Two new atom centered fragment descriptors and scoring function enhance classification of antibacterial activity

Classification of pharmacologic activity of a chemical compound is an essential step in any drug discovery process. We develop two new atom-centered fragment descriptors (vertex indices) - one based solely on topological considerations without discriminating atomor bond types, and another based on topological and electronic features. We also assess their usefulness by devising a method to rank and classify molecules with regard to their antibacterial activity. Classification performances of our method are found to be superior compared to two previous studies on large heterogeneous data sets for hit finding and hit-to-lead studies even though we use much fewer parameters. It is found that for hit finding studies topological features (simple graph) alone provide significant discriminating power, and for hit-to-lead process small but consistent improvement can be made by additionally including electronic features (colored graph). Our approach is simple, interpretable, and suitable for design of molecules as we do not use any physicochemical properties. The singular use of vertex index as descriptor, novel range based feature extraction, and rigorous statistical validation are the key elements of this study.

Effect Of Mo Doping On The Electrical Properties Of VO2 Phase

Solution combustion synthesis technique was adopted to synthesize V2O5, and Mo doped phases, The as-synthesized V2O5, has been reduced by a novel reduction technique to form VO2 typephase. The monophasic nature of the samples as revealed by XRD data and systematic shift in peak position indicated solid solubility up to 2 at % of Mo in VO2 lattice. The crystallite size was found to similar to 40 nm. Particle size measurement carried out using Transmission electron microscope ( TEM) agreed with XRD experiments. Scanning electron microscope revealed the morphology of the particles to be plate like and bimodal. Variation in the metal- insulator transition temperature as a function of doping was investigated by 4-probe electrical resistivity measurement on sintered ceramics.

C. N. R. Rao and the Growth of Solid State and Materials Chemistry as a Central Domain of Research

In celebrating Professor C. N. R. Rao's 80th birthday, this article recalls his singular contributions to solid state and materials chemistry for about sixty years. In so doing, the article also traces the growth of the field as a central domain of research in chemical sciences from its early origins in Europe. Although Rao's major work lies in solid state and materials chemistry - a field which he started and nurtured in India while its importance was being recognized internationally - his contributions to other areas of chemistry (and physics), viz., molecular spectroscopy, phase transitions, fullerenes, graphene, nanomaterials and multiferroics are equally significant. Illustrative examples of his work devoted to rare earth and transition metal oxides, defects and nonstoichiometry, metal-insulator transitions, investigation of crystal and electronic structures of a variety of solids by means of electron microscopies and photoelectron spectroscopy, superconducting cuprates, magnetoresistive manganites, multiferroic metal oxides of various structures and, last but not the least, development of new strategies for chemical synthesis of a wide variety of solids including nanomaterials and framework solids in different dimensionalities, are highlighted. The article also captures his exemplary role as a science teacher, science educationist and institution builder in post-Independence India.

Intermolecular interactions, charge-density distribution and the electrostatic properties of pyrazinamide anti-TB drug molecule: an experimental and theoretical charge-density study

An experimental charge-density analysis of pyrazinamide (a first line antitubercular drug) was performed using high-resolution X-ray diffraction data (sin theta/lambda)(max) = 1.1 angstrom(-1)] measured at 100 (2) K. The structure was solved by direct methods using SHELXS97 and refined by SHELXL97. The total electron density of the pyrazinamide molecule was modeled using the Hansen-Coppens multipole formalism implemented in the XD software. The topological properties of electron density determined from the experiment were compared with the theoretical results obtained from CRYSTAL09 at the B3LYP/6-31G** level of theory. The crystal structure was stabilized by N-H center dot center dot center dot N and N-H center dot center dot center dot O hydrogen bonds, in which the N3-H3B center dot center dot center dot N1 and N3-H3A center dot center dot center dot O1 interactions form two types of dimers in the crystal. Hirshfeld surface analysis was carried out to analyze the intermolecular interactions. The fingerprint plot reveals that the N center dot center dot center dot H and O center dot center dot center dot H hydrogen-bonding interactions contribute 26.1 and 18.4%, respectively, of the total Hirshfeld surface. The lattice energy of the molecule was calculated using density functional theory (B3LYP) methods with the 6-31G** basis set. The molecular electrostatic potential of the pyrazinamide molecule exhibits extended electronegative regions around O1, N1 and N2. The existence of a negative electrostatic potential (ESP) region just above the upper and lower surfaces of the pyrazine ring confirm the pi-electron cloud.

Evaluation of the intrinsic magneto-dielectric coupling in LaMn0.5Co0.5O3 single crystals

The magneto-dielectric coupling in (l00) oriented LaMn0.5Co0.5O3 single crystals has been investigated using temperature, frequency, and magnetic field dependent dielectric response. Electronic transport data divulges that polaronic hopping arises due to Emin-Holstein adiabatic small polarons. Spin realignment through external magnetic field favors faster polaronic hopping by lowering activation energy for dielectric relaxation. Finally, positive magneto-dielectricity and magnetoloss under increasing magnetic field at high frequency of the exciting ac field confirms intrinsic magneto-dielectric effect in disordered ferromagnetic-insulator LaMn0.5Co0.5O3. This study also emphasizes the need to use single crystals as well as the frequencies higher than the corresponding inverse relaxation time. (C) 2014 AIP Publishing LLC.

Influence of sputter power on structural and electrical properties of TiO2 films for Al/TiO2/Si gate capacitors

Titanium dioxide (TiO2) thin films were deposited onto p-Si substrates held at room temperature by reactive Direct Current (DC) magnetron sputtering at various sputter powers in the range 80-200W. The as-deposited TiO2 films were annealed at a temperature of 1023K. The post-annealed films were characterized for crystallographic structure, chemical binding configuration, surface morphology and optical absorption. The electrical and dielectric properties of Al/TiO2/p-Si structure were determined from the capacitance-voltage and current-voltage characteristics. X-ray diffraction studies confirmed that the as-deposited films were amorphous in nature. After post-annealing at 1023K, the films formed at lower powers exhibited anatase phase, where as those deposited at sputter powers >160W showed the mixed anatase and rutile phases of TiO2. The surface morphology of the films varied significantly with the increase of sputter power. The electrical and dielectric properties on the air-annealed Al/TiO2/p-Si structures were studied. The effect of sputter power on the electrical and dielectric characteristics of the structure of Al/TiO2/p-Si (metal-insulator-semiconductor) was systematically investigated. Copyright (c) 2014 John Wiley & Sons, Ltd.

Shape Memory Alloy based Active Chiral Composite Cells

Wing morphing is one of the emerging methodology towards improving aerodynamic efficiency of flight vehicle structures. In this paper a morphing structural element is designed and studied which has its origin in the well known chiral structures. The new aspect of design and functionality explored in this paper is that the chiral cell is actuated using thermal Shape Memory Alloy (SMA) actuator wires to provide directional motion. Such structure utilizes the potential of different actuations concepts based on actuator embedded in the chiral structure skin. This paper describes a new class of chiral cell structure with integrated SMA wire for actuation. Chiral topological constructs are obtained by considering passive and active load path decoupling and sub-optimal shape changes. Single cell of chiral honeycomb with actuators are analyzed using finite element simulation results and experiments. To this end, a multi-cell plan-form is characterized showing interesting possibilities in structural morphing applications. The applicability of the developed chiral cell to flexible wing skin, variable stiffness based design and controlling longitudinal-to-transverse stiffness ratio are discussed.

Frustration in Optical Lattices of Interacting Bosons

The realization of optical lattices of cold atoms has opened up the possibility of engineering interacting lattice systems of bosons and fermions, stimulating a frenzy of research over the last decade. More recently, experimental techniques have been developed to apply synthetic gauge fields to these optical lattices. As a result, it has become possible to study quantum Hall physics and the effects of frustration in lattices of cold atoms. In this article we describe the combined effect of frustration and interactions on the superfluidity of bosons. By focussing on a frustrated ladder of interacting bosons, we show that the effect of frustration is for ``chiral'' order to develop, which manifests itself as an alternating pattern of circulating supercurrents. Remarkably, this order persists even when superfluidity is lost and the system enters a Mott phase giving rise to a novel chiral Mott insulator. We describe the combined physics of frustration and interactions by studying a fully frustrated one dimensional model of interacting bosons. The model is studied using mean-field theory, a direct quantum simulation and a higher dimensional classical theory in order to offer a full description of the different quantum phases contained in it and transitions between the different phases. In addition, we provide physical descriptions of the chiral Mott insulator as a vortex-anitvortex super solid and indirect excitonic condensate in addition to obtaining a variational wavefunction for it. We also briefly describe the chiral Mott states arising in other microscopic models.

Evaluating FuncSION: A software for automated synthesis of design solutions for stimulating ideation during mechanical conceptual design

The goal of the work reported in this paper is to use automated, combinatorial synthesis to generate alternative solutions to be used as stimuli by designers for ideation. FuncSION, a computational synthesis tool that can automatically synthesize solution concepts for mechanical devices by combining building blocks from a library, is used for this purpose. The objectives of FuncSION are to help generate a variety of functional requirements for a given problem and a variety of concepts to fulfill these functions. A distinctive feature of FuncSION is its focus on automated generation of spatial configurations, an aspect rarely addressed by other computational synthesis programs. This paper provides an overview of FuncSION in terms of representation of design problems, representation of building blocks, and rules with which building blocks are combined to generate concepts at three levels of abstraction: topological, spatial, and physical. The paper then provides a detailed account of evaluating FuncSION for its effectiveness in providing stimuli for enhanced ideation.

Octahedral distortion induced magnetic anomalies in LaMn0.5Co0.5O3 single crystals

Single crystals of LaMn0.5Co0.5O3 belonging to the ferromagnetic-insulator and distorted perovskite class were grown using a four-mirror optical float zone furnace. The as-grown crystal crystallizes into an orthorhombic Pbnm structure. The spatially resolved 2D Raman scan reveals a strain-induced distribution of transition metal (TM)-oxygen (O) octahedral deformation in the as-grown crystal. A rigorous annealing process releases the strain, thereby generating homogeneous octahedral distortion. The octahedra tilt by reducing the bond angle TM-O-TM, resulting in a decline of the exchange energy in the annealed crystal. The critical behavior is investigated from the bulk magnetization. It is found that the ground state magnetic behavior assigned to the strain-free LaMn0.5Co0.5O3 crystal is of the 3D Heisenberg kind. Strain induces mean field-like interaction in some sites, and consequently, the critical exponents deviate from the 3D Heisenberg class in the as-grown crystal. The temperature-dependent Raman scattering study reveals strong spin-phonon coupling and the existence of two magnetic ground states in the same crystal. (C) 2014 AIP Publishing LLC.

Molecular topology of three ring nematogens from C-13-H-1 dipolar couplings

Molecules in their liquid crystalline phase undergo rotational motion about the long axis of the molecule and the shape adopted by the rotating molecule plays an important role in influencing the mesophase morphology. In this context, obtaining the topology and the relative orientation of the different sub-units are important steps. For studying the liquid crystalline phase, C-13 NMR spectroscopy is a convenient method and for certain specifically designed nematogens, 2-dimensional separated local field (2D-SLF) NMR spectroscopy provides a particularly simple and straightforward means of arriving at the molecular topology. We demonstrate this approach on two three ring based nematogens designed with a phenyl or a thiophene ring at one of the termini. From the C-13-H-1 dipolar couplings of the terminal carbon obtained using the 2D-SLF NMR technique, the order parameter of the local symmetry axis of the terminal phenyl ring as well as of the long molecular axis could be easily estimated. For the thiophene nematogen, the lack of symmetry of the thiophene moiety necessitates some additional computational steps. The results indicate that the thiophene unit has its local ordering axis oriented away from the long molecular axis by a small angle, consistent with a bent structure expected in view of the thiophene geometry. The experiment also demonstrates the ability of 2D-SLF NMR to provide high resolution spectra by separation of several overlapped resonances in terms of their C-13-H-1 dipolar couplings. The results are consistent with a rod-like topology of the core of the investigated mesogens. The investigation demonstrates the potential of 2D-SLF NMR C-13 spectroscopy for obtaining atomistic level information and its utility for topological studies of different mesogens.

On entanglement entropy functionals in higher-derivative gravity theories

In arXiv:1310.5713 1] and arXiv:1310.6659 2] a formula was proposed as the entanglement entropy functional for a general higher-derivative theory of gravity, whose lagrangian consists of terms containing contractions of the Riemann tensor. In this paper, we carry out some tests of this proposal. First, we find the surface equation of motion for general four-derivative gravity theory by minimizing the holographic entanglement entropy functional resulting from this proposed formula. Then we calculate the surface equation for the same theory using the generalized gravitational entropy method of arXiv:1304.4926 3]. We find that the two do not match in their entirety. We also construct the holographic entropy functional for quasi-topological gravity, which is a six-derivative gravity theory. We find that this functional gives the correct universal terms. However, as in the R-2 case, the generalized gravitational entropy method applied to this theory does not give exactly the surface equation of motion coming from minimizing the entropy functional.

Impact of Stone-Wales and lattice vacancy defects on the electro-thermal transport of the free standing structure of metallic ZGNR

We report the effect of topological as well as lattice vacancy defects on the electro-thermal transport properties of the metallic zigzag graphene nano ribbons at their ballistic limit. We employ the density function theory-Non equilibrium green's function combination to calculate the transmission details. We then present an elaborated study considering the variation in the electrical current and the heat current transport with the change in temperature as well as the voltage gradient across the nano ribbons. The comparative analysis shows, that in the case of topological defects, such as the Stone-Wales defect, the electrical current transport is minimum. Besides, for the voltage gradient of 0.5 Volt and the temperature gradient of 300 K, the heat current transport reduces by similar to 62 % and similar to 50% for the cases of Stones-Wales defect and lattice vacancy defect respectively, compared to that of the perfect one.

Characterization of Interactions Involving Bromine in 2,2-Dibromo2,3-dihydroinden-1-one via Experimental Charge Density Analysis

Experimental and theoretical charge density analyses on 2,2-dibromo-2,3-dihydroinden-1-one have been carried out to quantify the topological features of a short CBr....O halogen bond with nearly linear geometry (2.922 angstrom, angle CBr....O = 172.7 degrees) and to assess the strength of the interactions using the topological features of the electron density. The electrostatic potential map indicates the presence of the s-hole on bromine, while the interaction energy is comparable to that of a moderate OH....O hydrogen bond. In addition, the energetic contribution of CH.....Br interaction is demonstrated to be on par with that of the CBr....O halogen bond in stabilizing the crystal structure.

Computational Study of the Formation of Short Centrosymmetric N-center dot center dot center dot S Supramolecular Synthon and Related Weak Interactions in Crystalline 1,2,4-Triazoles

A comprehensive analysis of the crystal packing and the energetic features of a series of four biologically active molecules belonging to the family of substituted 4-(benzylideneamino)-3-(4-fluoro-3-phenoxyphenyl)-1H-1,2,4-triazole-5-(4 H)-thione derivatives have been performed based on the molecular conformation and the supramolecular packing. This involves the formation of a short centrosymmetric R-2(2)(8) NH...S supramolecular synthon in the solid state, including the presence of CH...S, CH...O, CH...N, CH...F, CH...Cl, CF...FC, CCl...ClC, and CH...pi intermolecular interactions along with pp stacking to evaluate the role of noncovalent interactions in the crystal. The presence of such synthons has a substantial contribution toward the interaction energy (-18 to -20 kcal/mol) as obtained from the PIXEL calculation, wherein the Coulombic and polarization contribution are more significant than the dispersion contribution. The geometrical characteristics of such synthons favor short distance, and the population of related molecules having these geometries is rare as has been obtained from the Cambridge Structural Database (CSD). Furthermore, their interaction energies have been compared with those present in our molecules in the solid state. The topological characteristics of the NH...S supramolecular synthon, in addition to related weak interactions, CH...N, CH...Cl, CF...FC, and CCl...ClC, have been estimated using the quantum theory of atoms in molecules (QTAIM). In addition, an analysis of the Hirshfeld surface and associated fingerprint plots of these four molecules also have provided a platform for the evaluation of the contribution of different atom...atom contacts, which contribute toward the packing of the molecules in solids.