Is the ruthenium analogue of compound I of cytochrome p450 an efficient oxidant? A theoretical investigation of the methane hydroxylation reaction

High-valent metal-oxo complexes catalyze C-H bond activation by oxygen insertion, with an efficiency that depends on the identity of the transition metal and its oxidation state. Our study uses density functional calculations and theoretical analysis to derive fundamental factors of catalytic activity, by comparison of a ruthenium-oxo catalyst with its iron-oxo analogue toward methane hydroxylation. The study focuses on the ruthenium analogue of the active species of the enzyme cytochrome P450, which is known to be among the most potent catalysts for C-H activation. The computed reaction pathways reveal one high-spin (HS) and two low-spin (LS) mechanisms, all nascent from the low-lying states of the ruthenium-oxo catalyst (Ogliaro, F.; de Visser, S. P.; Groves, J. T.; Shaik, S. Angew. Chem. Int. Ed. 2001, 40, 2874-2878). These mechanisms involve a bond activation phase, in which the transition states (TS's) appear as hydrogen abstraction species, followed by a C-O bond making phase, through a rebound of the methyl radical on the metal-hydroxo complex. However, while the HS mechanism has a significant rebound barrier, and hence a long lifetime of the radical intermediate, by contrast, the LS ones are effectively concerted with small barriers to rebound, if at all. Unlike the iron catalyst, the hydroxylation reaction for the ruthenium analogue is expected to follow largely a single-state reactivity on the LS surface, due to a very large rebound barrier of the HS process and to the more efficient spin crossover expected for ruthenium. As such, ruthenium-oxo catalysts (Groves, J. T.; Shalyaev, K.; Lee, J. In The Porphyrin Handbook; Biochemistry and Binding: Activation of Small Molecules, Vol. 4; Kadish, K. M., Smith, K. M., Guilard, R., Eds.; Academic Press: New York, 2000; pp 17-40) are expected to lead to more stereoselective hydroxylations compared with the corresponding iron-oxo reactions. It is reasoned that the ruthenium-oxo catalyst should have larger turnover numbers compared with the iron-oxo analogue, due to lesser production of suicidal side products that destroy the catalyst (Ortiz de Montellano, P. R.; Beilan, H. S.; Kunze, K. L.; Mico, B. A. J. Biol. Chem. 1981, 256, 4395-4399). The computations reveal also that the ruthenium complex is more electrophilic than its iron analogue, having lower hydrogen abstraction barriers. These reactivity features of the ruthenium-oxo system are analyzed and shown to originate from a key fundamental factor, namely, the strong 4d(Ru)-2p(O,N) overlaps, which produce high-lying pi(Ru-O), sigma(Ru-O), and sigma(Ru-N) orbitals and thereby to lead to a preference of ruthenium for higher-valent oxidation states with higher electrophilicity, for the effectively concerted LS hydroxylation mechanism, and for less suicidal complexes. As such, the ruthenium-oxo species is predicted to be a more robust catalyst than its iron-oxo analogue.     

Cycloaddition reactions of acrylonitrile on the Si(100)-2 x 1 surface

Multi-reference as well as single-reference quantum mechanical methods were adopted to study the potential energy surface along three possible surface reaction mechanisms of acrylonitrile on the Si(100)-2 x 1 surface. All three reactions occur via stepwise radical mechanisms. According to the computed potential energy surfaces, both [4+2] and [2+2](CN) cycloaddition products resulting from the reactions of surface dimers with the C[triple bond]N of acrylonitrile are expected, due to the negligible activation barriers at the surface. Another possible surface product, [2+2](CC), requires a 16.7 kcal/mol activation energy barrier. The large barrier makes this route much less favorable kinetically, even though this route produces the thermodynamically most stable products. Isomerization reactions among the surface products are very unlikely due to the predicted large activation barriers preventing thermal redistributions of the surface products. As a result, the distribution of the final surface products is kinetically controlled leading to a reinterpretation of recent experiments. An intermediate Lewis acid-base type complex appears in both the [4+2] and [2+2](CN) cycloadditions entrance channels, indicating that the surface may act as an electrophile/Lewis acid toward a strong Lewis base substrate.     

CuPd催化剂调节中间反应能垒提高电催化CO2生成二碳产物的选择性

过度的碳排放已造成了严重的全球环境问题,电催化CO2还原是一种利用间歇性过剩电能将CO2转化为有价值的化学物质的有效策略.在多种CO2还原产物中,二碳(C2)产物(如乙烯、乙醇)因其比一碳产物(如甲酸、甲烷、甲醇)具有更高的能量密度而备受关注.Cu是唯一能用电化学方法将CO2转化为多碳产物的单金属催化剂.如何提高Cu基催化剂上CO2还原为C2产物的效率已引起了极大关注.电催化还原CO2生成C2产物有两个重要步骤:一是参与碳碳偶联反应的CO*中间体的量(*代表中间体吸附在基底表面),二是碳碳偶联步骤的能垒.对于Cu单金属催化剂,虽然其表面碳碳偶联步骤的能垒相对较低,但是Cu对CO2的吸附能力和CO2*加氢能力并不高,导致在Cu表面不能生成足量的CO*中间体参与碳碳偶联反应,因而对C2产物的选择性和活性并不理想.与Cu单金属催化剂相反,在Pd单金属催化剂表面,CO*中间体的形成具有超快的反应动力学,但是CO*易在Pd表面中毒且后续碳碳偶联步骤的能垒极高,使其表面不能生成C2产物.为了充分发挥Cu(碳碳偶联步骤能垒较低)和Pd(CO*形成具有超快反应动力学)的双重优势,本文构建了一种紧密的CuPd(100)界面,以调节中间反应能垒,从而提高C2产率.密度泛函理论(DFT)计算表明,CuPd(100)界面增强了CO2的吸附,且降低了CO2*加氢步骤的能垒,从而能够催化生成更多的CO*中间体参与碳碳偶联反应.且CuPd(100)界面上CO2还原为C2产物的电位决定步骤能垒为0.61 eV,低于Cu(100)表面的(0.72 eV).本文采用了一种简便的湿化学法制备了CuPd(100)界面催化剂.X射线衍射和X射线光电子能谱测试以及扩展X射线吸收精细结构光谱结果表明,合成的是相分离的CuPd双金属催化剂,而非CuPd合金催化剂.同时高分辨透射电镜可以观察到清晰的CuPd(100)界面.由此可见,本文成功合成了CuPd(100)界面催化剂.程序升温脱附实验结果表明,CuPd(100)界面对CO2和CO*的吸附比Cu强,结果与理论预测一致.气体传感实验结果表明,CuPd(100)界面CO2*加氢能力比Cu强.为评估CuPd(100)界面催化剂的催化活性,进行了CO2电化学还原实验.结果表明,在0.1 mol/L的KHCO3电解液中,CuPd(100)界面催化剂在–1.4 VRHE下,C2产物的法拉第效率为50.3％ ±1.2％,是同电位下Cu催化剂的(23.6％ ±1.5％)的2.1倍,C2产物的选择性是Cu催化剂的2.4倍,且具有更高的电流密度和更大的电化学活性面积.本文通过调控中间反应能垒以合理设计铜基CO2还原电催化剂提供了参考.     

On the formation of phenyldiacetylene (C6H5CCCCH) and D5-phenyldiacetylene (C6D5CCCCH) studied under single collision conditions

The crossed molecular beam reactions of the phenyl and D5-phenyl radical with diacetylene (C(4)H(2)) was studied under single collision conditions at a collision energy of 46 kJ mol(-1). The chemical dynamics were found to be indirect and initiated by an addition of the phenyl/D5-phenyl radical with its radical center to the C1-carbon atom of the diacetylene reactant. This process involved an entrance barrier of 4 kJ mol(-1) and lead to a long lived, bound doublet radical intermediate. The latter emitted a hydrogen atom directly or after a few isomerization steps via tight exit transition states placed 20-21 kJ mol(-1) above the separated phenyldiacetylene (C(6)H(5)CCCCH) plus atomic hydrogen products. The overall reaction was determined to be exoergic by about 49 ± 26 kJ mol(-1) and 44 ± 10 kJ mol(-1) as determined experimentally and computationally, thus representing a feasible pathway to the formation of the phenyldiacetylene molecule in combustion flames of hydrocarbon fuel.     

Formation of a Criegee intermediate in the low-temperature oxidation of dimethyl sulfoxide

Dimethyl sulfoxide (DMSO) is the major sulfur-containing constituent of the Marine Boundary Layer. It is a significant source of H2SO4 aerosol/particles and methane sulfonic acid via atmospheric oxidation processes, where the mechanism is not established. In this study, several new, low-temperature pathways are revealed in the oxidation of DMSO using CBS-QB3 and G3MP2 multilevel and B3LYP hybrid density functional quantum chemical methods. Unlike analogous hydrocarbon peroxy radicals the chemically activated DMSO peroxy radical, [CH3S(=O)CH2OO*]*, predominantly undergoes simple dissociation to a methylsulfinyl radical CH3S*(=O) and a Criegee intermediate, CH2OO, with the barrier to dissociation 11.3 kcal mol(-1) below the energy of the CH3S(=O)CH2* + O2 reactants. The well depth for addition of O2 to the CH3S(=O)CH2 precursor radical is 29.6 kcal mol(-1) at the CBS-QB3 level of theory. We believe that this reaction may serve an important role in atmospheric photochemical and irradiated biological (oxygen-rich) media where formation of initial radicals is facilitated even at lower temperatures. The Criegee intermediate (carbonyl oxide, peroxymethylene) and sulfinyl radical can further decompose, resulting in additional chain branching. A second reaction channel important for oxidation processes includes formation (via intramolecular H atom transfer) and further decomposition of hydroperoxide methylsulfoxide radical, *CH2S(=O)CH2OOH over a low barrier of activation. The initial H-transfer reaction is similar and common in analogous hydrocarbon radical + O2 reactions; but the subsequent very low (3-6 kcal mol(-1)) barrier (14 kcal mol(-1) below the initial reagents) to beta-scission products is not common in HC systems. The low energy reaction of the hydroperoxide radical is a beta-scission elimination of *CH2S(=O)CH2OOH into the CH2=S=O + CH2O + *OH product set. This beta-scission barrier is low, because of the delocalization of the *CH2 radical center through the -S(=O) group, to the -CH2OOH fragment in the transition state structure. The hydroperoxide methylsulfoxide radical can also decompose via a second reaction channel of intramolecular OH migration, yielding formaldehyde and a sulfur-centered hydroxymethylsulfinyl radical HOCH2S*(=O). The barrier of activation relative to initial reagents is 4.2 kcal mol(-1). Heats of formation for DMSO, DMSO carbon-centered radical and Criegee intermediate are evaluated at 298 K as -35.97 +/- 0.05, 13.0 +/- 0.2 and 25.3 +/- 0.7 kcal mol(-1) respectively using isodesmic reaction analysis. The [CH3S*(=O) + CH2OO] product set is shown to form a van der Waals complex that results in O-atom transfer reaction and the formation of new products CH3SO2* radical and CH2O. Proper orientation of the Criegee intermediate and methylsulfinyl radical, as a pre-stabilized pre-reaction complex, assist the process. The DMSO radical reaction is also compared to that of acetonyl radical.     

PAH formation under single collision conditions: reaction of phenyl radical and 1,3-butadiene to form 1,4-dihydronaphthalene

The crossed beam reactions of the phenyl radical (C(6)H(5), X(2)A(1)) with 1,3-butadiene (C(4)H(6), X(1)A(g)) and D6-1,3-butadiene (C(4)D(6), X(1)A(g)) as well as of the D5-phenyl radical (C(6)D(5), X(2)A(1)) with 2,3-D2-1,3-butadiene and 1,1,4,4-D4-1,3-butadiene were carried out under single collision conditions at collision energies of about 55 kJ mol(-1). Experimentally, the bicyclic 1,4-dihydronaphthalene molecule was identified as a major product of this reaction (58 ± 15%) with the 1-phenyl-1,3-butadiene contributing 34 ± 10%. The reaction is initiated by a barrierless addition of the phenyl radical to the terminal carbon atom of the 1,3-butadiene (C1/C4) to form a bound intermediate; the latter underwent hydrogen elimination from the terminal CH(2) group of the 1,3-butadiene molecule leading to 1-phenyl-trans-1,3-butadiene through a submerged barrier. The dominant product, 1,4-dihydronaphthalene, is formed via an isomerization of the adduct by ring closure and emission of the hydrogen atom from the phenyl moiety at the bridging carbon atom through a tight exit transition state located about 31 kJ mol(-1) above the separated products. The hydrogen atom was found to leave the decomposing complex almost parallel to the total angular momentum vector and perpendicularly to the rotation plane of the decomposing intermediate. The defacto barrierless formation of the 1,4-dihydronaphthalene molecule involving a single collision between a phenyl radical and 1,3-butadiene represents an important step in the formation of polycyclic aromatic hydrocarbons (PAHs) and their partially hydrogenated counterparts in combustion and interstellar chemistry.     

Reaction of the i-C4H5 (CH2CCHCH2) radical with O2

The resonantly stabilized radical i-C(4)H(5) (CH(2)CCHCH(2)) is an important intermediate in the combustion of unsaturated hydrocarbons and is thought to be involved in the formation of polycyclic aromatic hydrocarbons through its reaction with acetylene (C(2)H(2)) to form benzene + H. This study uses quantum chemistry and statistical reaction rate theory to investigate the mechanism and kinetics of the i-C(4)H(5) + O(2) reaction as a function of temperature and pressure, and unlike most resonantly stabilized radicals we show that i-C(4)H(5) is consumed relatively rapidly by its reaction with molecular oxygen. O(2) addition occurs at the vinylic and allenic radical sites in i-C(4)H(5), with respective barriers of 0.9 and 4.9 kcal mol(-1). Addition to the allenic radical form produces an allenemethylperoxy radical adduct with only around 20 kcal mol(-1) excess vibrational energy. This adduct can isomerize to the ca. 14 kcal mol(-1) more stable 1,3-divinyl-2-peroxy radical via concerted and stepwise processes, both steps with barriers around 10 kcal mol(-1) below the entrance channel energy. Addition of O(2) to the vinylic radical site in i-C(4)H(5) directly forms the 1,3-divinyl-2-peroxy radical with a small barrier and around 36.8 kcal mol(-1) of excess energy. The 1,3-divinyl-2-peroxy radical isomerizes via ipso addition of the O(2) moiety followed by O atom insertion into the adjacent C-C bond. This process forms an unstable intermediate that ultimately dissociates to give the vinyl radical, formaldehyde, and CO. At higher temperatures formation of vinylacetylene + HO(2), the vinoxyl radical + ketene, and the 1,3-divinyl-2-oxyl radical + O paths have some importance. Because of the adiabatic transition states for O(2) addition, and significant reverse dissociation channels in the peroxy radical adducts, the i-C(4)H(5) + O(2) reaction proceeds to new products with rate constant of around 10(11) cm(3) mol(-1) s(-1) at typical combustion temperatures (1000-2000 K). For fuel-rich flames we show that the reaction of i-C(4)H(5) with O(2) is likely to be faster than that with C(2)H(2), bringing into question the importance of the i-C(4)H(5) + C(2)H(2) reaction in initiating ring formation in sooting flames.     

Photoinduced mechanism of formation and growth of polycyclic aromatic hydrocarbons in low-temperature environments via successive ethynyl radical additions

A novel ethynyl addition mechanism (EAM) has been established computationally as a practicable alternative to high-temperature hydrogen-abstraction-C2H2-addition (HACA) sequences to form polycyclic aromatic hydrocarbon (PAH) -like species under low-temperature conditions in the interstellar medium and in hydrocarbon-rich atmospheres of planets and their moons. Initiated by an addition of the ethynyl radical (C2H) to the ortho-carbon atom of the phenylacetylene (C6H5C2H) molecule, the reactive intermediate loses rapidly a hydrogen atom, forming 1,2-diethynylbenzene. The latter can react with a second ethynyl molecule via addition to a carbon atom of one of the ethynyl side chains. A consecutive ring closure of the intermediate leads to an ethynyl-substituted naphthalene core. Under single-collision conditions as present in the interstellar medium, this core loses a hydrogen atom to form ethynyl-substituted 1,2-didehydronaphthalene. However, under higher pressures as present, for example, in the atmosphere of Saturn's moon Titan, three-body reactions can lead to a stabilization of this naphthalene-core intermediate. We anticipate this mechanism to be of great importance to form PAH-like structures in the interstellar medium and also in hydrocarbon-rich, low-temperature atmospheres of planets and their moons such as Titan. If the final ethynyl addition to 1,2-diethynylbenzene is substituted by a barrierless addition of a cyano (CN) radical, this newly proposed mechanism can even lead to the formation of cyano-substituted naphthalene cores in the interstellar medium and in planetary atmospheres.     

Addition of one and two units of C2H to styrene: a theoretical study of the C10H9 and C12H9 systems and implications toward growth of polycyclic aromatic hydrocarbons at low temperatures

Various mechanisms of the formation of naphthalene and its substituted derivatives have been investigated by ab initio G3(MP2,CC)∕B3LYP∕6-311G?? calculations of potential energy surfaces for the reactions of one and two C(2)H additions to styrene combined with RRKM calculations of product branching ratios under single-collision conditions. The results show that for the C(2)H + styrene reaction, the dominant routes are H atom eliminations from the initial adducts; C(2)H addition to the vinyl side chain of styrene is predicted to produce trans or cis conformations of phenylvinylacetylene (t- and c-PVA), whereas C(2)H addition to the ortho carbon in the ring is expected to lead to the formation of o-ethynylstyrene. Although various reaction channels may lead to a second ring closure and the formation of naphthalene, they are not competitive with the direct H loss channels producing PVAs and ethynylstyrenes. However, c-PVA and o-ethynylstyrene may undergo a second addition of the ethynyl radical to ultimately produce substituted naphthalene derivatives. α- and β-additions of C(2)H to the side chain in c-PVA are calculated to form 2-ethynyl-naphthalene with branching ratios of about 30% and 96%, respectively; the major product in the case of α-addition would be cis-1-hexene-3,5-diynyl-benzene produced by an immediate H elimination from the initial adduct. C(2)H addition to the ethynyl side chain in o-ethynylstyrene is predicted to lead to the formation of 1-ethynyl-naphthalene as the dominant product. The C(2)H + styrene → t-PVA + H∕c-PVA + H∕ o-ethynylstyrene, C(2)H + c-PVA → 2-ethynyl-naphthalene + H, and C(2)H + o-ethynylstyrene → 1-ethynyl-naphthalene + H reactions are calculated to occur without a barrier and with high exothermicity, with all intermediates, transition states, and products lying significantly lower in energy than the initial reactants, and hence to be fast even at very low temperature conditions prevailing in Titan's atmosphere or in the interstellar medium. If styrene and C(2)H are available and overlap, the sequence of two C(2)H additions can result in the closure of a second aromatic ring and thus provide a viable route to the formation of 1- or 2-ethynyl-naphthalene. The analogous mechanism can be extrapolated to the low-temperature growth of polycyclic aromatic hydrocarbons (PAH) in general, as a step from a vinyl-PAH to an ethynyl-substituted PAH with an extra aromatic ring.     

Partial oxidation of 4-tert-butyltoluene catalyzed by homogeneous cobalt and cerium acetate catalysts in the Br-/H2O2/acetic acid system: insights into selectivity and mechanism

The partial oxidation of 4-tert-butyltoluene to 4-tert-butylbenzaldehyde by hydrogen peroxide in glacial acetic acid, catalyzed by bromide ions in combination with cobalt(II) acetate or cerium(III) acetate, has been studied in detail. Based on the observed differences in reaction rates and product distributions for the different catalysts, a reaction mechanism involving two independent pathways is proposed. After the initial formation of a benzylic radical species, either oxidation of this intermediate by the metal catalyst or reaction with bromine generated in situ occurs, depending on which catalyst is used. The first pathway leads to the exclusive formation of 4-tert-butylbenzaldehyde, whereas reaction of the radical intermediate with bromine leads to formation of the observed side products 4-tert-butylbenzyl bromide and its hydrolysis and solvolysis products 4-tert-butylbenzyl alcohol and 4-tert-butylbenzyl acetate, respectively. The cobalt(II) catalysts Co(OAc)(2) and Co(acac)(2) are able to quickly oxidize the radical intermediate, thereby largely preventing the bromination reaction (i.e., side-product formation) from occurring, and yield the aldehyde product with 75-80 % selectivity. In contrast, the cerium catalyst studied here exhibits an aldehyde selectivity of around 50 % due to the competing bromination reaction. Addition of extra hydrogen peroxide leads to an increased product yield of 72 % (cerium(III) acetate) or 58 % (cobalt(II) acetate). Product inhibition and the presence of increasing amounts of water in the reaction mixture do not play a role in the observed low incremental yields.     

A crossed beam and ab initio investigation on the formation of vinyl boron monoxide (C2H3BO; X1A') via reaction of boron monoxide (11BO; X2Σ+) with ethylene (C2H4; X1A(g))

The reaction dynamics of the boron monoxide radical ((11)BO; X(2)Σ(+)) with ethylene (C(2)H(4); X(1)A(g)) were investigated at a nominal collision energy of 12.2 kJ mol(-1) employing the crossed molecular beam technique and supported by ab initio and statistical (RRKM) calculations. The reaction is governed by indirect scattering dynamics with the boron monoxide radical attacking the carbon-carbon double bond of the ethylene molecule without entrance barrier with the boron atom. This addition leads to a doublet radical intermediate (O(11)BH(2)CCH(2)), which either undergoes unimolecular decomposition through hydrogen atom emission from the C1 atom via a tight transition state located about 13 kJ mol(-1) above the separated products or isomerizes via a hydrogen shift to the O(11)BHCCH(3) radical, which also can lose a hydrogen atom from the C1 atom. Both processes lead eventually to the formation of the vinyl boron monoxide molecule (C(2)H(3)BO; X(1)A'). The overall reaction was determined to be exoergic by about 40 kJ mol(-1). The reaction dynamics are also compared to the isoelectronic ethylene (C(2)H(4); X(1)A(g)) - cyano radical (CN; X(2)Σ(+)) system studied earlier.     

[Co(TPP)]-Catalyzed Formation of Substituted Piperidines

Radical cyclization via cobalt(III)-carbene radical intermediates is a powerful method for the synthesis of (hetero)cyclic structures. Building on the recently reported synthesis of five-membered N-heterocyclic pyrrolidines catalyzed by Co^II porphyrins, the [Co(TPP)]-catalyzed formation of useful six-membered N-heterocyclic piperidines directly from linear aldehydes is presented herein. The piperidines were obtained in overall high yields, with linear alkenes being formed as side products in small amounts. A DFT study was performed to gain a deeper mechanistic understanding of the cobalt(II)-porphyrin-catalyzed formation of pyrrolidines, piperidines, and linear alkenes. The calculations showed that the alkenes are unlikely to be formed through an expected 1,2-hydrogen-atom transfer to the carbene carbon. Instead, the calculations were consistent with a pathway involving benzyl-radical formation followed by radical-rebound ring closure to form the piperidines. Competitive 1,5-hydrogen-atom transfer from the β-position to the benzyl radical explained the formation of linear alkenes as side products.     

Hydrogen transfer in the formation and destruction of retrograde products in coal conversion

The conversion of coals to volatiles or liquids during pyrolysis and liquefaction is notoriously limited by the formation of retrograde products. Analysis of literature data for coals with grafted structures and for polymeric coal models demonstrates that the formation of volatile products from these materials does not correlate primarily with the weakness of the original bonding but correlates with the facility for retrogressive reaction. This analysis suggests further that simple recombination of resonance-stabilized radicals does not tend to yield true retrograde products, except in the case of aryloxy radicals. For pure hydrocarbon structural elements, radical addition to aromatic systems appears to be a key class of retrograde reactions, where the key factor is the kinetics of radical or H-atom loss from a cyclohexadienyl intermediate. We have used a mechanistic numerical model with a detailed set of radical reactions and thermochemically based kinetic parameters operating on a limited set of hydrocarbon structures to delineate important factors in mitigating retrograde processes. The modeling results show (1) how the "better" radical scavengers may reduce retrograde reaction at short reaction times but actually tend to increase it at longer times; (2) that the beneficial effects of H2 pressure at short reaction times are not primarily due to lowering of harmful radical concentrations by scavenging, nor to the maintenance of donor content; (3) that the benefit is due to the small population of free H-atoms thus produced, which are very active in causing increased scission of strong bonds; and (4) that under some conditions retrograde products are actually generated faster with added H2, but at longer reaction times and higher temperatures this temporary disadvantage of H2 is overcome by increased hydrogenolysis of those earlier-produced retrograde products. Thus, not only the cleavage of critical bonds in the original coal structures but also the net prevention of retrogression may be due to the H-transfer-induced cleavage of strong bonds.     

The possibility of the decomposition of 2'-deoxyribose moiety of thymidine induced by the low energy electron attachment

To evaluate the possibility of the decomposition of 2-deoxyribose moiety of thymidine induced by low energy electrons (LEE) attachment, the transition states and the energy barriers of the bond breaking processes of the ribose of the nucleoside have been studied theoretically by applying the density functional theory with the double zeta basis sets (DZP++). The energy barriers for the breakage of the C-C bonds (C(1')-C(2'), C(2')-C(3'), C(3')-C(4'), and C(4')-C(5')) of the ribose group of the radical anion of thymidine are found to be high (ca. 42-57 kcal/mol). The total energies of the C-C bond-broken products are significantly higher than that of the radical anion dT(*-). The decomposition of dT(*-) through the C-C bond rupture is unlikely to take place. The rupture of the C(1')-O(4') bond of dT(*-) needs an activation energy as low as 10.4 kcal/mol. However, the reversed reaction (C(1')-O(4') bond formation) needs the activation energy low as 0.3 kcal/mol. Therefore, the intermediate product LM1(C1')-(O4') is unlikely to be stable and the C(1')-O(4') bond-broken is not favored. The activation energy of the C(4')-O(4') bond rupture process amounts to 20.5 kcal/mol. The total energy of the C(4')-O(4') bond broken product is about 6.5 kcal/mol lower than that of the reactant dT(*-). The subsequent N1-glycosidic bond breaking process is found to have a very low energy barrier. Therefore, the LEE-induced base release through the C(4')-O(4') bond rupture might be a possible pathway.     

How Is Methane Formed and Oxidized Reversibly When Catalyzed by Ni‐Containing Methyl‐Coenzyme M Reductase?

Ni‐containing methyl‐coenzyme M reductase (MCR) is capable of catalyzing methane formation and has recently been observed to also be able to catalyze the reverse reaction, the anaerobic oxidation of methane. The forward reaction has been extensively studied theoretically before and was found to consist of two steps. The first step is rate‐limiting and the second step was therefore treated at a lower level. For an accurate treatment of the reverse reaction, both steps have to be studied at the same level. In the present paper, the mechanisms for the reversible formation and oxidation of methane catalyzed by MCR have been investigated using hybrid density functional theory with recent developments, in particular including dispersion effects. An active‐site model was constructed based on the X‐ray crystal structure. The calculations indicate that the MCR reaction is indeed reversible and proceeds via a methyl radical and a Ni‐S(CoM) intermediate with reasonable reaction barriers in both directions. In a competing mechanism, the formation of the crucial Ni‐methyl intermediate, was found to be strongly endergonic by over 20 kcal mol^?1 (including a barrier) with dispersion and entropy effects considered, and thus would not be reachable in a reasonable time under natural conditions.     

Density functional investigation on electron-transfer catalysis of cycloreversion of cyclobutane: radical anion mechanism

The mechanism of cycloreversion of cyclobutane radical anion (c-C(4)H(8) (-)) has been investigated at the UB3LYP/6-31++G(d,p) level, and compared with those of neutral c-C(4)H(8) and c-C(4)H(8) (+) radical cation. Although both c-C(4)H(8) (-) and C(2)H(4) are shown to be Rydberg states unstable with respect to electron ejection, the activation barrier for the "rotating" cycloreversion of c-C(4)H(8) (-) (37.3 kcal/mol) is lower by about 25.2 kcal/mol than that of c-C(4)H(8), and even the intervention of tetramethylene radical anion intermediate may reduce the activation barrier for the cycloreversion of c-C(4)H(8) by about 8.4 kcal/mol, mainly due to stronger electron-deficiency of intermediate biradical species than close-shell cyclobutanes. For the cycloreversion for c-C(4)H(8) (-), side isomerization reaction may be efficiently prevented by the low kinetic stability of tetramethylene radical anion intermediate towards dissociation, just different from the radical cation case. Our theoretical results have suggested the possibility of electron-attachment catalysis of the cycloreversion of some electron-deficient substituted cyclobutanes.     

In search of radical intermediates in the reactions catalyzed by lysine 2,3-aminomutase and lysine 5,6-aminomutase

High-level ab initio calculations have been used to study radical intermediates in the reactions catalyzed by lysine 2,3-aminomutase (2,3-LAM) and lysine 5,6-aminomutase (5,6-LAM). The reactions of these enzymes with the substrate analogues 4-oxalysine (4-OL), 4-thialysine (4-TL), or trans-4,5-dehydrolysine (t-4,5-DL) are rationalized in terms of stabilization provided by the substituent to the adjacent radical center. Large changes in the exothermicity accompanying the initial H-abstraction are observed relative to the lysine reference values that follow the series 4-OL < 4-TL < t-4,5-DL. These changes have the primary effect of increasing the endothermicity for subsequent ring-closure to form the putative aziridinylcarbinyl radical intermediate. Such stabilization is consistent with experimental observations of the substrate-derived radical (S*) in the reaction of 2,3-LAM with 4-TL as well as the ability of t-4,5-DL to act as an irreversible inhibitor of 2,3-LAM. Our calculations suggest that 4-TL and trans-3,4-dehydrolysine may also permit experimental characterization of S* radicals in the reactions catalyzed by 5,6-LAM. Strategies for modifying PLP are presented that might lead to the first observation of the aziridinylcarbinyl radical intermediate (I*) in the aminomutase-catalyzed reactions.     

Reactions of the OOH radical with guanine: Mechanisms of formation of 8-oxoguanine and other products

The mutagenic product 8-oxoguanine (8-oxoGua) is formed due to intermediacy of peroxyl (OOR) radicals in lipid peroxidation and protein oxidation-induced DNA damage. The mechanisms of these reactions are not yet understood properly. Therefore, in the present study, the mechanisms of formation of 8-oxoGua and other related products due to the reaction of the guanine base of DNA with the hydroperoxyl radical (OOH) were investigated theoretically employing the B3LYP and BHandHLYP hybrid functionals of density functional theory and the polarizable continuum model for solvation. It is found that the reaction of the OOH radical with guanine can occur following seven different mechanisms leading to the formation of various products including 8-oxoGua, its radicals, 5-hydroxy-8-oxoguanine and CO₂. The mechanism that yields 8-oxoGua as an intermediate and 5-hydroxy-8-oxoGua as the final product was found to be energetically most favorable.     

纤维素热解形成左旋葡聚糖机理的理论研究

采用密度泛函理论UB3LYP/6-31G(d)方法,对模型化合物纤维二糖热解反应机理进行了量子化学理论计算研究。设计了三种可能的热解反应途径,对各种反应的反应物、产物、中间体和过渡态的结构进行了能量梯度全优化,计算了不同温度下热解反应的标准热力学和动力学参数。计算结果表明,糖苷键均裂而形成两个自由基中间体IM₁a和IM₁b,吸收热量为321.26kJ/mol,中间体IM₁a经过渡态TS₁a进一步形成左旋葡聚糖P₁,反应势垒为202.72kJ/mol;与分步反应相比,纤维二糖经过渡态TS₂协同反应直接形成左旋葡聚糖P₁和吡喃葡萄糖P₂的反应势垒低于分步反应的总势垒,其反应势垒为377.54kJ/mol;H⁺的加入有利于糖苷键的断裂,断裂形成的中间体IM₃很难进一步反应形成左旋葡聚糖。     

Novel pathways for oxygen insertion into unactivated C-H bonds by dioxiranes. Transition structures for stepwise routes via radical pairs and comparison with the concerted pathway

The oxygen insertion into C-H bonds (of methane, isobutane, and acetone) by dioxiranes (parent dioxirane and dimethyldioxirane) to give alcohols was studied with the DFT theory, using both restricted and unrestricted B3LYP methods, and 6-31G(d) and 6-311+G(d,p) basis sets to evaluate the feasibility of stepwise mechanisms and their competition with the concerted counterpart. Confirming previous results by other authors, we have located, with the RB3LYP method, concerted TSs in which the oxygen bound to be inserted interacts very strongly with the hydrogen atom and very weakly with the carbon atom of the C-H bond. These TSs nicely explain all the experimental observations (e.g., configuration retention at the chiral centers), but all of them exhibit an RHF --> UHF wave function instability that preclude considering them as genuine transition structures. We also were able to characterize, with UB3LYP methods, two alternative two-step processes that can lead to final products (alcohol + carbonyl compound) via singlet radical pair intermediates. For the first step of both processes we located genuine diradicaloid TSs, namely, TSs rad,coll and TSs rad,perp, that have stable wave functions. In TSs rad,coll the alkane C-H bond tends to be collinear with the breaking O(1)- - -O(2) bond while in TSs rad,perp the alkane C-H bond is almost perpendicular to the O(1)- - -O(2) bond. The first step, of both processes, can represent an example of a "molecule induced homolysis" reaction: collision between alkane and dioxirane brings about the homolytic cleavage of the dioxirane O-O bond and the hydrogen abstraction follows afterward to produce the diradicaloid TS that then falls down to a singlet radical pair. This hypothesis was fully confirmed by IRC analysis in the case of TSs rad,coll. The possible pathways that lead from the intermediate radical pair to final products are discussed as well as the hypothesis that the radical collinear TSs may collapse directly to products in a "one-step nonconcerted" process. However, diradical mechanisms cannot explain the experimental data as satisfactorily as the concerted pathway does. As for computational predictions about competition of diradical vs concerted mechanisms, they strongly depend (i) on the alkane C-H type, (ii) on whether gas phase or solution is considered, and (iii) on the basis set used for calculations. In short, the concerted TS benefits, with respect to the corresponding diradicaloid TSs, of alkyl substitution at the C-H center, solvation effects, and basis set extension. Actually, in the case of DMD reactions with methane and acetone, the diradicaloid TSs are always (both in gas phase and in solution and with both the basis sets used) strongly favored over their concerted counterpart. In the case of DMD reaction with isobutane tertiary C-H bond the large favor for the diradicaloid TSs over the concerted TS, predicted in gas phase by the B3LYP/6-31G(d) method, progressively decreases as a result of basis set extension and introduction of solvent effects: the higher theory level [B3LYP/6-311+G(d,p)] suggests that in acetone solution TS conc has almost the same energy as TS rad,perp while TS rad,coll resides only 2 kcal/mol higher.