Insights into colistin-mediated fluorescence labelling of bacterial LPS.

Gram-negative bacterial infections are becoming untreatable due to their ability to mutate, and the gradual development of their resistance to the available antimicrobials. In recent times colistin, a drug of last resort, started losing its efficacy towards multidrug-resistant bacterial infections. Colistin targets bacterial endotoxin lipopolysaccharides (LPS) and destabilises the cytoplasmic membrane by disrupting the outer LPS membrane. In this study, we have tried to label the bacterial LPS, the main constituent of the cytoplasmic membrane of bacterial cells, to try to understand the interaction mechanism of LPS with colistin. The chemosensor, naphthaldehyde appended furfural (NAF) that selectively recognises colistin can label LPS, by showing its fluorescence signals. The computationally derived three-dimensional structure of LPS has been introduced to speculate on the possible binding mode of colistin with LPS, and this was also thoroughly studied with the help of quantum mechanics and molecular dynamics energy minimisation. Fluorescence microscopy and FE-SEM microscopic studies were also used to observe the change in the structural morphology of colistin-sensitive and resistant Salmonella typhi in different experimental conditions.

Mechanistic insight highlights the key steps and significance of metal in Ir(III)-catalysed C-H activated chromones generation.

A mild C-H activation reaction catalysed by an Ir(III)-complex to generate chromones from salicylaldehydes at room temperature has been studied theoretically to explore the reaction mechanism. The DFT study reveals that the key point of the catalytic cycle is cyclometallation, more precisely it is in the C-H metallation step where the significance of the metal becomes obvious. The favourable pathway includes several steps, namely, coordination of the substrate with the metal catalyst, O-H metallation, C-H metallation, denitrogenation, migration insertion, proton transfer, and demetallation. On removal of one pivalic acid, the metal is activated and the C-H metallation proceeds via oxidative addition followed by reductive elimination. The DFT study clearly indicated that, although there are two possibilities for cyclometallation, it only proceeds via O-H metallation followed by stepwise C-H metallation. The effect of substituents on the mechanism was also been studied. The low energetic span obtained for this catalytic cycle implies that the reaction can proceed at room temperature, and this is consistent with the experimental result.

Acetic Acid-Catalyzed Regioselective C(sp2)-H Bond Functionalization of Indolizines: Concomitant Involvement of Synthetic and Theoretical Studies.

An atom economical and environmentally benign protocol has been developed for the regioselective C(sp2)-H bond functionalization of indolizines. The acetic acid-catalyzed cross-coupling reaction proceeds under metal-free conditions, producing a wide range of synthetically useful indolizine derivatives. The present protocol showed good functional group tolerance and broad substrate scope in good to excellent yields. Quantum mechanical investigation using density functional theory (DFT) has played a crucial role in understanding that acetic acid is the key player in determining the actual pathway as the catalyst and its ultrafast nature. Different pathways involving inter- and intramolecular proton transfer, with or without acetic acid, were investigated. Calculated results revealed that a proton shuttle mechanism is involved for the least energetic, most favorable acetic acid-catalyzed pathway. Furthermore, regioselectivity has also been explained theoretically.

A Zn(II)-Coordination Polymer for the Instantaneous Cleavage of Csp3-Csp3 Bond and Simultaneous Reduction of Ketone to Alcohol.

Two coordination polymers of Zn(II) and Cu(II) with n-butylmalonic acid have been achieved in this work. The crystallographic structural descriptions along with the sedimentary rock-type microstructural morphology of these two coordination polymers (CPs) have been explored. The reactivity of ß-hydroxy ketones with these two CPs has also been investigated. The Zn(II)-CP shows a specific reactivity with ß-hydroxy ketone at room temperature and in open air conditions. Through a microcolumn-based filtration technique, the Zn(II)-CP shows the capability to break the Csp3-Csp3 σ bonds of ß-hydroxy ketone and simultaneously reduce the associated ketone to alcohol. Such conversion has been progressed without the use of any additional external reducing agent and any chemical workup or column chromatographic purification protocol. Other similar type CPs of Cu(II) and Mn(II) with n-butylmalonic acid completely failed to show similar reactivity with ß-hydroxy ketone. On the basis of much experimental evidence, the most possible mechanistic pathway of the reactivity between ß-hydroxy ketone and Zn(II)-CP has also been proposed through this work.

A semiconducting supramolecular Co(ii)-metallohydrogel: an efficient catalyst for single-pot aryl-S bond formation at room temperature.

A novel mechanically stable supramolecular Co(ii)-metallohydrogel has been synthesized. Cobalt(ii) nitrate hexahydrate and monoethanolamine, as a low molecular weight organic gelator, are used to get the gel. The mechanical stability of the supramolecular hydrogel was analyzed. The morphology of the supramolecular metallohydrogel was scrutinized. The semiconducting features of the metallohydrogel were studied. The conducting properties of the Co(ii)-metallohydrogel establish a Schottky barrier diode type nature. The catalytic nature of the Co(ii)-metallohydrogel based room temperature single pot aryl-S coupling reaction was explored. Most interestingly, the Co(ii)-metallohydrogel based catalytic aryl-S coupling reaction does not require any column-chromatographic purification protocol to get pure aryl-thioethers. Thus, through this work a semiconducting Schottky barrier diode application and catalytic role in the room temperature single pot aryl-S coupling reaction of a supramolecular Co(ii)-metallohydrogel have been explored.

Au-Catalyzed Hexannulation and Pt-Catalyzed Pentannulation of Propargylic Ester Bearing a 2-Alkynyl-phenyl Substituent: A Comparative DFT Study.

The mechanistic pathways of metal-catalyzed pentannulation and hexannulation of aromatic enediyne were studied quantum mechanically with Pt and Au salts. In agreement with the experimental facts, our result shows that the pentannulation favors over the hexannulation under Pt-catalyzed conditions and the reverse possibility favors when the Pt salt is replaced with an Au one. The Pt-catalyzed reaction involves a long-range acyl migration that follows the cyclization step. Our study reveals that such migration takes place under the assistance of a ligand of the metal atom. Moreover, the variation of aromaticity (probed by the change of the nucleus-independent chemical shift (0) value) in the cyclization steps shows that both processes maintain the development of the aromatic character of the generated intermediate during the progress of the reaction.

Theoretical Study on the Mechanism of Rearrangement Reactions of Bicyclic Derivatives of Cyclopropane to Monocyclic Derivatives under the Catalysis of Pt-Salt.

In this paper, the mechanistic studies on the isomerization of hydroxyl and silyl derivatives of bicyclic cyclopropanes under the catalytic action of Zeise's salt have been reported. The catalytic activity of both the monomeric and the dimeric forms of Zeise's salt has been studied by applying the high-level quantum mechanical method. Results from this investigation reveal that the reaction goes favorably under the catalysis of the dimeric form of Zeise's salt. The calculated activation barrier for the catalytic process using Zeise's dimer reveals that the rearrangement occurs with an activation barrier of 19-25 kcal mol-1. Depending on the nature of substituents present on the substrate, formation of various products has been explained. This study also includes the heteronuclear counter part of Zeise's dimer where one of the Pt-metals is replaced by palladium (Pd) and nickel (Ni) successively. The calculated activation barrier using these heteronuclear catalysts is found to be close enough to that calculated for the catalytic pathway using Zeise's dimer.

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.

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

An endo-ß-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 K(m) and V(max) 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 ß-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.

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.

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.

Theoretical studies on the pyridoxal-5'-phosphate dependent enzyme dopa decarboxylase: effect of thr 246 residue on the co-factor-enzyme binding and reaction mechanism.

Decarboxylation of amino acid is a key step for biosynthesis of several important cellular metabolites in the biological systems. This process is catalyzed by amino acid decarboxylases and most of them use pyridoxal-5'-phosphate (PLP) as a co-factor. PLP is bound to the active site of the enzyme by various interactions with the neighboring amino acid residues. In the present investigation, density functional theory (DFT) and real-time dynamics studies on both ligand-free and ligand-bound dopa decarboxylases (DDC) have been carried out in order to elucidate the factors responsible for facile decarboxylation and also for proper binding of PLP in the active site of the enzyme. It has been found that in the crystal structure Asp271 interacts with the pyridine nitrogen atom of PLP through H-bonding in both native and substrate-bound DDC. On the contrary, Thr246 is in close proximity to the oxygen of 3-OH ofPLP pyridine ring only in the substrate-bound DDC. In the ligand-free enzyme, the distance between the oxygen atom of 3-OH group of PLP pyridine ring and oxygen atom of Thr246 hydroxyl group is not favorable for hydrogen bonding. Thus, present study reveals that hydrogen bonding with 03 of PLP with a hydrogen bond donor residue provided by the enzyme plays an important role in the decarboxylation process.