Theoretical study of the hydroboration reaction of cyclopropane with borane

The hydroboration of cyclopropane has been investigated using the B3LYP density functional method employing several split-valence basis sets. It is shown that the reaction proceeds via an intermediate weakly bound complex and a three-centered transition state. Calculations at higher levels of theory were also performed at the geometries optimized at the B3LYP level, but only slight changes in the barriers were observed. Structural parameters for the transition state are also reported.     

Theoretical study of the catalytic reaction mechanism of MndD

Manganese-dependent homoprotocatechuate 2,3-dioxygenase (MndD) is an enzyme taking part in the catabolism of aromatic compounds in the environment. It uses molecular oxygen to perform an extradiol cleavage of the ring of the ortho-dihydroxylated aromatic compound homoprotocatechuate. A theoretical investigation of the reaction path for MndD was performed using hybrid density functional theory with the B3LYP functional, and a catalytic mechanism has been suggested. Models of different size were built from the crystal structure of the enzyme and were used in the search for intermediates and transition states. It was found that the substrate first binds at the active site as a monoanion. Next the dioxygen is bound, forming a hydroperoxo intermediate. The O–O bond, activated in this way undergoes homolytic cleavage leading to an oxyl and then to an extra epoxide radical with subsequent opening of the aromatic ring. The lactone ring is then hydrolyzed by the Mn-bound OH group, and the final product is obtained in the last reaction steps. Alternative reaction paths were considered, and their calculated barriers were found to be higher than for the suggested mechanism. The selectivity between the extra- and intra-cleavage pathways was found to be determined by the barriers for the decay of the radical state.Electronic Supplementary Material Supplementary material is available for this article at and is accessible for authorized users.     

The reaction between nitrite and oxyhemoglobin: a mechanistic study

The nitrite anion (NO(-)(2)) has recently received much attention as an endogenous nitric oxide source that has the potential to be supplemented for therapeutic benefit. One major mechanism of nitrite reduction is the direct reaction between this anion and the ferrous heme group of deoxygenated hemoglobin. However, the reaction of nitrite with oxyhemoglobin (oxyHb) is well established and generates nitrate and methemoglobin (metHb). Several mechanisms have been proposed that involve the intermediacy of protein-free radicals, ferryl heme, nitrogen dioxide (NO(2)), and hydrogen peroxide (H(2)O(2)) in an autocatalytic free radical chain reaction, which could potentially limit the usefulness of nitrite therapy. In this study we show that none of the previously published mechanisms is sufficient to fully explain the kinetics of the reaction of nitrite with oxyHb. Based on experimental data and kinetic simulation, we have modified previous models for this reaction mechanism and show that the new model proposed here is consistent with experimental data. The important feature of this model is that, whereas previously both H(2)O(2) and NO(2) were thought to be integral to both the initiation and propagation steps, H(2)O(2) now only plays a role as an initiator species, and NO(2) only plays a role as an autocatalytic propagatory species. The consequences of uncoupling the roles of H(2)O(2) and NO(2) in the reaction mechanism for the in vivo reactivity of nitrite are discussed.     

Baker's yeast flavocytochrome b2. A mechanistic study of the dehydrohalogenation reaction

It has been shown that reduced flavocytochrome b2 not only catalyzes reduction of bromopyruvate [P. Urban, P.M. Alliel and F. Lederer (1983) Eur. J. Biochem. 134, 275-281] but also transforms it into pyruvate in a reductive elimination process. The dehydrohalogenation reaction also takes place when oxidized enzyme acts on bromolactate, but the reaction is more difficult to observe under these conditions because of its low efficiency compared to the normal oxidative process. The maximal rates of pyruvate production from bromopyruvate and chloropyruvate differ by a factor of less than 10, whereas elimination from fluoropyruvate cannot be detected. These results support a mechanism in which the dehydrohalogenation reaction takes place from a carbanion intermediate of the normal reductive-oxidative pathway.     

A reaction of the superoxide radical with tetrapyrroles

Bilirubin and biliverdin were bleached during exposure to the aerobic xanthine oxidase reaction. Enzymic scavenging of O₂^?, by Superoxide dismutase, inhibited, whereas enzymic scavenging of H₂O₂, by catalase, did not. Increasing the rate of production of O₂^? without increasing the turnover rate of xanthine oxidase, by increasing pO₂, accelerated the bleaching of the biliverdin. Moreover, a scavenger of OH·, such as benzoate, or an inactivating chelating agent for iron, such as diethylenetriamine pentaacetate or desferrioxamine mesylate, did not inhibit. It follows that O₂^? can directly attack these tetrapyrroles. Kinetic competition between Superoxide dismutase and bilirubin yielded a value for k_{bilirubin, O2^?} = 2.3 × 10⁴ M^?1s^?1 at pH 8.3 and at 23 °C. A similar experiment for biliverdin yielded a value for k_{bilirubin, O2^?} = 7 × 10⁴ M^?1s^?1.     

Theoretical study on primary reaction of photosynthetic bacteria

Theoretical calculation was carried out on the primary electron donor P₈₇₀ of photosynthetic bacteria. The results show that: (i) the bimolecular structure of the primary electron donor is more advantageous in energy than monomolecular structure; (ii) the initial configuration of primary electron donor is no longer stable and changes to the configuration with lower energy and chemical reactivity after the charge separation. In the P₈₇₀, such structural change is completed through the rotation of C₃ acetyl, so the oxygen atom of acetyl interacts with the magnesium atom of another bacterio-chlorophyll molecule, and the total energy and chemical reactivity are reduced evidently. It is suggested that the structural change of the primary electron donor is important in preventing the occurrence of charge recombination during the primary reaction and maintaining the high efficiency of the conversion of sun-light to chemical energy. A new mechanism of primary reaction has been proposed, which can give reasonable explanations to the results of kinetic and site mutation studies.     

The reaction of superoxide radical with N-acetylcysteine

The interaction of superoxide radicals with N-acetylcysteine (RSH) in an aqueous solution of pH 7 using the technique of steady state radiolysis has been investigated in this paper. The radiolytic yield of the products (G value) of RSH consumption and disulfide of N-acetylcysteine (RSSR) formation has been determined. The G value of the products is not dependent on the concentration of RSH (at the plateau of dilution curve) or on the inverse of the square root of the dose rate (dose rate)(-1/2), from which it is concluded that in this reaction there is no character of chain reaction. The disulfide of N-acetylcysteine is the only sulfur final product. Hydrogen peroxide is not a reaction product, and accordingly the reaction of O(2)(*-) with RSH does not proceed via hydrogen atom abstraction from RSH. A reaction mechanism is proposed, and an overall rate constant of 68 M(-1) s(-1) has been estimated.     

Further insights into the reaction of melatonin with hydroxyl radical

Recent interest has focused on the use of exogenous melatonin as an antioxidant, particularly to scavenge the highly cytotoxic hydroxyl radical (HO(z.rad;)) which may be generated in many pathological conditions. However, in vitro and in vivo studies aimed at assessing the antioxidant properties of melatonin have produced conflicting results. While it is known that HO(z.rad;) reacts with melatonin at a diffusion limited rate, very little is known about the products of this reaction. In this investigation it is shown that incubation of melatonin with a Fenton-type HO(z.rad;)-generating system at pH 7.4 forms a complex mixture of primary products. These include 2-hydroxymelatonin, which was isolated as its more stable oxindole tautomer, 4- and 6-hydroxymelatonin, N-acetyl-N(2)-formyl-5-methoxykynurenine and 7,7(')-bi-(5-methoxy-N-acetyltryptamine-4-one). Reaction pathways that might lead to these products are described. The differing biological effects of these products, while currently incompletely understood, might account for the controversy concerning the antioxidant properties of melatonin.     

Quantitation of the hydroxyl radical by reaction with dimethyl sulfoxide

This investigation was conducted to validate the use of dimethyl sulfoxide (DMSO) as a quantitative molecular probe for the generation of hydroxyl radicals (HO.) in aqueous systems. Reaction of HO. with DMSO produces methane sulfinic acid as a primary product, which can be detected by a simple colorimetric assay. To evaluate this method for estimating total HO. production, we studied three model systems, including the Fenton reaction, gamma irradiation of water, and ultraviolet photolysis of hydrogen peroxide, for which the theoretical maximum yield of HO. could be calculated and compared to measured DMSO oxidation. The results confirm that 0.05 to 1 M DMSO may be used to capture nearly all of the expected HO. radicals formed. Thus, methane sulfinic acid production from DMSO holds promise as an easily measured marker for HO. formation in aqueous systems pretreated with DMSO.     

Theoretical mechanistic study of the formic acid decomposition assisted by a Ru(II)-phosphine catalyst

There is considerable evidence, which we discuss, indicating that compressibility and available free space in the crystal lattice are among the factors that govern the sensitivity of an explosive compound. Expanding and extending earlier work, we demonstrate, for 25 explosives, that there is an overall general tendency for greater impact sensitivity as the estimated free space per molecule increases. More specific relationships can be discerned by looking at subgroups of the compounds. The nitramine sensitivities, most of which are quite high, increase nearly linearly but only very gradually with free space. The nitroaromatics cover a wide range of sensitivities but all have an approximately similar intermediate level of free space. The remaining types of compounds show a reasonable sensitivity–free space relationship with one outlier: FOX-7 (1,1-diamino-2,2-dinitroethylene).     

Kinetic and mechanistic studies on the reaction of melilotate hydroxylase with deuterated melilotate.

Melilotate has been synthesized from melilotate by iodiantion followed by reductive deiodination in the presence of deuterated hydrazine. The deuterated melilotate has been employed in investigations of the reaction mechanism of melilotate hydroxylase. Stopped-flow spectrophotometry has revealed no isotope effect in the formation or decay of the oxygenated intermediate which is observed when reduced melilotate hydroxylase reacts with molecular oxygen. Steady-state analysis has corroborated this result, and in addition shows that there is no isotope effect in the reductive cycle of the enzyme mechanism. This analysis does reveal a reproducible 8% decrease in Vmax for the enzyme when using deuterated melilotate. These observations are compatible with the thesis that the above intermediate is an oxygenated form of the reduced flavine prosthetic group and that the last step of the proposed mechanism is rapid and involves a primary isotope effect. The existence of the NIH shift mechanism has been studied using combined gas chromatography-mass spectrometry. No evidence could be obtained for intramolecular migration of deuterium during the hydroxylation reaction. However, the small amount of migration expected when phenols are hydroxylated precludes elimination of the NIH shift as a possibility.     

Sterol C24-methyltransferase: mechanistic studies of the C-methylation reaction with 24-fluorocycloartenol

The mechanism of the C-methylation reaction was studied with the allylic substrate analog 24-fluorocycloartenol 10 assayed with soybean sterol C24-methyltransferase (SMT). 10 is an effective competitive inhibitor (Ki = 32 microM) of the SMT, and the electron-withdrawing alpha-fluorine substituent was shown to suppress the rate of the C-methylation reaction by one order of magnitude relative to the natural cycloartenol substrate, kcat = 0.02 min(-1) versus 0.6 min(-1); alternately 10 can prevent the critical hydride shift of H24 to C25 to afford time-dependent inactivation of SMT (k(inact) = 0.32 min(-1)).     

Difference between histidine and histamine in the mechanistic pathway of the fluorescence reaction with ortho-phthalaldehyde

Histamine reacts with ortho-phthalaldehyde (OPA) in an alkaline medium to form an unstable fluorescent adduct (Fbase-Hm). Acidification of the solution to pH 2-4 gives a stable and highly fluorescent adduct (Facid-Hm). In contrast, histidine develops a relatively stable fluorescent adduct (Fbase-Hd) with OPA in an alkaline medium. Upon acidification of the solution, however, only trace amounts of the alternative fluorescent adduct (Facid-Hd) are produced although Fbase-Hd disappears similarly to Fbase-Hm. In this paper, the reaction pathway of histidine with OPA was clarified by the kinetic analysis of formation and degradation of Fbase-Hd. In comparing the results of this study with the previous ones for histamine (T. Yoshimura et al., 1987, Anal. Biochem., 164, 132-137), we elucidate the difference between histamine and histidine in the mechanism of fluorescence reaction with OPA. The presence of the carboxyl group in histidine not only stabilizes Fbase-Hd in an alkaline medium but also prevents the formation of a 1:2 adduct of histidine and OPA, the precursor of Facid-Hd.     

Carbenic vs. ionic mechanistic pathway in reaction of cyclohexanone with bromoform

The extensive computation study was done to elucidate the mechanism of formation dibromoepoxide from cyclohexanone and bromoform. In this reaction, the formation of dihaloepoxide 2 is postulated as a key step that determines the distribution and stereochemistry of products. Two mechanistic paths of reaction were investigated: the addition of dibromocarbene to carbonyl group of ketone, and the addition of tribromomethyl carbanion to the same (C=O) group. The mechanisms for the addition reactions of dibromocarbenes and tribromomethyl carbanions with cyclohexanone have been investigated using ab initio HF/6-311++G** and MP2/6-311+G* level of theory. Solvent effects on these reactions have been explored by calculations which included a continuum polarizable conductor model (CPCM) for the solvent (H(2)O). The calculations showed that both mechanisms are possible and are exothermic, but have markedly different activation energies.     

Mechanism of reaction of nitrogen dioxide radical with hydroxycinnamic acid derivatives: A pulse radiolysis study

Nitrogen dioxide radical (NO^·₂) is known as a toxic agent produced in the metabolism of nitrates and nitrites. By the use of the pulse radiolysis technique, the mechanism of the reaction of NO^·₂ radical with hydroxycinnamic acid derivatives (HCA) was studied and the rate constants have been measured. The rate constants were found to be 7.4 × 10⁸, 7.2 × 10⁸, 8.6 × 10⁸ dm³ mol^-1s^-1 for ferulic acid, sinapic acid and caffeic acid, respectively. The reactions produce the corresponding phenoxyl radical.     

The reaction of superoxide radical with catalase. Mechanism of the inhibition of catalase by superoxide radical

We have studied the time course of the absorption of bovine liver catalase after pulse radiolysis with oxygen saturation in the presence and absence of superoxide dismutase. In the absence of superoxide dismutase, catalase produced Compound I and another species. The formation of Compound I is due to the reaction of ferric catalase with hydrogen peroxide, which is generated by the disproportionation of the superoxide anion (O-2). The kinetic difference spectrum showed that the other species was neither Compound I nor II. In the presence of superoxide dismutase, the formation of this species was found to be inhibited, whereas that of Compound I was little affected. This suggests that this species is formed by the reaction of ferric catalase with O-2 and is probably the oxy form of this enzyme (Compound III). The rate constant for the reaction of O-2 and ferric catalase increased with a decrease in pH (cf. 4.5 X 10(4) M-1 s-1 at pH 9 and 4.6 X 10(6) M-1 s-1 at pH 5.). The pH dependence of the rate constant can be explained by assuming that HO2 reacts with this enzyme more rapidly than O-2.     

On the mechanistic origin of damped oscillations in biochemical reaction systems

A generalized reaction scheme for the kinetic interaction of two reactants in a metabolic pathway has been examined in order to establish what minimal mechanistic patterns are required to support a damped oscillatory transient-state kinetic behaviour of such a two-component system when operating near a steady state. All potentially oscillating sub-systems inherent in this scheme are listed and briefly characterized. The list includes several mechanistic patterns that may be frequently encountered in biological system (e.g. involving feedback inhibition, feed-forward activation, substrate inhibition or product activation), but also draw attention to some hitherto unforeseen mechanisms by which the kinetic interaction of two metabolites may trigger damped oscillations. The results can be used to identify possible sources of oscillations in metabolic pathways without detailed knowledge about the explicit rate equations that apply.     

Theoretical and experimental evidence of the photonitration pathway of phenol and 4-chlorophenol: a mechanistic study of environmental significance

Light-induced nitration pathways of phenols are important processes for the transformation of pesticide-derived secondary pollutants into toxic derivatives in surface waters and for the formation of phytotoxic compounds in the atmosphere. Moreover, phenols can be used as ˙NO(2) probes in irradiated aqueous solutions. This paper shows that the nitration of 4-chlorophenol (4CP) into 2-nitro-4-chlorophenol (NCP) in the presence of irradiated nitrate and nitrite in aqueous solution involves the radical ˙NO(2). The experimental data allow exclusion of an alternative nitration pathway by ˙OH + ˙NO(2). Quantum mechanical calculations suggest that the nitration of both phenol and 4CP involves, as a first pathway, the abstraction of the phenolic hydrogen by ˙NO(2), which yields HNO(2) and the corresponding phenoxy radical. Reaction of phenoxyl with another ˙NO(2) follows to finally produce the corresponding nitrated phenol. Such a pathway also correctly predicts that 4CP undergoes nitration more easily than phenol, because the ring Cl atom increases the acidity of the phenolic hydrogen of 4CP. This favours the H-abstraction process to give the corresponding phenoxy radical. In contrast, an alternative nitration pathway that involves ˙NO(2) addition to the ring followed by H-abstraction by oxygen (or by ˙NO(2) or ˙OH) is energetically unfavoured and erroneously predicts faster nitration for phenol than for 4CP.     

Factors relevant in the reaction of pyrroloquinoline quinone with amino acids. Analytical and mechanistic implications

In order to reveal the stability of pyrroloquinoline quinone (PQQ) in complex samples, its reaction on incubation with amino acids was followed spectrophotometrically by monitoring oxygen consumption, and with a biological assay. For several alpha-amino acids, the formation of a yellow coloured compound (lambda max = 420 nm) was accompanied by oxygen uptake and disappearance of biological activity from the reaction mixture. The yellow product appeared to be an oxazole of PQQ, the exact structure depending on the amino acid used. Oxazole formation also occurred under anaerobic conditions with concomitant formation of PQQH2, suggesting that PQQ is able to oxidize the presumed oxazoline to the oxazole. Besides the condensation reaction, there is also a catalytic cycle in which an aldimine adduct of PQQ and the amino acid is converted into the aminophenol form of the cofactor and an aldehyde resulting from oxidative decarboxylation of the amino acid. Addition of NH4+ salts, as well as that of certain divalent cations, greatly stimulated both the cyclic and the linear reaction. With basic amino acids, oxazole formation scarcely occurred. However, as oxygen consumption was observed (provided that certain divalent cations were present), conversion of these compounds took place. A reaction scheme is proposed accounting for the products formed and the effects observed. Since NH4+ ions activate several quinoproteins (PQQ-containing enzymes) and divalent cations (Ca2+, Fe2+, and Cu2+) are additional (co)factors in certain metallo quinoproteins, the effects of metal ions observed here could be related to the mechanistic features of these enzymes. Although all oxazoles were converted to PQQ by acid hydrolysis, PQQ was not detected when hydrolysis was carried out in the presence of tryptophan, a compound which appeared to have a deleterious effect on the cofactor under this condition. The results here described explain why analysis methods for free PQQ in complex samples fail in certain cases, or are not quantitative.