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.     

The nature and function of the catalytic centres of the DMSO reductases

Density functional theory calculations have been performed to probe aspects of the function of the reaction centres of the DMSO reductase enzymes, in respect of catalysis of oxygen atom transfer (OAT). The first comparison between Mo and W at the active site of these enzymes has been accomplished by a consideration of the reaction profile for OAT from DMSO to [MoIV(OMe)(S2C2H2)2]1- versus that for the corresponding reaction with [WIV(OMe)(S2C2H2)2]1-. Both reaction profiles involve two transition states separated by a well-defined intermediate; however, whilst the second transition state (TS2) is clearly rate-limiting for the Mo system, the two transition states have a similar energy for the W system. The activation energy for OAT from DMSO to [WIV(OMe)(S2C2H2)2]1- is ca. 23 kJ mol-1 lower for the corresponding reaction with Mo, consistent with the significantly faster rate of reduction of DMSO by Rhodobacter capsulatus W-DMSO reductase than by its Mo counterpart. Consistent with the principle of the entatic state, the geometrical constraints imposed by the protein on the metal centre of the Mo- and W-DMSO reductases facilitate OAT by favouring a trigonal prismatic geometry for the transition state TS2 that is close to that observed for the metal in the oxidised form of each of these enzymes. The effects of different tautomers of a simplified form of the pyran ring-opened, dihydropterin state of the molybdopterin cofactor on the reaction profile for OAT have been considered. The major effect, a significant lowering of the activation barrier associated with TS2, is observed for a protonated form of a tautomer that involves conjugation between the pyrazine and metallodithiolene rings.     

Theoretical investigations on thermal rearrangement reactions of (aminomethyl)silane

Thermal rearrangement reactions of (aminomethyl)silane H(3)SiCH(2)NH(2) were studied by ab initio calculations at the G3 level. The results show that two dyotropic reactions could happen when H(3)SiCH(2)NH(2) is heated. In one reaction, the silyl group migrates from the carbon to the nitrogen atom while a hydrogen atom shifts from the nitrogen to the carbon atom, forming (methylamino)silane CH(3)NHSiH(3) (reaction A). This reaction can proceed via three paths: a path involving two consecutive steps with two transition states and one intermediate metastable carbene species (A-1); and two concerted paths (A-2 and A-3). In the other reaction, the amino group migrates from the carbon to the silicon atom while a hydrogen atom shifts from the silicon to the carbon atom, via a double three-membered ring transition state, forming aminomethylsilane CH(3)SiH(2)NH(2) (reaction B). Reaction rate constants, changes (DeltaS(#), DeltaH, and DeltaG) in thermodynamic functions and equilibrium constants of the reactions were calculated with the MP2(full)/6-311G(d,p) optimized geometries, harmonic vibrational frequencies and G3 energies of reactants, transition states, intermediates and products with statistical mechanical methods and the conventional transition-state theory (TST) with Wigner tunneling approximation over a temperature range 400-1800 K.     

Hydrogen transfer between sulfuric acid and hydroxyl radical in the gas phase: competition among hydrogen atom transfer, proton-coupled electron-transfer, and double proton transfer

In an attempt to assess the potential role of the hydroxyl radical in the atmospheric degradation of sulfuric acid, the hydrogen transfer between H2SO4 and HO* in the gas phase has been investigated by means of DFT and quantum-mechanical electronic-structure calculations, as well as classical transition state theory computations. The first step of the H2SO4 + HO* reaction is the barrierless formation of a prereactive hydrogen-bonded complex (Cr1) lying 8.1 kcal mol(-1) below the sum of the (298 K) enthalpies of the reactants. After forming Cr1, a single hydrogen transfer from H2SO4 to HO* and a degenerate double hydrogen-exchange between H2SO4 and HO* may occur. The single hydrogen transfer, yielding HSO4* and H2O, can take place through three different transition structures, the two lowest energy ones (TS1 and TS2) corresponding to a proton-coupled electron-transfer mechanism, whereas the higher energy one (TS3) is associated with a hydrogen atom transfer mechanism. The double hydrogen-exchange, affording products identical to reactants, takes place through a transition structure (TS4) involving a double proton-transfer mechanism and is predicted to be the dominant pathway. A rate constant of 1.50 x 10(-14) cm(3) molecule(-1) s(-1) at 298 K is obtained for the overall reaction H2SO4 + HO*. The single hydrogen transfer through TS1, TS2, and TS3 contributes to the overall rate constant at 298 K with a 43.4%. It is concluded that the single hydrogen transfer from H2SO4 to HO* yielding HSO4* and H2O might well be a significant sink for gaseous sulfuric acid in the atmosphere.     

The roles of benzoic acid and water on the Michael reactions of pentanal and nitrostyrene catalyzed by diarylprolinol silyl ether

The roles of benzoic acid and water on the Michael reaction of pentanal and nitrostyrene catalyzed by diarylprolinol silyl ether are revealed by density functional theory calculations. The calculations demonstrate that the benzoic acid is ready to attack the catalysts and form a hydrogen bond between the hydrogen atom of the COOH of benzoic acid and one of the N atoms of the catalyst. The complex formed from pentanal, catalyst and benzoic acid attacks nitroalkene and forms transition states. Finally, the transition states hydrolyze and the products are formed. The calculations demonstrate that the stereoselectivity is dominated by the steric hindrance of the 2-substituent groups, and the benzoic acid can increase the reaction rate evidently by decreasing the activation energies; however, H(3)O(+) or strong acid may prevent the formation of the transition states between enamines and nitroalkenes. The employed solvent can decrease the activation energies and promote the proton transfer from benzoic acid onto the catalyst 2. The calculated enantiomeric excess values are in good agreement with the experimental results. These calculations also reveal that the role of benzoic acid is dependent on the sophisticated structures of the catalysts and provide a valuable index for the structural design of new catalysts and selection of additives or co-catalysts.     

甲烷在清洁 Pd(111) 及氧改性的 Pd(111) 表面解离的密度泛函理论研究

 采用广义梯度近似 (GGA) 的密度泛函理论 (DFT) 并结合平板模型, 研究了 CH4 在清洁 Pd(111) 及 O 改性的 Pd(111) 表面发生 C朒 键断裂的反应历程. 优化了裂解过程中反应物、过渡态和产物的几何构型, 获得了反应路径上各物种的吸附能及反应的活化能. 结果表明, CH4 采用一个 H 原子指向表面的构型在 Pd(111) 表面的顶位吸附, CH3 的最稳定的吸附位置为顶位, OH, O 和 H 的最稳定吸附位置均为面心立方. CH4 在清洁 Pd(111) 表面裂解的活化能为 0.97 eV, 低于它在 O 原子改性 (O 没有参与反应) 的 Pd(111) 表面的活化能 1.42 eV, 说明表面氧原子抑制了 CH4 中 C朒 键的断裂. 当亚表面 O 原子和表面 O 原子 (O 参与反应) 共同存在时, C朒 键断裂的活化能为 0.72 eV, 低于只有表层氧存在时的活化能 (1.43 eV), 说明亚表面的 O 原子对 CH4 分子的活化具有促进作用. CH4 在 O 原子改性的 Pd(111) 表面裂解生成 CH3 和 H, 以及生成 CH3 和 OH 的反应活化能分别为 1.42 和 1.43 eV, 说明 CH4 在 O 原子改性的 Pd(111) 表面发生这两种反应的难易程度相当.     

The reaction of atomic oxygen with methanethiol. A theoretical study of the structures and the potential energy surface

Ab initio calculations at the Hartree-Fock, MP2 and MP4 levels were performed to find structures of the equilibrium and transition states and the reaction energies and energies of activation of several competing reaction pathways of O (3P)+CH3SH. A 6-31G* basis set was used in all calculations. The mechanism of hydrogen atom abstraction from the S-H group methanethiol was found to be very competitive with the oxygen atom addition to the sulfur atom.     

Quantum Chemical Study of the Reactions between Pd+/Pt+ and H2O/H2S

The study of the reactions of water and hydrogen sulfide with palladium and platinum cations has been completed in this work, in both low‐ and high‐spin states. Our calculations predict that only the formation of platinum sulfide is exothermic (in both spin states), whereas for the remaining species the oxides and sulfides are found to be more reactive than their corresponding bare metal cations. An in‐depth analysis of the reaction paths leading to metal oxide and sulfide species is given, including various minima, and several important transition states. All results have been compared with existing experimental and theoretical data, and earlier works covering the reaction of nickel cation with water and hydrogen sulfide to observe the trends for the group 10 transition metals.     

Full dimensional time-dependent quantum dynamics study of the H + NH3 --> H2 + NH2 reaction

A rigorous full dimensional time-dependent wave packet method has been developed for the reactive scattering between an atom and a tetra-atomic molecule. The method has been applied to the hydrogen abstraction reaction H+NH(3)-->H(2)+NH(2). Initial state-selected total reaction probabilities are investigated for the reactions from the ground vibrational state and from four excited vibrational states of ammonia. The total reaction probabilities from two lowest "tunneling doublets" due to the inversion barrier for the umbrella bending motion of NH(3) and from two pairs of doubly degenerate vibrational states of NH(3) are also inspected. Integral cross sections and rate constants are calculated for the reaction from the ground state with the centrifugal-sudden approximation. The calculated results are compared with those from the previous seven dimensional calculations [M. Yang and J. C. Corchado, J. Chem. Phys. 126, 214312 (2007)]. This work shows that the full dimensional rate constants are a factor of 3 larger than the corresponding seven dimensional calculated values at T=200 K and are overall smaller than those obtained from the variational transition state theory in the whole temperature region. The work also reveals that nonreactive NH bonds of NH(3) cannot be treated as spectators due to the fact that three NH bonds are coupled with each other during the reaction process.     

Influence of hydrogen bonding on hydrogen-atom abstraction reactions of dehydropyridinium cations in the gas phase

The reactions of several substituted, positively charged dehydropyridinium cations with cyclohexane, methanol, and tetrahydrofuran have been examined in a Fourier-transform ion cyclotron resonance mass spectrometer. All of the charged monoradicals react with the neutral reagents exclusively via hydrogen atom abstraction. For cyclohexane, there is a good correlation between the reaction efficiencies and the calculated electron affinities at the radical sites; that is, the greater the electron affinity of the charged monoradical at the radical site, the faster the reaction. The reaction efficiencies with methanol and tetrahydrofuran, however, do not correlate with the calculated electron affinities. Density functional theory (DFT) calculations indicate that for these reagents a stabilizing hydrogen bonding interaction exists in the hydrogen atom abstraction transition states for some of the charged monoradicals but not for others. At both the MPW1K and G3MP2B3 levels of theory, there is a good correlation between the calculated activation enthalpies and the observed reaction efficiencies, although the G3MP2B3 method provides a slightly better correlation than the MPW1K method. The extent of enhancement in the reaction efficiencies caused by the hydrogen bonding interactions parallels the calculated hydrogen bond lengths in the transition states.     

Theoretical study of water-assisted hydrolytic deamination mechanism of adenine

The water-assisted hydrolytic deamination mechanism of adenine was studied using density functional method at B3LYP/6-311G(d,p) level. Intrinsic reaction coordinate (IRC) calculations were performed on the transition states to verify whether it is the real transition states that connect the corresponding intermediates. Single-point calculations were carried out on the previous optimized geometries obtained during IRC calculations. The activation energies have also been calculated using G3MP2//B3LYP/6-311G(d,p) method. The water molecules attack the adenine and a tetrahedral intermediate forms. Then, two different intermediates have been obtained through different bond rotations. In pathway a, the second water molecule takes part in the formation of transition state and acts as a bridge to transfer hydrogen atom, while in pathway b, the second water molecule does not involve in the creation of transition state and only acts as a medium. The energy barriers are 23.40 and 37.17 kcal/mol for pathways a and b, respectively. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Computational Study of the Mechanism and Selectivity of Palladium‐Catalyzed Propargylic Substitution with Phosphorus Nucleophiles

The mechanism and sources of selectivity in the palladium‐catalyzed propargylic substitution reaction that involves phosphorus nucleophiles, and which yields predominantly allenylphosphonates and related compounds, have been studied computationally by means of density functional theory. Full free‐energy profiles are computed for both H‐phosphonate and H‐phosphonothioate substrates. The calculations show that the special behavior of H‐phosphonates among other heteroatom nucleophiles is indeed reflected in higher energy barriers for the attack on the central carbon atom of the allenyl/propargyl ligand relative to the ligand‐exchange pathway, which leads to the experimentally observed products. It is argued that, to explain the preference of allenyl‐ versus propargyl‐phosphonate/phosphonothioate formation in reactions that involve H‐phosphonates and H‐phosphonothioates, analysis of the complete free‐energy surfaces is necessary, because the product ratio is determined by different transition states in the respective branches of the catalytic cycle. In addition, these transition states change in going from a H‐phosphonate to a H‐phosphonothioate nucleophile.     

乙炔与氢化锂单体和二聚体加成反应中的HOMO-HOMO相互作用

用前线分子轨道分析乙炔与氢化锂单体和二聚体加成反应的过渡态.结果表明,在其反应过渡态形成过程中,反应物间的HOMO-LUMO和HOMO-HOMO相互作用均起重要作用.较强烈的HOMO-HOMO相互作用与过渡态附近反应由亲电性加成向亲核性加成转变相关,该反应特性的转变又与LiH中的氢原子在反应中的电荷转移相关.     

The arginine anomaly: arginine radicals are poor hydrogen atom donors in electron transfer induced dissociations

Arginine amide radicals are generated by femtosecond electron transfer to protonated arginine amide cations in the gas phase. A fraction of the arginine radicals formed (2-amino-5-dihydroguanid-1'-yl-pentanamide, 1H) is stable on the 6.7 micros time scale and is detected after collisional reionization. The main dissociation of 1H is loss of a guanidine molecule from the side chain followed by consecutive dissociations of the 2-aminopentanamid-5-yl radical intermediate. Intramolecular hydrogen atom transfer from the guanidinium group onto the amide group is not observed. These results are explained by ab initio and density functional theory calculations of dissociation and transition state energies. Loss of guanidine from 1H is calculated to require a transition state energy of 68 kJ mol(-)(1), which is substantially lower than that for hydrogen atom migration from the guanidine group. The loss of guanidine competes with the reverse migration of the arginine alpha-hydrogen atom onto the guanidyl radical. RRKM calculations of dissociation kinetics predict the loss of guanidine to account for >95% of 1H dissociations. The anomalous behavior of protonated arginine amide upon electron transfer provides an insight into electron capture and transfer dissociations of peptide cations containing arginine residues as charge carriers. The absence of efficient hydrogen atom transfer from charge-reduced arginine onto sterically proximate amide group blocks one of the current mechanisms for electron capture dissociation. Conversely, charge-reduced guanidine groups in arginine residues may function as radical traps and induce side-chain dissociations. In light of the current findings, backbone dissociations in arginine-containing peptides are predicted to involve excited electronic states and proceed by the amide superbase mechanism that involves electron capture in an amide pi* orbital, which is stabilized by through-space coulomb interaction with the remote charge carriers.     

Theoretical exploration of hydrogen loss from Al3H9

The Al(3)H(9) and Al(3)H(7) potential energy surfaces were explored using quantum chemistry calculations to investigate the H(2) loss mechanism from Al(3)H(9), which provide new insights into hydrogen production from bulk alane, [AlH(3)](x), a possible energy storage material. We present results of B3LYP/6-311++G(d,p) calculations for the various Al(3)H(9) and Al(3)H(7) optimized local minima and transition state structures along with some reaction pathways for their interconversion. We find the energy for Al(3)H(9) decomposition into Al(2)H(6) and AlH(3) is slightly lower than that for H(2) loss and Al(3)H(7) formation, but the calculations show that H(2) loss from Al(3)H(9) is a lower energy process than for losing hydrogen from either Al(2)H(6) or AlH(3). We found four transition state structures and reaction pathways for Al(3)H(9) → Al(3)H(7) + H(2), where the lowest energy activation barrier is around 25-73 kJ/mol greater than the experimental value for H(2) loss from bulk alane. Intrinsic reaction coordinate calculations show that the H(2) loss pathway involves considerable rearrangement of the H atom positions around a single Al center. Three of the pathways start with the formation of an AlH(3) moiety, which then enables a terminal H on the AlH(3) to get within 1.1 to 1.2 ? of a nearby bridging H atom. The bridging and terminal H atoms eventually combine to form H(2) and leave Al(3)H(9). One implication of these H(2) loss reaction pathways is that, since the H atoms in bulk alanes are all at bridging positions, if a similar H(2) loss mechanism were to apply to bulk alane, then H(2) loss would most likely occur on the bulk alane surface or at a defect site where there should be more terminal H atoms available for reaction with nearby bridging H atoms.     

Theoretical study on the kinetics and branching ratios of the gas phase reactions of 1, 1-Dichlorodimethylether (DCDME) with Cl atom

Quantum mechanical calculations are carried out on the reactions of CH₃OCHCl₂ (DCDME) with Cl atom by means of DFT and couple cluster methods. The geometries of the reactants, products, and transition states involved in the reaction pathways are optimized at BHandHLYP level of theory using 6-311G(d,p) basis set. Transition states are searched on the potential energy surface involved during the reaction channels, and each of the transition states is characterized by the presence of only one imaginary frequency. The existence of transition states on the corresponding potential energy surface is ascertained by performing intrinsic reaction coordinate calculation. Single point energy calculations are performed at CCSD(T) level using the same basis set. The hydrogen abstraction rate constant for the title reaction is calculated at 298 K and atmospheric pressure using the canonical transition state theory including tunneling correction. The calculated value for rate constant as 1.204 × 10^?12 cm³ molecule^?1 s^?1 is found to be in very good agreement with the recent experimental data. The percentage contributions of both reaction channels are also reported at 298 K.     

Theoretical study of the reaction mechanism of proton transfer in glycinamide

To investigate the tautomerism of glycinamide that is induced by proton transfer, we present detailed theoretical studies on the reaction mechanism of both the isolated gas phase and H₂O‐assisted proton transfer process of glycinamide, using density functional theory calculations by means of the B3LYP hybrid functional. Twenty‐six geometries, including 10 significant transition states, were optimized, and these geometrical parameters are discussed in detail. The relative order of the activation energy for hydrogen atom transfer of all the conformers has been systematically explored in this essay. For the amido hydrogen atom transfer process, the relative order of the activation energy is: IV < II < III < I, while in the carbonic hydrogen atom transfer process, the relative order is IV > II > III > I. Meanwhile, the most favorable structure for both the amido hydrogen atom transfer and the carbonic hydrogen atom transfer has been found. The involvement of the water molecule not only can stabilize the transition states and the ground states, but can also reduce the activation energy greatly. The superior catalytic effect of H₂O has been discussed in detail. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2006     

Communication: non-adiabatic coupling and resonances in the F + H2 reaction at low energies

Quantum reactive scattering calculations on accurate potential energy surfaces predict that at energies below ～5 meV, the reaction of F atoms with H(2) is dominated by the Born-Oppenheimer (BO) forbidden reaction of the spin-orbit excited F((2)P(1∕2)) atom. This non-BO dominance is amplified by low-energy resonances corresponding to quasi-bound states of the HF(v = 3, j = 3) + H product channel. Neglect of non-adiabatic coupling between the electronic states of the F atom leads to a qualitatively incorrect picture of the reaction dynamics at low energy.     

An ab initio study on thermal rearrangement reactions of 1-silylprop-2-en-1-ol H3SiCH(OH)CH=CH2

The thermal rearrangement reactions of 1-silylprop-2-en-1-ol H3SiCH(OH)CH=CH2 were studied by ab initio calculations at the G2(MP2) and G3 levels. The reaction mechanisms were revealed through ab initio molecular orbital theory. On the basis of the MP2(full)/6-31G(d) optimized geometries, harmonic vibrational frequencies of various stationary points were calculated. The reaction paths were investigated and confirmed by intrinsic reaction coordinate (IRC) calculations. The results show that the thermal rearrangements of H3SiCH(OH)CH=CH2 happen in two ways. One is via the Brook rearrangement reactions (reaction A), and the silyl group migrates from carbon atom to oxygen atom passing through a double three-membered ring transition state, forming allyloxysilane CH2=CHCH2OSiH3. In the other, the reactant undergoes a dyotropic rearrangement; the hydroxyl group migrates from carbon atom to silicon atom coupled with a simultaneous migration of a hydrogen atom from silicon atom to carbon atom, forming allylsilanol CH2=CHCH2SiH2OH (reaction B). The barriers for reactions A and B were computed to be 343.5 and 203.7 kJ/mol, respectively, at the G3 level. The changes of the thermodynamic functions, entropy (DeltaS), entropy (DeltaS(doubledagger)) for the transition state, enthalpy (DeltaH), and free energy (DeltaG) were calculated by using the MP2(full)/6-31G(d) optimized geometries, and harmonic vibrational frequencies of reactants, transition states, and products with statistical mechanical methods, and equilibrium constant K(T) and reaction rate constant k(T) in canonical variational transition-state theory (CVT) with centrifugal-dominant small-curvature tunneling approximation (SCT) were calculated over a temperature range 400-1300 K. The conventional transition-state theory (TST) rate constants were also calculated for the purposes of comparison. The influences of the vinyl group attached to the center carbon of the alpha-silyl alcohols on reactions were discussed.     

氧杂环丁烷热解机理的量子化学研究

本文利用半经验分子轨道理论研究了氧杂环丁烷热解为甲醛和乙烯的反应机理计算是采用半经验方法AM1进行的, 各种驻点全部运用Berny梯度方法优化. 同时, 对过渡态的结构进行了振动分析的确证. 计算表明: 1)不存在协同的同面-同面反应途径的过渡态, 其驻点只是一个二级鞍点; 2) 协同的同面-异面反应途径需要经过一个能量很高的过渡态; 3)有利的反应途径是包含了双自由基中间体的分步过程。