A theoretical study of radical-only and combined radical/carbocationic mechanisms of arachidonic acid cyclooxygenation by prostaglandin H synthase

Prostaglandin H synthase catalyzes the oxygenation of arachidonic acid into the cyclic endoperoxide, prostaglandin G₂ (PGG₂), and the subsequent reduction of PGG₂ to the corresponding alcohol, prostaglandin H₂ (PGH₂), the precursor of all prostaglandins and thromboxanes. Both radical abstraction by a neighboring tyrosyl radical and combined radical/carbocationic models have been proposed to explain the cyclooxygenase part of this reaction. We have used density functional theory calculations to study the mechanism of the formation of the cyclooxygenated product PGG₂. We found an activation free energy for the initial hydrogen abstraction by the tyrosine radical of 15.6 kcal/mol, and of 14.5 kcal/mol for peroxo bridge formation, in remarkable agreement with the experimental value of 15.0 kcal/mol. Subsequent steps of the radical-based mechanism were found to happen with smaller barriers. A combined radical/carbocation mechanism proceeding through a sigmatropic hydrogen shift was ruled out, owing to its much larger activation free energy of 36.5 kcal/mol. Supplementary material is available in the online version of this article at http://dx.doi.org/10.1007/s00214-003-0476-9. Electronic Supplementary MaterialSupplementary material is available in the online version of this article at Electronic Supplementary Material: Supplementary material is available in the online version of this article at     

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.     

Computational investigation of hydrogen abstraction from 2-aminoethanol by the 1,5-dideoxyribose-5-yl radical: a model study of a reaction occurring in the active site of ethanolamine ammonia lyase

Hydrogen abstraction from 2-aminoethanol by the 5'-deoxyadenosyl radical, which is formed upon Co--C bond homolysis in coenzyme B(12), was investigated by theoretical means with employment of the DFT (B3LYP) and ab initio (MP2) approaches. As a model system for the 5'-deoxyadenosyl moiety the computationally less demanding 1,5-dideoxyribose was employed; two conformers, which differ in ring conformation (C2- and C3-endo), were considered. If hydrogen is abstracted from "free" substrate by the C2-endo conformer of the 1,5-dideoxyribose-5-yl radical, the activation enthalpy is 16.7 kcal mol(-1); with the C3-endo counterpart, the value is 17.3 kcal mol(-1). These energetic requirements are slightly above the activation enthalpy limit (15 kcal mol(-1)) determined experimentally for the rate-determining step of the sequence, that is, hydrogen delivery from 5'-deoxyadenosine to the product radical. The activation enthalpy is lower when the substrate interacts with at least one amino acid from the active site. According to the computations, when a His model system partially protonates the substrate the activation enthalpy is 4.5 kcal mol(-1) for the C3-endo conformer and 5.8 kcal mol(-1) for the C2-endo counterpart. As hydrogen abstraction from the fully as well as the partially protonated substrate is preceded by the formation of quite stable encounter complexes, the actual activation barriers are around 13-15 kcal mol(-1). A synergistic interaction of 2-aminoethanol with two amino acids where His partially protonates the NH(2) group and Asp partially deprotonates the OH group of the substrate results in an activation enthalpy of 12.4 kcal mol(-1) for the C3-endo conformer and 13.2 kcal mol(-1) for the C2-endo counterpart. However, if encounter complexes exist in the active site, the actual activation barriers are much higher (>25 kcal mol(-1)) than that reported for the rate-determining step. These findings together with previous computations suggest that the energetics of the initial hydrogen abstraction decrease with an interaction of the substrate with only a protonating auxiliary, but for the rearrangement of the radical the synergistic effects of two auxiliaries are essential to pull the barrier below the limit of 15 kcal mol(-1).     

Gas-phase kinetics study of reaction of OH radical with CH3NHNH2 by second-order multireference perturbation theory

The gas-phase kinetics of H-abstraction reactions of monomethylhydrazine (MMH) by OH radical was investigated by second-order multireference perturbation theory and two-transition-state kinetic model. It was found that the abstractions of the central and terminal amine H atoms by the OH radical proceed through the formation of two hydrogen bonded preactivated complexes with energies of 6.16 and 5.90 kcal mol(-1) lower than that of the reactants, whereas the abstraction of methyl H atom is direct. Due to the multireference characters of the transition states, the geometries and ro-vibrational frequencies of the reactant, transition states, reactant complexes, and product complexes were optimized by the multireference CASPT2/aug-cc-pVTZ method, and the energies of the stationary points of the potential energy surface were refined at the QCISD(T)/CBS level via extrapolation of the QCISD(T)/cc-pVTZ and QCISD(T)/cc-pVQZ energies. It was found that the abstraction reactions of the central and two terminal amine H atoms of MMH have the submerged energy barriers with energies of 2.95, 2.12, and 1.24 kcal mol(-1) lower than that that of the reactants respectively, and the abstraction of methyl H atom has a real energy barrier of 3.09 kcal mol(-1). Furthermore, four MMH radical-H(2)O complexes were found to connect with product channels and the corresponding transition states. Consequently, the rate coefficients of MMH + OH for the H-abstraction of the amine H atoms were determined on the basis of a two-transition-state model, with the total energy E and angular momentum J conserved between the two transition-state regions. In units of cm(3) molecule(-1) s(-1), the rate coefficient was found to be k(1) = 3.37 × 10(-16)T(1.295) exp(1126.17/T) for the abstraction of the central amine H to form the CH(3)N(?)NH(2) radical, k(2) = 2.34 × 10(-17)T(1.907) exp(1052.26/T) for the abstraction of the terminal amine H to form the trans-CH(3)NHN(?)H radical, k(3) = 7.41 × 10(-20)T(2.428) exp(1343.20/T) for the abstraction of the terminal amine H to form the cis-CH(3)NHN(?)H radical, and k(4) = 9.13 × 10(-21)T(2.964) exp(-114.09/T) for the abstraction of the methyl H atom to form the C(?)H(2)NHNH(2) radical, respectively. Assuming that the rate coefficients are additive, the total rate coefficient of these theoretical predictions quantitatively agrees with the measured rate constant at temperatures of 200-650 K, with no adjustable parameters.     

The "somersault" mechanism for the p-450 hydroxylation of hydrocarbons. The intervention of transient inverted metastable hydroperoxides

A series of model theoretical calculations are described that suggest a new mechanism for the oxidation step in enzymatic cytochrome P450 hydroxylation of saturated hydrocarbons. A new class of metastable metal hydroperoxides is described that involves the rearrangement of the ground-state metal hydroperoxide to its inverted isomeric form with a hydroxyl radical hydrogen bonded to the metal oxide (MO-OH --> MO....HO). The activation energy for this somersault motion of the FeO-OH group is 20.3 kcal/mol for the P450 model porphyrin iron(III) hydroperoxide [Por(SH)Fe(III)-OOH(-)] to produce the isomeric ferryl oxygen hydrogen bonded to an *OH radical [Por(SH)Fe(III)-O....HO(-)]. This isomeric metastable hydroperoxide, the proposed primary oxidant in the P450 hydroxylation reaction, is calculated to be 17.8 kcal/mol higher in energy than the ground-state iron(III) hydroperoxide Cpd 0. The first step of the proposed mechanism for isobutane oxidation is abstraction of a hydrogen atom from the C-H bond of isobutane by the hydrogen-bonded hydroxyl radical to produce a water molecule strongly hydrogen bonded to anionic Cpd II. The hydroxylation step involves a concerted but nonsynchronous transfer of a hydrogen atom from this newly formed, bound, water molecule to the ferryl oxygen with a concomitant rebound of the incipient *OH radical to the carbon radical of isobutane to produce the C-O bond of the final product, tert-butyl alcohol. The TS for the oxygen rebound step is 2 kcal/mol lower in energy than the hydrogen abstraction TS (DeltaE() = 19.5 kcal/mol). The overall proposed new mechanism is consistent with a lot of the ancillary experimental data for this enzymatic hydroxylation reaction.     

Car-Parrinello molecular dynamics study of the rearrangement of the valeramide radical cation

Car-Parrinello molecular dynamics (CPMD) studies of neutral (1) and ionized (1 (+.)) valeramide are performed with the aim of providing a rationalization for the unusual temperature effect on the dissociation pattern of 1(+.) observed in mass spectrometric experiments. According to CPMD simulations of neutral valeramide 1 performed at approximately 500 K, the conformation with the fully relaxed carbon backbone predominates (96 %). Conformational changes involving folding of the carbon backbone into conformers that would allow intramolecular H transfers are predicted not to take place spontaneously at this temperature because of the barrier heights associated with these transitions (3.5 and 6.9 kcal mol(-1)), which cannot be overcome by thermal motion alone. For 1(+.), CPMD simulations performed at approximately 300 K reveal a substantial stability of a conformation in which the carbon backbone is fully relaxed; no reaction is observed even after 7 ps. However, when conformers with already folded carbon-backbones are used as initial geometries in the CPMD simulations, the gamma-hydrogen migration (McLafferty rearrangement resulting in C(3)H(6)) is already completed within 2 ps. For this important process, the free activation energy associated with both a required conformational change and the subsequent H transfer equals 4.5 kcal mol(-1), while for the formally related delta-H shift (which eventually gives rise to the elimination of C(2)H(4)/C(2)H(5.)) it amounts to 7.0 kcal mol(-1). Since the barriers associated with conformational changes are energetically more demanding than those of the corresponding hydrogen transfers, 1(+.) is essentially trapped by conformational barriers and long-lived at approximately 300 K. At elevated temperatures (500 K), the preferred reaction (within 7.3 ps) in the CPMD simulation corresponds to the McLafferty rearrangement. The estimated free activation energy associated with this process amounts to 2.5 kcal mol(-1), while the free activation energy for the delta-H transfer equals 4.4 kcal mol(-1). This relatively small free activation energy for the McLafferty rearrangement might cause dissociation of a substantial fraction of 1(+.) prior to the time-delayed mass selection, which would reduce the C3/C2 ratio in the experiments conducted with metastable ions that have a lifetime in the order of some micros at a source temperature of 500 K.     

Elimination of water from the carboxyl group of GlyGlyH+

The elimination of water from the carboxyl group of protonated diglycine has been investigated by density functional theory calculations. The resulting structure is identical to the b(2) ion formed in the mass spectrometric fragmentation of protonated peptides (therefore named "b2" in this study). The most stable geometry of the fragment ion ("b2") is an O-protonated diketopiperazine. However, its formation is kinetically disfavored as it requires a free energy of 58.2 kcal/mol. The experimentally observed N-protonated oxazolone is 3.0 kcal/mol less stable. The lowest energy pathway for the formation of the "b2" ion requires a free energy of 37.5 kcal/mol and involves the proton transfer from the amide oxygen of protonated diglycine to the hydroxyl oxygen. Fragmentation initiated by proton transfer from the terminal nitrogen has also a comparable free energy of activation (39.4 kcal/mol). Proton transfer initiating the fragmentation, from the highly basic terminal nitrogen or amide oxygen to the less basic hydroxyl oxygen is feasible at energies reached in usual mass spectrometric experiments. Amide N-protonated diglycine structures are precursors of mainly y(1) ions rather than "b2" ions. In the lowest energy fragmentation channels, proton transfer to the hydroxylic oxygen, bond breaking and formation of an oxazolone ring occur concertedly but asynchronously. Proton transfer to hydroxyl oxygen and cleavage of the corresponding C-O bond take place at the early stages of the fragmentation step, while ring closure to form an oxazolone geometry occurs at the later stages of the transition. The experimentally observed low kinetic energy release is expected to be due to the existence of a strongly hydrogen bonded protonated oxazolone-water complex in the exit channel. Whereas the threshold energy for "b2" ion formation (37.1 kcal/mol) is lower than for the y(1) ion (38.4 kcal/mol), the former requires a tight transition state with an activation entropy, DeltaS++ = -1.2 cal/mol.K and the latter has a loose transition state with DeltaS++ = +8.8 cal/mol.K. This leads to y(1) being the major fragment ion over a wide energy range.     

Preparation and reactivity of [D3d]-octahedrane: the most stable (CH)12 hydrocarbon

The synthesis of the (CH)12 hydrocarbon [D(3d)]-octahedrane (heptacyclo[6.4.0.0(2,4).0(3,7).0(5,12).0(6,10).0(9,11)]dodecane) 1 and its selective functionalization retaining the hydrocarbon cage is described. The B3LYP/6-311+G* strain energy of 1 is 83.7 kcal mol(-1) (4.7 kcal mol(-1) per C-C bond) which is significantly higher than that of the structurally related (CH)16 [D(4d)]-decahedrane 2 (75.4 kcal mol(-1); 3.1 kcal mol(-1) per C-C bond) and (CH)20 [I(h)]-dodecahedrane 3 (51.5 kcal mol(-1); 1.7 kcal mol(-1) per C-C bond); the heats of formation for 1-3 computed according to homodesmotic equations are 52, 35, and 4 kcal mol(-1). Catalytic hydrogenation of 1 leads to consecutive opening of the two cyclopropane rings to give C2-bisseco-octahedrane (pentacyclo[6.4.0.0(2,6).0(3,11).0(4,9)]dodecane) 16 as the major product. Although 1 is highly strained, its carbon skeleton is kinetically quite stable: Upon heating, 1 does not decompose until above 180 degrees C. The B3LYP/6-31G* barriers for the S(R)2 attack of the tBuO. and Br3C. radicals on a carbon atom of one of the cyclopropane fragments (Delta(298) = 27-28 kcal mol(-1)) are higher than those for hydrogen atom abstraction. The latter barriers are virtually identical for the abstraction from the C1-H and C2-H positions with the tBuO. radical (DeltaG(298) = 17.4 and 17.9 kcal mol(-1), respectively), but significantly different for the reaction at these positions with the Br3C. radical (DeltaG(298) = 18.8 and 21.0 kcal mol(-1)). These computational results agree well with experiments, in which the chlorination of 1 with tert-butyl hypochlorite gave a mixture of 1- and 2-chlorooctahedranes (ratio 3:2). The bromination with carbon tetrabromide under phase-transfer catalytic (PTC) conditions (nBu4NBr/NaOH) selectively gave 1-bromooctahedrane in 43 % isolated yield. For comparison, the PTC bromination was also applied to 2,4-dehydroadamantane yielding 54 % 7-bromo-2,4-dehydroadamantane.     

Direct ESR detection of pentadienyl radicals and peroxyl radicals in lipid peroxidation: mechanistic insight into regioselective oxygenation in lipoxygenases

Well-resolved ESR spectra of free pentadienyl radicals have been observed under photoirradiation of di-tert-butylperoxide (Bu(t)OOBu(t)) and polyunsaturated fatty acids in the absence of O(2), allowing us to determine the hfc values. The hfc values of linoleyl radical indicate that the spin density is the largest at the C-11 position. The linoleyl radical is readily trapped by O(2) to produce the peroxyl radical (11-HPO.) in which O(2) is added mainly at the C-11 position of the pentadienyl radical as indicated by the comparison of the ESR spectra of peroxyl radicals derived from linoleic acid and [11,11-(2)H(2)]linoleic acid. The peroxyl radical (13-HPO.), which is initially formed by the hydrogen abstraction from 13-(S)-hydroperoxy-9(Z),11(E)-octadecadienoic acid (13-HPOD) by Bu(t)O., is found to isomerize to 11-HPO. via removal of O(2) from 13-HPO. and addition of O(2) to linoleyl radical to produce 11-HPO. . This finding supports an idea of O(2) entering via a specific protein channel, which determines the stereo- and regiochemistry of the biradical combination between O(2) and linoleyl radical in lipoxygenases.     

Intramolecular hydrogen bonding and hydrogen atom abstraction in gas-phase aliphatic amine radical cations

The intramolecular hydrogen atom abstraction by the nitrogen atom in isolated aliphatic amine radical cations is examined experimentally and with composite high-level ab initio methods of the G3 family. The magnitude of the enthalpy barriers toward H-atom transfer varies with the shape and size of the cyclic transition state and with the degree of substitution at the nitrogen and carbon atoms involved. The lower barriers are found for 1,5- and 1,6-abstraction, for chairlike transition states, for abstraction reactions in ionized primary amines, and for abstraction of H from tertiary carbon atoms. In most cases, the internal energy required for 1,4-, 1,5-, and 1,6-hydrogen atom abstraction to occur is less than that required for gas-phase fragmentation by simple cleavage of C-C bonds, which explains why H-atom transfer can be reversible and result in extensive H/D exchange prior to the fragmentation of many low-energy deuterium labeled ionized amines. The H-atom transfer to nitrogen is exothermic for primary amine radical cations and endothermic for tertiary amines. It gives rise to a variety of distonic radical cations, and these may undergo further isomerization. The heat of formation of the gauche conformers of the gamma-, delta-, and epsilon-distonic isomers is up to 25 kJ mol(-1) lower than that of the corresponding trans forms, which is taken to reflect C-H-N hydrogen bonding between the protonated amino group and the alkyl radical site.     

QM/MM modeling of the hydroxylation of the androstenedione substrate catalyzed by cytochrome P450 aromatase (CYP19A1)

CYP19A1 aromatase is a member of the Cytochrome P450 family of hemeproteins, and is the enzyme responsible for the final step of the androgens conversion into the corresponding estrogens, via a three‐step oxidative process. For this reason, the inhibition of this enzyme plays an important role in the treatment of hormone‐dependent breast cancer. The first catalytic subcycle, corresponding to the hydroxilation of androstenedione, has been proposed to occur through a first hydrogen abstraction and a subsequent oxygen rebound step. In present work, we have studied the mechanism of the first catalytic subcycle by means of hybrid quantum mechanics/molecular mechanics methods. The inclusion of the protein flexibility has been achieved by means of Free Energy Perturbation techniques, giving rise to a free energy of activation for the hydrogen abstraction step of 13.5 kcal/mol. The subsequent oxygen rebound step, characterized by a small free energy barrier (1.5 kcal/mol), leads to the hydroxylated products through a highly exergonic reaction. In addition, an analysis of the primary deuterium kinetic isotopic effects, calculated for the hydrogen abstraction step, reveals values (～10) overpassing the semiclassical limit for the C? H, indicating the presence of a substantial tunnel effect. Finally, a decomposition analysis of the interaction energy for the substrate and cofactor in the active site is also discussed. According to our results, the role of the enzymatic environment consists of a transition state stabilization by means of dispersive and polarization effects. © 2015 Wiley Periodicals, Inc.     

Ab initio investigation on the reaction path and rate for the gas-phase reaction of HO + H2O <--> H2O + OH

This article describes an ab initio investigation on the potential surfaces for one of the simplest hydrogen atom abstraction reactions, that is, HO + H2O <--> H2O + OH. In accord with the findings in the previously reported theoretical investigations, two types of the hydrogen-bonding complexes [HOH--OH] and [H2O--HO] were located on the potential energy surface. The water molecule acts as a hydrogen donor in the [HOH--OH] complex, while the OH radical acts as a hydrogen donor in the [H2O--HO] complex. The energy evaluations at the MP2(FC) basis set limit, as well as those through the CBS-APNO procedure, have provided estimates for enthalpies of association for these complexes at 298 K as -2.1 approximately -2.3 and -4.1 approximately -4.3 kcal/mol, respectively. The IRC calculations have suggested that the [H2O--HO] complex should be located along the reaction coordinate for the hydrogen abstraction. Our best estimate for the classical barrier height for the hydrogen abstraction is 7.8 kcal/mol, which was obtained from the CBS-APNO energy evaluations. After fitting the CBS-APNO potential energy curve to a symmetrical Eckart function, the rate constants were calculated by using the transition state theory including the tunneling correction. Our estimates for the Arrhenius parameters in the temperature region from 300 to 420 K show quite reasonable agreement with the experimentally derived values.     

Chemistry of the t-butoxyl radical: evidence that most hydrogen abstractions from carbon are entropy-controlled

Absolute rate constants and Arrhenius parameters for hydrogen abstractions (from carbon) by the t-butoxyl radical ((t) BuO.) are reported for several hydrocarbons and tertiary amines in solution. Combined with data already in the literature, an analysis of all the available data reveals that most hydrogen abstractions (from carbon) by (t) BuO. are entropy controlled (i.e., TdeltaS > deltaH, in solution at room temperature). For substrates with C-H bond dissociation energies (BDEs) > 92 kcal/mol, the activation energy for hydrogen abstraction decreases with decreasing BDE in accord with the Evans-Polanyi equation, with alpha approximately 0.3. For substrates with C-H BDEs in the range from 79 to 92 kcal/mol, the activation energy does not vary significantly with C-H BDE. The implications of these results in the context of the use of (t) BuO. as a chemical model for reactive oxygen-centered radicals is discussed.     

Reaction mechanism between carbonyl oxide and hydroxyl radical: a theoretical study

The reaction mechanism of carbonyl oxide with hydroxyl radical was investigated by using CASSCF, B3LYP, QCISD, CASPT2, and CCSD(T) theoretical approaches with the 6-311+G(d,p), 6-311+G(2df, 2p), and aug-cc-pVTZ basis sets. This reaction involves the formation of H2CO + HO2 radical in a process that is computed to be exothermic by 57 kcal/mol. However, the reaction mechanism is very complex and begins with the formation of a pre-reactive hydrogen-bonded complex and follows by the addition of HO radical to the carbon atom of H2COO, forming the intermediate peroxy-radical H2C(OO)OH before producing formaldehyde and hydroperoxy radical. Our calculations predict that both the pre-reactive hydrogen-bonded complex and the transition state of the addition process lie energetically below the enthalpy of the separate reactants (DeltaH(298K) = -6.1 and -2.5 kcal/mol, respectively) and the formation of the H2C(OO)OH adduct is exothermic by about 74 kcal/mol. Beyond this addition process, further reaction mechanisms have also been investigated, which involve the abstraction of a hydrogen of carbonyl oxide by HO radical, but the computed activation barriers suggest that they will not contribute to the gas-phase reaction of H2COO + HO.     

Reactions of ·OH with thymine studied using density functional theory

We studied three possible reactions of a free ·OH radical with thymine by using density functional theory calculations. The results indicate that there is no energy barrier in the reactions of a free ·OH radical adding to the C₆ position of thymine, while the reactions of a free ·OH radical adding to the C₅ position of thymine and the reaction of an ·OH abstracting a hydrogen from the C₅ methyl group should overcome the energy barriers of ～0.70 kcal/mol and ～1.88 kcal/mol, respectively. The C₆‐hydroxylated radical formed is energetically more favorable than the C₅‐hydroxylated radical. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

Thermally activated mechanisms of hydrogen abstraction by growth precursors during plasma deposition of silicon thin films

Hydrogen abstraction by growth precursors is the dominant process responsible for reducing the hydrogen content of amorphous silicon thin films grown from SiH(4) discharges at low temperatures. Besides direct (Eley-Rideal) abstraction, gas-phase radicals may first adsorb on the growth surface and abstract hydrogen in a subsequent process, giving rise to thermally activated precursor-mediated (PM) and Langmuir-Hinshelwood (LH) abstraction mechanisms. Using results of first-principles density functional theory (DFT) calculations on the interaction of SiH(3) radicals with the hydrogen-terminated Si(001)-(2x1) surface, we show that precursor-mediated abstraction mechanisms can be described by a chemisorbed SiH(3) radical hopping between overcoordinated surface Si atoms while being weakly bonded to the surface before encountering a favorable site for hydrogen abstraction. The calculated energy barrier of 0.39 eV for the PM abstraction reaction is commensurate with the calculated barrier of 0.43-0.47 eV for diffusion of SiH(3) on the hydrogen-terminated Si(001)-(2x1) surface, which allows the radical to sample the entire surface for hydrogen atoms to abstract. In addition, using the same type of DFT analysis we have found that LH reaction pathways involve bond breaking between the silicon atoms of the chemisorbed SiH(3) radical and the film prior to hydrogen abstraction. The LH reaction pathways exhibit energy barriers of 0.76 eV or higher, confining the abstraction only to nearest-neighbor hydrogens. Furthermore, we have found that LH processes compete with radical desorption from the hydrogen-terminated Si(001)-(2x1) surface and may be suppressed by the dissociation of chemisorbed SiH(3) radicals into lower surface hydrides. Analysis of molecular-dynamics simulations of the growth process of plasma deposited silicon films have revealed that qualitatively similar pathways for thermally activated hydrogen abstraction also occur commonly on the amorphous silicon growth surface.     

The benzene+OH potential energy surface: intermediates and transition states

The potential energy surface for the interaction between benzene and hydroxyl radical is studied in detail using quantum mechanical methods, with a particular focus on the hydrogen abstraction pathway. Geometric parameters are optimized using a variety of density functional methods as well as perturbation theory. Energies are refined using coupled cluster singles and doubles with perturbative triples [CCSD(T)] extrapolated to the complete basis set limit. At our most reliable level of theory, complexation energies are found to be (with zero-point corrected energies in parentheses) 3.7 (2.8) kcal/mol for the benzene-hydroxyl radical complex and 2.9 (-1.7) kcal/mol for the phenyl radical-water complex. The barrier to H abstraction lies 6.5 (4.2) kcal/mol above the infinitely separated benzene and hydroxyl radical monomers.     

Ab initio MO and TST calculations for the rate constant of the HNO+NO2→HONO+NO reaction

Potential-energy surfaces for various channels of the HNO+NO₂ reaction have been studied at the G2M(RCC,MP2) level. The calculations show that direct hydrogen abstraction leading to the NO+cis-HONO products should be the most significant reaction mechanism. Based on TST calculations of the rate constant, this channel is predicted to have an activation energy of 6–7 kcal/mol and an A factor of ca. 10⁻¹¹ cm³ molecule⁻¹ s⁻¹ at ambient temperature. Direct H-abstraction giving NO+trans-HONO has a high barrier on PES and the formation of trans-HONO would rather occur by the addition/1,3-H shift mechanism via the HN(O)NO₂ intermediate or by the secondary isomerization of cis-HONO. The formation of NO+HNO₂ can take place by direct hydrogen transfer with the barrier of ca. 3 kcal/mol higher than that for the NO+cis-HONO channel. The formation of HNO₂ by oxygen abstraction is predicted to be the least significant reaction channel. The rate constant calculated in the temperature range 300–5000 K for the lowest energy path producing NO+cis-HONO gave rise to © 1998 John Wiley & Sons, Inc. Int J Chem Kinet 30: 729–736, 1998     

Molecular description of indigo oxidation mechanisms initiated by OH and OOH radicals

In this work, we report a quantum chemistry mechanistic study of the hydroxyl (?OH) and hydroperoxyl (?OOH) radicals initiated oxidation of indigo, within the density functional theory framework. All possible hydrogen abstraction and radical addition reaction pathways have been considered. We find that the reaction between a free indigo molecule and an ?OH radical occurs mainly through two competing mechanisms: H-abstraction from an NH site and ?OH addition to the central C═C double bond. Although the latter is favored, both channels occur, the indigo chromophore group structure is modified, and thus the color is changed. This mechanism adequately accounts for the loss of chromophore in urban air, including indoor air such as in museums and in urban areas. Regarding the reactivity of indigo toward ?OOH radicals, only ?OOH-addition to the central double bond is thermodynamically feasible. The corresponding transition state free energy value is about 10 kcal/mol larger than the one for the ?OH initiated oxidation. Therefore, even considering that the ?OOH concentration is considerably larger than the one of ?OH, this reaction is not expected to contribute significantly to indigo oxidation under atmospheric conditions.     

Chemisorbed benzoate-to-benzene conversion via phenyl radicals on Cu(110): kinetic observation of conformational effects

The adsorption and decomposition of benzoic acid on the Cu(110) surface has been investigated using temperature-programmed reaction (TPR) spectroscopy and scanning tunneling microscopy (STM). The benzoate species is found to exist in two conformations: a phase containing upright species at monolayer saturation and a phase containing many tilted species at lower coverages. Thermal decomposition begins to occur near 500 K, yielding benzene and CO2. It is found that phenyl radicals, generated preferentially from the tilted benzoate species, efficiently abstract H atoms from undecomposed benzoate species to produce benzene in a rate-controlling process with an activation energy of about 29 kcal/mol. Using deuterium atom substitution at the 4-C position on the benzoate ring, it is found that the hydrogen abstraction reaction is selective for 2-,3- and 5-,6-C-H bonds. This observation indicates that the mobile phenyl radical is surface bound and preferentially attacks C-H bonds which are nearest the Cu surface binding the benzoate species, either as an upright species or as a tilted species.