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.     

Isotopic effect on the cage-induced quenching of OH(A)/OD(A) inside small argon clusters

In this paper we report on the isotopic effect on the cage-induced excited-state quenching inside small Ar(m) clusters (m<10(2)) solvated in large Ne(N) clusters (N approximately 7.5x10(3)). Excited OH(A)/OD(A) fragments are produced by photodissociation of H2O and D2O molecules and the quenching agents are correspondingly H or D atoms. The decrease of the fluorescence yield with the size of the cluster m>m0 is observed in both cases and it is attributed to the formation of the cage of argon atoms around the doped molecule. Interestingly, more atoms are needed to induce the fluorescence quenching of OD*(A) fragments, m0=21+/-3, compared to the electronically excited state quenching of OH*(A) molecules, 11+/-2. A diffusion model containing two free parameters, the quenching cross section sigmaq and the number of argon atoms forming the cage m0, explains the effect in terms of the residence time of the hydrogen atom inside the cage. We suggest that the melting of the doped rare gas clusters is responsible for the different predissociation dynamics. The quenching cross section obtained from the experimental data is in good agreement with former experiments.     

Modeling the fragmentation dynamics of ionic clusters inside helium nanodroplets: the case of He100Ne4+

We present simulation results on the effect of a helium nanodroplet environment on the fragmentation dynamics of embedded molecular systems. The helium atoms are treated explicitly, with zero-point effects taken into account through an effective helium-helium interaction potential. The ionized neon tetramer is used as a model molecular system because, like all the small rare-gas clusters, it fragments extensively upon ionization. All the nonadiabatic effects between electronic states of the ionized neon cluster are taken into account. The results reveal a predominance of Ne2+ and HepNe2+ fragments and the absence of bare Ne+ fragments, in agreement with available experimental data. The neutral monomer fragments exhibit a rather wide kinetic energy distribution that can be fitted to the sum of two Boltzmann distributions, one with a low kinetic energy and the other with a higher kinetic energy. This indicates that cooling by helium atom evaporation is more efficient than was believed so far, as suggested by recent experimental results. Purely classical calculations are shown to strongly overestimate the amount of cage effect (cooling), clearly indicating the need to take into account zero-point effects.     

Isotope effects on the unimolecular dissociation of ionized 3-methyl-2-butanol: reactions via a long-lived C-H-C hydrogen-bridged ion-neutral complex

A pronounced isotope effect causes metastable CD3CHOHCH(CH3)2+* ions to expell C3H6D2 in preference to C3H7D in a ratio of approximately 33:1; a number of related compounds show similar effects. High-level ab initio calculations suggest that the reactant alcohol molecular ion possesses an extraordinarily long alpha-carbon-carbon bond and that the reaction proceeds via the formation of an intermediate hydrogen-bridged complex of propane and ionized vinyl alcohol, in which the bridging hydrogen atom is almost midway between the two carbon termini. The isotopic preference reflects the difference between the zero-point vibrational energies of the isotopically different product pairs rather than kinetic isotope effects on the hydrogen atom transfer reactions that precede dissociation.     

Vibrational ground state properties of H(5)(+) and its isotopomers from diffusion Monte Carlo calculations

Diffusion Monte Carlo computations, with and without importance sampling, of the zero-point properties of H(5)(+) and its isotopomers using a recent high accuracy global potential energy surface are presented. The global minimum of the potential possesses C(2v) symmetry, but the calculations predict a D(2d) geometry for zero-point averaged structure of H(5)(+) with one H atom "in the middle" between two HH diatoms. The predicted zero-point geometries of the deuterated forms have H in the middle preferred over D in the middle and for a nonsymmetric arrangement of D atoms the preferred arrangement is one which maximizes the number of D as the triatomic ion. We speculate on the consequences of these preferences in scattering of H(2)+H(3)(+) and isotopomers at low energies, such as those in the interstellar medium.     

Isotope effect of proton and deuteron adsorption site on zeolite-templated carbon using path integral molecular dynamics

To analyze the proton/deuteron (H/D) isotope effect on the stable adsorption sites on zeolite-templated carbon (ZTC), we have performed path integral molecular dynamics simulations including thermal and nuclear quantum effects with the semi-empirical PM3 potential at 300?K. Here, for the adsorption sites of additional proton (H*) and deuteron (D*), we chose different five carbon atoms labeled as ??-, ??₁-, ??₂-, ??-, and ??-carbons from edge to bottom for inside of buckybowl (C₃₆H₁₂ and C₃₆D₁₂). The stable adsorption sites of D* are observed on all carbon atoms, while those of H* are not observed on ??-carbon atom, but only on ??-, ??₁-, ??₂-, and ??-carbon atoms. This result is explained by the fact that H* can easily go over the barrier height for hydrogen transferring from ??- to ??₂-carbons at 300?K, since the zero-point energy of H* is greater than that of D*.     

Photodissociation and caging of HBr and HI molecules on the surface of large rare gas clusters

Photodissociation experiments were carried out at a wavelength of 243 nm for single HBr and HI molecules adsorbed on the surface of large Nen, Arn, Krn and Xen clusters. The average size is about = 130; the size ranges = 62-139 for the system HBr-Arn and = 110-830 for HI-Xen were covered. In this way the dependence of the photodissociation dynamics on both the size and the rare gas host cluster was investigated. The main observable is the kinetic energy distribution of the outgoing H atoms. The key results are that we do not find any size dependence for either system but that we observe a strong dependence on the rare gas clusters. All systems exhibit H atoms with no energy loss that indicate direct cage exit and those with nearly zero energy that are an indication of complete caging. The intensity ratio of caged to uncaged H atoms is largest for Nen, decreases with increasing mass of the cage atoms, and is weakest for Xen. On the basis of accompanying calculations this behaviour is attributed to the large amplitude motion of the light H atom. This leads to direct cage exit and penetration of the atom through the cluster with different energy transfer per collision depending on the rare gas atoms. The differences between HBr and HI molecules are attributed to different surface states, a flat and an encapsulated site.     

A discharge investigation of hydrogen and deuterium atom formation, and parahydrogen and orthodeuterium reconversion

Hydrogen is flowed through a mild tesla-coil discharge and trapped at 3.8 K: New infrared absorptions of H2 are induced by interaction with trapped H atoms and H- anions. High purity parahydrogen and orthodeuterium samples are 1%-9% reconverted depending on the discharge pressure and recombination of atoms. Annealing the solid samples to 7 K reveals growth in p-H2 induced by o-H2, which shows that H atom recombination produces thermal nuclear spin populations. Similar results are found in discharge experiments with HD and on annealing solid HD. The observed increase in induced HD absorption by J = 1, H2 and D2 molecules formed on recombination gives approximately 1% for the H[D] atom concentration in our solid HD samples.     

The sticking of H and D atoms on a graphite (0001) surface: the effects of coverage and energy dissipation

Classical trajectory methods are used to examine the trapping and sticking of H and D atoms on the graphite (0001) surface. Total energy calculations based on density functional theory are used to construct the model potential energy surface, and graphite clusters of up to 121 atoms are considered. For hydrogen to chemisorb, the bonding carbon must pucker out of the surface plane by roughly 0.4 A. For incident energies above the 0.2 eV barrier, any trapped H atoms must rapidly dissipate their excess energy into the surrounding lattice within a few vibrations of the C-H stretch in order to remain bound. For sufficiently large clusters, the C-H bond stabilizes within about 0.1 ps. The sticking probability for D at 150 K is in the range of 5%-10%, more-or-less consistent with the most recent measurements in the limit of zero coverge. Variation with isotope and substrate temperature is weak. We estimate that the sticking cross section for adsorption at the para site, directly across the sixfold carbon ring from an already adsorbed H atom, can be four or more times larger that the zero coverage sticking cross section.     

High-precision quantum thermochemistry on nonquasiharmonic potentials: converged path-integral free energies and a systematically convergent family of generalized Pitzer-Gwinn approximations

Accurate quantum mechanical (QM) vibrational-rotational partition functions for HOOD, D(2)O(2), H(18)OOH, H(2)(18)O(2), D(18)OOH, and H(18)OOD are determined using a realistic potential energy surface for temperatures ranging from 300 to 2400 K by using the TT-FPI-ESPE path-integral Monte Carlo method. These data, together with our prior results for H(2)O(2), provide benchmarks for testing approximate methods of estimating isotope effects for systems with torsional motions. Harmonic approximations yield poor accuracy for these systems, and although the well-known Pitzer-Gwinn (PG) approximation provides better results for absolute partition functions, it yields the same results as the harmonic approximation for isotope effects because these are intrinsically quantal phenomena. We present QM generalizations of the PG approximation that can provide high accuracy for both isotope effects and absolute partition functions. These approximations can be systematically improved until they approach the accurate result and converge rapidly. These methods can also be used to obtain affordable estimates of zero-point energies from accurate partition functions-even those at relatively high temperatures.     

Imaging the reaction dynamics of OH + CD4. 3. Isotope effects

Isotope effects in the reaction of hydroxyl radical with methane are investigated in a crossed-beam experiment. By exploiting different combinations of OH/OD + CH4/CD4/CHD3, a total of eight isotopically variant reactions are examined to decipher the dynamical consequence of both primary and secondary isotope effects. The most prominent observation is from isotopic substitution of the transferred atom (primary isotope effect), which yields more stretch-excited water product for the D atom case than H atom. The opposite is found, however, for excitations in bending and combination modes. The secondary isotope effects, from either substituted hydroxyl radical or the three H atoms that are not being abstracted, are relatively minor and manifest themselves in spreading the vibrational distribution of the water coproducts.     

Classical studies of H atom trapping on a graphite surface

The trapping and sticking of H and D atoms on the graphite (0001) surface is examined over the energy range 0.1-0.9 eV. Total electronic energy calculations based on density functional theory are used to develop a potential energy surface that allows for the full three-dimensional motion of the incident atom and the reconstruction of the bonding carbon atom, which must pucker out of the surface to form a stable bond. Classical methods are used to compute trapping cross sections as a function of incident energy. The C-H bond, once formed, rapidly dissociates without a mechanism to dissipate its excess energy. However, a number of long-lived trapping resonances exist, and for impact parameters below 1 A or so, several percent of the incident H atoms can remain trapped for 1 ps or more. This long-time trapping probability increases significantly when additional lattice degrees of freedom are added to carry energy away from the C-H stretch. Trapping can also increase with an increasing collision impact parameter, as H vibrations parallel to the surface become excited, leaving less energy in the C-H stretch. The trapping cross section at 1 ps reaches a maximum of 0.2 A2 for an H atom energy of 0.3 eV. Assuming that any atoms remaining trapped after 1 ps fully relax and stick, we estimate a lower bound for the sticking probability of H and D to be 0.024 and 0.050, respectively, about an order of magnitude below the experimental values.     

Observation of hydrogen in deuterated methane hydrate by maximum entropy method with neutron powder diffraction

The crystal structure of deuterated methane hydrate (structure I, space group: Pm(-)3n) was investigated by neutron powder diffraction at temperatures of 7.7-185 K. The scattering amplitude density distribution was examined by a combination of Rietveld method and maximum entropy method (MEM). The distribution of the D atoms in both D(2)O and CD(4) molecules was clarified from three-dimensional graphic images of the scattering amplitude density. The MEM results showed that there were low-density sites for the D atom of D(2)O in a particular location within the D(2)O cage at low temperatures. The MEM provided more reasonable results because of the decrease in the R factor that is attainable by this method. Accordingly, the low-density sites for the D atom of D(2)O probably exist within the D(2)O cage. This suggests that a spatial disorder of the D atom of D(2)O occurs at these sites and that hydrogen bonds between D(2)O molecules become partially weakened. With regard to the CD(4) molecules, there were high-density sites for the D atom of CD(4), and the density distribution of the C and D atoms was observed separately in the scattering amplitude density image. Consequently, the C-D bonds of CD(4) were not observed clearly because the CD(4) molecules had an orientational disorder. The D atoms of CD(4) were displaced from the line between the C and O atoms, and were located near the face center of the polygon in the cage. Accordingly, the D atoms of CD(4) were not bonded to specific O atoms. This result is consistent with the hydrophobicity of the CD(4) molecule. We also report the difference between the small and the large cages in the density distribution map and the temperature dependence of the scattering amplitude density.     

Semiquantal analysis of hydrogen bond

The semiquantal time-dependent Hartree (SQTDH) theory is applied to the coupled Morse and modified Lippincott-Schroeder (LS) model potentials of hydrogen bond. The structural correlation between the heavy atoms distance and the proton position, the geometric isotope effect, the energy of hydrogen bond formation, and the proton vibrational frequency shift are examined in a broad range of structural parameters. In particular, the geometric isotope effect is found to depend notably on the choice of the potential model, for which the LS potential gives the isotope shift of the heavy atoms distance in the range of 0.02-0.04 A, in quantitative agreement with the experimental findings from assortment of hydrogen bonding crystals. The fourth-order expansion approximation to the semiquantal extended potential was confirmed to be highly accurate in reproducing the full SQTDH results. The approximation is computationally efficient and flexible enough to be applied to general models of hydrogen bond.     

Comments on a model for isotope effects on Henry's law constants in aqueous solution

A model has been proposed in the literature for isotope effects on Henry's law constants in which the motion of the dissolved molecule surrounded by a solvent cage is approximated by the motion of a particle in a cubic box. The isotope effect then arises from the three free translations of the gas phase molecule which become the restricted translations of a particle in a box for the dissolved molecule. The theoretical equation for the isotope effect is derived here on the basis of this model. Zero-point energy arguments have been used in the literature in conjunction with this model to deduce solvent cage dimensions from observed isotope effect data. These arguments are shown here to be theoretically wrong. The correct theory for the particle in a box model gives much larger dimensions for the solvent cage than the incorrect zero-point energy argument.     

Spin-orbit relaxation of Cl(2P1/2) and F(2P1/2) in a gas of H2

The authors present quantum scattering calculations of rate coefficients for the spin-orbit relaxation of F(2P1/2) atoms in a gas of H2 molecules and Cl(2P1/2) atoms in a gas of H2 and D2 molecules. Their calculation of the thermally averaged rate coefficient for the electronic relaxation of chlorine in H2 agrees very well with an experimental measurement at room temperature. It is found that the spin-orbit relaxation of chlorine atoms in collisions with hydrogen molecules in the rotationally excited state j=2 is dominated by the near-resonant electronic-to-rotational energy transfer accompanied by rotational excitation of the molecules. The rate of the spin-orbit relaxation in collisions with D2 molecules increases to a great extent with the rotational excitation of the molecules. They have found that the H2/D2 isotope effect in the relaxation of Cl(2P1/2) is very sensitive to temperature due to the significant role of molecular rotations in the nonadiabatic transitions. Their calculation yields a rate ratio of 10 for the electronic relaxation in H2 and D2 at room temperature, in qualitative agreement with the experimental measurement of the isotope ratio of about 5. The isotope effect becomes less significant at higher temperatures.     

The effect of zero-point energy differences on the isotope dependence of the formation of ozone: a classical trajectory study

The effect of zero-point energy differences (DeltaZPE) between the possible fragmentation channels of highly excited O(3) complexes on the isotope dependence of the formation of ozone is investigated by means of classical trajectory calculations and a strong-collision model. DeltaZPE is incorporated in the calculations in a phenomenological way by adjusting the potential energy surface in the product channels so that the correct exothermicities and endothermicities are matched. The model contains two parameters, the frequency of stabilizing collisions omega and an energy dependent parameter Delta(damp), which favors the lower energies in the Maxwell-Boltzmann distribution. The stabilization frequency is used to adjust the pressure dependence of the absolute formation rate while Delta(damp) is utilized to control its isotope dependence. The calculations for several isotope combinations of oxygen atoms show a clear dependence of relative formation rates on DeltaZPE. The results are similar to those of Gao and Marcus [J. Chem. Phys. 116, 137 (2002)] obtained within a statistical model. In particular, like in the statistical approach an ad hoc parameter eta approximately 1.14, which effectively reduces the formation rates of the symmetric ABA ozone molecules, has to be introduced in order to obtain good agreement with the measured relative rates of Janssen et al. [Phys. Chem. Chem. Phys. 3, 4718 (2001)]. The temperature dependence of the recombination rate is also addressed.     

Energy transfer of highly vibrationally excited naphthalene. II. Vibrational energy dependence and isotope and mass effects

The vibrational energy dependence, H and D atom isotope effects, and the mass effects in the energy transfer between rare gas atoms and highly vibrationally excited naphthalene in the triplet state were investigated using crossed-beam/time-sliced velocity-map ion imaging at various translational collision energies. Increase of vibrational energy from 16 194 to 18 922 cm(-1) does not make a significant difference in energy transfer. The energy transfer properties also remain the same when H atoms in naphthalene are replaced by D atoms, indicating that the high vibrational frequency modes do not play important roles in energy transfer. They are not important in supercollisions either. However, as the Kr atoms are replaced by Xe atoms, the shapes of energy transfer probability density functions change. The probabilities for large translation to vibration/rotation energy transfer (T-->VR) and large vibration to translation energy transfer (V-->T) decrease. High energy tails in the backward scatterings disappear, and the probability for very large vibration to translation energy transfer such as supercollisions also decreases.     

Deuterium enrichment of interstellar methanol explained by atom tunneling

We calculate, down to low temperature and for different isotopes, the reaction rate constants for the hydrogen abstraction reaction H + H(3)COH → H(2) + CH(2)OH/CH(3)O. These explain the known abundances of deuterated forms of methanol in interstellar clouds, where CH(2)DOH can be almost as abundant as CH(3)OH. For abstraction from both the C- and the O-end of methanol, the barrier-crossing motion involves the movement of light hydrogen atoms. Consequently, tunneling plays a dominant role already at relatively high temperature. Our implementation of harmonic quantum transition state theory with on the fly calculation of forces and energies accounts for these tunneling effects. The results are in good agreement with previous semiclassical and quantum dynamics calculations (down to 200 K) and experimental studies (down to 295 K). Here we extend the rate calculations down to lower temperature: 30 K for abstraction from the C-end of methanol and 80 K for abstraction from the OH-group. At all temperatures, abstraction from the C-end is preferred over abstraction from the O-end, more strongly so at lower temperature. Furthermore, the tunneling behavior strongly affects the kinetic isotope effects (KIEs). D + H(3)COH → HD + CH(2)OH has a lower vibrationally adiabatic barrier than H + H(3)COH → H(2) + CH(2)OH, giving rise to an inverse KIE (k(H)/k(D) < 1) at high temperature, in accordance with previous experiments and calculations. However, since tunneling is more facile for the light H atom, abstraction by H is favored over abstraction by D below ~135 K, with a KIE k(H)/k(D) of 11.2 at 30 K. The H + D(3)COD → HD + CD(2)OD reaction is calculated to be much slower than the D + H(3)COH → HD + CH(2)OH, in agreement with low-temperature solid-state experiments, which suggests the preference for H (as opposed to D) abstraction from the C-end of methanol to be the mechanism by which interstellar methanol is deuterium-enriched.     

Investigation of protonation and rotational isomerization of 6-dimethylaminofulventungsten tricarbonyl in acidic media by dynamic 1H NMR spectroscopy

Rotational isomerization of 6-dimethylaminofulventungsten tricarbonyl in media of various acidities has been studied by dynamic ¹H NMR spectroscopy, and the kinetic parameters of the rotation about the C(6)N bond have been determined. The rate of rotation about this bond increases in weakly acidic media and decreases in strongly acidic solutions with respect to that in the parent complex. This dependence indicates that the complex has dual reactivity in protonation, i.e. in weakly acidic media the protonation involves the nitrogen atom, and in highly acidic solutions the tungsten atom. On increasing the acidity of the medium the ammonium form of the complex is converted into the W-protonated complex. A study of deuterium exchange in acidic media has shown that the H or D atom attached to the W atom may be readily exchange for the deuteron (or the proton, respectively) of the acid, while the H atoms of the cyclopentadienyl ring do not undergo deuterium exchange under the conditions investigated. Protonation involving the Cp ring of the complex was not observed.