Model studies of DNA C5' radicals. Selective generation and reactivity of 2'-deoxyadenosin-5'-yl radical

The reaction of hydrated electrons (e(aq)(-)) with 8-bromo-2'-deoxyadenosine has been investigated by radiolytic methods coupled with product studies and addressed computationally by means of DFT-B3LYP calculations. Pulse radiolysis revealed that this reaction was complete in approximately 0.3 mus, and, at this time, no significant absorption was detected. The spectrum of a transient developed in 20 mus has an absorbance in the range 300-500 nm (epsilon(max) congruent with 9600 M(-1) cm(-1) at 360 nm), and it was assigned to aromatic aminyl radical 3. Computed vertical transitions (TD-UB3LYP/6-311+G) are in good agreement with the experimental observations. Radical 3 is obtained by the following reaction sequence: one-electron reductive cleavage of the C-Br bond that gives the C8 radical, a fast radical translocation from the C8 to C5' position, and an intramolecular attack of the C5' radical at the C8,N7 double bond of the adenine moiety. The rate constant for the cyclization is 1.6 x 10(5) s(-1). On the basis of the theoretical findings, the cyclization step is highly stereospecific. The rate constants for the reactions of C5' and aminyl 3 radicals with different oxidants were determined by pulse radiolysis methods. The respective rate constants for the reaction of 2'-deoxyadenosin-5'-yl radical with dioxygen, Fe(CN)(6)(3)(-), and MV(2+) in water at ambient temperature are 1.9 x 10(9), 4.2 x 10(9), and 2.2 x 10(8) M(-1) s(-1). The value for the reaction of aminyl radical 3 with Fe(CN)(6)(3-) is 8.3 x 10(8) M(-1) s(-1), whereas the reaction with dioxygen is reversible. Tailored experiments allowed the reaction mechanism to be defined in some detail. A synthetically useful radical cascade process has also been developed that allows in a one-pot procedure the conversion of 8-bromo-2'-deoxyadenosine to 5',8-cyclo-2'-deoxyadenosine in a diastereoisomeric ratio (5'R):(5'S) = 6:1 and in high yield, by reaction with hydrated electrons in the presence of K(4)Fe(CN)(6).     

Gaseous reaction mechanism of C2F radical with water

The kinetic properties of the carbon-fluorine radicals are little understood except those of CFn (n =1-3). In this article, a detailed mechanistic study was reported on the gas-phase reaction between the simplest pi-bonded C2F radical and water as the first attempt to understand the chemical reactivity of the C2F radical. Various reaction channels are considered. The most kinetically competitive channel is the quasi-direct hydrogen-abstraction route forming P5 HCCF + OH. At the CCSD(T)/6-311+G(2d,2p)//B3LYP/6-311G(d,p)+ZPVE, CCSD(T)/6-311+G(3df,2p)//QCISD/6-311G(d,p)+ZPVE and Gaussian-3//B3LYP/6-31G(d) levels, the overall H-abstraction barriers (4.5, 4.7, and 4.2 kcal/mol) for the C2F + H2O reaction are comparable to the corresponding values (5.5, 3.7, and 5.7 kcal/mol) for the analogous C2H + H2O reaction. This suggests that C2F is a reactive radical like the extensively studied C2H, in contrast to the situation of the CF and CF2 radicals that have much lower reactivity than the corresponding hydrocarbon species. Thus, the C2F radical is expected to play an important role in the combustion processes of the carbon-fluorine chemistry. Furthermore, addition of a second H2O can catalyze the reaction with the H-abstraction barrier significantly reduced to a marginally zero value (0.5 kcal/mol). This is also indicative of the potential relevance of the title reactions in the low-temperature atmospheric chemistry.     

自由基环化制备β-内酰胺的理论研究

使用密度泛函方法在UB3LYP/6-311＋＋G(3df, 2p)水平上对自由基环化合成β-内酰胺的四种反应途径进行理论研究. 结合Marcus理论对影响反应的热力学及动力学因素进行分析, 发现氨基甲酰基自由基4-exo环合反应是理想的动力学控制过程; 酰胺自由基的4-exo环合反应与5-endo环合反应相比是动力学有利的转化过程; 单取代的酰胺烷基自由基的4-exo环合反应是一类动力学和热力学都较为不利的反应; 羰基自由基加成亚胺N＝C双键的4-exo环合反应与5-endo环合反应相比动力学不利而热力学有利.     

Radicals masquerading as electrophiles: a computational study of the intramolecular addition reactions of acyl radicals to imines

Ab initio calculations using 6-311G**, cc-pVDZ, and aug-cc-pVDZ, with (MP2, QCISD, CCSD(T)) and without (UHF) electron correlation, and density functional methods (BHandHLYP and B3LYP) predict that cyclization of the 5-aza-5-hexenoyl and (E)-6-aza-5-hexenoyl radicals proceed to afford the 5-exo products. At the CCSD(T)/cc-pVDZ//BHandHLYP/cc-pVDZ level of theory, energy barriers (deltaE(double dagger)) of 36.1 and 47.0 kJ mol(-1) were calculated for the 5-exo and 6-endo pathways for the cyclization of the 5-aza-5-hexenoyl radical. On the other hand, at the same level of theory, deltaE(double dagger) of 38.9 and 45.4 kJ mol(-1) were obtained for the 5-exo and 6-endo cyclization modes of (E)-6-aza-5-hexenoyl radical, with exothermicities of about 27 and 110 kJ mol(-1) calculated for the exo and endo modes, respectively. Under suitable experimental conditions, the 6-endo cyclization product is likely to dominate. Analysis of the molecular orbitals involved in these ring-closure reactions indicate that both reactions at nitrogen are assisted by dual orbital interactions involving simultaneous SOMO-pi* and LP-pi* overlap in the transitions states. Interestingly, the (Z)-6-aza-5-hexenoyl radical, that cannot benefit from these dual orbital effects is predicted to ring-close exclusively in the 5-exo fashion.     

SiH2自由基与HNCO反应机理的理论研究

采用密度泛函理论B3LYP方法研究了SiH₂自由基与HNCO的反应机理, 并在B3LYP/6-311＋＋G**水平上对反应物、中间体、过渡态进行了全几何参数优化, 通过频率分析和内禀反应坐标(IRC)确定了中间体和过渡态. 为了得到更精确的能量值, 又用QCISD(T)/6-311＋＋G**方法计算了在B3LYP/6-311＋＋G**水平优化后的各个驻点的相对能量. 计算结果表明SiH₂自由基与HNCO的反应有五条反应通道, 其中顺式反应通道SiH₂＋HNCO→IM3→ TS4→IM5→TS5→IM6→SiH₂NH＋CO反应能垒最低, 为主反应通道.     

FC(O)O自由基与NO2反应的量子化学研究

用量子化学DFT, MP2, G3和G3MP2方法对FC(O)O自由基与NO₂的反应机理进行了理论研究. 优化了反应势能面上各驻点的几何结构, 通过内禀反应坐标(IRC)计算和振动分析, 确认了反应中的过渡态, 并用过渡态理论(TST)计算了相关反应的速率常数.     

Transition states for deactivation reactions in the modeled 2,2,6,6‐tetramethyl‐1‐piperidinyloxy‐mediated free‐radical polymerization of acrylonitrile

The geometries and energetics of transition states (TS) for radical deactivation reactions, including competitive combination and disproportionation reactions, have been studied for the modeled 2,2,6,6‐tetramethyl‐1‐piperidinyloxy (TEMPO)‐mediated free‐radical polymerization of acrylonitrile with quantum mechanical calculations at the DFT/UB3‐LYP/6‐311+G(3df,2p)//(U)AM1 level of theory (where DFT is density functional theory, AM1 is Austin model 1, and UAM1 is unrestricted Austin model 1). A method providing reasonable starting geometries for an effective search for TS between the TEMPO radical and 1‐cyanopropyl radical mimicking the growing polyacrylonitrile macroradical is shown. For the hydrogen atom abstraction reaction by the TEMPO radical from the 1‐cyanopropyl radical, practically one TS has been found, whereas for the combination reaction of the radicals, several TS have been found, mainly differing in out‐of‐plane angle α of the N? O bond in the TEMPO structure. α in the TS is correlated with the activation energy, ΔE, determined from the single‐point calculation at the DFT UB3‐LYP/6‐311+G(3df, 2p)//UAM1 level for the combination reaction of CH₃AN· with the TEMPO radical. The theoretical activation energy for the coupling reaction from DFT UB3‐LYP/6‐311+G(3df, 2p)//UAM1 calculations has been estimated to be 11.6 kcal mol^?1, that is, only about 4.5 times smaller than ΔE for the disproportionation reaction obtained with the DFT UB3‐LYP/6‐311+G(3df, 2p)//(U)AM1 approach. © 2005 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 44: 914–927, 2006     

Reactions of o-benzyne with propargyl and benzyl radicals: potential sources of polycyclic aromatic hydrocarbons in combustion

The kinetics and mechanisms of the reactions of o-benzyne with propargyl and benzyl radicals have been investigated computationally. The possible reaction pathways have been explored by quantum chemical calculations at the M06-2X/6-311+G(3df,2p)//B3LYP/6-311G(d,p) level and the mechanisms have been investigated by the Rice-Ramsperger-Kassel-Marcus theory/master-equation calculations. It was found that the o-benzyne associates with the propargyl and benzyl radicals without pronounced barriers and the activated adducts easily isomerize to five-membered ring species. Indenyl radical and fluorene + H were predicted to be dominantly produced by the reactions of o-benzyne with propargyl and benzyl radicals, respectively, with the rate constants close to the high-pressure limits at temperatures below 2000 K. The related reactions on the two potential energy surfaces, namely, the reaction between fulvenallenyl radical and acetylene and the decomposition reactions of indenyl and α-phenylbenzyl radicals were also investigated. The high reactivity of o-benzyne toward the resonance stabilized radicals suggested a potential role of o-benzyne as a precursor of polycyclic aromatic hydrocarbons in combustion.     

Theoretical elucidation of kinetic and thermodynamic control of radical addition regioselectivity

The cyclizations of two structurally similar 2-oxo-5-hexenyl-type radicals have been investigated by ab initio and density functional (UB3LYP/6-31+G**//UHF/6-31G* and UB3LYP/6-31G*//UB3LYP/6-31G*) calculations. The origin of apparently contradictory reports of 6-endo and 5-exo cyclizations is determined. Kinetic control favors 6-endo cyclization, while thermodynamic control gives 5-exo cyclization, and the observation of different products from different research groups arises from the difference in experimental conditions used by the two groups. The outcome of a new cyclization reaction was predicted by using these theoretical techniques. Kinetic control is predicted to yield exclusively the products of 6-endo cyclization, while thermodynamic control would lead to an approximately equal mixture of one 6-endo and one 5-exo cyclized product. Experimental studies revealed that the reaction yields only the products of 6-endo cyclization through kinetic control.     

Cyanomethylidyne: a reactive carbyne radical.

The cyanomethylidyne radical (CCN) has been a long-standing subject of extensive structural and spectroscopic studies. However, its chemical reactivity has received rather little attention. Recently, we studied the reaction of CCN with the simplest alkane, CH4, which follows a mechanism of carbyne insertion-dissociation rather than that of direct H abstraction proposed by a recent experimental study. However, we are aware that alkanes like CH4 bear no electron lone pairs and thus are not ideal diagnostic molecules for distinguishing between the carbyne-insertion and H-abstraction mechanisms. Hence, we chose a series of sigma-bonded molecules HX (X=OH, NH2, and F) which bear electron lone pairs and are better diagnostics for carbyne-insertion behavior. The new results at the CCSD(T)/6-311+G(2df,p)//B3LYP/6-311G(d,p)+ZPVE, CCSD(T)/aug-cc-pVTZ//B3LYP/6-311G(d,p)+ZPVE, G2M(CC1), and MC-QCISD//B3LYP/6-31G(d)+ZPVE levels definitively confirm the carbyne-insertion behavior of the CCN radical towards HX. In addition, we make the first attempt to understand the reactivity of the CCN radical toward pi-bonded molecules, using the CCN+C2H2 model reaction. This reaction involves carbenoid addition to the C[triple chemical bond]C bond without a potential-energy barrier to form a C3 three-membered cyclic intermediate followed by H extrusion. Therefore, the reactions of CCN with both sigma- and pi-bonded molecules conclusively show that CCN is a reactive carbyne radical and may be more reactive than the well-known CN radical. Future experimental studies, especially on product characterization, are strongly desired to test our proposed carbyne mechanism. The studied reactions of CCN with CH4, NH3, H2O, and C2H2 could be of interest to combustion science and astrophysics, and they could provide efficient routes to form novel cyano-containing molecules in interstellar space.     

Myers–Saito and Schmittel cyclizations of enyne-(hetero)-1,2,3-trienes: A DFT study on the structure–reactivity relationship

The Myers–Saito (C²–C⁷) cyclization and the alternative Schmittel (C²–C⁶) cyclization of enyne-1,2,3-triene 1R and its hetero analogues 2R–5R were investigated by using pure density functional theory method (BPW91) in connection with the 6-311G(d, p) basis set. It has been shown that heteroatom-containing reactants lower significantly reaction barriers for both cyclization modes and reduce the difference between the barrier of the C²–C⁷ cyclization mode and that of the C²–C⁶ one. The Myers–Saito cyclization of 4R is associated with the smallest reaction barrier and the highest exothermicity. Whereas the Schmittel cyclization of 4R is exothermic, all the others are predicted to be endothermic.     

Theoretical study of electroreductive intramolecular coupling of nonconjugated olefinic and aromatic ketones

The electroreductive cyclization of hept-6-en-2-one, octa-7-en-2-one, and 5-phenylpentan-2-one was investigated by ab initio (UHF/6-311++G**) and density functional (UB3LYP/6-311++G**) calculation methods. The high regio- and stereoselectivities previously reported for olefinic ketones (exo-trans) and 5-arylpentan-2-ones (endo-trans) were reconfirmed. These experimental results well agree with the computational outcome for the transition states in the intramolecular coupling of ketyl radicals generated by one-electron transfer to the ketones.     

Ab initio and density functional calculations on the pericyclic vs pseudopericyclic mode of conjugated nitrile ylide 1, 5-electrocyclizations

Ab initio (MP2/6-311+G and MP4(SDTQ)/6-311+G//MP2/6-311+G) and density functional (B3LYP/6-311+G) calculations on the ring closure reactions of conjugated nitrile ylides 1a-e, 3, and 6 to the corresponding oxazoles 2a, 5, 7, and 8; thiazoles 2b and 4; imidazole 2c; and pyrroles 2d and 2e, respectively, are reported. Vinyl nitrile ylides 1d and 1e cyclize with a substantially higher barrier than nitrile ylides containing a heteroatom. Geometric features as well as electronic structures as obtained by NBO analysis are indicative of a pericyclic, monorotatory 1, 5-electrocyclization of 1d and 1e. For nitrile ylides where X = heteroatom, a pseudopericyclic heteroelectrocyclization pathway, characterized by in-plane attack of the heteroatom's lone pair at the nitrile ylide group, is found. For 3 and 6, where two different cyclization products are possible, the calculated barriers and reaction energies are in line with the experimentally observed direction of reaction. Vinyl nitrile ylides 1d and 1e are characterized by an allene, acyl substituted derivatives 1a, 1b, 3, and 6 by a propargyl type structure. The nitrogen derivative 1c represents an intermediate case.     

A density functional theory study on the reaction mechanism of hydrazones with α-oxo-ketenes: Comparison between stepwise 1,3-dipolar cycloaddition and Diels–Alder pathways

Density functional theory calculations have been performed at the B3LYP/6-311+G(d,p) and M06-2X/6-31G(d,p) levels to obtain an insight into the nature of the stepwise cycloaddition reactions of hydrazones with α-oxo-ketenes. Three reaction pathways are possible, two Diels–Alder reactions and a 1,3-dipolar cycloaddition (1,3-DC) reaction. Despite the high energy required for 1,2-hydrogen shift in hydrazone to form an azomethine imine, 1,3-DC reaction among the possible pathways is the most favorable. The mechanism has been explained on the basis of transition state stabilities, global and local reactivity indices of the reactants, intrinsic reaction coordinate calculation, and the electron localization function topological analysis of the bonding changes along the 1,3-DC reaction. The computed free energies and enthalpies agree with the experimental outcome.     

锗烯与异硫氰酸反应机理的量子化学研究

采用密度泛函理论B3LYP方法研究了GeH2自由基与HNCS的反应机理,并在B3LYP/6-311++G**水平上对反应物,中间体,过渡态进行了全几何参数优化,通过频率分析和IRC确定中间体和过渡态。为了得到更精确的能量值,用QCISD(T)/6-311++G**方法计算了各个驻点的单点能,计算结果表明单重态的锗烯与异硫氰酸的反应有抽提硫、插入N-H键、抽提亚氨基的路径,而经由三元环中间体的抽提硫反应GeH2+HNCS→IM3→TS2→IM4→TS3→IM5→GeH2S+HNC(P1),反应能垒最低,为主反应通道,甲锗硫醛和异氰氢酸为主产物。锗烯经由四元环中间体抽提硫的反应为竞争反应通道。     

Mechanism and Kinetics of the Reaction of Nitrosamines with OH Radical: A Theoretical Study

The reaction of nitrosodimethylamine, nitrosoazetidine, nitrosopyrrolidine, and nitrosopiperidine with the hydroxyl radical has been studied using electronic structure calculations in gas and aqueous phases. The rate constant was calculated using variational transition state theory. The reactions are initiated by H‐atom abstraction from the αC─H group of nitrosamines and leads to the formation of alkyl radical intermediate. In the subsequent reactions, the initially formed alkyl radical intermediate reacts with O₂ forming a peroxy radical. The reaction of peroxy radical with other atmospheric oxidants, such as HO₂ and NO radicals, is studied. The structures of the reactive species were optimized by using the density functional theory methods, such as M06‐2X, MPW1K, and BHandHLYP, and hybrid methods G3B3. The single‐point energy calculations were also performed at CCSD(T)/6‐311+G(d,p)// M062X/6‐311+G(d,p) level. The calculated thermodynamical parameters show that the reactions corresponding to the formation of intermediates and products are highly exothermic. We have calculated the rate constant for the initial H‐atom abstraction and subsequent favorable secondary reactions using canonical variational transition state theory over the temperature range of 150–400 K. The calculated rate constant for initial H‐atom abstraction reaction is ∼3 × 10⁻¹² cm³ molecule⁻¹ s⁻¹ and is in agreement with the previous experimental results. The calculated thermochemical data and rate constants show that the reaction profile and kinetics of the reactions are less dependent on the number of methyl groups present in the nitrosoamines. Furthermore, it has been found that the atmospheric lifetime of nitrosamines is around 5 days in the normal atmospheric OH concentration.     

Thermochemical and kinetic analyses on oxidation of isobutenyl radical and 2-hydroperoxymethyl-2-propenyl radical

In recognition of the importance of the isobutene oxidation reaction in the preignition chemistry associated with engine knock, the thermochemistry, chemical reaction pathways, and reaction kinetics of the isobutenyl radical oxidation at low to intermediate temperature range were computationally studied, focusing on both the first and the second O2 addition to the isobutenyl radical. The geometries of reactants, important intermediates, transition states, and products in the isobutenyl radical oxidation system were optimized at the B3LYP/6-311G(d,p) and MP2(full)/6-31G(d) levels, and the thermochemical properties were determined on the basis of ab initio, density functional theory, and statistical mechanics. Enthalpies of formation for several important intermediates were calculated using isodesmic reactions at the DFT and the CBS-QB3 levels. The kinetic analysis of the first O2 addition to the isobutenyl radical was performed using enthalpies at the CBS-QB3 and G3(MP2) levels. The reaction forms a chemically activated isobutenyl peroxy adduct which can be stabilized, dissociate back to reactants, cyclize to cyclic peroxide-alkyl radicals, and isomerize to the 2-hydroperoxymethyl-2-propenyl radical that further undergoes another O2 addition. The reaction channels for isomerization and cyclization and further dissociation on this second O2 addition were analyzed using enthalpies at the DFT level with energy corrections based on similar reaction channels for the first O2 addition. The high-pressure limit rate constants for each reaction channel were determined as functions of temperature by the canonical transition state theory for further kinetic model development.     

AIM Study on the Reaction of CH2SH Radical with Fluorine Atom

The reaction of CH2SH radical with fluorine atom was studied at the levels of B3LYP/6-311G(d,p) and MP2(Full)/6-311G(d,p). The computational results show that the reaction has three channels and proceeds by the addition of fluorine atoms on carbon or sulfur sites of CH2SH, forming initial intermediates. The calculated results show that the channel in which fluorine attaches to the carbon atom to form CH2S and HF, is the most likely reaction pathway. Topological analysis of electron density was carried out for the three channels. The change trends of the chemical bonds on the reaction paths were discussed. The energy transition states and the structure transition regions (states) of the three channels were found. The calculated results show that the structure transition regions are broad in unobvious exothermic reactions or unobvious endothermic reactions, and are narrow in obvious exothermic reactions or obvious endothermic reactions.     

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

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

*H atom and *OH radical reactions with 5-methylcytosine

The reactions between either a hydrogen atom or a hydroxyl radical and 5-methylcytosine (5-MeCyt) are studied by using the hybrid kinetic energy meta-GGA functional MPW1B95. *H atom and *OH radical addition to positions C5 and C6 of 5-MeCyt, or *OH radical induced H-abstraction from the C5 methyl group, are explored. All systems are optimized in bulk solvent. The data presented show that the barriers to reaction are very low: ca. 7 kcal/mol for the *H atom additions and 1 kcal/mol for the reactions involving the *OH radical. Thermodynamically, the two C6 radical adducts and the *H-abstraction product are the most stable ones. The proton hyperfine coupling constants (HFCC), computed at the IEFPCM/MPW1B95/6-311++G(2d,2p) level, agree well with B3LYP results and available experimental and theoretical data on related thymine and cytosine radicals.