Pressure effects on enzyme-catalyzed quantum tunneling events arise from protein-specific structural and dynamic changes

The rate and kinetic isotope effect (KIE) on proton transfer during the aromatic amine dehydrogenase-catalyzed reaction with phenylethylamine shows complex pressure and temperature dependences. We are able to rationalize these effects within an environmentally coupled tunneling model based on constant pressure molecular dynamics (MD) simulations. As pressure appears to act anisotropically on the enzyme, perturbation of the reaction coordinate (donor-acceptor compression) is, in this case, marginal. Therefore, while we have previously demonstrated that pressure and temperature dependences can be used to infer H-tunneling and the involvement of promoting vibrations, these effects should not be used in the absence of atomistic insight, as they can vary greatly for different enzymes. We show that a pressure-dependent KIE is not a definitive hallmark of quantum mechanical H-tunneling during an enzyme-catalyzed reaction and that pressure-independent KIEs cannot be used to exclude tunneling contributions or a role for promoting vibrations in the enzyme-catalyzed reaction. We conclude that coupling of MD calculations with experimental rate and KIE studies is required to provide atomistic understanding of pressure effects in enzyme-catalyzed reactions.     

Tunneling proton transfer in biological systems. Role of temperature and pressure

The possibilities of hydrogen atom tunneling transfer in biological liquids are discussed. Basic mechanisms of temperature and pressure effects on the tunneling rate constant are considered: the reorganization of reagents and the medium due to the transfer of H atoms and changes in the value and shape of the chemical reaction potential barrier upon intermolecular and soft intramolecular vibrations. Expressions are derived for the tunneling transition rate constant and kinetic isotopic effect as functions of temperature and pressure. It is found that the temperature dependence of the isotope effect is mainly affected by the second mechanism only. The theory is compared with the literature??s experimental data on the temperature dependence of the isotope effect. It is shown that experiments are described well by the theory at sensible values of the fitting parameters.     

Examining the importance of dynamics,barrier compression and hydrogen tunnelling in enzyme catalysed reactions

Nuclear quantum mechanical tunnelling is important in enzyme-catalysed H-transfer reactions. This viewpoint has arisen after a number of experimental studies have described enzymatic reactions with kinetic isotope effects that are significantly larger than the semiclassical limit. Other experimental evidence for tunnelling, and the potential role of promoting vibrations that transiently compress the reaction barrier, is more indirect, being derived from the interpretation of e.g. mutational analyses of enzyme systems and temperature perturbation studies of reaction rates/kinetic isotope effects. Computational simulations have, in some cases, determined exalted kinetic isotope effects and tunnelling contributions, and identified putative promoting vibrations. In this review, we present the available evidence – both experimental and computational – for environmentally-coupled Htunnelling in several enzyme systems, namely aromatic amine dehydrogenase and members of the Old Yellow Enzyme family. We then consider the relative importance of tunnelling contributions to these reactions. We find that the tunnelling contribution to these reactions confers a rate enhancement of ～1000-fold. Without tunnelling, a 1000-fold reduction in activity would seriously impair cellular metabolism. We therefore infer that tunnelling is crucial to host organism viability thereby emphasising the general importance of tunnelling in biology.     

The kinetics of isotope exchange reactions: Use of initial rates to measure isotope effects on carbon acid ionization

Multistep hydrogen isotope exchange reactions, such as the íonization of a carbon acid via a carbanion intermediate in a protic solvent, when conducted using an isotopic tracer to monitor the exchange, have the unusual feature that their rate-determining steps always refer to the transfer of the tracer isotope and never to the isotope present in macroscopic amounts. This property of these reactions is discussed and rationalized using a free energy versus reaction coordinate diagram. It is further shown that this property does not invalidate a commonly used method of measuring kinetic isotope effects on carbon acid ionization in which rates of incorporation of tritium tracers into RH and RD substrates are compared, despite the fact that tritium transfer is rate determining in both exchanges, but it is valid only if initial rate measurements are used. When the comparison is made in a protio solvent, e.g., H₂O, the portion of the initial reaction which may be used depends strongly on the magnitude of the isotope effect. It ranges from less than 1% tritium incorporation for large isotope effects to 10% or more for isotope effects near unity. On the other hand, when a deuterated solvent, e.g., D₂O, is used, the range of validity of the method for large isotope effects is extended dramatically.     

Generalized Swain–Schaad relations including tunneling and temperature dependence

The Swain–Schaad relation, which relates the kinetic isotope effects of the three hydrogen isotopes, is extended by including tunneling and temperature dependence. The new version shows that the effect of tunneling on the Swain–Schaad exponent is opposite to that usually assumed and depends on the degree of assistance the tunneling receives from other vibrations.     

Dependence of transition state structure on substrate: the intrinsic C-13 kinetic isotope effect is different for physiological and slow substrates of the ornithine decarboxylase reaction because of different hydrogen bonding structures

Ornithine decarboxylase is the first and the rate-controlling enzyme in polyamine biosynthesis; it decarboxylates l-ornithine to form the diamine putrescine. We present calculations performed using a combined quantum mechanical and molecular mechanical (QM/MM) method with the AM1 semiempirical Hamiltonian for the wild-type ornithine decarboxylase reaction with ornithine (the physiological substrate) and lysine (a "slow" substrate) and for mutant E274A with ornithine substrate. The dynamical method is variational transition state theory with quantized vibrations. We employ a single reaction coordinate equal to the carbon-carbon distance of the dissociating bond, and we find a large difference between the intrinsic kinetic isotope effect for the physiological substrate, which equals 1.04, and that for the slow substrate, which equals 1.06. This shows that, contrary to a commonly accepted assumption, kinetic isotope effects on slow substrates are not always good models of intrinsic kinetic isotope effects on physiological substrates. Furthermore, analysis of free-energy-based samples of transition state structures shows that the differences in kinetic isotope effects may be traced to different numbers of hydrogen bonds at the different transition states of the different reactions.     

Noncovalent Hydrogen Isotope Effects

Zero-point energies (ZPE) and isotope effects, induced by intermolecular, noncovalent vibrations, are computed and tested by experimental data. The ZPE differences of H- and D-complexes of water with hydrogen, methane, and water molecules are about 100–300 cal/mol; they result to isotope effects IE of 1.20–1.70. Semi-ionic bonds between metal ions and water ligands in M(H₂O) ₆ ²⁺ complexes are much stronger; their ZPEs are about 12–14 kcal/mol per molecule and result to IE of 1.9–2.1 at 300 K. Protonated (deuterated) water and biwater exhibit the largest ZPE differences and isotope effects; the latter are 25–28 and 12–13 for water and biwater, respectively. Noncovalent IEs contribute markedly into the experimentally measured effects and explain many anomalous and even magic properties of the effects, such as the dependence of IE on the solvents and on the presence of the third substances, enormously large isotope effects at the mild conditions, the difference between IEs measured in the reactions of individual protiated and deuterated compounds and those measured in their mixture. Noncovalent IEs are not negligible and should be taken into account to make correct and substantiated conclusions on the reaction mechanisms. The kinetic equations are derived for the total isotope effects, which include noncovalent IEs as additive factors.     

Quantum effects in ab-initio calculations of rate constants for chemical reactions occuring in the condensed phase

An overview of recent advances in the development of methods designed to calculate rate constants for chemical reactions obeying mass action kinetic equations in condensed phases is presented. A general framework addressing mixed quantum-classical systems is elaborated that enables quantum features such as tunneling effects, zero-point vibrations, dynamic quantum coherence, and non-adiabatic effects to be calculated. An efficient Monte Carlo sampling method for performing ab-initio calculations of rate constants and isotope effects in chemical processes in condensed phases is outlined, and the connection of isotope effects to reaction mechanism is explored     

Vibrational energy relaxation of the bend fundamental of dilute water in liquid chloroform and d-chloroform

The population lifetimes of the bend fundamental of dilute water in liquid chloroform (8.5 ps) and d-chloroform (28.5 ps) display an interesting solvent isotope effect. As the lowest excited vibrational state of the molecule, the water bend fundamental relaxes directly to the ground state with about 1600 cm-1 of energy released to the other degrees of freedom. The strong solvent isotope effect along with the large energy gap indicates the participation of solvent vibrational modes in this vibrational energy relaxation process. We calculate the vibrational energy relaxation rates of the water bend in chloroform and d-chloroform using the Landau-Teller formula with a new potential model developed and parametrized self-consistently to describe the chloroform-water interaction. The computed values are in reasonable agreement with the experimental results, and the trend for the isotope effect is correct. It is found that energy transfer to the solvent vibrations does indeed play an important role. Nevertheless, no single dominant solvent accepting mode can be identified; the relaxation appears to involve both the bend and the C-Cl stretches, and frequency changes of all of these modes upon deuteration contribute to the observed solvent isotope effect.     

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.     

AN EXAMPLE OF HOW PHOTOPHYSICAL PROPERTIES CAN INFLUENCE THE MAGNITUDE OF SOLVENT ISOTOPE EFFECTS UPON PHOTO-OXIDATION REACTIONS

Abstract Substantial isotope effects have been observed for the dye sensitised photo-oxidation of 1,3-diphenyl-2-pyrazoline in both polar and non polar solvents, implicating singlet oxygen as a reactive intermediate. By way of contrast, a solvent isotope effect upon the direct photo-oxidation of the pyrazoline was only observed when a protic solvent (methanol) was used. It was found that the photophysical properties (e.g. quantum yields and fluorescence lifetimes) of pyrazolines are sensitive to the isotopic composition of protic solvents but not aprotic solvents. The solvent isotope effect observed for the direct photo-oxidation reaction in methanol may not therefore be a true indication of the participation of singlet oxygen. Since this reaction may not be singlet oxygen mediated, an alternative mechanism is proposed.     

Chlorine kinetic isotope effects on the haloalkane dehalogenase reaction.

We have found chlorine kinetic isotope effects on the dehalogenation catalyzed by haloalkane dehalogenase from Xanthobacter autotrophicus GJ10 to be 1.0045 +/- 0.0004 for 1,2-dichloroethane and 1.0066 +/- 0.0004 for 1-chlorobutane. The latter isotope effect approaches the intrinsic chlorine kinetic isotope effect for the dehalogenation step. The intrinsic isotope effect has been modeled using semiempirical and DFT theory levels using the ONIOM QM/QM scheme. Our results indicate that the dehalogenation step is reversible; the overall irreversibility of the enzyme-catalyzed reaction is brought about by a step following the dehalogenation.     

Effect of pressure on a heavy-atom isotope effect of yeast alcohol dehydrogenase

Hydrostatic pressure causes a monophasic decrease in the (13)C primary isotope effect expressed on the oxidation of benzyl alcohol by yeast alcohol dehydrogenase. The primary isotope effect was measured by the competitive method, using whole-molecule mass spectrometry. The effect is, therefore, an expression of isotopic discrimination on the kinetic parameter V/K, which measures substrate capture. Moderate pressure increases capture by activating hydride transfer, the transition state of which must therefore have a smaller volume than the free alcohol plus the capturing form of enzyme [Cho, Y.-K.; Northrop, D. B. Biochemistry 1999, 38, 7470-7475]. The decrease in the (13)C isotope effect with increasing pressure means that the transition state for hydride transfer from the heavy atom must have an even smaller volume, measured here to be 13 mL.mol(-1). The pressure data factor the kinetic isotope effect into a semiclassical reactant-state component, with a null value of k(12)/k(13) = 1, and a transition-state component of Q(12)/Q(13) = 1.028 (borrowing Bell's nomenclature for hydrogen tunneling corrections). A similar experiment involving a deuterium isotope effect previously returned the same volume and null value, plus a pressure-sensitive isotope effect [Northrop, D. B.; Cho, Y.-K. Biochemistry 2000, 39, 2406-2412]. Consistent with precedence in the chemical literature, the latter suggested a possibility of hydrogen tunneling; however, it is unlikely that carbon can engage in significant tunneling at ambient temperature. The fact that the decrease in activation volumes for hydride transfer is equivalent when one mass unit is added to the carbon end of a scissile C-H bond and when one mass unit is added to the hydrogen end is significant and suggests a common origin.     

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.     

A fragment molecular-orbital-multicomponent molecular-orbital method for analyzing HD isotope effects in large molecules

We have developed a fragment molecular orbital (FMO)-multi-component MO (MC_MO) method to analyze isotope effect due to differences between the quantum effects of protons and deuterons for large molecules such as proteins and DNA. The FMO-MC_MO method enables the determination of both the electronic and the protonic (deuteronic) wave functions simultaneously, and can directly express isotope effects, including coupling effects between nuclei and electrons. In our calculations of two polyglycines, which serve as prototypes for biological molecules, by this method, we clearly observed the geometrical relaxation induced by the HD isotope effect in the intramolecular hydrogen bonding portions of the molecules. The HD isotope effect on the interfragment interaction energy, including that of the hydrogen bonding parts, was also demonstrated: the hydrogen bond was weakened by replacement of hydrogen with deuterium. We also developed electrostatic potential approximations for use in the FMO-MC_MO calculations, and the accuracy of the energy differences induced by the isotope effect was independent of the approximation level of the FMO-MC_MO. Our results confirmed that the FMO-MC_MO method is a powerful tool for the detailed analysis of changes in hydrogen bonding and interaction energies induced by the HD isotope effect for large biological molecules.     

Non-linear signal response functions and their effects on the statistical and noise cancellation properties of isotope ratio measurements by multi-collector plasma mass spectrometry

A nebulizer-centric response function model of the analytical inductively coupled argon plasma ion source was used to investigate the statistical frequency distributions and noise reduction factors of simultaneously measured flicker noise limited isotope ion signals and their ratios. The response function model was extended by assuming i) a single gaussian distributed random noise source (nebulizer gas pressure fluctuations) and ii) the isotope ion signal response is a parabolic function of the nebulizer gas pressure.Model calculations of ion signal and signal ratio histograms were obtained by applying the statistical method of translation to the non-linear response function model of the plasma. Histograms of Ni, Cu, Pr, Tl and Pb isotope ion signals measured using a multi-collector plasma mass spectrometer were, without exception, negative skew. Histograms of the corresponding isotope ratios of Ni, Cu, Tl and Pb were either positive or negative skew. There was a complete agreement between the measured and model calculated histogram skew properties.The nebulizer-centric response function model was also used to investigate the effect of non-linear response functions on the effectiveness of noise cancellation by signal division. An alternative noise correction procedure suitable for parabolic signal response functions was derived and applied to measurements of isotope ratios of Cu, Ni, Pb and Tl. The largest noise reduction factors were always obtained when the non-linearity of the response functions was taken into account by the isotope ratio calculation.Possible applications of the nebulizer-centric response function model to other types of analytical instrumentation, large amplitude signal noise sources (e.g., lasers, pumped nebulizers) and analytical error in isotope ratio measurements by multi-collector plasma mass spectrometry are discussed.     

Spectroscopic identification of the CO-H2O 2-1 cluster trapped in an argon matrix

The infrared spectra of the carbon monoxide-water cluster as well as the CO monomer and dimer in an argon matrix at cryogenic temperatures have been reinvestigated on the basis of the isotope substitution experiment with 12CO and 13CO. Lines due to the CO-H2O 2-1 cluster in the matrix have been unambiguously identified in the CO and OH stretching regions. The isotope effect on the vibrational frequency of the cluster is observed in the CO stretching vibration but neither in the symmetric nor antisymmetric OH stretching vibrations. Each of the two vibrational lines due to the two CO vibrations of the CO-H2O 2-1 cluster is examined by comparing the expected spectral features at a 12CO/13CO ratio on a simulation with those observed experimentally. The migration of the trapped molecules (CO and H2O) in the matrix is discussed, in which the observed spectral change with the deposition temperature from 14 K to 30 K is explained.     

Isotope effects on miscibility of 1-butyl-3-methylimidazolium tetrafluoroborate with butanols

The liquid-liquid miscibility temperatures as a function of composition and deuterium substitution have been experimentally determined for the binary mixtures of 1-butyl-3-methylimidazolium tetrafluroborate with 1-butanol, isobutyl alcohol, 2-butanol, and tert-butyl alcohol and their deuterated forms (OH/OD substitution). All systems exhibit upper critical solution temperatures (UCSTs) with a visible effect of branching in alcohols. Deuteration of alcohols in the hydroxyl group results in a decrease of the UCST of the given system and the largest shift is observed for tert-butyl alcohol. These solvent isotope effects nicely correlate with the polarity expressed by dielectric constants or E(T)(30) parameters of alcohols. The effect of the isotope substitution on the miscibility of ILs with butanols can be rationalized by using the statistical-mechanical theory of the isotope effects coupled with a phenomenological g(E) model. Following this procedure one finds that the isotope shift of UCST is associated mainly with the zero-point energy contribution.     

Isotope Effects on Chemical Shifts in the Study of Hydrogen Bonds in Small Molecules

This review is giving a short introduction to the techniques used to investigate isotope effects on NMR chemical shifts. The review is discussing how isotope effects on chemical shifts can be used to elucidate the importance of either intra- or intermolecular hydrogen bonding in ionic liquids, of ammonium ions in a confined space, how isotope effects can help define dimers, trimers, etc., how isotope effects can lead to structural parameters such as distances and give information about ion pairing. Tautomerism is by advantage investigated by isotope effects on chemical shifts both in symmetric and asymmetric systems. The relationship between hydrogen bond energies and two-bond deuterium isotope effects on chemical shifts is described. Finally, theoretical calculations to obtain isotope effects on chemical shifts are looked into.     

Hydrogen/deuterium adsorption and absorption properties on and in palladium using a combined plane wave and localized basis set method

Detailed information on the H/D isotope effects for adsorption on the surface and absorption in the bulk is important for understanding the nuclear quantum effect. To achieve this, we developed a new theoretical approach, namely, the combined plane wave and localized basis set (CPLB) method. By using the multicomponent quantum chemical method, which takes into account the quantum effect of a proton or deuteron, with the localized part of the CPLB method, direct analysis of the H/D isotope effect about adsorption and absorption is carried out. In this study, we performed a theoretical investigation of the H/D isotope effects for adsorption on a Pd(111) surface and absorption in bulk Pd. We clearly showed an H/D isotope effect on geometry during adsorption and absorption. Our developed CPLB approach is a powerful tool for analyzing the quantum nature of H/D in surface, bulk, and inhomogeneous systems.