Variational transition state theory with multidimensional tunnelling and kinetic isotope effects in the reactions of C2H6, C2H5D and C2D6 with .CCl3 to produce CHCl3 and CDCl3

ABSTRACT

Rate constants for the reactions of C₂H₆, C₂H₅D and C₂D₆ with .CCl₃. for the production of CHCl₃ and CDCl₃ (k₁, k₂, k₃ and k₄) were computed using variational transition state theory coupled with hybrid-meta density functional theory (MPWB1K) over the temperature range of 200–2900 K. The ground-state vibrational adiabatic potential was plotted for all channels. Small- and large-curvature tunnelling were determined to include quantum effects in the calculation of rate constants. Harmonic vibrational frequencies along the reaction path were calculated in curvilinear coordinates with scaled frequencies. Anharmonicity was included in the lowest-frequency torsion. The position of formation and dissociation of bonds was specified using the variation in harmonic vibrational frequencies along the reaction path. Representative tunnelling energy and the thermally averaged transmission probability at 298 K (P(E)exp?( ? ΔE/RT)) were determined for the reactions in which tunnelling is important. The kinetic isotope effect was used to calculate the considerable contributions of tunnelling and vibration. The expressions for rate constants were determined using nonlinear least-square fitting over the temperature range of 200–2900 K.     

Primary kinetic hydrogen isotope effects in deprotonations of a nitroalkane by intramolecular phenolate groups

Rate constants and kinetic isotope effects have been determined for the formation of nitronate anions from the ethers 1‐(2‐methoxyphenyl)‐2‐nitropropane, 7 (X = H, L = H and D) and 1‐(2‐methoxy‐5‐nitrophenyl)‐2‐nitropropane, 7 (X = NO₂, L = H and D), and from the corresponding phenols, 1‐(2‐hydroxyphenyl)‐2‐nitropropane, 3 (X = H, L = H and D), and 1‐(2‐hydroxy‐5‐nitrophenyl)‐2‐nitropropane, 3 (X = NO₂, L = H and D), in aqueous basic medium. For the ethers 7 , rates of deprotonation by hydroxide are comparable with those found for deprotonations of 2‐nitropropane, with k^H/k^D (25 °C) = 7.7 and 7.8, respectively. In both the cases, the isotope effects are conventionally temperature dependent. For the corresponding phenols 3 , conditions have been established under which the deprotonations of the nitroalkane are dominated by intramolecular deprotonation by the kinetically first‐formed phenolate anion, with an estimated effective molarity EM ～ 250. For 3 (X = H, L = H or D), k^H/k^D (25 °C) = 7.8, with E ? E = 6.9 kJ mol^?1 and A^H/A^D = 0.5. For 3 (X = NO₂, L = H or D), rates of intramolecular deprotonation are reduced 30‐fold, and an elevated kinetic isotope effect is found (k^H/k^D (25 °C) = 10.7). Activation parameters (E ? E = 17.8 kJ mol^?1 and A^H/A^D = 0.008) are compatible with an enhanced tunnelling contribution to reactivity in the H‐isotopomer. Copyright © 2009 John Wiley & Sons, Ltd.     

细胞色素P450 2E1催化下乙醛羟基化反应动力学同位素效应的理论研究

采用建立在Eyring绝对反应速率理论基础上的计算模型,对细胞色素P4502E1催化下乙醛羟基化反应动力学同位素效应进行了理论研究.计算表明,乙醛羟基化反应的动力学同位素效应大小约为5.0(Wigner量子校正后约为7.0左右),远比烷烃羟基化反应的动力学同位素效应要小的多.这个反应对温度比较敏感,所以反应存在明显的量子隧穿现象.文中还对动力学同位素效应给出了相应的过渡态构型方面的解释.     

Rate coefficients and kinetic isotope effects of the abstraction reaction of H atoms from methylsilane

ABSTRACT

Thermal rate constants for chemical reactions using improved canonical variational transition state theory (ICVT) with small-curvature tunnelling (SCT) contributions in a temperature range 180–2000 K are reported. The general procedure is used with high-quality ab initio computations and semi-classical reaction probabilities along the minimum energy path (MEP). The approach is based on a vibrational adiabatic reaction path and is applied to the multiple-channel hydrogen abstraction reaction H + SiH₃CH₃ → products and its isotopically substituted variants. All the degrees of freedom are optimised and harmonic vibrational frequencies and zero-point energies are calculated at the MP2 level with the cc-pVTZ basis set. Single-point energies are calculated at a higher level of theory; CCSD(T)-F12a/VTZ-F12. ICVT/SCT rate constants show that the quantum tunnelling contributions at low temperatures are relatively important and the H-abstraction channel from SiH₃ group of SiH₃CH₃ is the major pathway. The total rate constants are given by the following expression: k_tot(ICVT/SCT) = 2.29 10^?18 T^2.42 exp(?350.9/T) cm³ molec^?1 s^?1. These calculated rates are in agreement with the available experiments. The ICVT/SCT method is further exploited to predict primary and secondary kinetic isotope effects, respectively).     

Transesterification of an RNA model in buffer solutions in H2O and D2O

Transesterification of a phosphodiester bond of RNA models has been studied in various buffer solutions, under neutral and slightly alkaline conditions in H₂O and D₂O. The results show that imidazole is the only buffer system where a clear buffer catalysis on the cleavage of a phosphodiester bond is observed. The rate enhancement in sulphonic acid buffers is smaller, and a sulphonate base, particularly, is inactive as a catalyst. The rate‐enhancing effect of imidazole is, however, catalytic, and the catalytic inactivity of sulphonate buffers can be attributed to their structure and/or charge. The catalysis by imidazole is a complex system which, in addition to first‐order reactions, involves a process that shows a second‐order dependence in imidazole concentration. The latter reaction becomes significant in acidic imidazole buffers (pH < pK_a), as the buffer concentration increases. The kinetic solvent deuterium isotope effect k_H/k_D, referring to first‐order catalysis by imidazole base, is 2.3 ± 0.3. That referring to second‐order catalysis is most probably much larger, but an accurate value could not be obtained. Copyright © 2007 John Wiley & Sons, Ltd.     

Insights into the elimination mechanisms employed for the degradation of different hexachlorocyclohexane isomers using kinetic isotope effects and docking studies

Modern DFT functional as well as the continuum solvation model have been applied in order to theoretically predict carbon, chlorine and hydrogen kinetic isotope effects (KIEs) during aerobic degradation of four hexachlorocyclohexane isomers (α, β, δ and γ). A small model of the hexachlorocyclohexane dehydrochlorinase (LinA) active site comprising its catalytic dyad has been constructed based on the receptor–ligand complexes suggested by docking studies and compared to the respective reaction modeled in aqueous solution. In‐depth analysis of chlorine and hydrogen KIEs patterns clearly indicates different transition states in aqueous solution and in the model mimicking the protein active site. Although all isomers seem to undergo a concerted E2 mechanism, the contribution of proton transfer and carbon–chlorine leaving group bond stretch in the transition states differs for the different isomers giving rise to totally different magnitudes of predicted isotope effects. Copyright © 2013 John Wiley & Sons, Ltd.     

Measurement of stable isotope activities in saline aqueous solutions using optical spectroscopy methods

The requirement to measure the stable isotopic compositions of saline pore fluids by optical methods has prompted a re-evaluation of the isotopic salt effect for common salts. Hydrogen and oxygen isotopic salt effects were measured at room temperature (21°C) by optical methods. For hydrogen isotopes, our results agree well with those of previous studies and better define these effects at low temperatures. In contrast, measured oxygen isotope salt effects disagree within error for NaCl and CaCl₂ solutions from those reported previously. Subtle differences between measurement methods may account for the discrepancy. In studies that involve highly saline fluids, the isotopic salt effect must be taken into account because modern methods that measure stable isotopic compositions as activities or concentrations may be not directly comparable to historical data sets.     

The kinetic and solvent deuterium isotope effects in the 4- and 5-positions of the indole ring on the enzymatic decomposition of L-tryptophan

The kinetic and solvent deuterium isotope effects in the 4- and 5-positions of the indole ring on the enzymatic decomposition of l-tryptophan catalysed by the enzyme TPase (EC. 4.1.99.1) were determined. The isotope effects were investigated by the non-competitive method using [4′-²H]-l-tryptophan, which was enriched in deuterium in 70% in the 4-position. The numerical values of isotope effects for 100% enrichment in deuterated label in that position were calculated by approximation. Those same isotope effects were determined for [5′-²H]-l-tryptophan fully deuteriated in the 5′ -position.     

Solvent isotope effects on the hydration of alkaline cations: H/D secondary isotope effects on electrostatic interactions

We investigate H/D secondary isotope effects on the binding energies of water alkaline cation complexes, Alk⁺(X₂O)_n (X = H, D; Alk = Li, Na, K; n = 1 ? 4), using the any particle molecular orbital approach. Our results reveal that deuteration reduces water’s capacity to solvate alkaline cations. An explanation to this behaviour is proposed in terms of the observed changes in distances, partial charges, electrostatic potentials and polarisation induced by deuteration.     

Non-linear dynamics of stable carbon and hydrogen isotope signatures based on a biological kinetic model of aerobic enzymatic methane oxidation

The non-linear dynamics of stable carbon and hydrogen isotope signatures during methane oxidation by the methanotrophic bacteria Methylosinus sporium strain 5 (NCIMB 11126) and Methylocaldum gracile strain 14 L (NCIMB 11912) under copper-rich (8.9 µM Cu²⁺), copper-limited (0.3 µM Cu²⁺) or copper-regular (1.1 µM Cu²⁺) conditions has been described mathematically. The model was calibrated by experimental data of methane quantities and carbon and hydrogen isotope signatures of methane measured previously in laboratory microcosms reported by Feisthauer et al. [1 Feisthauer S, Vogt C, Modrzynski J, Szlenkier M, Krüger M, Siegert M, Richnow HH. Different types of methane monooxygenases produce similar carbon and hydrogen isotope fractionation patterns during methane oxidation. Geochim Cosmochim Acta. 2011;75:1173–1184. doi: 10.1016/j.gca.2010.12.006[Crossref], [Web of Science ®] , [Google Scholar]] M. gracile initially oxidizes methane by a particulate methane monooxygenase and assimilates formaldehyde via the ribulose monophosphate pathway, whereas M. sporium expresses a soluble methane monooxygenase under copper-limited conditions and uses the serine pathway for carbon assimilation. The model shows that during methane solubilization dominant carbon and hydrogen isotope fractionation occurs. An increase of biomass due to growth of methanotrophs causes an increase of particulate or soluble monooxygenase that, in turn, decreases soluble methane concentration intensifying methane solubilization. The specific maximum rate of methane oxidation υ_m was proved to be equal to 4.0 and 1.3 mM mM^?1 h^?1 for M. sporium under copper-rich and copper-limited conditions, respectively, and 0.5 mM mM^?1 h^?1 for M. gracile. The model shows that methane oxidation cannot be described by traditional first-order kinetics. The kinetic isotope fractionation ceases when methane concentrations decrease close to the threshold value. Applicability of the non-linear model was confirmed by dynamics of carbon isotope signature for carbon dioxide that was depleted and later enriched in ¹³C. Contrasting to the common Rayleigh linear graph, the dynamic curves allow identifying inappropriate isotope data due to inaccurate substrate concentration analyses. The non-linear model pretty adequately described experimental data presented in the two-dimensional plot of hydrogen versus carbon stable isotope signatures.     

Real‐time measurement of H/D exchange in a microdialysis Raman quartz cell

We present here a novel quartz cell for monitoring H/D exchange in biomolecules using Raman spectroscopy. This cell is combined with a syringe to pump heavy water through a hollow microdialysis fibre, which is inserted into the cell. The deuterium efflux into the sample has been studied as a function of the molecular weight cut‐off of the microdialysis fibre and compared with other microcell systems comprising conventional glass capillaries. The fastest D₂O efflux that we have obtained (k_d = 0.38 ± 0.008 min⁻¹) permits to measure exchange rates of 2.5 min⁻¹ or less. Application of this cell to deuterium exchange in glyceraldehyde‐3‐phosphate dehydrogenase reveals a class of H‐atoms highly resistant to deuteration, which is consistent with a previous infrared study on this protein. Copyright © 2009 John Wiley & Sons, Ltd.     

Observation of 18O/16O isotope effects at the cathode of a polymer electrolyte membrane fuel cell

¹⁸O/¹⁶O isotope effects were observed at the cathode of a polymer electrolyte membrane fuel cell at 25 and 35°C. Results of experiments in which the ¹⁸O/¹⁶O isotope ratios of the oxygen gases supplied to and exhausted from the cell were measured revealed that the lighter isotope ¹⁶O reacted more preferentially to form water molecules at the cathode than the heavier one, ¹⁸O. The value of the oxygen isotope separation factor, S₁, defined as the ratio of the ¹⁸O/¹⁶O isotope ratios of the oxygen gases supplied to and exhausted from the cell, ranged from 1.0030 to 1.0139, and tended to decrease with decreasing rate of oxygen utilisation (θ) and with increasing flow rate of the feed oxygen gas (D_F). The value of another separation factor, S₂, defined as the ratio of the ¹⁸O/¹⁶O isotope ratios of the exhausted oxygen gas and oxygen having reacted to form water molecules at the cathode, ranged from 1.0049 to 1.0304. The S₂ value was much less affected by the change in θ and D_F than the S₁ value with the majority of the S₂ value being in the range of 1.0240–1.0304.     

Exploring acetylene chemistry in superbasic media: A theoretical study of the effect of water on vinylation and ethynylation reactions with acetylene in KOH/DMSO and NaOH/DMSO systems

A rapidly developing approach adding new dimensions to acetylene chemistry relying on employment of high basicity media such as alkali metal hydroxide suspensions in dimethyl sulfoxide (DMSO) has been, for the first time, investigated theoretically using ab initio models. Extending our recently introduced model of superbase catalysis with a nondissociated KOH (or NaOH) participation, we present here a model for a superbasic reaction center with the first solvation shell explicitly included. The alkali metal hydroxides in a DMSO solution were found to form KOH·5DMSO and NaOH·4DMSO complexes that are stabilized due to the interligand interaction. Our present MP2/6‐311++G**//B3LYP/6‐31+G* computations show that 1 and 2 water molecules can build themselves into the MOH close surrounding without substantially perturbing the DMSO ligands and easily travel between different insertion positions. Our results predict that the activation energies in the series of reactions of nucleophilic addition to a triple bond with water, methanol, methanethiol, sodium hydrosulfide, and acetone in the presence of dihydrated complexes should be larger than those obtained with the participation of monohydrated ones, which is in fair agreement with the experimental findings. The present model also explains an increase in the ethynylation reaction yield in the presence of water by suppression of the competitive enolization reaction.     

D2/H2 quantum sieving in microporous carbons: a theoretical study on the effects of pore size and pressure

The adsorption of hydrogen and deuterium in slit-shaped carbon pores is studied by grand canonical Monte Carlo simulations. All interactions are assumed to be of Lennard–Jones type, while the Feynman–Hibbs expression is used to account for quantum effects. The interaction energy of both isotopes inside the slit pore space is discussed thoroughly. Furthermore, pure component adsorption isotherms of both isotopes were simulated at 77?K for pressures up to 20?bar in slit pores having widths of up to 2.0?nm. According to our simulations, in equilibrium, slit pores reveal slight deuterium selectivity over hydrogen, and this quantum-based selectivity depends both on pressure and pore size.     

Anilinolysis of O‐butyl phenyl phosphonochloridothioate in acetonitrile: Synthesis,characterization, kinetic study,and reaction mechanism

This paper describes a simple optimized method for the synthesis of O‐butyl phenyl phosphonochloridothioate ( 4 ) under mild conditions. The target compounds were characterized by ¹H‐nuclear magnetic resonance (NMR), ¹³C‐NMR, and ³¹P‐NMR spectroscopy, as well as mass spectroscopy. The apparent structure of 4 was confirmed by optimization using the B3LYP/6‐311 + G(d,p) level in the Gaussian 09 program in acetonitrile. The nucleophilic substitution reactions of 4 with X‐anilines (XC₆H₄NH₂) and deuterated X‐anilines (XC₆H₄ND₂) were investigated kinetically in acetonitrile at 55.0°C. The free energy relationship with X in the anilines looked biphasic concave upwards with a break region between X = H and X = 3‐MeO, giving large negative ρ_X and small positive β_X values. The deuterium kinetic isotope effects were secondary inverse (k_H/k_D < 1: 0.789‐0.995) and the magnitudes, (k_H/k_D), increased when the nucleophiles were changed from weakly basic to strongly basic anilines. A concerted S_N2 mechanism is proposed on the basis of the selectivity parameters and the variation trend of the deuterium kinetic isotope effects with X.     

Theoretical study of stereodynamics for the reaction O(3P) +D2 (v=0, j=0) to OD+D and isotope effect

Quasi-classical trajectory (QCT) calculations have been performed to study the product polarization behaviours in the reaction O(³P) + D₂ (v= 0, j= 0)→OD + D. By running trajectories on the ³A′ and ³A″ potential energy surfaces (PESs), vector correlations such as the distributions of the polarization-dependent differential cross sections (PDDCSs), the angular distributions of P(θ_r) and P(ø_r) are presented. Isotope effect is discussed in this work by a comprehensive comparison with the reaction O(³P) + H₂ (v= 0, j= 0) → H + H. Common characteristics as well as differences are discussed in product alignment and orientation for the two reactions. The isotope mass effect differs on the two potential energy surfaces: the isotope mass effect has stronger influence on P(θ_r) and PDDCSs of the ³A′ PES while the opposite on P(ø_r) of the ³A″ potential energy surface.     

Reaction pathway and H/D kinetic isotope effects of the triple proton transfer in a 7‐hydroxyquinoline‐methanol complex in the ground state: A computational approach

Multiple proton transfer (PT) is an essential process in long‐range proton transport such as proton relay in enzymes. 7‐Hydroxyquinoline (7HQ) undergoes alcohol‐mediated PT in both the excited and ground states, and this system has been investigated as a biomimetic model. In the present study, the reaction pathway of triple PT in a 7HQ‐methanol cluster, 7HQ·(MeOH)₂, in the ground state has been investigated using density functional theory calculations to clarify the reaction mechanism and the origin of the experimentally observed kinetic isotope effect (KIE). The PT takes place in an asynchronous concerted fashion, in which the oxygen atom in 7HQ first accepts a proton from the directly hydrogen‐bonded MeOH. The rate constants and primary H/D KIEs have been estimated with canonical variational transition state theory in combination with the small curvature tunneling approximation. The tunneling effect on the PT rate is significant, and the KIE is much greater than 1 at room temperature. The rule of the geometric mean for the KIEs breaks down because of the asynchronicity in the motions of 3 protons and tunneling effect. In addition, the rate constant is smaller, the KIE is larger, and the activation energy is higher compared with the experimental values in heptane solution, suggesting that the PT dynamics in solution is governed by not only the intrinsic PT process but also thermal fluctuation of the solute and solvent molecules, which plays an important role in the configurational change of the 7HQ·(MeOH)₂ complex.     

Primary 1H/2H isotope effect in the NMR chemical shift of HClO4 salts of 1,8‐bis(dimethylamino)naphthalene derivatives

The primary ¹H/²H isotope effect for a number of protonated naphthalene proton sponges (DMAN‐s) was measured and correlated with the δ(¹H) value and IR spectroscopic characteristics of the [NHN]⁺ hydrogen bonds. A particular role of the unusual anharmonicity expressed in the isotopic ratio ISR ? is discussed when the fundamental vibrational levels are close to the barrier top for proton/deuteron motion. Copyright © 2007 John Wiley & Sons, Ltd.     

N-Sulfonic acid poly(4-vinylpyridinium) hydrogen sulfate as an efficient and reusable solid acid catalyst for one-pot synthesis of xanthene derivatives in dry media under ultrasound irradiation

N-Sulfonic acid poly(4-vinylpyridinium) hydrogen sulfate catalyzed efficiently the synthesis of xanthene derivatives under ultrasonic irradiation at room temperature, which has prompted various concerns involving cost and environmental persistence. This methodology shows the effect of presence of anion hydrogen sulfate as an important and effective factor on the promotion of the one-pot multi-components and condensation reactions. The catalyst can be recovered by simple filtration and used for several times without a significant loss of catalytic activity.     

Temperature and set field dependence of exchange bias training effects in Co/NiO/[Co/Pt] heterostructures with orthogonal easy axes

Training effects in a new class of exchange biased ferromagnet/antiferromagnet/ferromagnet trilayers (Co/NiO/[Co/Pt]₃) with mutually orthogonal easy axes have been measured and successfully modeled. Previous experiments have demonstrated an enhanced blocking temperature as well as the ability to isothermally field tune the magnitude of the room temperature in-plane exchange bias. These effects have been attributed to the presence of the [Co/Pt] multilayer with perpendicular magnetic anisotropy, which variably pins the backside NiO domains. Here we show that the tuning of the exchange bias and the blocking temperature enhancement are highly dependent on both the temperature and the in-plane remanence of the normally out-of-plane [Co/Pt] multilayer, achieved using modest in-plane set fields. Training effects and their dependence on temperature and in-plane remanence are modeled using a thermodynamic approach. The in-plane remanence of the [Co/Pt] acts only to set the equilibrium exchange bias value and sets the scale for the blocking temperature; it has no effect on the training. We conclude that training effects occur only at the Co/NiO interface and that the relaxation towards equilibrium is confined to this interface. The field enhanced blocking temperature and isothermal tuning of exchange bias in these magnetic heterostructures with mutually orthogonal easy axes could play a role in the enhancement of exchange bias effects in future spin-valve devices. A thorough knowledge of the training effects is essential to account for the fundamental relaxation mechanisms that occur with repeated field cycling.