Gourab Kanti Das

Mechanism of the Gold(III)-Catalyzed Isomerization of Substituted Allenes to Conjugated Dienes: A DFT Study

The mechanism of gold(III) [Au(III)]-catalyzed isomerization of alkyl-substituted allenes to conjugated dienes in the presence of a nitroso compound (additive) was studied quantum mechanically using hybrid density functional PBE0 with 6-31G** basis set for lighter atoms and (aug)-ccpVDZ basis set and LANL2 electron core potential for Au atom. Several pathways, involving the nitroso compound in a free or bound state to the gold-allene (GA) complex, were investigated. Calculated results reveal that the unbound nitroso compound acts as a better proton transferring agent in the isomerization process and utilizes its own nitrogen atom to carry the proton. While comparing the efficiency of other basic reagents to carry out the process, it appeared that the moderate basicity of the nitroso compound plays a crucial role to reduce the activation barrier of the reaction pathway. A similar pathway was also investigated using a gold(I) [Au(I)] catalyst and found to be less favorable than the process catalyzed by a Au(III) catalyst. All these facts agree well with the experimental reports for the reaction.

Ligand-assisted acyl migration in Au-catalyzed isomerization of propargylic ester to diketone: a DFT study.

Gold-catalyzed isomerization of propargylic ester to a diketone derivative is a fascinating example for the generation of the C-C bond in organoaurate chemistry as it is one of the few reactions that exploit the nucleophilicity of organoaurates to a migrating acyl group. The proposed mechanistic pathway, involving the formation of a four-membered intermediate, has never been substantiated by any theoretical or experimental evidence. Detailed theoretical calculation suggests that the formation of an alkylideneoxoniumcyclobutene intermediate is highly unlikely. Instead, an acyl migration, assisted by the chlorine ligand in the square planar geometry of metal complex offers an alternative mechanism that can justify the reasonable activation barrier and the associated stereochemical feature involved in the reaction. The initial mandatory steps of the catalytic process such as allene formation (af) and rotamerization of allene-bound gold complex (ra) are found to be quite facile. However, the final step, acyl migration (am), that takes place through the formation of an intermediate with C-Cl bond, acts as the rate-determining step of the reaction. The mechanism also justifies the lack of sufficient activity of Au(I) salt to catalyze the isomerization process.

Cloning, overexpression, and characterization of a novel alkali-thermostable xylanase from Geobacillus sp. WBI

An endo‐β‐1,4‐xylanase gene xynA of a thermophilic Geobacillus sp. WBI from “hot” compost was isolated by PCR amplification. The gene encoding 407 residues were overexpressed in E. coli and purified by Ni‐NTA chromatography. The purified enzyme (47 kDa) had a broad pH optimum of 6.0 to 9.0, and was active between 50 and 90 °C. The enzyme retained 100% of its activity when incubated at 65 °C for 1 h under alkaline condition (pH 10.0) and retained 75% activity at pH 11.0. The Km and Vmax of the enzyme were 0.9 mg ml−1 and 0.8 µmol ml−1 min−1, respectively. In molecular dynamics simulation at 338 K (65 °C), the enzyme was found to be stable. At an elevated temperature (450 K) specific α‐helix and β‐turns of the proteins were most denatured. The denaturation was less in WBI compared with its highest homolog G. stearothermophilus T‐6 xylanase with difference of six residues. The results predict that these regions are responsible for the improved thermostability observed over related enzymes. The present work encourages further experimental demonstration to understand how these regions contribute thermostability to WBI xylanase. The study noted that WBI produces a xylanase with unique characteristics, specifically alkali‐thermostability.

Utilization of MeOH as a C1 Building Block in Tandem Three-Component Coupling Reaction

Ru(II) catalyzed tandem synthesis of α-branched methylated ketones via multicomponent reactions following the hydrogen borrowing process is described. This nonphosphine-based air and moisture stable catalyst efficiently produced various methylated ketones using methanol as a methylating agent. This system was found to be highly effective in three-component coupling between methanol, primary alcohols, and methyl ketones. A proposed catalytic cycle for the α-methylation is supported by DFT calculations as well as kinetic experiments.

Ionic liquid supported acid additive stabilizes the transition structure of organocatalytic asymmetric direct aldol reaction by proton donation: A quantum mechanical study

ONIOM studies were performed on the transition structure (TS) of organocatalytic direct aldol reaction by using ionic liquid supported benzoic acid (ILS-PhCO2H) as an additive. Results obtained from this computation suggest direct involvement of ILS-PhCO2H in the TS as a proton donor. It has also come out from the present study that, the counter ion of the ILS-acid additive may also play significant role to maintain the proper TS geometry by holding the organocatalyst and the acid additive close together during the course of reaction.

DFT study on the mechanism of 1,3-hydrogen disposition in Isopentenyl pyrophosphate catalyzed by Isopentenyl pyrophosphate: Dimethylallyl pyrophosphate isomerase

Biosynthesis of polyterpenoid and related molecules are largely accomplished via mevalonate pathway. One of the vital steps in this pathway is the inter-conversion of two intermediates isopentenyl pyrophosphate (IPP) and dimethylallyl pyrophosphate (DMAPP) catalyzed by IPP:DMAPP isomerase (IDI). The crystal structure of the enzyme, bound to the substrate analogues and inhibitors, revealed possible mechanism of this inter-conversion; however, none of them could affirm the true nature of the transition state through which the process is taking place. Our DFT study on the pathway of this isomerization reaction at the active site of the enzyme suggests a favorable concerted mechanism that occurs through a single transition structure without generating any carbocation intermediate. In this mechanism, the Cys-67 residue acts as proton donor whereas Glu-116 acts as proton acceptor. The mechanism also reveals the active involvement of other two components present at the active site. A crystallographic water molecule (Wat508) and Glu-87 assist to reprotonate the conjugate base of cysteine residue through a proton shuttle mechanism while forming the transition structure of the isomerization reaction.

Study on first reported (2,5) ene cyclisation: does it really follow a concerted pathway?

Theoretical calculation reveals that the reported (2,5) ene cyclization reaction follows a stepwise pathway, which results in a thermodynamically less stable compound through intramolecular proton abstraction; the presence of an external molecule, capable of abstracting a proton, directs the reaction to form thermodynamically more stable compound as a major product.

Theoretical study on the mechanism of Robinson's synthesis of tropinonet

Ab initio quantum mechanical calculation reveals that the first Mannich reaction in Robinsons tropinone synthesis involves both carbon–carbon bond formation and water elimination, which is followed by tautomerisation and a second Mannich reaction to form the protonated tropinone.