Twist‐dependent stacking energy of base‐pair steps in B‐DNA geometry: A density functional theory approach

Stacking energy of all the 10 unique DNA base‐pair steps (bp step) are calculated using density functional theory within the ultrasoft pseudopotential plane wave method and local density approximation for the exchange‐correlation functional. We have studied the dependence of stacking energy on twist angle, an aspect found difficult to explain using classical theory. We have found that the twist angle for different bp steps at stacking energy minimum matches extremely well with the values of average twist obtained from B‐DNA crystal structure data. This indicates that the use of a proper quantum chemical method to calculate the π‐π electronic interactions may explain stacking energy without incorporating hydrophobic interaction through solvent or effect of backbone through pseudobond. From the twist angle‐dependent stacking energy profile, we have also generated the probability distributions of twist for all the bp steps and calculated the variance of the distribution. Our calculated variances show similar trend to that of the experimental data for which sufficient numbers of data are available. The TA, AT, and CG doublets show large variances among the 10 possible bp steps, indicating their maximum flexibility. This might be the case of unusual deformation observed at the TATA‐box while binding to TBP protein. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2008     

Perturbing π-clouds with Substituents to Study the Effects on Reaction Dynamics of gauche-1,3-Butadiene to Bicyclobutane Electrocyclization

The conical intersection (CI) governs the ultra-fast relaxation of excited states in a radiationless manner and are observed mainly in photochemical processes. In the current work, we investigated the effects of substituents on the reaction dynamics for the conversion of gauche-1,3-butadiene to bicyclobutane via photochemical electrocyclization. We incorporated both electron withdrawing (−F) and donating (−CH₃) groups in the conjugated system. In our study, we optimized the minimum energy conical intersection (MECI) geometries using the multi-configurational state-averaged CASSCF approach, whereas, to study the ground state reaction pathways for the substituted derivatives, dispersion corrected, B3LYP-D3 functional was used. The non-adiabatic surface hopping molecular dynamics simulations were performed to observe the behaviour of electronic states involved throughout the photoconversion process. The results obtained from the multi-reference second-order perturbation correction of energy at the XMS-CASPT2 level of theory, topography analysis, and non-adiabatic dynamics suggest that the −CH₃ substituted derivatives can undergo faster thermal conversion to the product in the ground state with a smaller activation energy barrier compared to −F substituted derivative. Our study also reveals that the GBUT to BIBUT conversion follows both conrotatory and disrotatory pathways, whereas, on substitution with −F or −CH₃, the conversion proceeds via the conrotatory pathway.     

On the decay of the ozonide radical in aqueous alkaline solutions

In flash photolysis of an oxygenated aqueous potassium persulphate solution at pH 12.5 the decay of the ozonide radical has been found to follow $\text{3}\text{2}$ order kinetics which has been explained by reactions O^?₃ + O^? ? 2 O^?₂ and O^?₃ + HO₂ → 2 O₂ + OH^?     

Confined systems and the modified virial theorem from semiclassical considerations

We show that two simple semiclassical strategies, one based on the Wilson–Sommerfeld rule and the other on the uncertainty principle, yield the exact modified form of the virial theorem for confined systems. An alternative, easier quantum mechanical route to arrive at this result is also sketched. Pilot calculations on confined oscillators reveal decisive trends. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

New pyridine carboxamide ligands and their complexation to copper(II). X-Ray crystal structures of mono-, di, tri- and tetranuclear copper complexes

Seven new pyridine dicarboxamide ligands H2L(1-7) have been synthesised from condensation reactions involving pyridine-2,6-dicarboxylic acid (H2dipic), pyridine-2,6-dicarbonyl dichloride or 2,6-diaminopyridine with heterocyclic amine or carboxylic acid precursors. Crystallographic analyses of N,N'-bis(2-pyridyl)pyridine-2,6-dicarboxamide monohydrate (H2L8 x H2O), N,N'-bis[2-(2-pyridyl)methyl]pyridine-2,6-dicarboxamide and N,N'-bis[2-(2-pyridyl)ethyl]pyridine-2,6-dicarboxamide monohydrate revealed extensive intramolecular hydrogen bonding interactions. 2,6-Bis(pyrazine-2-carboxamido)pyridine (H2L6) and 2,6-bis(pyridine-2-carboxamido)pyridine (H2L7) reacted with copper(II) acetate monohydrate to give tricopper(II) complexes [Cu3(L)2(mu2-OAc)2]. X-Ray crystallography confirmed deprotonation of the amidic nitrogen atoms and that the (L6,7)2- ligands and acetate anions hold three copper(II) ions in approximately linear fashion. H2L8. Reacted with copper(II) tetrakis(pyridine) perchlorate to give [Cu(L8)(OH2)]2 x 2H2O, in which (L8)2- was tridentate through the nitrogen atoms of the central pyridine ring and the deprotonated carboxamide groups at one copper centre, with one of the terminal pyridyl rings coordinating to the other copper atom in the dimer. The corresponding reaction using H2L7 gave [Cu3(L7)2(py)2][ClO4]2, which transformed during an attempted recrystallisation from ethanol under aerobic conditions to a tetracopper(II) complex [Cu4(L7)2(L7-O)2].     

Single‐phase TiO2 formation by plasma oxidation of titanium thin films

Synthesis of titanium oxide film by plasma oxidization of the metallic films is investigated. Argon/oxygen gas mixture in the pressure range 30 × 10^?2 mbar is used for plasma processing at a frequency of 250 kHz. The plasma‐oxidized films are annealed in a tube furnace in argon atmosphere to establish crystalline‐phase formation. X‐ray diffraction and Raman spectroscopic results manifest peaks corresponding to rutile TiO₂. Ultraviolet‐Visible (UV‐Vis) spectroscopic analysis confirms the bandgap of rutile TiO₂, and photoluminescence spectra exhibit peaks due to oxygen defects. Homogeneity across the film's thickness and the nature of the film substrate interface is studied by depth profiling acquired using secondary ion mass spectrometry. Copyright © 2015 John Wiley & Sons, Ltd.     

A new chelating resin containing 2-aminothiophenol: Synthesis characterization and determination of mercury in waste water using <Superscript>203</Superscript>Hg radiotracer

A new stable chelating resin was synthesized by incorporating 2-aminothiophenol into Merrifield polymer through C-N covalent bond and characterized by elemental analysis, IR and thermal study. The sorption capacity of the newly formed resin for Hg²⁺ as a function of pH has been studied using ²⁰³Hg radioisotope. The resin exhibits no affinity to alkali or alkaline earth metal ions and common anions. The separation of mercury(II) in presence of different alkali and alkaline earth metal ions (Na⁺, K⁺, Mg²⁺, Ca²⁺, Sr²⁺, Ba²⁺), common anions (ClO₄ ⁻, SO₄ ²⁻) and other diverse ions (Ag⁺, Cu²⁺, Pb²⁺, Fe³⁺, Ni²⁺ and Zn²⁺) has been checked. In column operation it has been observed that Hg²⁺ content of the waste water can be removed at usual pH of natural water. Mercury was determined by isotope dilution method and the concentration of Hg²⁺ in the waste water spiked with ²⁰³Hg was found to be 0.05 to 0.09 μg/ml.     

Electrokinetic actuation of an uncharged polarizable dielectric droplet in charged hydrogel medium

Electrokinetic transport of an uncharged nonconducting microsized liquid droplet in a charged hydrogel medium is studied. Dielectric polarization of the liquid drop under the action of an externally imposed electric field induces a non-homogeneous charge density at the droplet surface. The interactions of the induced surface charge of the droplet with the immobile charges of the hydrogel medium generates an electric force to the droplet, which actuates the drop through the charged hydrogel medium. A numerical study based on the first principle of electrokinetics is adopted. Dependence of the droplet velocity on its dielectric permittivity, bulk ionic concentration, and immobile charge density of the gel is analyzed. The surface conduction is significant in presence of charged gel, which creates a concentration polarization. The impact of the counterion saturation in the Debye layer due to the dielectric decrement of the medium is addressed. The modified Nernst–Planck equation for ion transport and the Poisson equation for the electric field is considered to take into account the dielectric polarization. A quadrupolar vortex around the uncharged droplet is observed when the gel medium is considered to be uncharged, which is similar to the induced charge electroosmosis around an uncharged dielectric colloid in free-solution. We find that the induced charge electrokinetic mechanism creates a strong recirculation of liquid within the droplet and the translational velocity of the droplet strongly depends on its size for the dielectric droplet embedded in a charged gel medium.     

Oscillating laminar electrokinetic flow in infinitely extended circular microchannels

This article addresses the problem of oscillating laminar electrokinetic liquid flow in an infinitely extended circular microchannel. Based on the Debye-Huckel approximation for low surface potential at the channel wall, a complex variable approach is used to obtain an analytical solution for the flow. The complex counterparts of the flow rate and the current are linearly dependent on the pressure gradient and the external electric field. This property is used to show that Onsager's principle of reciprocity continues to be valid (involving the complex quantities) for the stated problem. During oscillating pressure-driven flow, the electroviscous effect for a given value of the normalized reciprocal electrical double-layer (EDL) thickness is observed to attain a maximum at a certain normalized frequency. In general, an increasing normalized frequency results in a reduction of EDL effects, leading to (i). a volumetric flow rate in the case of streaming potential approaching that predicted by the theory without EDL effects, and (ii). a reduction in the volumetric flow rate in the case of electroosmosis.     

Anomalous behaviour in the SmA*–SmCA* pre‐transitional regime of a chiral swallow‐tailed antiferroelectric liquid crystal

The temperature‐ and electric field‐dependent dielectric relaxation and polarisation of a new chiral swallow tailed antiferroelectric liquid crystal, i.e. 1‐ethylpropyl (S)‐2‐{6‐[4‐(4′‐decyloxyphenyl)benzoyloxy]‐2‐naphthyl}propionate (abbreviated as EP10PBNP), were investigated. The electric field‐induced dielectric loss spectra of EP10PBNP revealed electroclinic and anomalous dielectric behaviour in the chiral smectic A (SmA*)–chiral antiferroelectric smectic C (SmC_A*) pre‐transitional regime. From an analysis of thermal hysteresis of the dielectric constant, electric field‐induced polarisation and dielectric loss spectra, the appearance of a ferrielectric‐like mesophase is observed followed by an unstable SmC_A* phase in the SmA*–SmC_A* pre‐transitional regime.