemisorption of molecular hydrogen. The observed saturation fractional coverage of 1.42 results from a steady-state balance of adsorption of gas-phase atomic hydrogen and reaction of gas-phase hydrogen with chemisorbed hydrogen adatoms, which produces molecular hydrogen that desorbs from the surface at a temperature at least 150 K below the temperature of recombinative desorption of two hydrogen adatoms. The cross section of this direct reaction of hydrogen was found to be remarkably large, approximately 40% of the cross section for chemisorption of the gas-phase atomic hydrogen. The reaction was found not to depend on surface temperature nor was there an observable kinetic isotope effect.

Hydrogen tunneling in the flavoenzyme monoamine oxidase B.

Competitive kH/kT and kD/kT kinetic isotope effects on p-methoxybenzylamine oxidation by the 8 alpha-S-cysteinyl flavin adenine dinucleotide (FAD)-dependent enzyme monoamine oxidase B (MAO-B) have been measured as a function of temperature. At pH 7.5, exponents relating observed kH/kT and kD/kT isotope effects indicate the presence of a temperature-dependent change in rate-limiting step. At lower temperature (e.g., 2 degrees C), the presence of multiple rate-limiting steps (commitments) is clearly indicated from the size of the exponent and individual isotope effects. Noncompetitive kH/kD isotope effect measurements indicate a trend in observed isotope effects between pH 9.0 and 6.0, with isotope effects increasing at lower pH. Primary and secondary kH/kT and kD/kT isotope effects were therefore measured as a function of temperature at pH 6.1. Exponents relating primary and secondary kH/kT and kD/kT in the 10-43 degrees C range are 3.13 +/- 0.04 and 2.36 +/- 0.13, respectively, and do not systematically change with temperature. These data indicate that commitments, if present, remain constant across this temperature range. The temperature dependence of the observed primary isotope effects gives values for the ratios of Arrhenius prefactors of 0.13 +/- 0.03 (AH/AT) and 0.52 +/- 0.05 (AD/AT). Both values are well below the lower limits predicted in the absence of tunneling contributions to the reaction coordinate, indicating that both deuterium and protium tunneling take place in this reaction. The presence of a temperature independent commitment contribution cannot be rigorously ruled out; however, the effect of such a commitment on the observed AH/AT and AD/AT values is shown to be quite small.

Low-temperature proton transport in clathrates

The impedance spectra are measured for protonated and deuterated clathrates, HClO4⋅5.5H2O and DClO4⋅5.5D2O, between 10 and 300 K. The conductance is investigated between 80 K and room temperature and the dielectric constant between 10 and 120 K. The data show deviation from the Arrhenius behavior of conductance in the low-temperature regime. A description of proton conductivity is developed on the basis of quantum theory of an elementary act of proton tunneling between donor–acceptor sites interacting with environmental fluctuations. Several models of the elementary act are considered. The mechanism, most consistent with the obtained data, incorporates—strong coupling of the proton with local vibrational modes of the closest environment and system diabatic transitions along these vibrational ‘‘coordinates’’—fluctuations of the tunneling barrier for the proton. At low temperatures the motion along the vibrational coordinates is no longer purely classical and the slow mode tunneling takes place. The latter gives rise to a curvature in the Arrhenius plots apprehended as a decrease of the apparent activation energy at lower temperatures. The observed isotope effect is in line with the lower deuteron tunneling probability due to doubling the mass, though other parameters may also be affected by deuteration.

Solvent hydrogen isotope effects and anion inhibition of CO2 hydration catalysed by carbonic anhydrase from Pisum sativum.

Chloroplast carbonic anhydrase from Pisum sativum has been studied to elucidate the catalytic mechanism and to test if the mechanism proposed for human carbonic anhydrase II is also valid for pea carbonic anhydrase. The catalytic activity was found to depend on the chemical nature of the buffer. Barbital buffer gives the highest turnover number at infinite buffer concentration and the lowest Km value with respect to the buffer, while the kinetic parameters obtained in the imidazole-type buffer, 1-methylimidazole, do not differ from those obtained using the biological-type buffer Mops. The anion inhibition of CO2 hydration was investigated using SCN- at pH 6-9. The binding of the anion was found to be pH dependent with the strongest interaction at low pH. We obtained an uncompetitive inhibition pattern at high pH and noncompetitive inhibition patterns at pH 7 and low pH. The catalytic mechanism was further tested by measurements of the solvent hydrogen isotope effects on the kinetic parameters for CO2 hydration. The observed effects were comparatively small with a kcat value of approximately 2 irrespective of the pH. The effect on kcat/Km and on Km changes when going from high pH to pH 7 and low pH. At high pH, the solvent isotope effect in Km is at least 3, giving a value below 1 for kcat/Km, while at pH 7 and low pH the major effect is found in kcat/Km with values of 2.6 and 2.9. The dependence of the CO2-hydration activity on the buffer concentration is in agreement with a ping-pong mechanism with buffer acting as a second substrate. This is analogous to the behaviour of human carbonic anhydrase II. The inhibition patterns and the observed isotope effects at high pH can also be explained within the framework of the catalytic mechanism for human carbonic anhydrase II, with a rate-determining and buffer-dependent part. The results are consistent with a mechanism involving a proton transfer that contributes to rate limitation. However, the isotope effects found at pH 7 and low pH indicate that some part of the mechanism has changed. Moreover, we cannot decide whether the mechanism for pea carbonic anhydrase involves an internal proton-shuttle group, or if the buffer molecule acts in a direct proton transfer from the zinc-coordinated water.

Pair Breaking and Isotope Effect ind-Wave Superconductivity

The question as to whether d -wave superconductivity is compatible with the small but nonvanishing isotope effects observed in high- T c copper oxides is addressed. On the assumption that a n o n phonon mechanism, most likely via antiferromagnetic spin fluctuations, is dominant in both normal and superconducting states, only a few percent contribution to the quasi-particle damping rate from the electron-phonon interaction gives rise to a correct order of the observed isotope effects. The heavier the isotope mass, the lower T c becomes, since the damping increases via lowering in frequency of the phonon spectrum. The pairing and pair-breaking effects for YBa 2 Cu 3 O 7 and La 1.85 Sr 0.15 CuO 4 are examined, and the impurity-concentration dependence of T c is briefly discussed.

Theory for the observed isotope effects on the formation of multiple products by different kinetic mechanisms of cytochrome P450 enzymes

Cytochrome P450 systems are unusual in that many of them can convert a substrate to a number of different metabolites. Several kinetic mechanisms may be envisioned by which the metabolites may be formed. In each of the mechanisms, the substrate combines with the enzyme in different orientations to form a set of (ES) complexes that then are activated to a set of (EOS) complexes. The fate of these (EOS) complexes determines the kinetic mechanism. In the "parallel pathway" mechanism, the (EOS) complexes are so stable and rigid they cannot be converted either directly or indirectly to complexes with different orientations; the orientation of the (ES) complexes thus determines which metabolite will be formed. In the "nondissociative" mechanisms, the complexes are not rigid; instead they undergo interconversion while the substrate remains in the active site of the enzyme. In the "dissociative" mechanisms, the (EOS) complexes dissociate to (EO) and (S), but recombine to form (EOS) complexes with either the same or different orientations. Steady-state equations describing the deuterium isotope effects for these kinetics mechanisms have been derived and solved for competitive experiments, in which equal concentrations of both deuterated and nondeuterated substrates are present in incubation mixtures, and for noncompetitive experiments, in which only one of the substrates is present. The equations reveal that comparisons of the isotope effects on the formation of a metabolite by a pathway that does not involve the abstraction of a deuterium from a deuterated substrate (the non-deuterium abstraction pathway) in both experiments can differentiate between the kinetic mechanisms. A value of 1.0 for (v)H/(v)D in the competitive experiment, but < 1.0 to > 1.0 for the value of (Vmax/Km)H/(Vmax/Km)D in the noncompetitive experiment, is diagnostic for the "dissociative" mechanisms. Values of 1.0 in both kinds of experiments are diagnostic for the "parallel pathway" mechanism. Values of < 1.0 in both types of experiments are diagnostic for the "nondissociative" mechanisms. The equations also predict possible unusual substrate-inhibitor interactions when the "dissociative" mechanism is operative.

Kinetic Deuterium Isotope Effects in the combustion of formulated nitramine propellants

AbstractThe kinetic deuterium isotope effect was used to investigate the rate‐limiting process in the combustion of formulated nitramine propellants. Model propellant formulations containing either octahydro‐1,3,5,7‐tetranitro‐1,3,5,7‐tetrazocine (HMX), hexahydro‐1,3,5‐trinitro‐1,3,5‐triazine (RDX), or their deuteriated analogues were pressed into pellets and burned under nitrogen pressure in a window bomb. The magnitudes of the observed deuterium isotope effects indicate that the HMX and RDX exert significant control over the combustion phenomenon of the propellants studied. Furthermore, assuming a consistent mechanism between decomposition and combustion, the observed isotope effects suggest that a carbon‐hydrogen bond rupture in HMX or RDX is the rate‐controlling step in the combustion of the model nitramine propellants. Observed isotope effect values for HMX‐CW5 and RDX‐CW5 formulated propellants at 1000 psig (6.99 MPa) pressure were 1.29 ± 0.09 and 1.24 ± 0.07, respectively, compared to a theoretical estimate of 1.29 for a primary effect due to CH bond rupture at 673 K.

Isotope effects in the dissociation dynamics of energetic hydrogen scattered from Cu(111) under glancing angles of incidence

We have scattered fast beams of H 2 and D 2 and their positive ions from Cu(111) under glancing angles of incidence. By directly measuring the relative velocity ν of the dissociation fragments we obtain the kinetic energy released in the internuclear coordinate as a function of the final orientation of the internuclear axis. These distributions exhibit a strong isotope effect for the case of neutral beam scattering, and no isotope effect for incident ion beam scattering. We propose a dissociation mechanism for neutral molecules which assumes multiple electronic excitation—relaxation cycles during scattering, with the detailed dynamics determined by the propagation times per cycle on each of the participating states. We attribute the observed isotope effect to a velocity induced change in the electron—hole pair excitation density, which determines the propagation time of the system on the lower state. We propose that the dissociation dynamics of H + 2 and D + 2 ions at Cu(111) is determined both by this mechanism (for charge transfer to the X 1∑ + g state) and direct dissociation via the b 3∑ + u state, with a branching ratio of the order of unity.