Valence bond calculations of hydrogen transfer reactions: a general predictive pattern derived from theory

Hydrogen abstraction reactions of the type X(*) + H-H' --> X-H + H'(*) (X = F, Cl, Br, I) are studied by ab initio valence bond methods and the VB state correlation diagram (VBSCD) model. The reaction barriers and VB parameters of the VBSCD are computed by using the breathing orbital valence bond and valence bond configuration interaction methods. The combination of the VBSCD model and semiempirical VB theory leads to analytical expressions for the barriers and other VB quantities that match the ab initio VB calculations fairly well. The barriers are influenced by the endo- or exothermicity of the reaction, but the fundamental factor of the barrier is the average singlet-triplet gap of the bonds that are broken or formed in the reactions. Some further approximations lead to a simple formula that expresses the barrier for nonidentity and identity hydrogen abstraction reactions as a function of the bond strengths of reactants and products. The semiempirical expressions are shown to be useful not only for the model reactions that are studied in this work, but also for other nonidentity and identity hydrogen abstraction reactions that have been studied in previous articles.     

Reactivity of isobutane on zeolites: a first principles study

In this work, ab initio and density functional theory methods are used to study isobutane protolytic cracking, primary hydrogen exchange, tertiary hydrogen exchange, and dehydrogenation reactions catalyzed by zeolites. The reactants, products, and transition-state structures are optimized at the B3LYP/6-31G* level, and the final energies are calculated using the CBS-QB3 composite energy method. The computed activation barriers are 52.3 kcal/mol for cracking, 29.4 kcal/mol for primary hydrogen exchange, 29.9 kcal/mol for tertiary hydrogen exchange, and 59.4 kcal/mol for dehydrogenation. The zeolite acidity effects on the reaction barriers are also investigated by changing the cluster terminal Si-H bond lengths. The analytical expressions between activation barriers and zeolite deprotonation energies for each reaction are proposed so that accurate activation barriers can be obtained when using different zeolites as catalysts.     

Systematic QM/MM investigation of factors that affect the cytochrome P450-catalyzed hydrogen abstraction of camphor

The hydrogen abstraction reaction of camphor in cytochrome P450(cam) has been investigated in the native enzyme environment by combined quantum mechanical/molecular mechanical (QM/MM) calculations and in the gas phase by density functional calculations. This work has been motivated by contradictory published QM/MM results. In an attempt to pinpoint the origin of these discrepancies, we have systematically studied the factors that may affect the computed barriers, including the QM/MM setup, the optimization procedures, and the choice of QM region, basis set, and protonation states. It is found that the ChemShell and QSite programs used in the published QM/MM calculations yield similar results at given geometries, and that the discrepancies mainly arise from two technical issues (optimization protocols and initial system preparation) that need to be well controlled in QM/MM work. In the course of these systematic investigations, new mechanistic insights have been gained. The crystallographic water 903 placed near the oxo atom of Compound I lowers the hydrogen abstraction barrier by ca. 4 kcal/mol, and thus acts as a catalyst for this reaction. Spin density may appear at the A-propionate side chain of the heme if the carboxylate group is not properly screened, which might be expected to happen during protein dynamics, but not in static equilibrium situations. There is no clear correlation between the computed A-propionate spin density and the hydrogen abstraction barrier, and hence, no support for a previously proposed side-chain mediated transition state stabilization mechanism. Standard QM/MM optimizations yield an A-propionate environment close to the X-ray structure only for protonated Asp297, and not for deprotonated Asp297, but the computed barriers are similar in both cases. An X-ray like A-propionate environment can also be obtained when deprotonated Asp297 is included in the QM region and His355 is singly protonated, but this Compound II-type species with a closed-shell porphyrin ring has a higher hydrogen abstraction barrier and should thus not be mechanistically relevant.     

Rearrangement and hydrogen scrambling pathways of the toluene radical cation: a computational study

A computational study is undertaken to provide a unified picture for various rearrangement reactions and hydrogen scrambling pathways of the toluene radical cation (1). The geometries are optimized with the BHandHLYP density functional, and the energies are computed with the ab initio CCSD(T) method, in conjunction with the 6-311+G(d,p) basis set. In particular, four channels have been located, which may account for hydrogen scrambling, as they are found to have overall barriers lower than the observed threshold for hydrogen dissociation. These are a stepwise norcaradiene walk involved in the Hoffman mechanism, a rearrangement of 1 to the methylenecyclohexadiene radical cation (5) by successive [1,2]-H shifts via isotoluene radical cations, a series of [1,2]-H shifts in the cycloheptatriene radical cation (4), and a concerted norcaradiene walk. In addition, we have also investigated other pathways such as the suggested Dewar-Landman mechanism, which proceeds through 5, via two consecutive [1,2]-H shifts. This pathway is, however, found to be inactive as it involves too high reaction barriers. Moreover, a novel rearrangement pathway that connects 5 to the norcaradiene radical cation (3) has also been located in this work.     

On the difference between hydrogen fluoride and hydrogen chloride crystals

The geometrical and energetical parameters of hydrogen fluoride and hydrogen chloride crystals are calculated using the periodic Hartree–Fock method with 6-31G and 6-31G(d,p) basis sets. The comparison of the stabilisation energies reveals that HCl crystals are about 75% less stable than HF crystals. The activation energy for collective proton movements are computed and discussed in view of data of isolated infinite chains. The barriers of 13.1 and 40.0 kcal mol⁻¹ at 6-31G(d,p) level are found for HF and HCl crystals.     

High-level ab initio studies of hydrogen abstraction from prototype hydrocarbon systems

Symmetric and nonsymmetric hydrogen abstraction reactions are studied using state-of-the-art ab initio electronic structure methods. Second-order M?ller-Plesset perturbation theory (MP2) and the coupled-cluster singles, doubles, and perturbative triples [CCSD(T)] methods with large correlation consistent basis sets (cc-pVXZ, where X = D,T,Q) are used in determining the transition-state geometries, activation barriers, and thermodynamic properties of several representative hydrogen abstraction reactions. The importance of basis set, electron correlation, and choice of zeroth-order reference wave function in the accurate prediction of activation barriers and reaction enthalpies are also investigated. The ethynyl radical (*CCH), which has a very high affinity for hydrogen atoms, is studied as a prototype hydrogen abstraction agent. Our high-level quantum mechanical computations indicate that hydrogen abstraction using the ethynyl radical has an activation energy of less than 3 kcal mol(-1) for hydrogens bonded to an sp(2) or sp(3) carbon. These low activation barriers further corroborate previous studies suggesting that ethynyl-type radicals would make good tooltips for abstracting hydrogens from diamondoid surfaces during mechanosynthesis. Modeling the diamond C(111) surface with isobutane and treating the ethynyl radical as a tooltip, hydrogen abstraction in this reaction is predicted to be barrierless.     

First‐principles study of molecular hydrogen dissociation on doped Al12X (X = B,Al, C,Si, P,Mg, and Ca) clusters

Inspired by the concept of superatom via substitutionally doping an Al₁₃ magic cluster, we investigated the H₂ molecule dissociation on the doped icosahedral Al₁₂X (X = B, Al, C, Si, P, Mg, and Ca) clusters by means of density functional theory. The computed reaction energies and activation barriers show that the concept of superatom is still valid for the catalysis behavior of doped metal clusters. The hydrogen dissociation behavior on metal clusters characterized by the activation barrier and reaction energy can be tuned by controllable doping. Thus, doped Al₁₂X clusters might serve as highly efficient and low‐cost catalysts for hydrogen dissociation. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2009     

A theoretical study of the effects of transition metal dopants on the adsorption and dissociation of hydrogen on nickel clusters

The structure, stability, adsorption, and dissociation of H₂ on nickel clusters doped with late transition metals were investigated using density functional theory with the BP86 functional. Molecular hydrogen physisorption occurred at a vertex atom with a low coordination number. Charge transfer between clusters and the H₂ molecule stabilized the physisorption. The chemisorption of H₂ occurred at the bridge sites, without any structural or spin change of the clusters. Among the pentamer clusters, Cd, Zn, and Au had the lowest chemisorption energies, while Ir and Pt had higher chemisorption energies for hydrogen. The computed reaction energies and activation barriers for the dissociation mechanism showed that dopants such as Rh, Pd, Pt, and Au have endothermic reaction energies and low activation barriers. This facilitates the reversible adsorption/dissociation of the H₂ molecule on these metal‐doped clusters. The dopant atoms play a major role in modulating the physisorption, chemisorption, and dissociation mechanism of H₂ on nickel clusters. © 2013 Wiley Periodicals, Inc.     

Reactivity of alkanes on zeolites: a computational study of propane conversion reactions

In this work, quantum chemical methods were used to study propane conversion reactions on zeolites; these reactions included protolytic cracking, primary hydrogen exchange, secondary hydrogen exchange, and dehydrogenation reactions. The reactants, products, and transition-state structures were optimized at the B3LYP/6-31G level and the energies were calculated with CBS-QB3, a complete basis set composite energy method. The computed activation barriers were 62.1 and 62.6 kcal/mol for protolytic cracking through two different transition states, 30.4 kcal/mol for primary hydrogen exchange, 29.8 kcal/mol for secondary hydrogen exchange, and 76.7 kcal/mol for dehydrogenation reactions. The effects of basis set for the geometry optimization and zeolite acidity on the reaction barriers were also investigated. Adding extra polarization and diffuse functions for the geometry optimization did not affect the activation barriers obtained with the composite energy method. The largest difference in calculated activation barriers is within 1 kcal/mol. Reaction activation barriers do change as zeolite acidity changes, however. Linear relationships were found between activation barriers and zeolite deprotonation energies. Analytical expressions for each reaction were proposed so that accurate activation barriers can be obtained when using different zeolites as catalysts, as long as the deprotonation energies are first acquired.     

Peroxy and alkoxy radicals from 2-methyl-3-buten-2-ol

Quantum mechanical calculations were used to determine the structure and energetics of peroxy radicals (P1 and P2) and alkoxy radicals (A1-A3) formed in the atmospheric degradation of 2-methyl-3-buten-2-ol. At the level of theory employed (B3LYP/6-31G(d,p)) low energy conformers were identified with zero, one, or two hydrogen bonds. The beta C-C scission (decomposition) reactions are computed to occur with low barriers, and the 1,5 H-shift (isomerization) reaction of A2 is computed to be of negligible importance. Scission 2 of A2 is computed to be about 93% of the fate of A2, with the balance being scission 1. The new BB1K functional of Truhlar was employed to investigate activation barriers for single intramolecular H-atom transfers across the OH...O* hydrogen bonds, but the barriers to these reactions appear to be too high for these reactions to be important. Extensive searches for transition states for simultaneous double intramolecular H-atom transfer across OH...OH...O* hydrogen bond pairs were unsuccessful.     

From atomic to molecular anions: a neutral receptor captures cyanide using strong C-H hydrogen bonds

The multifaceted character of cyanide as an acceptor of hydrogen bonds from a receptor has been examined for the first time using electronic-structure theory and spectroscopic measurements (UV/Vis and NMR titrations). Motivated by the similar size and charge of the cyanide pseudohalide and the monoatomic chloride ion, strong interactions of cyanide with a rigid macrocyclic triazolophane receptor have been predicted by theory and confirmed by experimental findings. It was found that both anions bind with similar strength in the gas phase (computed) and in the solution phase (experimental) via C-H hydrogen bonds. Theoretical calculations predict that the heterodiatomic cyanide prefers to bind in the plane of the macrocycle along the north-south axis. Examination of the possible binding modes reveal low computed barriers for in-plane rotation. The predicted model is consistent with the experimental data. Overall, the binding of a molecular anion within the cavity of a triazolophane receptor has been characterized where the computed and experimental binding energies are consistent with the classification of cyanide as a pseudohalide in the context of supramolecular chemistry.     

Quantum dynamical examination of surprisal theory for the three-dimensional hydrogen exchange reaction

Quantum dynamical rotational excitation probabilities have been computed as a function of the reaction coordinate for the three-dimensional hydrogen exchange reaction. The results are used to examine surprisal theory, with particular emphasis on the definition of the “prior distribution”.     

Quantum chemical study of hydrogen abstraction reactions of the ethynyl radical with hydrogen compounds (C2H+HX)

We have theoretically investigated the hydrogen abstraction reactions of ethynyl radical with simple hydrogen compounds, C₂H+HX, using quantum chemical computations. Computations have been performed using the density functional theory with the recently proposed MPW1K functional and the 6-311++G(3df,2p) basis set. An analysis of the resulting energy barriers for hydrogen abstraction reactions has been carried out using the bond dissociation energy of the breaking X–H bond and DFT-based reactivity parameters to rationalize the reaction behavior.     

Low-temperature catalytic decomposition of hydrogen sulfide into hydrogen and diatomic gaseous sulfur

The thermodynamics of three pathways of the hydrogen sulfide decomposition reaction is considered. In the thermal process, the gas-phase dissociation of hydrogen sulfide yields hydrogen and diatomic singlet sulfur. Over sulfide catalysts, the reaction proceeds via the formation of disulfane (H₂S₂) as the key surface intermediate. This intermediate then decomposes to release hydrogen into the gas phase, and adsorbed singlet sulfur recombines into cyclooctasulfur. Over metal catalysts, H₂S decomposes via dissociation into surface atoms followed by the formation of gaseous hydrogen and gaseous triplet disulfur. The last two pathways are thermodynamically forbidden in the gas phase and can take place at room temperature only on the surface of a catalyst. An alternative mechanism is suggested for hydrogen sulfide assimilation in the chemosynthesis process involving sulfur bacteria. To shift the hydrogen sulfide decomposition equilibrium toward the target product (hydrogen), it is suggested that the reaction should be conducted at room temperature as a three-phase process over a solid catalyst under a layer of a solvent that can dissolve hydrogen sulfide and sulfur. In this case, it is possible to attain an H₂S conversion close to 100%. Therefore, hydrogen sulfide can be considered as an inexhaustible source of hydrogen, a valuable chemical and an environmentally friendly energetic product.     

Model studies of the chemisorption of hydrogen and oxygen on nickel surfaces

Atomic chemisorption of hydrogen and oxygen on the Ni(100) surface has been studied using an Effective Core Potential (ECP) approach described in a previous paper. Clusters of up to 50 nickel atoms have been used to model the surface. The computed chemisorption energies are 62 kcal/mol (exp. 63 kcal/mol) for hydrogen and 106 kcal/mol (exp. 115–130 kcal/mol) for oxygen. Correlating the adsorbate and the cluster-adsorbate bonds is extremely important for obtaining accceptable results, particularly for oxygen. Reasonable convergence of chemisorption energies is obtained with 40–50 cluster atoms for both hydrogen and oxygen. For hydrogen the addition of a third cluster layer stabilizes the results considerably. Both hydrogen and oxygen are adsorbed at (or close to) the four-fold hollow site. The calculated barriers for surface migration are also in good agreement with the experimental estimates. The calculated equilibrium heights above the surface are on the other hand too high compared with experiments. This disagreement is believed to be due to core-valence correlation effects, which are not incorporated in the present ECP. The cluster convergence for the height above the surface is much slower than for the chemisorption energy.     

Theoretical Studies on the Reaction Mechanism of 1-Chloroethane with Hydroxyl Radical

The reaction mechanism of 1-chloroethane with hydroxyl radical has been inves- tigated by using density functional theory (DFT) B3LYP/6-31G (d, p) method. All bond dissociation enthalpies were computed at the same theoretical level. It was found that hydrogen abstraction pathway is the most favorable. There are two hydrogen abstraction pathways with activation barriers of 0.630 and 4.988 kJ/mol, respectively, while chlorine abstraction pathway was not found. It was observed that activation energies have a more reasonable correlation with the reaction enthalpy changes (△Hr) than with bond dissociation enthalpies (BDE).     

Mechanism of the hydrogen transfer from the OH group to oxygen-centered radicals: proton-coupled electron-transfer versus radical hydrogen abstraction

High-level ab initio electronic structure calculations have been carried out with respect to the intermolecular hydrogen-transfer reaction HCOOH+.OH-->HCOO.+H(2)O and the intramolecular hydrogen-transfer reaction .OOCH2OH-->HOOCH(2)O.. In both cases we found that the hydrogen atom transfer can take place via two different transition structures. The lowest energy transition structure involves a proton transfer coupled to an electron transfer from the ROH species to the radical, whereas the higher energy transition structure corresponds to the conventional radical hydrogen atom abstraction. An analysis of the atomic spin population, computed within the framework of the topological theory of atoms in molecules, suggests that the triplet repulsion between the unpaired electrons located on the oxygen atoms that undergo hydrogen exchange must be much higher in the transition structure for the radical hydrogen abstraction than that for the proton-coupled electron-transfer mechanism. It is suggested that, in the gas phase, hydrogen atom transfer from the OH group to oxygen-centered radicals occurs by the proton-coupled electron-transfer mechanism when this pathway is accessible.     

Thermochemistry and kinetics of hydrogen abstraction by methyl radical from polycyclic aromatic hydrocarbons

Thermodynamic and kinetic properties relating to hydrogen abstraction by methyl radical from various sites in polycyclic aromatic hydrocarbons (PAHs) have been investigated. The reaction enthalpies (298 K), barriers (0 K), and activation energies and pre-exponential factors (700-1100 K), have been calculated by means of density functional theory, specifically with B3-LYP/6-311G(d,p) geometries, followed by BMK/6-311+G(3df,2p) single-point energy calculations. For uncongested sites in the PAHs, a reasonable correlation is obtained between reactivities (as characterized by the reaction barriers) and reaction enthalpies. This is reflected in a Bell-Evans-Polanyi (BEP) relationship. However, for congested sites, abstraction is accompanied both by lower reaction enthalpies (due to relief of steric strain) and also by reduced reactivities (due to significantly increased steric hindrance effects in the transition structures), so that the BEP relationship does not hold. In addition, the reaction enthalpies and kinetic parameters for the series of linear acenes indicate that abstraction is more difficult from the central rings.     

Theoretical study of the gas-phase reaction of hydrogen isocyanate with water

Transition states for the two probable pathways for the gas-phase hydrolysis of hydrogen isocyanate have been determined using the MINDO /3 method. Activation barriers obtained showed that the one-step mechanism is preferred to the two-step mechanism involving an intermediate. It was shown that the reaction of polymeric water has lower activation barrier than the reaction of monomeric water. Energy and charge decomposition analysis showed that in the former less energy is required in the deformation of molecules for the transition state (TS ) formation due to the cyclic flow of electronic charges in the TS .     

Study in the effect of annealing on hydrogen retention properties of C‐90%SiC films

Carbon‐rich silicon carbide (C‐90%SiC) films as hydrogen barriers were deposited on the surface of stainless steel substrates with magnetron sputtering, and then bombarded by argon ion beam. In order to remove the argon atoms reserved during films preparation, some samples with the prepared C‐90%SiC films were thermally annealed for 30 min at 473, 673 and 873 K in vacuum, respectively. These samples together with the un‐annealed ones were then irradiated by a 5 keV hydrogen ion beam. SEM was used to investigate the surface micrograph of those films and SIMS was used to measure the mass spectra of positive species and the depth distribution of argon and hydrogen in the samples. A remarkable decrease in hydrogen intensity in the substrates with annealing indicates that annealing for removing argon can effectively improve hydrogen retention properties of the C‐90%SiC films. Copyright © 2008 John Wiley & Sons, Ltd.