Mechanism of Nucleophilic Aromatic Substitution of 1-Chloro-2,4-dinitrobenzene by Glutathione in the Gas Phase and in Solution. Implications for the Mode of Action of Glutathione S-Transferases

Human mitochondrial glutathione transferases: Kinetic parameters and accommodation of a mitochondria-targeting group in substrates

Glutathione-S-transferases are key to the cellular detoxification of xenobiotics and products of oxidative damage. GSTs catalyse the reaction of glutathione (GSH) with electrophiles to form stable thioether adducts. GSTK1-1 is the main GST isoform in the mitochondrial matrix, but the GSTA1-1 and GSTA4-4 isoforms are also thought to be in the mitochondria with their distribution altering in transformed cells, thus potentially providing a cancer specific target. A mitochondria-targeted version of the GST substrate 1-chloro-2,4-dinitrobenzene (CDNB), MitoCDNB, has been used to manipulate the mitochondrial GSH pool. To finesse this approach to target particular GST isoforms in the context of cancer, here we have determined the kcat/Km for the human isoforms of GSTK1-1, GSTA1-1 and GSTA4-4 with respect to GSH and CDNB. We show how the rate of the GST-catalysed reaction between GSH and CDNB analogues can be modified by both the electron withdrawing substituents, and by the position of the mitochondria-targeting triphenylphosphonium on the chlorobenzene ring to tune the activity of mitochondria-targeted substrates. These findings can now be exploited to selectively disrupt the mitochondrial GSH pools of cancer cells expressing particular GST isoforms.

Molecular perspectives and recent advances in microbial remediation of persistent organic pollutants

Nutrition and pollution stress stimulate genetic adaptation in microorganisms and assist in evolution of diverse metabolic pathways for their survival on several complex organic compounds. Persistent organic pollutants (POPs) are highly lipophilic in nature and cause adverse effects to the environment and human health by biomagnification through the food chain. Diverse microorganisms, harboring numerous plasmids and catabolic genes, acclimatize to these environmentally unfavorable conditions by gene duplication, mutational drift, hypermutation, and recombination. Genetic aspects of some major POP catabolic genes such as biphenyl dioxygenase (bph), DDT 2,3-dioxygenase, and angular dioxygenase assist in degradation of biphenyl, organochlorine pesticides, and dioxins/furans, respectively. Microbial metagenome constitutes the largest genetic reservoir with miscellaneous enzymatic activities implicated in degradation. To tap the metabolic potential of microorganisms, recent techniques like sequence and function-based screening and substrate-induced gene expression are proficient in tracing out novel catabolic genes from the entire metagenome for utilization in enhanced biodegradation. The major endeavor of today's scientific world is to characterize the exact genetic mechanisms of microbes for bioremediation of these toxic compounds by excavating into the uncultured plethora. This review entails the effect of POPs on the environment and involvement of microbial catabolic genes for their removal with the advanced techniques of bioremediation.

Dehalogenation of aromatics by nucleophilic aromatic substitution

Nucleophilic aromatic substitution has been implicated as a mechanism for both the biotic and abiotic hydrodehalogenation of aromatics. Two mechanisms for the aqueous dehalogenation of aromatics involving nucleophilic aromatic substitution with hydride as a nucleophile are investigated using a validated density functional and continuum solvation protocol. For chlorinated and brominated aromatics, nucleophilic addition ortho to carbon-halogen bonds via an anionic intermediate is predicted to be the preferred mechanism in the majority of cases, while concerted substitution is predicted to be preferred for most fluorinated aromatics. Nucleophilic aromatic substitution reactions with the hydroxide and hydrosulfide anions as nucleophiles are also investigated and compared.

Phosphonate-anchored monolayers for antibody binding to magnetic nanoparticles

Targeted delivery of magnetic iron oxide nanoparticles (IONPs) to a specific tissue can be achieved by conjugation with particular biological ligands on an appropriately functionalized IONP surface. To take best advantage of the unique magnetic properties of IONPs and to maximize their blood half-life, thin, strongly bonded, functionalized coatings are required. The work reported herein demonstrates the successful application of phosphonate-anchored self-assembled monolayers (SAMs) as ultrathin coatings for such particles. It also describes a new chemical approach to the anchoring of antibodies on the surface of SAM-coated IONPs (using nucleophilic aromatic substitution). This anchoring strategy results in stable, nonhydrolyzable, covalent attachment and allows the reactivity of the particles toward antibody binding to be activated in situ, such that prior to the activation the modified surface is stable for long-term storage. While the SAMs do not have the well-packed crystallinity of other such monolayers, their structure was studied using smooth model substrates based on an iron oxide layer on a double-side polished silicon wafer. In this way, atomic force microscopy, ellipsometry, and contact angle goniometry (tools that could not be applied to the nanoparticles' surfaces) could contribute to the determination of their monomolecular thickness and uniformity. Finally, the successful conjugation of IgG antibodies to the SAM-coated IONPs such that the antibodies retain their biological activity is verified by their complexation to a secondary fluorescent antibody.

Gas phase reactions of 1,3,5-triazine: proton transfer, hydride transfer, and anionic σ-adduct formation

The gas phase reactivity of 1,3,5-triazine with several oxyanions and carbanions, as well as amide, was evaluated using a flowing afterglow-selected ion flow tube mass spectrometer. Isotopic labeling, H/D exchange, and collision induced dissociation experiments were conducted to facilitate the interpretation of structures and fragmentation processes. A multi-step (→ HCN + HC(2)N (2) (-) → CN(-) + 2 HCN) and/or single-step (→ CN(-) + 2 HCN) ring-opening collision-induced fragmentation process appears to exist for 1,3,5-triazinide. In addition to proton and hydride transfer reactions, the data indicate a competitive nucleophilic aromatic addition pathway (S(N)Ar) over a wide range of relative gas phase acidities to form strong anionic σ-adducts (Meisenheimer complexes). The significant hydride acceptor properties and stability of the anionic σ-adducts are rationalized by extremely electrophilic carbon centers and symmetric charge delocalization at the electron-withdrawing nitrogen positions. The types of anion-arene binding motifs and their influence on reaction pathways are discussed.

Rate-determining factors in nucleophilic aromatic substitution reactions

Quantum chemical calculations (OPBE/6-311++G(d,p)) have been performed to uncover the electronic factors that govern reactivity in the prototypical S(N)Ar reaction. It was found that intrinsic nucleophilicity--expressed as the critical energy (the energy required for forming the Meisenheimer structure Ph(X)(2)(-)) in the identity substitution reaction X(-) + PhX --> X(-) + PhX (Ph = phenyl)--shows the following approximate trend: NH(2)(-) approximately OH(-) approximately F(-) >> PH(2)(-) approximately SH(-) approximately Cl(-) > AsH(2)(-) approximately SeH(-) approximately Br(-). The periodic trends are discussed in terms of molecular properties (proton affinity of X(-) expressing Lewis basicity of the nucleophile and C(1s) orbital energy expressing Lewis acidity of the substrate) based on a dative bonding model. Furthermore, the stepwise progress of the reactions and the critical structures are analyzed applying energy decomposition analysis. Increased stability, and thereby increased intrinsic nucleophilicity, correlates with decreasing aromatic character of the Meisenheimer structure. This apparent contradiction is explained in consistency with the other observations using the same model.

A novel hydrolytic dehalogenase for the chlorinated aromatic compound chlorothalonil

Dehalogenases play key roles in the detoxification of halogenated aromatics. Interestingly, only one hydrolytic dehalogenase for halogenated aromatics, 4-chlorobenzoyl-coenzyme A (CoA) dehalogenase, has been reported. Here, we characterize another novel hydrolytic dehalogenase for a halogenated aromatic compound from the 2,4,5,6-tetrachloroisophthalonitrile (chlorothalonil)-degrading strain of Pseudomonas sp. CTN-3, which we have named Chd. Chd catalyzes a hydroxyl substitution at the 4-chlorine atom of chlorothalonil. The metabolite of the Chd dehalogenation, 4-hydroxy-trichloroisophthalonitrile, was identified by reverse-phase high-performance liquid chromatography (HPLC), tandem mass spectrometry (MS/MS), and nuclear magnetic resonance (NMR). Chd dehalogenates chlorothalonil under anaerobic and aerobic conditions and does not require the presence of cofactors such as CoA and ATP. Chd contains a putative conserved domain of the metallo-beta-lactamase superfamily and shows the highest identity with several metallohydrolases (24 to 29%). Chd is a monomer (36 kDa), and the isoelectric point (pI) of Chd is estimated to be 4.13. Chd has a dissociation constant (K(m)) of 0.112 mM and an overall catalytic rate (k(cat)) of 207 s(-1) for chlorothalonil. Chd is completely inhibited by 1,10-phenanthroline, diethyl pyrocarbonate, and N-bromosuccinic acid. Site-directed mutagenesis of Chd revealed that histidines 128 and 157, serine 126, aspartates 45, 130 and 184, and tryptophan 241 were essential for the dehalogenase activity. Chd differs from other reported hydrolytic dehalogenases based on the analysis of amino acid sequences and catalytic mechanisms. This study provides an excellent dehalogenase candidate for mechanistic study of hydrolytic dehalogenation of halogenated aromatic compound.

Aromatic C-F activation by complexes containing the {Pt2S2} core via nucleophilic substitution: a combined experimental and theoretical study

The C-F bond activation of perfluorobenzene and perfluoropyridine have been achieved by means of the complex [Pt(2)(mu-S)(2)(dppp)(2)], where dppp denotes 1,3-bis(diphenylphosphino)propane. The reaction with the first substrate requires a long time (five days) and high temperature (reflux in toluene) to yield [Pt(o-S(2)C(6)F(4))(dppp)] and [Pt(3)(mu(3)-S)(2)(dppp)(3)]F(2), and involves replacement of two fluorides in the ortho position. In contrast, the reaction with perfluoropyridine is much faster (15 min at 0 degrees C) yielding [Pt(2)(mu-S){mu-(p-SC(5)F(4)N)}(dppp)(2)]F, which implies the C-F activation in the para position with respect the pyridine nitrogen. The mechanism of both reactions has been studied computationally and the geometries of the transition states are consistent with an S(N)Ar mechanism where a sulfido bridging ligand replaces the fluoride anion. The energy barriers corresponding to the first and the second fluoride substitution are 131.7 and 137.1 kJ mol(-1) for perfluorobenzene and 85.9 and 142.7 kJ mol(-1) for perfluoropyridine, respectively. The different energy barrier of the first substitution explains the different experimental conditions required and the various products obtained for these reactions.

Theoretical study of general base-catalyzed hydrolysis of aryl esters and implications for enzymatic reactions

In this work, the mechanism of general base-catalyzed hydrolysis of aryl esters is investigated in vacuo with density functional theory and in solutions with a polarized continuum model. The hydrolysis is found to proceed via a concerted mechanism featuring simultaneous addition and elimination steps accompanied by proton transfers, consistent with experimental evidence. Reasonable agreement with measured kinetic isotope effects provides additional validation. It is found that solvation substantially lowers the transition state energy, but has a small effect on the reaction exothermicity. An enzyme oxyanion hole, modeled by an ammonia molecule hydrogen bonded to the acyl carbonyl oxygen, is found to stabilize the near-tetrahedral transition state. Implications of these findings for the hydrolysis step of the dehalogenation reaction catalyzed by 4-chlorobenzoyl-CoA dehalogenase are discussed.

Atmospheric pressure ion/molecule reactions for the selective detection of nitroaromatic explosives using acetonitrile and air as reagents

Acetonitrile vapor and air are useful reagents for the selective detection of nitroaromatic compounds using atmospheric pressure ion/molecule reactions. Reagent ions CH2CN- and CN- generated from acetonitrile, and O-*, OH- and OOH- produced from the oxygen in air, react with vapor-phase and condensed-phase nitroaromatics in the course of atmospheric pressure chemical ionization (APCI) and desorption atmospheric pressure chemical ionization (DAPCI), respectively. The homogeneous and the heterogeneous phase reactions both lead to the formation of the same anionic adducts. These adducts have characteristic fragmentation patterns upon collisional activation, which makes these two reagents valuable for the selective detection of particular nitroaromatics, including explosives present as components of complex mixtures. Complementary information is available from the two reagents because their different chemistry facilitates analyte identification. DAPCI is demonstrated to be a useful ambient detection method for nitroaromatic explosives absorbed on surfaces.

QM/MM studies of the enzyme-catalyzed dechlorination of 4-chlorobenzoyl-CoA provide insight into reaction energetics

The conversion of 4-chlorobenzoyl-CoA to 4-hydroxybenzoyl-CoA catalyzed by 4-chlorobenzoyl-CoA dehalogenase is investigated using combined QM/MM approaches. The calculated potential of mean force at the PM3/CHARMM level supports the proposed nucleophilic aromatic substitution mechanism. In particular, a Meisenheimer intermediate was found, stabilized by hydrogen bonds between the benzoyl carbonyl of the ligand and two backbone amide NHs at positions 64 and 114. Mutation of Gly113 to Ala significantly increases the barrier by disrupting the hydrogen bond with the Gly114 backbone. The formation of the Meisenheimer complex is accompanied by significant charge redistribution and structural changes in the substrate benzoyl moiety, consistent with experimental observations. Theoretical results suggest that the reaction rate is limited by the formation of the Meisenheimer complex, rather than by its decomposition. A kinetic model based on the calculated free energy profile is found to be consistent with the experimental time course data.

Meisenheimer complexes bonded at carbon and at oxygen

The carbon-bonded gas-phase Meisenheimer complex of 2,4,6-trinitrotoluene (TNT) and the nitromethyl carbanion CH(2)NO(2)(-) (m/z 60) is generated for the first time by chemical ionization using nitromethane as the reagent gas. Collision-induced dissociation (CID) of the Meisenheimer complex furnishes deprotonated TNT, a result of the higher gas-phase acidity of TNT than nitromethane. The formation of Meisenheimer complexes with CH(2)NO(2)(-) in the gas phase is selective to highly electron-deficient compounds such as dinitrobenzene and trinitrobenzene and does not occur with organic molecules with lower electron-affinity such as methanol, methylamine, propionaldehyde, acetone, ethyl acetate, chloroform, toluene, m-methoxytoluene, and even nitrobenzene and p-fluoronitrobenzene. As such, the reaction allows selective detection of TNT in mixtures. Meisenheimer complexes between CH(2)NO(2)(-) and the three dinitrobenzene isomers display distinctive fragmentations. The oxygen-bonded sigma-complex of TNT with the deprotonated hemiacetal anion CH(3)OCH(2)O(-) (m/z 61), represents a different type of Meisenheimer complex. It displays characteristic fragmentation involving loss of HNO(2) upon CID. The combination of a selective ion/molecule reaction (Meisenheimer complex formation) followed by a characteristic CID process provides a second novel and highly selective approach to the detection of TNT and closely related compounds in mixtures. The assay is readily implemented using neutral loss scans in a triple quadrupole mass spectrometer. Gas-phase reactions of denitrosylated TNT with benzaldehyde produce the corresponding dihydrofuran in an aldol condensation, a result that parallels the corresponding condensed-phase reaction.

Computational chemistry study of the environmentally important acid-catalyzed hydrolysis of atrazine and related 2-chloro-s-triazines

Many chlorine-containing pesticides, for example 2-chloro-s-triazines, are of great concern both environmentally and toxicologically. As a result, ascertaining or predicting the fate and transport of these compounds in soils and water is of current interest. Transformation pathways for 2-chloro-s-triazines in the environment include dealkylation, dechlorination (hydrolysis), and ring cleavage. This study explored the feasibility of using computational chemistry, specifically the hybrid density functional theory method, B3LYP, to predict hydrolysis trends of atrazine (2-chloro-N4-ethyl-N6-isopropyl-1,3,5-triazine-2,4-diamine) and related 2-chloro-s-triazines to the corresponding 2-hydroxy-s-triazines. Gas-phase energetics are described on the basis of calculations performed at the B3LYP/6-311++G(d,p)//B3LYP/6-31G* level of theory. Calculated free energies of hydrolysis (delta h G298) are nearly the same for simazine (2-chloro-N4,N6-diethyl-1,3,5-triazine-2,4-diamine), atrazine, and propazine (2-chloro-N4,N6-di-isopropyl-1,3,5-triazine-2,4-diamine), suggesting that hydrolysis is not significantly affected by the side-chain amine-nitrogen alkyl substituents. High-energy barriers also suggest that the reactions are not likely to be observed in the gas phase. Aqueous solvation effects were examined by means of self-consistent reaction field methods (SCRF). Molecular structures were optimized at the B3LYP/6-31G* level using the Onsager model, and solvation energies were calculated at the B3LYP/6-311++G(d,p) level using the isodensity surface polarizable continuum model (IPCM). Although the extent of solvent stabilization was greater for cationic species than neutral ones, the full extent of solvation is underestimated, especially for the transition state structures. As a consequence, the calculated hydrolysis barrier for protonated atrazine is exaggerated compared with the experimentally determined one. Overall, the hydrolysis reactions follow a concerted nucleophilic aromatic substitution (SNAr) pathway.

Trimethylsilyl- and trimethylstannyldimethylphosphane--convenient and versatile reagents for the synthesis of polyfluoroaryldimethylphosphanes

Trimethylsilyldimethylphosphane (Me3SiPMe2) and the corresponding tin compound (Me3SnPMe2) were used as reagents for the substitution of fluorine by the Me2P group in polyfluoroarenes C6F5X (X = F, H, Cl, CF3) and C5NF5. The reactions occur even under mild conditions (T = 0-20 C), either in benzene or without solvent, to give as a rule 4-X-1-(dimethylphosphano)tetrafluorobenzenes (XC6F4PMe2, 1-4) and 4-(dimethylphosphano)tetrafluoropyridine (C5NF4PMe2, 5), respectively, in yields between 75 and 95%. In the case of C6F6, double substitution is also observed, which affords 1,4-bis(dimethylphosphano)tetrafluorobenzene (6). A very efficient route to the compounds XC6F4PMe2 (X = F, H, Cl, CF3) and C5NF4PMe2 was developed as a one-pot reaction of the corresponding fluoroarenes with tetramethyldiphosphane (P2Me4) and trimethyltin hydride (Me3SnH) at moderate temperatures. This process was tested for C6F6 and perfluorobiphenyl which gave C6F5PMe2 (1) and 4,4'-bis(dimethylphosphano)octafluorobiphenyl (7), respectively. The results, which included kinetic measurements that used the intensities of the 31P signals, revealed the influence of the substrate type on the rate of reaction in the sequence: C5NF5>C6F5CF3> C6F5Cl, C6F5PMe2>C6F5H>C6F6>> C6H5F. Ab initio calculations were carried out on the model reactions of pentafluoropyridine with silylphosphane, phosphane or phosphide to discriminate between possible reaction mechanisms. The novel phosphanes were characterised by spectroscopic investigations (NMR, MS), by preparation of the related thiophosphanes ArFP(=S)Me2 (8-14), their spectroscopic and analytic data and single crystal X-ray diffraction studies on five of these derivatives.

The importance of reactant positioning in enzyme catalysis: a hybrid quantum mechanics/molecular mechanics study of a haloalkane dehalogenase

Hybrid quantum mechanics/molecular mechanics calculations using Austin Model 1 system-specific parameters were performed to study the S(N)2 displacement reaction of chloride from 1,2-dichloroethane (DCE) by nucleophilic attack of the carboxylate of acetate in the gas phase and by Asp-124 in the active site of haloalkane dehalogenase from Xanthobacter autotrophicus GJ10. The activation barrier for nucleophilic attack of acetate on DCE depends greatly on the reactants having a geometry resembling that in the enzyme or an optimized gas-phase structure. It was found in the gas-phase calculations that the activation barrier is 9 kcal/mol lower when dihedral constraints are used to restrict the carboxylate nucleophile geometry to that in the enzyme relative to the geometries for the reactants without dihedral constraints. The calculated quantum mechanics/molecular mechanics activation barriers for the enzymatic reaction are 16.2 and 19.4 kcal/mol when the geometry of the reactants is in a near attack conformer from molecular dynamics and in a conformer similar to the crystal structure (DCE is gauche), respectively. This haloalkane dehalogenase lowers the activation barrier for dehalogenation of DCE by 2-4 kcal/mol relative to the single point energies of the enzyme's quantum mechanics atoms in the gas phase. S(N)2 displacements of this sort in water are infinitely slower than in the gas phase. The modest lowering of the activation barrier by the enzyme relative to the reaction in the gas phase is consistent with mutation experiments.

Solvolytic enolization of scytalone

[reaction--see text] The major conformation of scytalone has an envelope shape with C3 forming the flap and the C3 hydroxyl in the equatorial position as determined by quantum mechanical calculations and corroborated by NMR. The C2 axial pro-R is slower to exchange with solvent than the equatorial pro-S hydrogen. Modeling the transition state for enolate formation points to a deprotonation through the flipped envelope conformation in which the C3-hydroxyl and the C2 pro-S hydrogen are axial.

Ab initio Study of Nucleophilic Aromatic Substitution of Polyfluorobenzene

Calculations at ab initio levels of theory of the nucleophilic aromatic substitution of pentafluoronitrobenzene with amines demonstrate an addition–elimination mechanism (SNAr), with the rate-determining step at the second transition state involving C–F bond breaking, and support the ortho-selectivity of the reactions based on the stability of the second transition states.

Non-enzymatic and enzymatic hydrolysis of alkyl halides: a haloalkane dehalogenation enzyme evolved to stabilize the gas-phase transition state of an SN2 displacement reaction

The semiempirical PM3 method, calibrated against ab initio HF/6-31+G(d) theory, has been used to elucidate the reaction of 1, 2-dichloroethane (DCE) with the carboxylate of Asp-124 at the active site of haloalkane dehalogenase of Xanthobacter autothropicus. Asp-124 and 13 other amino acid side chains that make up the active site cavity (Glu-56, Trp-125, Phe-128, Phe-172, Trp-175, Leu-179, Val-219, Phe-222, Pro-223, Val-226, Leu-262, Leu-263, and His-289) were included in the calculations. The three most significant observations of the present study are that: (i) the DCE substrate and Asp-124 carboxylate, in the reactive ES complex, are present as an ion-molecule complex with a structure similar to that seen in the gas-phase reaction of AcO- with DCE; (ii) the structures of the transition states in the gas-phase and enzymatic reaction are much the same where the structure formed at the active site is somewhat exploded; and (iii) the enthalpies in going from ground states to transition states in the enzymatic and gas-phase reactions differ by only a couple kcal/mol. The dehalogenase derives its catalytic power from: (i) bringing the electrophile and nucleophile together in a low-dielectric environment in an orientation that allows the reaction to occur without much structural reorganization; (ii) desolvation; and (iii) stabilizing the leaving chloride anion by Trp-125 and Trp-175 through hydrogen bonding.