Structure, stability, and dynamics of canonical and noncanonical base pairs: quantum chemical studies

The importance of non-Watson-Crick base pairs in the three-dimensional structure of RNA is now well established. The structure and stability of these noncanonical base pairs are, however, poorly understood. We have attempted to understand structural features of 33 frequently occurring base pairs using density functional theory. These are of three types, namely (i) those stabilized by two or more polar hydrogen bonds between the bases, (ii) those having one polar and another C-H...O/N type interactions, and (iii) those having one H-bond between the bases and another involving one of the sugars linked to the bases. We found that the base pairs having two polar H-bonds are very stable as compared to those having one C-H...O/N interaction. Our quantitatively analysis of structures of these optimized base pairs indicates that they possess a different amount of nonplanarity with large propeller or buckle values as also observed in the crystal structures. We further found that geometry optimization does not modify the hydrogen-bonding pattern, as values of shear and open angle of the base pairs remain conserved. The structures of initial crystal geometry and final optimized geometry of some base pairs having only one polar H-bond and a C-H...O/N interaction, however, are significantly different, indicating the weak nature of the nonpolar interaction. The base pair flexibility, as measured from normal-mode analysis, in terms of the intrinsic standard deviations of the base pair structural parameters are in conformity with those calculated from RNA crystal structures. We also noticed that deformation of a base pair along the stretch direction is impossible for all of the base pairs, and movements of the base pairs along shear and open are also quite restricted. The base pair opening mode through alteration of propeller or buckle is considerably less restricted for most of the base pairs.     

A pH dependent transport and back transport of americium(III) through the cellulose triacetate composite polymer membrane of cyanex-301 and TBP: role of H-bonding interactions

Transport of Am(III) was studied through the composite polymer membrane of Cyanex-301 [bis(2,4,4-trimethylpentyl)dithiophosphinic acid] and tri-n-butylphosphate (TBP). Depending on the pH of the strip solution containing alpha-hydroxyisobutyric acid (AHIBA), the transport behaviour of Am(III) was changed significantly. After approximately 70% of the Am(III) transported to the strip side, interestingly, back transport of Am(III) was observed at a pH of 3.5. The back transport phenomenon was not so significant at pH 1 and 5.7. The back transport of Am(III) was attributed to the transport of AHIBA from strip to the feed side due to its interaction with TBP in the membrane and the attainment of Donnan equilibrium because of the presence of Na(+) in the feed as the driving ion. The experimental observations were rationalized using the hydrogen bonding interaction energies obtained through ab initio molecular orbital and DFT calculations.     

Optimization of separation and detection conditions for the multiresidue analysis of pesticides in grapes by comprehensive two-dimensional gas chromatography-time-of-flight mass spectrometry

A comprehensive GCxGC-TOFMS method was optimized for multiresidue analysis of pesticides using a combination of a non-polar (RTX-5MS, 10 m x 0.18 mm x 0.2 microm) and a polar capillary column (TR-50MS, 1 m x 0.1 mm x 0.1 microm), connected in series through a dual stage thermal modulator. The method resolved the co-elution problems as observed in full scan one-dimensional GC-MS analysis and allowed chromatographic separation of 51 pesticides within 24 min run time with library-searchable mass spectrometric confirmation. Four pesticides, viz. chlorpyrifos-methyl, vinclozoline, parathion-methyl and heptachlor could be baseline separated on GCxGC, which were otherwise closely eluting and interfering each other's detection in 1D GC-MS run. Similarly, it could be possible to separate myclobutanil, buprofezin, flusilazole and oxyfluorfen on GCxGC. Although in 1D GC-MS, these closely eluting compounds could be identified through deconvolution algorithm and 'peak-find' option of the Chromatof software but the spectral purity significantly improved on GCxGC analysis. Thorough optimization was accomplished for the oven temperature programming, ion source temperature and GCxGC parameters like modulation period, duration of hot pulses, modulation-offset temperature, acquisition rate, etc. to achieve best possible separation of the test compounds. The limit of detection significantly improved by 2-12 times on GCxGC-TOFMS against GC-TOFMS because of sharper and narrower peak shapes. The method was tested for grape matrix after preparing the samples using previously described method and recoveries of the entire test pesticides were within 70-110% at 10 ng/g level of fortification. GCxGC-TOFMS was found to be an excellent technique for library-based screening of pesticides with high accuracy and sensitivity.     

Temperature tunability of size in CdS nanoparticles and size dependent photocatalytic degradation of nitroaromatics

Size tunability of thiophenol capped CdS nanoparticles (NPs) has been achieved by controlling the temperatures in situ. Synthesis at 5 degrees C produced stable particles of smallest size having narrow size distribution and high photoluminescence quantum yield. The photoluminescence of thiophenol capped CdS NPs was quenched by the nitroaromatic compounds. The Stern-Volmer constant of dinitrobenzene was about 15-fold higher than nitrobenzene, which indicates that introduction of nitro groups in the benzene ring increases the quenching efficiency. Further, the as-prepared CdS NPs were found to display size dependent photocatalytic activity towards degradation of nitroaromatics. The catalytic efficiency of CdS quantum particles was quintupled with decrease in particle size from 5.8 to 3.8 nm. An empirical equation has been derived to correlate the catalytic efficiency of the nanoparticles with the twin factors operating in the quantum confinement regime: (i) change in surface to volume ratio and (ii) shift in conduction band edge.     

A Robust Electrochemical Sensor Based on Butterfly-shaped Silver Nanostructure for Concurrent Quantification of Heavy Metals in Water Samples

Heavy metals in drinking water have become a severe threat to human health. Detection of heavy metals has been achieved by electrochemical sensors that are modified with complex nanocomposites; however, reproducibility of these sensors is still a big challenge when applied in commercial settings. Here, a simple, very robust, and sensitive electrochemical sensor based on a screen-printed carbon electrode modified with butterfly-shaped silver nanostructure (AgNS/SPCE) has been developed for the concurrent determination of cadmium (II), lead (II), copper (II), and mercury (II) in water samples. The electrochemical behavior of the modified electrodes was investigated using cyclic voltammetry and differential pulse anodic stripping voltammetry. The AgNS/SPCE showed distinct peak potentials and a significant increase in the peak currents for all heavy metals, attributed to the high electrical conductivity and electrocatalytic activity of the synthesized butterfly-shaped AgNS. Moreover, the excellent stability and sensitivity towards simultaneous quantification of heavy metals have been obtained with detection limits of 0.4 ppb, 2.5 ppb, 7.3 ppb, and 0.7 ppb for Cd (II), Pb (II), Cu (II), and Hg (II), respectively. Besides, the constructed sensor was successfully applied to simultaneously quantify target heavy metals in spiked water samples. Owing to excellent sensitivity, high robustness, affordability, and fast response, the presented electrochemical sensor could be incorporated into a portable and miniaturized potentiostat device, making it a promising method for on-site water analysis.     

A brief review on <Emphasis Type="Italic">μ</Emphasis>SR studies of unconventional Fe- and Cr-based superconductors

Muon spin relaxation/rotation (μSR) is a vital technique for probing the superconducting gap structure, pairing symmetry and time reversal symmetry breaking, enabling an understanding of the mechanisms behind the unconventional superconductivity of cuprates and Fe-based high-temperature superconductors, which remain a puzzle. Very recently double layered Fe-based super- conductors having quasi-2D crystal structures and Cr-based superconductors with a quasi-1D structure have drawn considerable attention. Here we present a brief review of the characteristics of a few selected Fe- and Cr-based superconducting materials and highlight some of the major outstanding problems, with an emphasis on the superconducting pairing symmetries of these materials. We focus on μSR studies of the newly discovered superconductors ACa₂Fe₄As₄F₂ (A = K, Rb, and Cs), ThFeAsN, and A₂Cr₃As₃ (A = K, Cs), which were used to determine the superconducting gap structures, the presence of spin fluctuations, and to search for time reversal symmetry breaking in the superconducting states. We also briefly discuss the results of μSR investigations of the superconductivity in hole and electron doped BaFe₂As₂.     

Wilson–Sommerfeld quantization rule revisited

A fresh look at the origin of the Wilson–Sommerfeld quantization rule has been pursued to gain new insight. The rule is shown to provide states that satisfy several well‐known theorems of standard quantum mechanics. A few other useful results and scaling relations are also derived. They emerge to act as nice guiding rules of thumb in the course of rigorous computations. Certain features of true excited‐state densities can be understood. Goodness of approximate densities can be assessed. Compressed systems can be studied profitably. A route is also sketched that allows one to retrieve classical trajectories from near‐exact energy eigenfunctions for both bound and resonant states by exploiting this rule. Additionally, a discussion on semiclassical perturbation theory is presented emphasizing the asymptotic behavior. Pilot calculations demonstrate the success of the present endeavor under various circumstances. © 2001 John Wiley & Sons, Inc. Int J Quant Chem 82: 113–125, 2001     

Discussion on a possible neutrino detector located in India

We have identified some important and worthwhile physics opportunities with a possible neutrino detector located in India. Particular emphasis is placed on the geographical advantage with a stress on the complimentary aspects with respect to other neutrino detectors already in operation.     

Modeling quantum dynamics of photodetachment from closed‐shell anions: Static versus fluctuating well‐depth models

The electronic states of halide ions are modeled by a one‐dimensional Hamiltonian with a potential V(x)=−V₀e. The two parameters V₀ and σ are fixed by requiring V(x) to reproduce the experimentally observed ground‐state ionization potentials of the halide ions concerned. The potentials so generated are shown to support only one bound state in each case. The time‐dependent Fourier grid Hamiltonian method is used to follow the ionization dynamics in monochromatic light of fairly high intensities. The total Hamiltonian, in the most general case, reads H(t)=P/2m−V₀e−ϵ₀s(t)ex sin(ωt). For pulsed fields [s(t)=sin²(πt/t_p)], the computed ionization rate constants are seen to increase with increase in the peak intensity (ϵ₀) of the electric field of light. The possibility of additional transient bound states being generated at the high intensities of light and its possible consequences on the observed ionization rates are explored. The environmental effects on the dynamics are sought to be modeled by allowing the well depth (V₀) to fluctuate randomly [V₀(t)=V₀+ΔVR(t); R(t) randomly fluctuates between +1 and −1 with time, ΔV is fixed]. The ionization rate constants (k_ϵ) are shown to be significantly affected by fluctuations in V₀ and pass through a well‐defined minimum in each case for a certain specified frequency of fluctuation. An alternative model potential V(x)=−V₀e^−σx is also shown to yield similar results. ©1999 John Wiley & Sons, Inc. Int J Quant Chem 73: 469–478, 1999