A Reevaluation of the Ambident Reactivity of the Guanine Moiety Towards Hydroxyl Radicals

Radically different : Contrary to previous proposals, the main reaction of the HO^. radical with guanosine or 2′‐deoxyguanosine is the hydrogen abstraction from the NH₂ moiety to give a guanyl radical. This radical, characterized by a broad band in the visible region (around 610 nm), undergoes tautomerization to the most stable isomer.

     

自由基-氟代烯烃加成反应活性的理论研究

利用AMI半经验量化方法对一系列自由基-氟取代烯烃加成反应进行了计算，并用软硬酸碱规则的理论基础-广义微扰理论对计算结果进行了处理．发现该类烯烃与自由基加成的反应活性（以活化能来表示）可由该理论得到很好的解释、同时发现影响反应活性的主要因素是路易斯酸碱对之间的共价作用，而静电作用的影响则非常小。另外还发现，对于本文讨论的烯烃分子，两不饱和碳原子间存在有强的相互作用．     

羟基自由基引发的邻二甲苯大气氧化机理

采用量子化学、过渡态理论和单分子反应理论计算,研究了由羟基(OH)自由基引发的邻二甲苯(oX)大气氧化降解机理.在M06-2X/6-311++G(2df, 2p)水平上优化了反应物、过渡态和产物的结构,在ROCBSQB3水平上计算了反应势能面.采用过渡态理论计算了各个可能反应步骤的速率常数和反应通道的分支比,同时还采用单分子反应理论(RRKM-ME)计算探讨了反应的压力效应.计算发现,在大气中,邻二甲苯与OH的反应以苯环加成为主,首先形成两个加和物oX-1-OH (R1)和oX-3-OH (R3),它们随后与大气中的氧气发生反应.R1和R3与O₂可直接发生不可逆直接夺氢生成二甲基苯酚,或和O₂的可逆加成,生成双环自由基中间体.双环自由基将与大气中的氧气结合,形成双环过氧自由基,接着与NO或HO₂反应生成有机硝酸酯或有机过氧化氢化合物,或被还原为双环烷氧自由基,并最终生成产物,包括丁二酮、丁烯二醛、甲基乙二醛、4-氧-2-戊烯醛、2, 3-环氧丁二醛以及少量的乙二醛.这些产物中有机过氧化氢和甲基乙二醛被认为对二次气溶胶有较大的贡献.结合理论计算和文献报道的实验结果,提出了新的oX大气氧化机理,预测了在高NO浓度条件下可能产物的分支比,并与文献报道结果相比较.最后还讨论了温度对反应机理的影响.     

Correlation between the Structure of Thioureas and Their Reactivity toward Hydroperoxides and Peroxy Radicals

The behavior of thiourea derivatives in reactions simulating oxidative processes in carbon-chain polymers was studied. Based on the kinetic data obtained (reaction rate constants), correlations were revealed between the structures of thioureas and their reactivity in inhibition of oxidation of organic substrates.     

A Mass Spectrometric Approach for Probing the Stability of Bioorganic Radicals

Glycyl radicals are important bioorganic radical species involved in enzymatic catalysis. Herein, we demonstrate that the stability of glycyl‐type radicals (X‐^.CH‐Y) can be tuned on a molecular level by varying the X and Y substituents and experimentally probed by mass spectrometry. This approach is based on the gas‐phase dissociation of cysteine sulfinyl radical (X‐Cys‐Y) ions through homolysis of a C_α? C_β bond. This fragmentation produces a glycyl‐type radical upon losing CH₂SO, and the degree of this loss is closely tied to the stability of the as‐formed radical. Theoretical calculations indicate that the energy of the C_α? C_β bond homolysis is predominantly affected by the stability of the glycyl radical product through the captodative effect, rather than that of the parent sulfinyl radical. This finding suggests a novel experimental method to probe the stability of bioorganic radicals, which can potentially broaden our understanding of these important reactive intermediates.     

Substituent Effects on Photosensitized Splitting of Thymine Cyclobutane Dimer by an Attached Indole

In chromophore‐containing cyclobutane pyrimidine dimer (CPD) model systems, solvent effects on the splitting efficiency may depend on the length of the linker, the molecular conformation, and the oxidation potential of the donor. To further explore the relationship between chromophore structure and splitting efficiency, we prepared a series of substituted indole–T<>T model compounds 2 a – 2 g and measured their splitting quantum yields in various solvents. Two reverse solvent effects were observed: an increase in splitting efficiency in solvents of lower polarity for models 2 a – 2 d with an electron‐donating group (EDG), and vice versa for models 2 e – 2 g with an electron‐withdrawing group (EWG). According to the Hammett equation, the negative value of the slope of the Hammett plot indicates that the indole moiety during the T<>T‐splitting reaction loses negative charge, and the larger negative value implies that the repair reaction is more sensitive to substituent effects in low‐polarity solvents. The EDGs of the models 2 a – 2 d can delocalize the charge‐separated state, and low‐polarity solvents make it more stable, which leads to higher splitting efficiency in low‐polarity solvents. Conversely, the EWGs of models 2 e – 2 g favor destabilization of the charge‐separated state, and high‐polarity solvents decrease the destabilization and hence lead to more efficient splitting in high‐polarity solvents.     

Electron attachment to the DNA bases adenine and guanine and dehydrogenation of their anionic derivatives: Density functional study

Density functional theory (DFT) calculations have been used to explore electron attachment to the purines adenine and guanine and their hydrogen atom loss. Calculations show that the dehydrogenation at the N9 site in the adenine and guanine transient anions is the lowest‐cost channel of hydrogen loss, and the N9? H bond scission has Gibbs free energies of dissociation ΔG° of 8.8 kcal mol^?1 for the anionic adenine and 13.9 kcal mol^?1 for the anionic guanine. The relatively high feasibility of low‐energy electron (LEE)‐induced N9? H bond cleavage in the purine nucleobases arises from high electron affinities of their H‐deleted counterparts. Unlike adenine, other N? H bond dissociations are competitive with the N9? H bond fission in the anionic guanine. The replacement of hydrogen in the ring of purine has a significant effect on the N9? H bond fragmentation. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007     

流动注射-化学发光法测定水果提取物对羟自由基的清除率

建立了Fe2+-H2O2-亚甲基蓝化学发光体系用于水果对羟自由基清除率的测定。实验发现,在酸性介质中,Fe2+和H2O2在线生成的羟自由基(.OH)与亚甲基蓝反应能产生较强的化学发光,加入水果水提取物可以清除部分羟自由基,使化学发光强度降低。据此,结合流动注射技术,建立了测定水果水提取物对.OH清除率的化学发光新方法。将该方法应用于9种水果水提取物对.OH清除能力的研究,结果满意。     

Theoretical Studies on the Reactions of 1,1,2,2,3,3,4‐Heptafluorocyclopentane with Hydroxyl and Hydrogen Free Radicals

1,1,2,2,3,3,4‐Heptafluorocyclopentane (F7A) has considerable potential to be a new halon replacement due to its environmental friendliness and low‐toxicity. However, the reaction processes of F7A with hydroxyl and hydrogen free radicals, which are of great importance for investigating its fire suppression mechanisms, are still unclear. In this paper, ab inito and density functional theory are used to deduce the possible reaction pathways for the reactions of F7A with hydroxyl and hydrogen free radicals at the CCSD/cc‐pVDZ//B3LYP/6‐311++G (d,p) level of theory. Two distinct reaction pathways including ten elementary reaction channels for F7A with hydroxyl free radical, and five distinct reaction pathways including twenty elementary reaction channels for F7A with hydrogen free radical are investigated. The geometries, vibrational frequencies and reaction energy barriers are also determined. Based on the calculated results, the possible reaction mechanisms are proposed and discussed. The most feasible reaction channel for F7A with hydroxyl free radical is that leads to CH(OH)CH₂(CF₂)₃+·F, and the most feasible reaction channel for F7A with hydrogen free radical is that leads to (CF₂)₃CH₂CH·+HF. The study is helpful to further study its fire suppression mechanisms and promote it to be a new generation of halon replacement.     

羟自由基的分析研究进展

本文着重对电子自旋捕集法、高效液相色谱法和化学发光法在羟自由基检测中的应用情况进行了评述,引用文献41篇。     

一种表征羟基自由基的新型荧光探针

表征羟基自由基 (· OH)的方法主要有电子自旋共振法[1] 和芳环羟基化法[2 ,3] 两大类 .电子自旋共振法灵敏度不高 ,且仪器设备昂贵 ,不适于常规分析 .芳环羟基化法操作较简单 ,灵敏度高 ,但芳环羟基化的产物往往不止一种 ,使得定量测定变得复杂 .其它方法如高效液相色谱法[4 ] ,化学发光法[5] 等也有报道 .顺磁性氮氧化合物能有效地清除自由基 [6 ,7] ,同时也是一种芳烃单重激发态的有效猝灭剂 [8,9] .当顺磁性氮氧化合物与荧光分子共价结合 ,所形成的荧光分子 -氮氧自由基复合物 (即自旋标记荧光分子 )仍保留对自由基反应的活性 ,但由于…     

Theoretical Studies on the Hydrogen Bonds of Different Position Action Mechanisms of Thymine with Uracil

In this research, the hydrogen bonds Y···H-X(X = C, N; Y = N, O) of thymine and uracil have been theoretically studied. The results show that hydrogen bond leads to bond length elongation and stretches the frequency red-shift of N-H···Y. Meanwhile, the C-H···O bonds shorten and stretch the frequency blue-shift. They all belong to traditional hydrogen bonds. The intermolecular charge transfer caused by the intermolecular hyperconjugation ρ*(N–H) →n(Y) and intramolecular charge redistribution by intramolecular hyperconjugation ρ(C-H)→ρ*(C-N) play important roles in the formation of hydrogen bonds. According to the judgment standards proposed by Bader and Popelier, these hydrogen bonds have typical electron density topological properties. Electrostatic surface potential(ESP) is a useful physicochemical property of a molecule that provides insights into inter- and intramolecular associations, as well as the prediction of likely sites of electrophilic and nucleophilic metabolic attack.     

Quantum Mechanics/Molecular Mechanics Study on the Oxygen Binding and Substrate Hydroxylation Step in AlkB Repair Enzymes

AlkB repair enzymes are important nonheme iron enzymes that catalyse the demethylation of alkylated DNA bases in humans, which is a vital reaction in the body that heals externally damaged DNA bases. Its mechanism is currently controversial and in order to resolve the catalytic mechanism of these enzymes, a quantum mechanics/molecular mechanics (QM/MM) study was performed on the demethylation of the N¹‐methyladenine fragment by AlkB repair enzymes. Firstly, the initial modelling identified the oxygen binding site of the enzyme. Secondly, the oxygen activation mechanism was investigated and a novel pathway was found, whereby the catalytically active iron(IV)–oxo intermediate in the catalytic cycle undergoes an initial isomerisation assisted by an Arg residue in the substrate binding pocket, which then brings the oxo group in close contact with the methyl group of the alkylated DNA base. This enables a subsequent rate‐determining hydrogen‐atom abstraction on competitive σ‐ and π‐pathways on a quintet spin‐state surface. These findings give evidence of different locations of the oxygen and substrate binding channels in the enzyme and the origin of the separation of the oxygen‐bound intermediates in the catalytic cycle from substrate. Our studies are compared with small model complexes and the effect of protein and environment on the kinetics and mechanism is explained.     

A Mechanistic Study of the Effects of Antioxidants on the Formation of Malondialdehyde‐Like Products in the Reaction of Hydroxyl Radicals with Deoxyribose

The reactions of ^.OH radicals with deoxyribose, DR, form five different DR^. radicals, only one of which is transformed into malondialdehyde (MDA)‐like products. The radiolytic yield of the MDA‐like products increases with the increase in the DR concentration indicating that some of the initially formed “unproductive” radicals react with DR to form the “productive” radicals. The yield of the MDA‐like products also increases with the dose rate delivered to the solution suggesting that the formation of the MDA‐like products involves the reaction of the “productive” radicals with a radical. The addition of ascorbate, AH^?, to the solution decreases the yield of the MDA‐like products as expected from the relative rates of the reaction of DR and AH^? with ^.OH radicals. On the other hand the addition of the exogenous thiol, N‐acetylcysteine (NAC), to the solutions decreases the yield of the MDA‐like products considerably more than expected from the rate constants of the reaction with ^.OH radicals. The addition of the endogenous thiol, glutathione (GSH), to the solutions affects the yield of the MDA‐like products at low concentration less than expected and at “high” concentrations more than expected from the rate constant of the reaction. Addition of low concentration of AH^? to solutions containing GSH increases considerably its antioxidant activity whereas addition of small concentrations of AH^? to solutions containing NAC has no effect on its antioxidant activity. The results point out that the DR^. radicals react differently with NAC and GSH and that the GS^. and NAC^. radicals react differently with DR, the GS^. radical being considerably more active than the NAC^. radical. Thus it has to be concluded that the relative activity of antioxidants depends also on the rate constants of many secondary reactions and on the concentrations of all the solutes present in the system.     

铂钌团簇及电荷对甲醇活性的理论研究

采用密度泛函理论(DFT)对钌掺杂的铂团簇阳离子([Pt_nRu_m]⁺, m + n = 3, n ≥ 1)活化甲醇C―H和O―H键反应进行了理论研究;探讨了电荷对[Pt_nRu_m]团簇反应活性的影响。电荷分析表明:(1) [Pt₃]⁺团簇中正电荷在三个Pt原子上均匀分布;掺杂Ru原子后,正电荷主要分布在Ru原子上; (2)首先活化C―H键时[Pt_nRu_m]⁺的反应活性比[Pt_nRu_m]明显提高;首先活化O―H键时只有[Pt₃]⁺比[Pt₃]团簇的反应活性有明显提高。本研究可为金属团簇调控的C―H键和O―H键的活化提供更深入的理解。     

Theoretical Study on the Kinetics for the Reactions of Heptyl Radicals with Methanol

Ab initio study of the reactions of n-heptyl radicals(1-C₇H₁₅, 2-C₇H₁₅, 3-C₇H₁₅, and 4-C₇H₁₅) with methanol was conducted over the temperature range of 300-1500 K. Transition states for the reaction channels producing C₇H₁₅OH, CH₃, C₇H₁₅OCH₃, H, C₇H₁₆, CH₂OH and CH₃O were identified and the geometries of all stationary points were calculated at BB1K/MG3S level of theory. The potential barrier heights of the corresponding transition states were predicted by the CBS-QB3//BB1K and G4//BB1K methods, indicating that the eight H-abstraction channels are more kinetically favorable than the channels where OH transfers from CH₃OH to C₇H₁₅ and where the C₇H₁₅OCH₃+H products are given. The rate constants of H-abstraction channels were calculated with TST and TST/Eck. Both the forward and reverse rate constants have positive temperature dependence and the tunneling effect is only important at the temperature lower than 700 K. For the reactions of H-atom abstraction from methyl in CH₃OH by n-heptyl, a reverse and the corresponding forward rate constant are roughly equal. For the reactions of H-atom abstraction from OH in CH₃OH by n-heptyl, a reverse rate constant is larger by several orders of magnitude than the corresponding forward one.