Modulation of pyrene fluorescence in DNA probes depends upon the nature of the conformationally restricted nucleotide

The DNA probes (ODNs) containing a 2'-N-(pyren-1-yl)-group on the conformationally locked nucleosides [2'-N-(pyren-1-yl)carbonyl-azetidine thymidine, Aze-pyr (X), and 2'-N-(pyren-1-yl)carbonyl-aza-ENA thymidine, Aza-ENA-pyr (Y)], show that they can bind to complementary RNA more strongly than to the DNA. The Aze-pyr (X) containing ODNs with the complementary DNA and RNA duplexes showed an increase in the fluorescence intensity (measured at lambda em approximately 376 nm) depending upon the nearest neighbor at the 3'-end to X [dA ( approximately 12-20-fold) > dG ( approximately 9-20-fold) > dT ( approximately 2.5-20-fold) > dC ( approximately 6-13-fold)]. They give high fluorescence quantum yields (Phi F = 0.13-0.89) as compared to those of the single-stranded ODNs. The Aza-ENA-pyr (Y)-modified ODNs, on the other hand, showed an enhancement of the fluorescence intensity only with the complementary DNA (1.4-3.9-fold, Phi F = 0.16-0.47); a very small increase in fluorescence is also observed with the complementary RNA (1.1-1.7-fold, Phi F = 0.17-0.22), depending both upon the site of the Y modification introduced as well as on the chemical nature of the nucleobase adjacent to the modification site into the ODN. The fluorescence properties, thermal denaturation experiments, absorption, and circular dichroism (CD) studies with the X- and Y-modified ODNs in the form of matched homo- and heteroduplexes consistently suggested (i) that the orientation of the pyrene moiety is outside the helix of the nucleic acid duplexes containing a dT-d/rA base pair at the 3'-end of the modification site for both X and Y types of modifications, and (ii) that the microenvironment around the pyrene moiety in the ODN/DNA and ODN/RNA duplexes is dictated by the chemical nature of the conformational constraint in the sugar moiety, as well as by the nature of neighboring nucleobases. The pyrene fluorescence emission in both X and Y types of the conformationally restricted nucleotides is found to be sensitive to a mismatched base present in the target RNA: (i) The X-modified ODN showed a decrease ( approximately 37-fold) in the fluorescence intensity (measured at lambda em approximately 376 nm) upon duplex formation with RNA containing a G nucleobase mismatch (dT-rG pair instead of dT-rA) opposite to the modification site. (ii) In contrast, the Y-modified ODN in the heteroduplex resulted in a approximately 3-fold increase in the fluorescence intensity upon dT-rG mismatch, instead of matched dT-rA pair, in the RNA strand. Our data corroborate that the pyrene moiety is intercalated in the X-modified mismatched ODN/RNA (G mismatch) heteroduplex as compared to that of the Y-modified ODN/RNA (G mismatch) heteroduplex, in which it is located outside the helix.     

Characterization of an LED based photoreactor to degrade 4-chlorophenol in an aqueous medium using coumarin (C-343) sensitized TiO2

A detailed performance evaluation of a simple high intensity LED based photoreactor exploiting a narrow wavelength range of the LED to match the spectrum of a dye in a photocatalysis system is reported. A dye sensitized (coumarin-343, lambda max = 446 nm) TiO 2 photocatalyst was used for the degradation of 4-chlorophenol (4-CP) in an aqueous medium using the 436 nm LED based photoreactor. The LED reactor performed competitively with a conventional multilamp reactor and sunlight in the degradation of 4-CP. Light intensities entering the reaction vessel were measured by conventional ferrioxalate actinometry. The results can be fitted by approximate first order kinetic behavior in this system. Hydroxyl radicals were detected by spin trapping EPR, and effects of OH radical quenchers on kinetics suggest that the reaction is initiated by these radicals or their equivalents. LEDs operating at competitive intensities offer a number of advantages to the photochemist or the environmental engineer via long life, efficient current to light conversion, narrow bandwidth, forward directed output, and direct current power for remote operation. Matching light source spectrum to chromophore is a key.     

Terpyridine Based Heteroleptic Ruthenium Complexes: Influence of Donor and Acceptor Ligands in Photosensitization

We report heteroleptic ruthenium complexes of terpyridine (tpy) ligands with directly linked carboxylic acid anchors. These complexes feature methyl or methoxy-substituted ^4′−Phtpy as donor ligands. We prepared these heteroleptic complexes from the ruthenium (II) precursor via a milder route to preclude the homoleptic complex formation. The donor−acceptor arrangement of tpy ligands in these ruthenium complexes renders visible light absorption giving metal and ligand-to-ligand charge transfer excitations at c.a. 490 nm. We evaluate the effect of the tpy donor substituents on the light-harvesting ability in Dye-Sensitized Solar Cells (DSSCs) and compare their photosensitizing ability with heteroleptic complexes bearing phenyl spacer at the acceptor end. Further, scrutinizing their photovoltaic performance, we studied their electron transfer kinetics in DSSCs using electrochemical impedance spectroscopy. This paper presents the structure-photosensitization relationship of these heteroleptic ruthenium complexes through a combined experimental and computational approach.     

A Method of Computing the PI Index of Benzenoid Hydrocarbons Using Orthogonal Cuts

The Padmakar–Ivan (PI) index of a graph G is defined as PI , where for edge e=(u,v) are the number of edges of G lying closer to u than v, and is the number of edges of G lying closer to v than u and summation goes over all edges of G. The PI index is a Wiener–Szeged-like topological index developed very recently. In this paper, we describe a method of computing PI index of benzenoid hydrocarbons (H) using orthogonal cuts. The method requires the finding of number of edges in the orthogonal cuts in a benzenoid system (H) and the edge number of H – a task significantly simpler than the calculation of PI index directly from its definition. On the eve of 70th anniversary of both Prof. Padmakar V. Khadikar and his wife Mrs. Kusum Khadikar.     

Population Balance Model for Miniemulsion Polymerization, 2

Summary: The predictions of the model developed in Part 1 of this series are compared with experimental values taken from literature. Initially, the method of solution of the population balance equation and the simulation algorithm are given. Various radical entry mechanisms are discussed in adequate detail. Plausible arguments are given to identify the correct radical entry mechanism. An expression to evaluate the radical exit coefficient is given. Model predictions of a number of variables are discussed. These include average number of radicals per particle, particle phase monomer volume fraction, average number of radicals averaged over all particles, monomer volume fraction averaged over all particles, variation of nucleation rate, variation of fraction of droplets nucleated, variation of average diameter, variation of standard deviation, variation of polydispersity index, and development of particle size distribution with time. Finally, model predictions for the variation of conversion with time for five different initiator concentrations, number average diameter, standard deviation and full distribution are compared with experimental values.

Variation in the average number of radicals per particle with time, at different collocation points.     

Rubidium uranium trisulphate: A new chemical assay standard for uranium

Rubidium uranium trisulphate [Rb₂U(SO₄)₃] was prepared as a high purity compound of uranium in different lots of 250 g each. The compound was characterised and evaluated by chemical, atomic spectrosopic, infrared, X-ray diffraction and thermogravimetric methods for its use as a chemical assay standard for uranium. The compound is stoichiometric, pure, homogeneous and stable in atmospheric conditions. The solubility studies showed that Rb₂U(SO₄)₃ is easily soluble in mineral acids. An experiment based on Randomised Block Design was carried out to assign a value to the uranium content in Rb₂U(SO₄)₃ from the statistically analysed chemical data. The assigned value of [34.167±0.042]% to the uranium content is in close agreement with the theoretical value of 34.152%. Based on these studies, Rb₂U(SO₄)₃ is recommended as a chemical assay standard for uranium.     

Imaging in turbid media using quasi-ballistic photons

We study by means of experiments and Monte Carlo simulations, the scattering of light in random media, to determine the distance up to which photons travel along almost undeviated paths within a scattering medium, and are therefore capable of casting a shadow of an opaque inclusion embedded within the medium. Such photons are isolated by polarisation discrimination wherein the plane of linear polarisation of the input light is continuously rotated and the polarisation preserving component of the emerging light is extracted by means of a Fourier transform. This technique is a software implementation of lock-in detection. We find that images may be recovered to a depth far in excess of that predicted by the diffusion theory of photon propagation. To understand our experimental results, we perform Monte Carlo simulations to model the random walk behaviour of the multiply scattered photons. We present a new definition of a diffusing photon in terms of the memory of its initial direction of propagation, which we then quantify in terms of an angular correlation function. This redefinition yields the penetration depth of the polarisation preserving photons. Based on these results, we have formulated a model to understand shadow formation in a turbid medium, the predictions of which are in good agreement with our experimental results.     

Numerical simulation of low loss silicon photonic wire waveguide with multiple cladding layers

A different silicon photonic wire waveguide is proposed, which uses multiple thin cladding layers in order to reduce the index contrast between core and cladding interface. The reduced index contrast in the proposed waveguide has led to reduction in the scattering losses by 37% as compared to silicon wire waveguide for 400 nm × 220 nm waveguide dimension. The proposed waveguide has shown significant reduction in bending losses. It offers the bending loss of 0.0118 dB at the radius of 1 μm and 0.0063 dB for a radius of 2 μm at 1.55 μm wavelength as compared to 0.086 and 0.013 dB at the radius of 1 and 2 μm, respectively, offered by silicon photonic wire waveguide at 1.5 μm wavelength. The use of polymer material as top cladding layer resulted in decreasing the sensitivity of effective index against temperature for the designed waveguide by a factor of 2 as compared to silicon wire waveguide.