Rupa Mukhopadhyay

Heteroannulation through combined palladium catalysed and Friedel-Crafts reactions strategy: Synthesis of 3-alkylidene isoindolin-1-ones☆

Abstract The palladium-catalysed reactions of 2-iodobenzamides 1–5 with trimethylsilyl acetylene 6 led to 2-(2-trimethylsilyl)ethynyl benzamides 7–11 in excellent yields. The 2-(2-trimethylsilyl)ethynyl benzamides 7–11 underwent Friedel-Crafts reactions with acid chlorides 12–17 or anhydride 18 smoothly under mild conditions yielding the 3-alkylidene isoindolin-1-ones 19–38 .

Synthesis and characterization of water-soluble carbon nanotubes from mustard soot

Carbon nanotubes (CNT) has been synthesized by pyrolysing mustard oil using an oil lamp. It was made water-soluble (wsCNT) through oxidative treatment by dilute nitric acid and was characterized by SEM, AFM, XRD, Raman and FTIR spectroscopy. The synthesized wsCNT showed the presence of several junctions and defects in it. The presence of curved graphene structure (sp2) with frequent sp3 hybridized carbon is found to be responsible for the observed defects. These defects along with the presence of di- and tri-podal junctions showed interesting magnetic properties of carbon radicals formed by spin frustration. This trapped carbon radical showed ESR signal in aqueous solution and was very stable even under drastic treatment by strong oxidizing or reducing agents. Oxidative acid treatment of CNT introduced several carboxylic acid group functionalities in wsCNT along with the nicking of the CNT at different lengths with varied molecular weight. To evaluate molecular weights of these wsCNTs, an innovative method like gel electrophoresis using high molecular weight DNA as marker was introduced.

A convenient and highly regio and stereoselective method for the synthesis of (E)-3-alkylidene isobenzofuran-1(3H)-ones (phthalides)

Abstract 2-Iodobenzyl alcohol on treatment with acetylenic carbinols in the presence of a palladium catalyst and copper(I) iodide as a co-catalyst afforded disubstituted alkynes. Jones oxidation of the disubstituted alkynes led to (E)-3-alkylidene isobenzofuran-1(3H)-ones in good yields in a highly regio and stereoselective manner. The E-isomers were obtained exclusively instead of the more stable Z-isomers.

Structural effects of nogalamycin, an antibiotic antitumour agent, on DNA

The structural changes of DNA, induced by the antitumour antibiotic nogalamycin, have been studied by atomic force microscopy (AFM). The transformation in the tertiary structure of 4361bp long plasmid pBR322 DNA, after incubation with nogalamycin at 37 degrees C, has been monitored at the single molecule level. The AFM topographs of free DNA and the DNA-nogalamycin complex, incubated for 6, 12, 24, 36 and 48h, reveal a gradual change from the circular supercoiled form having strand crossovers to the more compact plectonemic superhelix. With increasing incubation time, the extent of plectonemic coiling increases, indicating increasing level of drug binding via intercalative mode. Supportive evidences are obtained from the CD and UV-vis spectroscopic studies. To our knowledge, this is the first report on an AFM imaging study of the effects of nogalamycin, an anthracyclin intercalator, on DNA.

An atomic force microscopy investigation on self-assembled peptide nucleic acid structures on gold(111) surface

Peptide Nucleic Acid (PNA) is an important alternative nucleic acid, which exhibits more effective DNA/RNA detection capabilities compared to DNA. Its potential utility in nucleic acid based detection technologies warrants detail understanding of its self-assembly behavior on solid substrates, e.g., gold. In the present study, we have applied high-resolution Atomic Force Microscopy (AFM) for obtaining direct visual information on PNA adsorption and formation of a self-assembled monolayer of PNA on gold(111) surface. We show from the molecularly resolved AFM data that PNA molecules form a well-defined 1-dimensional molecule-by-molecule ordering, over a considerable length scale (few hundred nm), as well as 2-dimensional ordering over a wide area of about 10 μm×10 μm, due to parallel positioning of the 1-dimensional ordered arrangements. The way the parameters like PNA concentration, incubation time, incubation temperature and PNA deposition methods can affect the formation of such ordered self-assembled PNA structures has been investigated. Some of the primary observations are that the minimum PNA concentration and incubation time for large scale (10 μm ×10 μm) 2-dimensional order formation are 0.5 μM and 4h, respectively. Furthermore, a dense and well-ordered layer over a large area could be better formed in case of immersion method compared to the droplet contact and droplet deposition methods. From the Reflection Absorption Infra Red Spectroscopy (RAIRS) data, indications for PNA concentration-driven reorientation of the PNA backbone towards more upright configuration on gold(111) surface, were obtained.

Heteroannulation through copper catalysis: a novel cyclisation leading to an unusual formation of 2-aroylquinoxalines

N-[(3′-Aryl)prop-2′-ynyl]-N,N′-1,2-phenylene di-p-tosylamides, 15–22, underwent an unusual ring closure with potassium carbonate (2 equiv.) and copper(I) iodide (10 mol%) in DMF at 100°C for 24 h to yield 2-aroylquinoxalines (23–30) instead of the expected 2-alkylidene-1,4-di-tosyl-1,2,3,4-tetrahydroquinoxalines (31).

Near-metallic behavior of warm holoferritin molecules on a gold(111) surface.

Ferritin, the iron-storage protein, holds great potential for bioelectronic applications because of the presence of an electronically conducting iron core. We have applied scanning tunneling microscopy (STM), a high-resolution imaging method based on direct tunneling, to visualize the ferritin molecules both in the iron-containing holo form and in the iron-free apo form, and we have probed the electron flow through the two forms of this protein by measuring the current-voltage response using scanning tunneling spectroscopy (STS). Clear distinctions could be made among the current-voltage responses of the metallic gold(111) substrate surface, holoferritin molecules, and apoferritin molecules at room temperature. When warmed to the near-physiological temperature of 40 °C, the current-voltage response of the holoferritin molecules exhibited no band gap resembling near-metallic behavior, and the apoferritin molecules exhibited only a reduced band gap.

Solid-state electron transport in Mn-, Co-, holo-, and Cu-ferritins: force-induced modulation is inversely linked to the protein conductivity.

In this work, solid-state electron transport through the three metal core reconstituted ferritins, namely, Mn(III)-ferritin, Co(III)-ferritin, and Cu(II)-ferritin, has been probed and compared to the electron transport via the naturally-occurring iron-containing holoferritin and the metal-free apoferritin using current sensing atomic force spectroscopy (CSAFS), which allows direct contact to be established with the protein molecules. The CSAFS results reveal that by applying compressional force, in varying degrees (17-66 nN) and for varying durations (1 min, 2 min, and 3 min), the electronic conductivity of these proteins can be increased (for greater amount of force applied or for prolonged application of force) or decreased (for lesser amount of force applied or for shorter application time). The compressional modulation of the electronic conductivities appears to be due to compression of the protein part. The observation of the order of electronic conductivities of Mn-, holo-, Co-, and Cu-ferritins at almost any specific force value being similar to that of the free metal conductivities indicates that the absolute conductivity values are directly influenced by the metal core. Importantly, we found that more conductive the protein is, less modulated it can be. These findings could be highly relevant in realizing metalloprotein-based bioelectronic devices, especially where the electrode-protein-electrode sandwich configurations are employed.

Compacting effect of BBR3464, a new-generation trisplatinum anticancer agent, on DNA

BBR3464 is a trinuclear platinum compound of formula [{trans-PtCl(NH(3))(2)}(2)-mu-trans-Pt(NH(3))(2){NH(2)(CH(2))(6)NH(2)}(2)](4+). It is a new-generation platinum chemotherapeutic agent that exhibits cytotoxicity at ten to thousand times lower dose limit compared to the well-known platinum drug cisplatin, in cisplatin-sensitive as well as in cisplatin-resistant cells. DNA is thought to be the primary cellular target of BBR3464. In this work, we have applied high-resolution atomic force microscopy (AFM) for the first time, to obtain direct information on BBR3464-induced structural changes of DNA. It is found that the DNA molecules get compacted after treatment with BBR3464, for the drug:DNA molar ratio and the drug treatment period of 0.01 and 48 h, respectively. These values of molar ratio and incubation period have been obtained previously, as a result of biochemical optimization studies carried out for achieving maximum drug effects. The DNA structural changes, as observed in AFM topographs, have been correlated to the bulk level spectroscopic information. A remark on the significance of BBR3464-induced DNA compaction with respect to the available AFM reports on DNA modification by cisplatin has been made.

Tunable 3D and 2D polystyrene nanoparticle assemblies using surface wettability, low volume fraction and surfactant effects

Polymer-based nanopatterning on metal surfaces is of increasing importance to a number of applications, including biosensors, bioelectronic devices and medical implants. Here we show that polycrystalline gold surfaces can be functionalized with monocomponent nanoparticle (NP) assemblies by a simple drop deposition method. Ordered 3D hexagonal close-packed structures consisting of 350 nm polystyrene (PS) NPs on hydrophobically modified gold surfaces from solutions of very low volume fraction (varphi = 0.0006) were obtained as a result of capillary force induced self-assembly, whilst 2D self-assembly of PS NPs was generated over large area on hydrophilic gold and TiO(2) surfaces by spin coating. Furthermore, we show that when Triton X-100 is added to the PS NP suspending medium longer range ordering is obtained. Our observations may initiate interesting applications in the areas of nanoengineering of metal-based sensors and as a means to design new nanostructures for biocompatible implant surfaces.