Can the ebselen derivatives catalyze the isomerization of peroxynitrite to nitrate?

The reaction of ebselen and its derivatives (1-7) with peroxynitrite anion (ONOO(-); PN) has been studied in gas phase and in aqueous, dichloromethane, benzene, and cyclohexane solutions using B3LYP/6-311+G(d,p)//B3LYP/6-311G(d,p) and PCM-B3LYP/6-311+G(d,p)//B3LYP/6-311G(d,p) approaches, respectively. It was shown that the reaction of 2 (R=H) with PN proceeds via 2 + PN --> 2-PN --> 2-TS1 (O-O activation) --> 2-O(NO(2)(-)()) --> 2-SeO + NO(2)(-) pathway with a rate-determining barrier of 25.3 (14.8) kcal/mol at the NO(2)(-) dissociation step (numbers presented without parentheses are enthalpies, and those in parentheses are Gibbs free energies). The NO(3)(-) formation process, starting from the complex 2-O(NO(2)(-)()), requires by (7.9) kcal/mol more energy than the NO(2)(-) dissociation process and is unlikely to compete with the latter. Thus, in the gas phase, the peroxynitrite --> nitrate isomerization catalyzed by complex 2 is unlikely to occur. It is shown that the NO(3)(-) formation process is slightly more favorably than the NO(2)(-) dissociation process for complex 4, with a strongest electron-withdrawing ligand R=CF(3). Therefore, complex 4 (as well as complex 6 with R=OH) is predicted to be a good catalyst for peroxynitrite <--> nitrite isomerization in the gas phase. Solvent effects (a) change the rate-determining step of the reaction 2 + PN from NO(2)(-) dissociation in the gas phase to O-O activation, which occurs with barriers of (13.9), (8.4), (8.4), and (8.2) kcal/mol in water, dichloromethane, benzene, and cyclohexane, respectively, and (b) significantly reduce the NO(2)(-) dissociation energy, while only slightly destabilizing the NO(3)(-) formation barrier, and make the peroxynitrite <--> nitrate isomerization process practically impossible, even for complex 4.     

Quantum mechanical study of the potential energy surface of the ClO + NO2 reaction

In the study of the reaction pathways of the ClO + NO2 reaction including reliable structures of the reactants, products, intermediates, and transition states as well as energies the MP2/6-311G(d), B3LYP/6-311G(d), and G2(MP2) methods have been employed. Chlorine nitrate, ClONO2, is formed by N-O association without an entrance barrier and is stabilized by 29.8 kcal mol(-1). It can undergo either a direct 1,3 migration of Cl or OCl rotation to yield an indistinguishable isomer. The corresponding barriers are 45.8 and 7.1 kcal mol(-1), respectively. ClONO2 can further decompose into NO3 + Cl with an endothermicity of 46.4 kcal mol(-1). The overall endothermicity of the NO2 + ClO --> NO3 + Cl reaction is calculated to be 16.6 kcal mol(-1). The formation of cis-perp and trans-perp conformer of chlorine preoxynitrite, ClOONO(cp) and ClOONO(tp), are exothermic by 5.4 and 3.8 kcal mol(-1), respectively. Calculations on the possible reaction pathways for the isomerization of ClOONO to ClONO2 showed that the activation barriers are too high to account for appreciable nitrate formation from peroxynitrite isomerization. All quoted relative energies are related to G2(MP2) calculations.     

Peroxynitrite decomposition activity of iron porphyrin complexes

Peroxynitrite (ONOO(-)/ONOOH), a putative cytotoxin formed by combination of nitric oxide (NO.) and superoxide (HO(2)(.)) radicals, is decomposed catalytically by micromolar concentrations of water-soluble Fe(III) porphyrin complexes, including 5,10,15,20-tetrakis(2',4',6'-trimethyl-3,5-disulfonatophenyl)porphyrinatoferrate(7-), Fe(TMPS); 5,10,15,20-tetrakis(4'-sulfonatophenyl)porphyrinatoiron(3-), Fe(TPPS); and 5,10,15,20-tetrakis(N-methyl-4'-pyridyl) porphyrinatoiron(5+), Fe(TMPyP). Spectroscopic (UV-visible), kinetic (stopped-flow), and product (ion chromatography) studies reveal that the catalyzed reaction is a net isomerization of peroxynitrite to nitrate (NO(3)(-)). One-electron catalyst oxidation forms an oxoFe(IV) intermediate and nitrogen dioxide, and recombination of these species is proposed to regenerate peroxynitrite or to yield nitrate. Michaelis-Menten kinetics are maintained accordingly over an initial peroxynitrite concentration range of 40-610 microM at 5.0 microM catalyst concentrations, with K(m) in the range 370-620 microM and limiting turnover rates in the range of 200-600 s(-1). Control experiments indicate that nitrite is not a kinetically competent reductant toward the oxidized intermediates, thus ruling out a significant role for NO(2)(.) hydrolysis in catalyst turnover. However, ascorbic acid can intercept the catalytic intermediates, thus directing product distributions toward nitrite and accelerating catalysis to the oxidation limit. Additional mechanistic details are proposed on the basis of these and various other kinetic observations, specifically including rate effects of catalyst and peroxynitrite concentrations, solution pH, and isotopic composition.     

Mechanism of nitrite formation by nitrate photolysis in aqueous solutions: the role of peroxynitrite, nitrogen dioxide, and hydroxyl radical

Photolysis of aqueous NO3(-) with lambda > or = 195 nm is known to induce the formation of NO2(-) and O2 as the only stable products. The mechanism of NO3- photolysis, however, is complex, and there is still uncertainty about the primary photoprocesses and subsequent reactions. This is, in part, due to photoisomerization of NO3(-) to ONOO(-) at lambda < 280 nm, followed by the formation of *OH and *NO2 through the decomposition of ONOOH (pKa = 6.5-6.8). Because of incomplete information concerning the mechanism of peroxynitrite (ONOOH/ONOO(-)) decomposition, previous studies were unable to account for all observations. In the present study aqueous nitrate solutions were photolyzed by monochromatic light in the range of 205-300 nm. It is shown that the main primary processes at this wavelength range are NO3(-) hv-->*NO2 + O*(-) (reaction 1) and NO3(-) hv--> ONOO(-) (reaction 2). Based on recent knowledge on the mechanisms of peroxynitrite decomposition and its reactions with reactive nitrogen and oxygen species, we determined Phi(1) and Phi(2) using different experimental approaches. Both quantum yields increase with decreasing the excitation wavelength, approaching Phi(1) = 0.13 and Phi(2) = 0.28 at 205 nm. It is also shown that the yield of nitrite increases with decreasing the excitation wavelength. The implications of these results on UV disinfection of drinking water are discussed.     

A Possible Reaction Channel from BrONO to BrNO2

A possible isomeriztion channel from BrONO( bromine nitrite) to BrNO2 (nitryl bromide) is predicted by means of MP2 and QCISD(T) (single-point) methods.The channel is a direct bromine abstraction reaction from BrONO molecule by NO2 in which the forward reaction barrier is 89.30 kJ/mol at final UQCISD(T)/6-311 G(2df)//UMP2/6-311G(d) level of theory with zero-point energies included,The result can explian the available experiments very well.     

Homolysis of the peroxynitrite anion detected with permanganate

The reaction of peroxynitrite with violet-colored MnO4- leads to the formation of green MnO42-. The rate constant for the reaction at pH 11.7, 5.5 mM ionic strength, and 25 degrees C, 0.020 +/- 0.001 s(-1), is independent of the MnO4- concentration; homolysis of ONOO- to NO* and O2*- is the rate-determining step. Both NO* and O2*- react with MnO4- with rate constants of (3.5 +/- 0.7) x 10(6) M(-1)s(-1) and (5.7 +/- 0.9) x 10(5) M(-1)s(-1), respectively. The activation volume and activation energy for breaking the N-O bond are 12.6 +/- 0.8 cm(3)mol(-1) and 102 +/- 2 kJ mol(-1), respectively. In combination with the known standard Gibbs energies of formation of NO* and O2*-, the rate of the reaction of NO* and O2*-, and the pKa of ONOOH, we find a standard Gibbs energy of formation of ONOO- of +68 +/- 1 kJ mol(-1), and of ONOOH of +31 +/- 1 kJ mol(-1).     

Proton affinity of methyl nitrite and methyl peroxynitrite: implications for measuring branching ratios of alkyl nitrates and nitrites

Geometry optimizations for methyl nitrite and methyl peroxynitrite, along with various protonated isomers for each, have been investigated using ab initio and density functional methods. The lowest energy structure for protonated methyl nitrite is a complex between CH3OH and NO(+). For methyl peroxynitrite, the lowest energy protonated structure is a complex between CH3OOH and NO(+). Their respective proton affinities are estimated to be 195.2 and 195.8 kcal/mol at the QCISD(T)/6-311++G(3df,3pd) level of theory. The results, compared with past studies, suggest an alternative method for directly measuring branching ratios for production of alkyl nitrates and nitrites.     

Reaction of the radical pair NO2* and CO3*- with 2-[6-(4'-amino)phenoxy-3H-xanthen-3-on-9-yl]benzoic acid (APF)

The fluorogenic indicator 2-[6-(4'-amino)phenoxy-3H-xanthen-3-on-9-yl]benzoic acid (APF) is used widely to detect and measure reactive nitrogen and oxygen species such as peroxynitrite, ONOO-, both in vivo and in vitro. We present in this work the results of a combined computational and experimental study to provide insights into the mechanism of the reaction of APF with the radical products of ONOO- reaction with CO2, namely NO2* and CO3*-. The experimental study on the inhibition of APF oxidation by HCO3- suggests that a direct reaction of APF with nitrosoperoxycarbonate, ONOOCO2-, is unlikely. The mechanism of APF action on NO2* and CO3*- was investigated using gas-phase and solvent modeled calculations at the MPW1K/6-311+G(d)//MPW1K/6-31G(d) level of theory. Our computational results suggest that two-electron oxidation of APF takes place in two rapid one-electron oxidation steps, the first being a proton-coupled electron transfer (PCET) between APF and NO2*, followed by addition of CO3*- and subsequent decomposition of the adduct to yield fluorescein.     

Quantum mechanical investigation of the atmospheric reaction CH3O2 + NO

The important stationary points on the potential energy surface of the reaction CH(3)O(2) + NO have been investigated using ab initio and density functional theory techniques. The optimizations were carried out at the B3LYP/6-311++G(d,p) and MP2/6-311++G(d,p) levels of theory while the energetics have been refined using the G2MP2, G3//B3LYP, and CCSD(T) methodologies. The calculations allow the proper characterization of the transition state barriers that determine the fate of the nascent association conformeric minima of methyl peroxynitrite. The main products, CH(3)O + NO(2), are formed through either rearrangement of the trans-conformer to methyl nitrate and its subsequent dissociation or via the breaking of the peroxy bond of the cis-conformer to CH(3)O + NO(2) radical pair. The important consequences of the proposed mechanism are (a) the allowance on energetic grounds for nitrate formation parallel to radical propagation under favorable external conditions and (b) the confirmation of the conformational preference of the homolytic cleavage of the peroxy bond, discussed in previous literature.     

Hydroxyl radical formation by O-O bond homolysis in peroxynitrous acid

Peroxynitrite decay in weakly alkaline media occurs by two concurrent sets of pathways which are distinguished by their reaction products. One set leads to net isomerization to NO(3)(-) and the other set to net decomposition to O(2) plus NO(2)(-). At sufficiently high peroxynitrite concentrations, the decay half-time becomes concentration-independent and approaches a limiting value predicted by a mechanism in which reaction is initiated by unimolecular homolysis of the peroxo O-O bond, i.e., the following reaction: ONOOH --> (*)OH + (*)NO(2). This dynamical behavior excludes alternative postulated mechanisms that ascribe decomposition to bond rearrangement within bimolecular adducts. Nitrate and nitrite product distributions measured at very low peroxynitrite concentrations also correspond to predictions of the homolysis model, contrary to a recent report from another laboratory. Additionally, (1) the rate constant for the reaction ONOO(-) --> (*)NO + (*)O(2)(-), which is critical to the kinetic model, has been confirmed, (2) the apparent volume of activation for ONOOH decay (DeltaV() = 9.7 +/- 1.4 cm(3)/mol) has been shown to be independent of the concentration of added nitrite and identical to most other reported values, and (3) complex patterns of inhibition of O(2) formation by radical scavengers, which are impossible to rationalize by alternative proposed reaction schemes, are shown to be quantitatively in accord with the homolysis model. These observations resolve major disputes over experimental data existing in the literature; despite extensive investigation of these reactions, no verifiable experimental evidence has been advanced that contradicts the homolysis model.     

GC-MS and HPLC methods for peroxynitrite (ONOO- and O15NOO-) analysis: a study on stability, decomposition to nitrite and nitrate, laboratory synthesis, and formation of peroxynitrite from S-nitrosoglutathione (GSNO) and KO2

Nitric oxide (˙NO) and superoxide (O(2)(-)˙) are ubiquitous in nature. Their reaction product peroxynitrite (ONOO(-)) and notably its conjugated peroxynitrous acid (ONOOH) are highly unstable in aqueous phase. ONOO(-)/ONOOH (referred to as peroxynitrite) isomerize and decompose to NO(3)(-), NO(2)(-) and O(2). Here, we report for the first time GC-MS and HPLC methods for the analysis of peroxynitrite in aqueous solution. For GC-MS analysis peroxynitrite in alkaline solution was derivatized to a pentafluorobenzyl derivative using pentafluorobenzyl bromide. O(15)NOO(-) was synthesized from H(2)O(2) and (15)NO(2)(-) and used as internal standard. HPLC analysis was performed on stationary phases consisting of Nucleosil? 100-5C(18)AB or Nucleodur? C(18) Gravity. The mobile phase consisted of a 10 mM aqueous solution of tetrabutylammonium hydrogen sulfate and had a pH value of 11.5. UV absorbance detection at 300 nm was used. HPLC allows simultaneous analysis of ONOO(-), NO(2)(-) and NO(3)(-). The GC-MS and HPLC methods were used to study stability, synthesis, formation from S-[(15)N]nitrosoglutathione (GS(15)NO) and KO(2), and isomerization/decomposition of peroxynitrite to NO(2)(-) and NO(3)(-) in aqueous buffer.     

偶氮苯磺酸衍生物的光致顺反异构化机理

基于密度泛函理论(DFT)中的B3LYP方法, 在6-311++G(d,p)水平上全优化得到了3,3'-偶氮苯磺酸(3,3'-AbS)在S0和T1态顺反异构化机理.在S0态存在两种异构化途径: 绕角NNC反转和绕NC键旋转相结合的形式和单纯的绕CNNC二面角旋转形式, 两种异构化途径的能垒分别为94.2和124.3 kJ·mol-1. 有必要指出的是, 在反转与旋转结合的途径上存在二次过渡态. 在T1态上仅存在旋转途径且其能垒为21.1 kJ·mol-1. 采用含时密度泛函理论(TD-DFT), 在B3LYP/6-311++G(d,p)水平上, 沿着基态的两种异构化途径计算得到了T1, S1, T2和S2态的垂直激发的势能剖面, 分析了可能的光致异构化途径. 当激发光波长为330 nm时, 反应物分子被激发到S2态, 然后弛豫到较低的能态S1发生异构化反应, 旋转途径存在两条活化途径: (1) 沿着S1/S0的圆锥交叉点衰变到产物; (2) 由S1态弛豫到T1态后, 在S0-T1-S0的区域发生异构化, 再转化到产物. 计算结果表明, 3,3'-AbS通过反转和旋转的结合形式实现在S0态的异构化, 而被激发后倾向于沿着旋转坐标作为其主要的异构化途径.     

硝基甲烷异构化反应势能面的ab initio研究

在B3LYP/6-311+ +G(2d,2p)水平上,优化得到硝基甲烷CH3NO2的10种异构体和23个异构化反应过渡态,并用G2MP2方法进行了单点能计算.根据计算得到的G2MP2相对能量,探讨了CH3NO2势能面上异构化反应的微观机理.研究表明,反应初始阶段的CH3NO2异构化过程具有较高的能垒,其中CH3NO2的两个主要异构化反应通道,即CH3NO2→CH3ONO和CH3NO2→CH2N(O)OH的活化能分别为270.3和267.8 kJ/mol,均高于CH3NO2的C-N键离解能.因而,从动力学角度考虑, CH3NO2的异构化反应较为不利.     

Inhibition of peroxynitrite-induced nitration of tyrosine by glutathione in the presence of carbon dioxide through both radical repair and peroxynitrate formation

Peroxynitrite (ONOO-/ONOOH) is assumed to react preferentially with carbon dioxide in vivo to produce nitrogen dioxide (NO2*) and trioxocarbonate(1-) (CO3*-) radicals. We have studied the mechanism by which glutathione (GSH) inhibits the NO2*/CO3*--mediated formation of 3-nitrotyrosine. We found that even low concentrations of GSH strongly inhibit peroxynitrite-dependent tyrosine consumption (IC50 = 660 microM) as well as 3-nitrotyrosine formation (IC50) = 265 microM). From the determination of the level of oxygen produced or consumed under various initial conditions, it is inferred that GSH inhibits peroxynitrite-induced tyrosine consumption by re-reducing (repairing) the intermediate tyrosyl radicals. An additional protective pathway is mediated by the glutathiyl radical (GS*) through reduction of dioxygen to superoxide (O2*-) and reaction with NO2* to form peroxynitrate (O2NOOH/O2NOO-), which is largely unreactive towards tyrosine. Thus, GSH is highly effective in protecting tyrosine against an attack by peroxynitrite in the presence of CO2. Consequently, formation of 3-nitrotyrosine by freely diffusing NO2* radicals is highly unlikely at physiological levels of GSH.     

Product distribution of peroxynitrite decay as a function of pH, temperature, and concentration.

The decay of peroxynitrite [O=NOO(-), oxoperoxonitrate(1-)] was examined as a function of concentration (0.050-2.5 mM), temperature (5-45 degrees C), and pH (2.2-10.0). Below 5 degrees C and pH 7, little amounts of the decomposition products nitrite and dioxygen are formed, even when the peroxynitrite concentration is high (2.5 mM). Instead, approximately > or =90% isomerizes to nitrate. At higher pH, decomposition increases at the expense of isomerization, up to nearly 80% at pH 10.0 at 5 degrees C and 90% at 45 degrees C. Much less nitrite and dioxygen per peroxynitrite are formed when the peroxynitrite concentration is lower; at 50 microM and pH 10.2, < or =40% decomposes. In contrast to two other reports (Pfeiffer, S.; Gorren, A. C. F.; Schmidt, K.; Werner, E. R.; Hansert, B.; Bohle, D. S.; Mayer, B. J. Biol. Chem. 1997, 272, 3465-3470, and Coddington, J. W.; Hurst, J. K.; Lymar, S. V. J. Am. Chem. Soc. 1999, 121, 2438-2443), we find that the extent of decomposition is dependent on the peroxynitrite concentration.     

CS与NO分子反应势能面的理论研究

应用量子化学从头计算和密度泛函理论(DFT)对CS分子和NO分子的反应机理进行了研究. 在B3LYP/6- 311G**和CCSD(T)/6-311G**水平上计算了CS分子与NO分子反应的二重态和四重态反应势能面. 计算结果表明, 二重态反应势能面中, CS分子的C端和NO的N端连接是主要的反应方式. 反应物先经过过渡态TS1, 形成具有直线结构的中间体1 (CSNO). 中间体1经过一系列异构化得到主要产物P₁ (CO＋SN). 此反应是放热反应, 反应热为－183.75 kJ/mol . 而四重态由于反应入口势垒过高, 是不重要的.     

Spectrophotometric studies of the reaction of quercetin with peroxynitrite at different pH

Peroxynitrite (ONOOH/ONOO-) which is formed in vivo under oxidative stress is a strong oxidizing and nitrating agent. It has been reported that several flavonoids, including quercetin, inhibit the peroxynitrite-induced oxidation and/or nitration of several molecules tested; however, the mechanism of their protective action against peroxynitrite is not univocally resolved. The kinetics of the reaction of quercetin with peroxynitrite was studied by stopped-flow as well as by conventional spectrophotometry under acidic, neutral and alkaline pH. The obtained results show that the protective mechanism of quercetin against peroxynitrite toxicity cannot be explained by direct scavenging of peroxynitrite. We propose that quercetin acts via scavenging intermediate radical products of peroxynitrite decomposition (it is an excellent scavenger of ·NO2) and/or via reduction of target radicals formed in the reaction with peroxynitrite.     

Pressure dependence of peroxynitrite reactions. Support for a radical mechanism

Activation volumes (delta V++) have been determined for several reactions of peroxynitrite using the stopped-flow technique. Spontaneous decomposition of ONOOH to NO3- in 0.15 M phosphate, pH 4.5, gave delta V++ = 6.0 +/- 0.7 and 14 +/- 1.0 cm3 mol-1 in the presence of 53 microM and 5 mM nitrite ion, respectively. One-electron oxidations of Mo(CN)8(4-) and Fe(CN)6(4-), which are first order in peroxynitrite and zero order in metal complex, gave delta V++ = 10 +/- 1 and 11 +/- 1 cm3 mol-1, respectively, at pH 7.2. The limiting yields of oxidized metal complex were found to decrease from 61 to 30% of the initially added peroxynitrite for Mo(CN)8(3-) and from 78 to 47% for Fe(CN)6(3-) when the pressure was increased from 0.1 to 140 MPa. The bimolecular reaction between CO2 and ONOO- was determined by monitoring the oxidation of Fe(CN)6(4-) by peroxynitrite in bicarbonate-containing 0.15 M phosphate, pH 7.2, for which delta V++ = -22 +/- 4 cm3 mol-1. The Fe(CN)6(3-) yield decreased by approximately 20% upon increasing the pressure from atmospheric to 80 MPa. Oxidation of Ni(cyclam)2+ by peroxynitrite, which is first order in each reactant, was characterized by delta V++ = -7.1 +/- 2 cm3 mol-1, and the thermal activation parameters delta H++ = 4.2 +/- 0.1 kcal mol-1 and delta S++ = -24 +/- 1 cal mol-1 K-1 in 0.15 M phosphate, pH 7.2. These results are discussed within the context of the radical cage hypothesis for peroxynitrite reactivity.     

Isomerization of free base porphyrin. Theoretical study

The photoinduced isomerization reaction of free base porphyrin molecule has been calculated using the DFT-B3LYP method combined with the 6-31G(d,p) basis set. To prove the accuracy of results, the 6-311G+(2p,2d) basis set was used. Two types of isomerization mechanisms were studied. It was found that the stepwise pathway of isomerization is the most appropriate. The geometric parameters of isomers and the transition structures of different multiplets are discussed. Zero-point energy and vibrational frequencies analysis are given.     

NO3-+Cl2→ClONO2+Cl-反应势能面和势能阱

采用密度泛函理论B3LYP方法和6-311+G(d)基组, 计算构建离子-分子气相反应NO3-+Cl2→ClONO2+Cl-的三维势能面. 三维反应势能面证明该反应没有过渡态和势能垒, 但是存在一个深达-55.0 kJ/mol的势能阱(以氯气分子和硝酸根离子相隔无穷远为参量). 在势能阱底部, 有个化合物(O2NOClCl)- 称为势阱化合物, 依赖于势能阱而稳定存在. 理论红外光谱预测低温红外光谱能检测该势阱化合物. 低温条件下, 该反应由热力学控制, 反应产物是势阱化合物(O2NOClCl)-. 当温度升高, 该反应由动力学控制, 势阱化合物(O2NOClCl)-不稳定, 发生分解反应, 重新生成NO3-和Cl2. 研究结果可用来解释低温时ClONO2与Cl-气相反应不能产生Cl2的原因.