Mutagenicity associated with O6-methylguanine-DNA damage and mechanism of nucleotide flipping by AGT during repair

Methylated guanine damage at O6 position (i.e. O6MG) is dangerous due to its mutagenic and carcinogenic character that often gives rise to G:C-A:T mutation. However, the reason for this mutagenicity is not known precisely and has been a matter of controversy. Further, although it is known that O6-alkylguanine-DNA alkyltransferase (AGT) repairs O6MG paired with cytosine in DNA, the complete mechanism of target recognition and repair is not known completely. All these aspects of DNA damage and repair have been addressed here by employing high level density functional theory in gas phase and aqueous medium. It is found that the actual cause of O6MG mediated mutation may arise due to the fact that DNA polymerases incorporate thymine opposite to O6MG, misreading the resulting O6MG:T complex as an A:T base pair due to their analogous binding energies and structural alignments. It is further revealed that AGT mediated nucleotide flipping occurs in two successive steps. The intercalation of the finger residue Arg 128 into the DNA double helix and its interaction with the O6MG: C base pair followed by rotation of the O6MG nucleotide are found to be crucial for the damage recognition and nucleotide flipping.

Synthesis and metallic probe induced conductance of Au tipped ultranarrow PbS rods

Au tipped ultranarrow PbS nanorods are synthesized. DFT electronic structure calculations and transport studies show that Au probes modify the nature and energies of PbS nanorod orbitals creating efficient electron conduction channels for enhanced conductance even at low applied bias.

A study of phase separation in ternary alloys

We have studied the evolution of microstructure when a disordered ternary alloy is quenched into a ternary miscibility gap. We have used computer simulations based on multicomponent Cahn-Hilliard (CH) equations for c(A) and c(B), the compositions (in mole fraction) of A and B, respectively. In this work, we present our results on the effect of relative interfacial energies on the temporal evolution of morphologies during spinodal phase separation of an alloy with average composition, c(A) = 1/4, c(B) = 1/4 and c(C) = 1/2. Interfacial energies between the 'A' rich, 'B' rich and 'C' rich phases are varied by changing the gradient energy coefficients. The phases associated with a higher interfacial energy are found to be more rounded than those with lower energy. Further, the kinetic paths (i.e. the history of A-rich, B-rich and C-rich regions in the microstructure) are also affected significantly by the relative interfacial energies of the three phases.

High-pressure studies on lithium fast-ion conductors

The variation of resistivity of the lithium fast-ion conductor Li3+y Ge1−yO4 (y = 0.25, 0.6, 0.72) has been studied with hydrostatic pressure up to 70 kbar and compared with that of Li16−2x Znx (GeO4)4(x = 1, 2). Both types showed pronounced resistivity maxima between 20–30 kbar and marked decrease thereafter. Measurements as a function of temperature between 120–300 K permitted the determination of activation energies and prefactors that also showed corresponding maxima. The activation volumes (ΔV) of the first type of compound varied between 4.34 to −4.90 cm3/mol at 300 K and decreased monotonically with increasing temperature. For the second type ΔV was much smaller, varied with pressure between 0.58 and −0.24 cm3/mol, and went through a maximum with increasing temperature. High-pressure studies were also conducted on aged samples, and the results are discussed in conjunction with results of impedance measurements and nuclear magnetic resonance (NMR) studies. The principal effect of pressure appears to be variations of the sum of interatomic potentials and hence barrier height, which also causes significant changes in entropy.

Two-channel Kondo physics in odd impurity chains

We study odd-membered chains of spin-1/2 impurities, with each end connected to its own metallic lead. For antiferromagnetic exchange coupling, universal two-channel Kondo (2CK) physics is shown to arise at low energies. Two overscreening mechanisms are found to occur depending on coupling strength, with distinct signatures in physical properties. For strong interimpurity coupling, a residual chain spin-1/2 moment experiences a renormalized effective coupling to the leads, while in the weak-coupling regime, Kondo coupling is mediated via incipient single-channel Kondo singlet formation. We also investigate models in which the leads are tunnel-coupled to the impurity chain, permitting variable dot filling under applied gate voltages. Effective low-energy models for each regime of filling are derived, and for even fillings where the chain ground state is a spin singlet, an orbital 2CK effect is found to be operative. Provided mirror symmetry is preserved, 2CK physics is shown to be wholly robust to variable dot filling; in particular, the single-particle spectrum at the Fermi level, and hence the low-temperature zero-bias conductance, is always pinned to half-unitarity. We derive a Friedel-Luttinger sum rule and from it show that, in contrast to a Fermi liquid, the Luttinger integral is nonzero and determined solely by the ``excess'' dot charge as controlled by gate voltage. The relevance of the work to real quantum dot devices, where interlead charge-transfer processes fatal to 2CK physics are present, is also discussed. Physical arguments and numerical renormalization-group techniques are used to obtain a detailed understanding of these problems.

Nature and strength of C-H center dot center dot center dot O interactions involving formyl hydrogen atoms: computational and experimental studies of small aldehydes

Structural and electronic properties of C-H center dot center dot center dot O contacts in compounds containing a formyl group are investigated from the perspective of both hydrogen bonding and dipole-dipole interactions, in a systematic and graded approach. The effects of a-substitution and self-association on the nature of the formyl H-atom are studied with the NBO and AIM methodologies. The relative dipole-dipole contributions in formyl C-H center dot center dot center dot O interactions are obtained for aldehyde dimers. The stabilities and energies of aldehyde clusters (dimer through octamer) have been examined computationally. Such studies have an implication in crystallization mechanisms. Experimental X-ray crystal structures of formaldehyde, acrolein and N-methylformamide have been determined in order to ascertain the role of C-H center dot center dot center dot O interactions in the crystal packing of formyl compounds.

Identity, energetics, dynamics and environment of interfacial water molecules in a micellar solution

The structure and energetics of interfacial water molecules in the aqueous micelle of cesium perfluorooctanoate have been investigated, using large-scale atomistic molecular dynamics simulations, with the primary objective of classifying them. The simulations show that the water molecules at the interface fall into two broad classes: bound and free, present in a ratio of 9:1. The bound water molecules can be further categorized on the basis of the number of hydrogen bonds (one or two) that they form with the surfactant headgroups. The hydrogen bonds of the doubly hydrogen-bonded species are found to be, on the average, slightly weaker than those in the singly bonded species. The environment around interfacial water molecules is more ordered than that in the bulk. The surface water molecules have substantially lower potential energy, because of interaction with the micelle. In particular, both forms of bound water have energies that are lower by �2.5-4.0 kcal/ mol. Entropy is found to play an important role in determining the relative concentration of the species.

Kinetics of catalytic degradation of polycarbonate in benzene

The degradation kinetics of polycarbonate [poly(bisphenol A carbonate)] in benzene catalyzed by commercial (rutile) TiO2 (BET surface area = 11 m(2)/g), anatase TiO2 (156 m(2)/g), and 1 atom % Pt/TiO2 (111 m2/g), prepared by the solution combustion technique, was investigated at various temperatures (230-280 degreesC) and 50 atm. The time evolution of the molecular weight distribution (MWD) was determined by gel permeation chromatography (GPC) and modeled with continuous distribution kinetics to obtain the degradation rate coefficients. The rate coefficients for the catalytic degradation of polycarbonate increased by factors of 20, 3.5, and 1.3 compared to the rate coefficients for thermal degradation when catalyzed by nanosized TiO2 anatase, Pt/TiO2 anatase, and commercial TiO2, respectively, at 280 degreesC. The increased catalytic activity of combustion for synthesized TiO2 and 1% Pt/TiO2 might be due to the increased acidity and BET surface area. The activation energies, determined from the temperature dependencies of the rate coefficients, were 16.3, 21.5, and 39.1 kcal/mol for commercial TiO2, combustion-synthesized Pt/TiO2, and anatase TiO2, respectively.

Electric Field Directed Growth of Molecular Wires of Charge Transfer Molecules on Prefabricated Metal Electrodes

Molecular wires of charge transfer molecules were formed by co-evaporating the 7 7 8 8-Tetracyanoquinodimethane [TCNQ] (acceptor) and Tetrathiafulvalene [TTF] (donor) molecules across prefabricated metal electrodes. Molecular wires of TTF TCNQ were also formed by evaporating single complex of TTF:TCNQ across prefabricated metal electrodes The prefabricated metal electrodes were made using electron beam lithography on SiO2 and glass cover slip substrates. Even though TTF: TCNQ wires grown from both co-evaporation and evaporation techniques show semiconductor like behavior in temperature dependence of resistance they show different activation energies due the difference in stoichiometry of TTF and TCNQ.

Dark Matter Halo Properties as Deduced from the Observed H I Scale Height Data, in The Low-Frequency Radio Universe

We use the HΙ scale height data along with the HΙ rotation curve as constraints to probe the shape and density profile of the dark matter halos of M31 (Andromeda) and the superthin, low surface brightness (LSB) galaxy UGC 07321. We model the galaxy as a two component system of gravitationally-coupled stars and gas subjected to the force field of a dark matter halo. For M31, we get a flattened halo which is required to match the outer galactic HΙ scale height data, with our best-fit axis ratio (0.4) lying at the most oblate end of the distributions obtained from cosmological simulations. For UGC 07321, our best-fit halo core radius is only slightly larger than the stellar disc scale length, indicating that the halo is important even at small radii in this LSB galaxy. The high value of the gas velocity dispersion required to match the scale height data can explain the low star-formation rate of this galaxy.

Structural Variability in the Monofluoroethynylbenzenes Mediated through Interactions Involving ``Organic'' Fluorine

Competition among weak intermolecular interactions can lead to polymorphism, the appearance of various crystalline forms of a substance with comparable cohesive energies. The crystal structures of 2-fluorophenylacetylene (2FPA) and 3-fluorophenylacetylene (3FPA), both of which are liquids at ambient conditions, have been determined by in situ cryocrystallization. Both compounds exhibit dimorphs, with one of the forms observed in common, P2(1), Z = 2 and the other form being Pna2(1), Z = 4 for 2FPA and P2(1)/c, Z = 12 for 3FPA. Variations in the crystal structures of the dimorphs of each of these compounds arise from subtle differences in the way in which weak intermolecular interactions such as C-H center dot center dot center dot pi and C-H center dot center dot center dot F are manifested. The interactions involving ``organic'' fluorine, are entirely different from those in the known structure of 4-fluorophenylacetylene (4FPA), space group P2(1)/c, Z = 4. The commonalities and differences in these polymorphs of 2FPA and 3FPA have been analyzed in terms of supramolecular synthons and extended long-range synthon aufbau module (LSAM) patterns. These structures are compared with the three polymorphs of phenylacetylene, in terms of the T-shaped C-H center dot center dot center dot pi interaction, a feature common to all these structures.

Structure and Bonding in Stannadiphospholes and their Dianions SnC(2)P(2)R(2)(m) (R=H, tBu m=0,-2): A Comparative Study with C(5)H(5)(+) and C(5)H(5)(-) Analogues

The potential energy surfaces of both neutral and dianionic SnC(2)P(2)R(2) (R=H, tBu) ring systems have been explored at the B3PW91/LANL2DZ (Sn) and 6-311 + G* (other atoms) level. In the neutral isomers the global minimum is a nido structure in which a 1,2-diphosphocyclobutadiene ring (1,2-DPCB) is capped by the Sn. Interestingly, the structure established by Xray diffraction analysis, for R=tBu, is a 1,3-DPCB ring capped by Sn and it is 2.4 kcal mol(-1) higher in energy than the 1,2-DPCB ring isomer. This is possibly related to the kinetic stability of the 1,3-DPCB ring, which might originate from the synthetic precursor ZrCp(2)tBu(2)C(2)P(2). In the case of the dianionic isomers we observe only a 6 pi-electron aromatic structure as the global minimum, similarly to the cases of our previously reported results with other types of heterodiphospholes.([1,4,19]) The existence of large numbers of cluster-type isomers in neutral and 6 pi-planar structures in the dianions SnC(2)P(2)R(2)(2-) (R=H, tBu) is due to 3D aromaticity in neutral clusters and to 2D pi aromaticity of the dianionic rings. Relative energies of positional isomers mainly depend on: 1) the valency and coordination number of the Sn centre, 2) individual bond strengths, and 3) the steric effect of tBu groups. A comparison of neutral stannadiphospholes with other structurally related C(5)H(5)(+) analogues indicates that Sn might be a better isolobal analogue to P(+) than to BH or CH(+). The variation in global minima in these C(5)H(5)(+) analogues is due to characteristic features such as 1) the different valencies of C, B, P and Sn, 2) the electron deficiency of B, 3) weaker p pi-p pi bonding by P and Sn atoms, and 4) the tendency of electropositive elements to donate electrons to nido clusters. Unlike the C5H5+ systems, all C(5)H(5)(-) analogues have 6 pi-planar aromatic structures as global minima. The differences in the relative ordering of the positional isomers and ligating properties are significant and depend on 1) the nature of the pi orbitals involved, and 2) effective overlap of orbitals.

Size dependent microstructure for Ag-Ni nanoparticles

The Ag-Ni system is characterized by large differences in atomic sizes (14%) and a positive heat of mixing (+23 kJ mol(-1)). The binary equilibrium diagram for this system therefore exhibits a large miscibility gap in both solid and liquid state. This paper explores the size-dependent changes in microstructure and the suppression of the miscibility gap which occurs when free alloy particles of nanometer size are synthesized by co-reduction of Ag and Ni metal precursors. The paper reports that complete mixing between Ag and Ni atoms could be achieved for smaller nanoparticles (<7 nm). These particles exhibit a single-phase solid solution with face-centered cubic (fcc) structure. With increase in size, the nanoparticles revealed two distinct regions. One of the regions is composed of pure Ag. This region partially surrounds a region of fcc solid solution at an early stage of decomposition. Experimental observations were compared with the results obtained from the thermodynamic calculations, which compared the free energies corresponding to a physical mixture of pure Ag and Ni phases and a fcc Ag-Ni solid solution for different particle sizes. Results from the theoretical calculations revealed that, for the Ag-Ni system, solid solution was energetically preferred over the physical mixture configuration for particle sizes of 7 nm and below. The experimentally observed two-phase microstructure for larger particles was thus primarily due to the growth of Ag-rich regions epitaxially on initially formed small fcc Ag-Ni nanoparticles. (C) 2011 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Surface effects on stacking fault and twin formation in fcc nanofilms: A first-principles study

The free surface effects on stacking fault and twin formation in fcc metals (Al, Cu, and Ni) were examined by first-principles calculations based on density functional theory (DFT). It is found that the generalized planar fault (GPF) energies of Ni are much larger than bulk Ni with respect to Al and Cu. The discrepancy is attributed to the localized relaxation of Ni nanofilm to accommodate the large expansion of the inter-planar separation induced at the fault plane. The localized relaxation can be coupled to the electronic structure of Ni nanofilms. (C) 2011 Elsevier B.V. All rights reserved.

New Insights into Selective Heterogeneous Nucleation of Metal Nanoparticles on Oxides by Microwave-Assisted Reduction: Rapid Synthesis of High-Activity Supported Catalysts

Microwave-based methods are widely employed to synthesize metal nanoparticles on various substrates. However, the detailed mechanism of formation of such hybrids has not been addressed. In this paper, we describe the thermodynamic and kinetic aspects of reduction of metal salts by ethylene glycol under microwave heating conditions. On the basis of this analysis, we identify the temperatures above which the reduction of the metal salt is thermodynamically favorable and temperatures above which the rates of homogeneous nucleation of the metal and the heterogeneous nucleation of the metal on supports are favored. We delineate different conditions which favor the heterogeneous nucleation of the metal on the supports over homogeneous nucleation in the solvent medium based on the dielectric loss parameters of the solvent and the support and the metal/solvent and metal/support interfacial energies. Contrary to current understanding, we show that metal particles can be selectively formed on the substrate even under situations where the temperature of the substrate Is lower than that of the surrounding medium. The catalytic activity of the Pt/CeO(2) and Pt/TiO(2) hybrids synthesized by this method for H(2) combustion reaction shows that complete conversion is achieved at temperatures as low as 100 degrees C with Pt-CeO(2) catalyst and at 50 degrees C with Pt-TiO(2) catalyst. Our method thus opens up possibilities for rational synthesis of high-activity supported catalysts using a fast microwave-based reduction method.