SN2-like Reaction Research Articles

Stereochemistry of LinB-catalyzed biotransformation of δ-HBCD to 1R,2R,5S,6R,9R,10S-pentabromocyclododecanol

The haloalkane dehalogenase LinB from Sphingobium indicum B90A converts β-hexachlorocyclohexane (β-HCH), the most persistent HCH stereoisomer, to mono- and dihydroxylated metabolites. Recently, we reported that LinB also transforms α-, β- and γ-hexabromocyclododecanes (HBCDs), which are structurally related to HCHs. Here, we show that LinB catalyzes the hydroxylation of δ-HBCD to two pentabromocyclododecanols (PBCDOHs) and two tetrabromocyclododecadiols (TBCDDOHs). The stereochemistry of this enzymatic transformation was deduced from XRD crystal structure data of the substrate δ-HBCD and α2-PBCDOH, one of the biotransformation products. Five stereocenters of δ-HBCD are unchanged but the one at C6 is converted to an alcohol with inversion from S- to R-configuration in a nucleophilic, SN2-like substitution reaction. Only α2-PBCDOH with the 1R,2R,5S,6R,9R,10S-configuration is obtained but not its enantiomer. With only two of the 64 PBCDOHs formed, these transformations indeed are regio- and stereoselective. A conformational analysis revealed that the triple-turn motive, which is predominant in δ-HBCD and in several other HBCD stereoisomers, is also found in the product. This shows that LinB preferentially converted reactive bromine atoms but not those in the conserved triple-turn motive. The widespread contamination with HCHs triggered the bacterial evolution of dehalogenases which acquired the ability to convert these pollutants and their metabolites. We here demonstrate that LinB of S. indicum also transforms HBCDs regio- and stereoselectively following a similar mechanism.

Structural Analysis of Thermus thermophilus HB27 Mannosyl-3-phosphoglycerate Synthase Provides Evidence for a Second Catalytic Metal Ion and New Insight into the Retaining Mechanism of Glycosyltransferases

Mannosyl-3-phosphoglycerate synthase is a glycosyltransferase involved in the two-step synthetic pathway of mannosylglycerate, a compatible solute that accumulates in response to salt and/or heat stresses in many microorganisms thriving in hot environments. The three-dimensional structure of mannosyl-3-phosphoglycerate synthase from Thermus thermophilus HB27 in its binary complex form, with GDP-alpha-D-mannose and Mg(2+), shows a second metal binding site, about 6 A away from the mannose moiety. Kinetic and mutagenesis studies have shown that this metal site plays a role in catalysis. Additionally, Asp(167) in the DXD motif is found within van der Waals contact distance of the C1' atom in the mannopyranose ring, suggesting its action as a catalytic nucleophile, either in the formation of a glycosyl-enzyme intermediate according to the double-displacement S(N)2 reaction mechanism or in the stabilization of the oxocarbenium ion-like intermediate according to the D(N)*A(Nss) (S(N)i-like) reaction mechanism. We propose that either mechanism may occur in retaining glycosyltransferases with a GT-A fold, and, based on the gathered structural information, we identified an extended structural signature toward a common scaffold between the inverting and retaining glycosyltransferases.

Lithium Cuprate Coupling Reactions: Evaluation of Computational Methods for Determination of the Reaction Mechanisms

Several computational methods were evaluated for determining the gas-phase reaction mechanisms of lithium dimethylcuprate and dimethylcuprate anion with chloromethane and vinyl chloride. These methods include the B3LYP and M06 density functional theory (DFT) methods, the unscaled and spin-component-scaled Moller-Plesset perturbation theory (MP2, SCS-MP2, and SCSC-MP2), CCSD, and CCSD(T). The reaction of interest is an oxidative addition of the alkyl or vinyl halide to the Cu(I) species, resulting in a Cu(III) intermediate, which undergoes reductive elimination with coupling of the two alkyl fragments. Three possible oxidative addition pathways were examined, a concerted addition to Cu(I), an S(N)2-like reaction of Cu on the alkyl halide, and a radical mechanism. A concerted reductive elimination step was also investigated.

Unusual Mechanisms Can Dominate Reactions at Hyperthermal Energies: An Example from O(3P) + HCl → ClO + H

An unusual mechanism in the reaction, O(3P) + HCl --> ClO + H, dominates at hyperthermal collision energies. This mechanism applies to collision geometries in which the H atom in the HCl molecule is oriented toward the reagent O atom. As the Cl-O bond forms, the H atom experiences a strong repulsive force from both the O and Cl atoms. The ClO product scatters forward with respect to the initial velocity of the O atom, and the H atom scatters backward. This mechanism accounts for more than half the reactive trajectories at energies >110 kcal mol-1, but it does not involve motion near the minimum energy path, which favors an SN2-like reaction mechanism where the H atom is oriented away from the reagent O atom during the collision.

Characterization of Mouse Rt6.1 NAD:Arginine ADP-ribosyltransferase

Rat RT6 proteins, and perhaps mouse Rt6, identify a set of immunoregulatory T lymphocytes. Rat RT6.1 (RT6.1) and rat RT6.2 (RT6. 2) are NAD glycohydrolases, which catalyze auto-ADP-ribosylation, but not ADP-ribosylation of exogenous proteins. Mouse Rt6.1 (mRt6.1) also catalyzes auto-ADP-ribosylation. The activity of mouse cytotoxic T lymphocytes is reportedly inhibited by ADP-ribosylation of surface proteins, raising the possibility that mRt6 may participate in this process. The reactions catalyzed by mRt6, would, however, need to be more diverse than those of the rat homologues and include the ADP-ribosylation of acceptors other than itself. To test this hypothesis, mRt6.1 and rat RT6.2 were synthesized in Sf9 insect cells and rat mammary adenocarcinoma (NMU) cells. mRt6.1, but not rat RT6.2, catalyzed the ADP-ribosylation of guanidino-containing compounds (e.g. agmatine). Unlike RT6.2, mRt6.1 was a weak NAD glycohydrolase. In the presence of agmatine, however, the ratio of [adenine-14C]ADP-ribosylagmatine formation from [adenine-14C]NAD to [carbonyl-14C]nicotinamide formation from [carbonyl-14C]NAD was approximately 1.0, demonstrating that mRt6.1 is primarily a transferase. ADP-ribosylarginine hydrolase, which preferentially hydrolyzes the alpha-anomer of ADP-ribosylarginine, released [U-14C]arginine from ADP-ribosyl[U-14C]arginine synthesized by mRT6.1, consistent with the conclusion that mRt6.1 catalyzes a stereospecific Sn2-like reaction. Thus, mRt6.1 is an NAD:arginine ADP-ribosyltransferase capable of catalyzing a multiple turnover, stereospecific Sn2-like reaction.

On the mechanism of hydrolysis of sulfinate esters: oxygen isotope exchange and theoretical studies

A small but detectable amount of 18O loss at the sulfinyl oxygen was observed during acid hydrolysis of 18O-labelled methyl benzenesulfinate, while no detectable loss of the label was found during alkaline hydrolysis. The relative rates of the acid-catalysed isotope exchange and hydrolysis were evaluated to be about 1/200. This large difference in the rates seems to be incompatible with the reaction of water with the conjugate acid of the substrate protonated at the sulfinyl oxygen. A mechanism involving an SN2-like reaction at the sulfur through the protonation at the alkoxy oxygen of the substrate is proposed on the basis of theoretical calculations.

Phenoxenium ions: generations and reactions

The acid-catalyzed reaction of N-acyl- and N-sulfonylhydroxylamines with benzene proceeded smoothly to give C-C products; 2- and 4-hydroxybiphenyls. The reaction and the thermolysis of N-aryloxypyridinium salts involve common intermediates. The results of product analysis, the orientation of the reaction, effects of substituents on the nitrogen atom and on the phenyl ring suggested a mechanism involving a phenoxenium ion. The positive charge of the phenoxenium ion localized not on the oxygen atom but on the ortho and para carbons of the benzene ring. C-O product: diphenylethers are formed when the heterolysis of the N-O bonds is slow and the aromatic solvent has high nucleophilicity, suggesting an SN2-like reaction on the oxygen atom. The phenoxenium ions are also concerned with a rearrangement of O-arylhydroxylamine to 2-aminophenol. An ion-molecule pair involving phenoxenium ion and ammonia as an intermediate of the intramolecular ortho rearrangement.

Ion-molecule reactions in the gas phase. Part 1. Stereospecific nucleophilic substitution of tertiary alcohols by ammonia

A study of the chemical ionisation of two pairs of diastereoisomeric unsaturated tertiary alcohols with isobutane as the protonating gas shows that hydrogen bonding between the protonated hydroxy-group and the double bond can stabilize the quasi-molecular ion, if the geometry is correct. Therefore, it is possible to differentiate between two isomers. With ammonia, the most interesting phenomenon is an SN2-like reaction, in which the OH2+ group is replaced by NH3+, with Walden inversion.

Do cleavages of amides by serine proteases occur through a stepwise pathway involving tetrahedral intermediates?

The mechanism of the serine protease-catalyzed cleavage of amides (acylation) was examined in terms of the basicity of the functional groups participating in the catalysis. It is proposed that the reaction does not proceed through a stepwise pathway, as opposed to the cleavage of esters and anilides, which start with general base-catalyzed formation of the tetrahedral intermediate followed by its general acid-catalyzed breakdown. Instead, the proton abstracted from the hydroxyl group of the serine by the imidazolyl group of the histidine is donated to the nitrogen atom of the leaving group of the amide before the bond between the carbonyl carbon atom of the amide and the attacking serine oxygen atom is completed. Reactions proceed by a SN2-like reaction through the cooperation of acid catalysis by the imidazolyl cation and nucleophilic attack by the serine. The mechanisms of the enzymatic hydrolyses of anilides and esters proceed through a discrete tetrahedral intermediate, but the enzymatic hydrolyses of amides probably do not.