Cross metathesis on olefin-terminated monolayers on Si(111) using the Grubbs' catalyst

This paper reports the functionalization and patterning of olefin-terminated monolayers on Si(111) through cross metathesis. A simple, one-step synthesis of a diolefin--CH2=CH(CH2)9O(CH2)9CH=CH2--was developed from commercially available starting materials. Mixed partially olefin-terminated monolayers of this novel diolefin and 1-octadecene on hydrogen-terminated Si(111) were obtained. The olefins are raised above the rest of the monolayer and thus sterically accessible for further functionalization. Olefin-terminated monolayers were reacted with the Grubbs' first generation catalyst and olefins in solution that were terminated with fluorines, carboxylic acids, alcohols, aldehydes, and alkyl bromides. Characterization of these monolayers using X-ray photoelectron spectroscopy and horizontal attenuated total reflection infrared spectroscopy demonstrated that olefins on the surface had reacted via cross metathesis to expose fluorines, carboxylic acids, aldehydes, alcohols, and bromides. Through calibration experiments, we demonstrated a simple 1:1 correspondence between the ratio of olefins in solution used in the assembly and the final composition of the mixed monolayers. Finally, these monolayers on silicon were patterned on the micrometer-size scale by soft lithography using microfluidic channels patterned into poly(dimethylsiloxane) (PDMS) stamps. Micrometer-wide lines of polymer brushes were synthesized on these monolayers and characterized by scanning electron microscopy. In addition, olefin-terminated monolayers were patterned into micrometer-sized lines exposing carboxylic acids by cross metathesis with olefins in solution. This method of patterning is broadly applicable and can find applications in a variety of fields including the development of biosensors and nanoelectronics.     

A physicochemical model for analyzing DNA sequences

In search of an ab initio model to characterize DNA sequences as genes and nongenes, we examined some physicochemical properties of each trinucleotide (codon), which could accomplish this task. We constructed three-dimensional vectors for each double-helical trinucleotide sequence considering hydrogen-bonding energy, stacking energy, and a third parameter, which we provisionally identified with DNA-protein interactions. As this three-dimensional vector moves along any genome, the net orientation of the resultant vector should differ significantly for gene and nongene regions to make a distinction feasible, if the underlying model has some merits. An analysis of 331 prokaryotic genomes comprising a total of 294 786 experimentally verified genes (nonoverlapping) and an equal number of nongenes presents a proof of concept of the model without the need for further parametrization. Also, initial analyses on Saccharomyces cerevisiae and Arabidopsis thaliana suggest that the methodology is extendable to eukaryotes. The physicochemical model (ChemGenome1.0) introduced has the potential to be developed into a gene-finding algorithm and, more pressingly, could be employed for an independent assessment of the annotation of DNA sequences.     

pH-induced Conformational Isomerization of Bovine Serum Albumin Studied by Extrinsic and Intrinsic Protein Fluorescence

Serum albumins are multi-domain all α-helical proteins that are present in the circulatory system and aid in the transport of a variety of metabolites, endogenous ligands, drugs etc. Earlier observations have indicated that serum albumins adopt a range of reversible conformational isomers depending on the pH of the solution. Herein, we report the concurrent changes in the protein conformation and size that are inherent to the pH-induced conformational isomers of bovine serum albumin (BSA). We have investigated the fluorescence properties of both intrinsic (tryptophan) and extrinsic (ANS, pyrene) fluorophores to shed light into the structural features of the pH-dependent conformers. We have been able to identify a number of conformational isomers using multiple fluorescence observables as a function of pH titration. Our results indicate that at pH 3, a partially-folded, ‘molten-globule-like’ state is populated. Moreover, equilibrium unfolding studies indicated that the ‘molten-globule-like’ state unfolds in a non-cooperative fashion and is thermodynamically less stable than the native state. The fluorescence-based approach described in the present work has implications in the study of pH-induced conformational plasticity of other physiologically relevant proteins.     

Time delay factor can be used as a key factor for preventing the outbreak of a disease—Results drawn from a mathematical study of a one season eco-epidemiological model

Chatterjee and Chattopadhyay [Role of migratory bird population in an simple eco-epidemiological model, Math. Comp. Model. Dyn. Syst., in press] proposed and analyzed a one season eco-epidemiological model of susceptible and infective prey together with their predators. In such systems, time lags due to the gestation of the infective prey are of importance. In this paper we modify and analyze their model by taking this factor into consideration. Our analysis shows that the outbreak of the disease can be controlled by a careful and suitable increment of the time lag factor. Moreover, to preserve the stability of the coexisting equilibrium, the time lag factor plays an important role. To substantiate our analytical results, extensive numerical simulations are performed for a hypothetical set of parameter values.     

Luminescence,Plasmonic, and Magnetic Properties of Doped Semiconductor Nanocrystals

Introducing a few atoms of impurities or dopants in semiconductor nanocrystals can drastically alter the existing properties or even introduce new properties. For example, mid-gap states created by doping tremendously affect photocatalytic activities and surface controlled redox reactions, generate new emission centers, show thermometric optical switching, make FRET donors by enhancing the excited state lifetime, and also create localized surface plasmon resonance induced low energy absorption. In addition, researchers have more recently started focusing their attention on doped nanocrystals as an important and alternative material for solar energy conversion to meet the current demand for renewable energy. Moreover, the electrical and magnetic properties of the host are also strongly altered on doping. These beneficial dopant-induced changes suggest that doped nanocrystals with proper selections of dopant–host pairs may be helpful for generating designer materials for a wide range of current technological needs. How properties relate to the doping of a variety of semiconductor nanocrystals are summarized in this Review.     

Organic Donor–Acceptor Assemblies form Coaxial p–n Heterojunctions with High Photoconductivity

The formation of coaxial p–n heterojunctions by mesoscale alignment of self‐sorted donor and acceptor molecules, important to achieve high photocurrent generation in organic semiconductor‐based assemblies, remains a challenging topic. Herein, we show that mixing a p‐type π gelator (TTV) with an n‐type semiconductor (PBI) results in the formation of self‐sorted fibers which are coaxially aligned to form interfacial p–n heterojunctions. UV/Vis absorption spectroscopy, powder X‐ray diffraction studies, atomic force microscopy, and Kelvin‐probe force microscopy revealed an initial self‐sorting at the molecular level and a subsequent mesoscale self‐assembly of the resulted supramolecular fibers leading to coaxially aligned p–n heterojunctions. A flash photolysis time‐resolved microwave conductivity (FP‐TRMC) study revealed a 12‐fold enhancement in the anisotropic photoconductivity of TTV/PBI coaxial fibers when compared to the individual assemblies of the donor/acceptor molecules.     

Surfactant mediated sulfide estimation at trace level: Application to environmental samples

A simple spectrophotometric method has been developed for the quantification of dissolved sulfide based on its reaction with ferric iron and the subsequent reaction of ferrous iron with 1-nitroso-2-naphthol in alkaline medium. The insoluble iron(II)-ligand complex has been solubilized in micellar medium using neutral surfactant which facilitates the non extraction step. The method obeys Beer??s law in the concentration range 0.5?C8 ??g in 10 mL of aqueous phase. The complex showed an absorption maximum at 710 nm with ?? value of 4.11 × 10⁴ L/mol cm. The detection limit has been found to be 0.0036 ??g/mL. The interference of common cations and anions has been studied and the proposed method has been successfully applied to determine the sulfide in different sewage water samples.     

Structure and dynamics of a molecular hydrogel derived from a tripodal cholamide

Tripodal cholamide 1 is a supergelator of aqueous fluids. A variety of physical techniques, including cryo-transmission electron microscopy (TEM), circular dichroism (CD), steady-state fluorescence, time-resolved fluorescence, and dynamic light-scattering, were employed to understand the structure and dynamics of the gel. Fluorescent probes [ANS (8-anilinonaphthalene-1-sulfonic acid) and pyrene] reported two critical aggregation concentrations (CAC(1) and CAC(2)) of 1 in predominantly aqueous media, with the minimum gel concentration (MGC) being close to CAC(2). Fluorescence lifetime measurements with pyrene revealed ineffective quenching of pyrene fluorescence by oxygen, possibly caused by slower Brownian diffusion due to the enhanced viscosity in the gel phase. The study of the gelation kinetics by monitoring the ultrafast dynamics of ANS revealed a progressive increase in the aggregate size and the microviscosity of the aqueous pool encompassed by the self-assembled fibrillar network (SAFIN) during the gelation. The striking difference between microviscosity and bulk (macroscopic) viscosity of the gel is also discussed.     

A new pentacyclic pyrylium fluorescent probe that responds to pH imbalance during apoptosis

Efficient fluorophores with easy synthetic routes and fast responses are of great importance in clinical diagnostics. Herein, we report a new, rigid pentacyclic pyrylium fluorophore, PS-OMe, synthesised in a single step by a modified Vilsmeier–Haack reaction. Insights into the reaction mechanism facilitated a new reaction protocol for the efficient synthesis of PS-OMe which upon demethylation resulted in a “turn-on” pH sensor, PS-OH. This new fluorescent probe has been successfully used to monitor intracellular acidification at physiological pH. From the fluorescence image analysis, we were able to quantify the intracellular dynamic pH change during apoptosis. This new pH probe is a potential chemical tool for screening, drug discovery and dose determination in cancer therapy.

A modified Vilsmeier–Haack reaction resulted in the synthesis of a pyrylium based turn-on fluorescent pH probe. The probe can monitor minute acidification and dynamic pH variation in cells during apoptosis with therapeutic chemo drugs.