Crystal structures and binding studies of atovaquone and its derivatives with cytochrome bc(1): a molecular basis for drug design

Crystal structure of trans-atovaquone (antimalarial drug), its polymorph and its stereoisomer (cis) along with five other derivatives with different functional groups have been analyzed. Based on the conformational features of these compounds and the characteristics of the nature of intermolecular interactions, valuable insights into the atomistic details of protein-inhibitor interactions have been derived by docking studies. Atovaquone and its derivatives pack in the crystal lattice using intermolecular O-H center dot center dot center dot O hydrogen bond dimer motifs supported by surrogate weak interactions including C-H center dot center dot center dot O and C-H center dot center dot center dot Cl hydrogen bonds. The docking results of these molecules with cytochrome bc(1) show preferences to form N-H center dot center dot center dot O, O-H center dot center dot center dot O and O-H center dot center dot center dot Cl hydrogen bonds. The involvement of halogen atoms in the binding pocket appears to be significant and is contrary to the theoretically predicted mechanism of protein-ligand docking reported earlier based on mimicking experimental binding results of stigmatellin with cytochrome bc(1). The significance of subtle energy factors controlled by weak intermolecular interactions appears to play a major role in drug binding.

Growth-temperature dependent physical properties of SnS nanocrystalline thin films

In this article we have demonstrated the influence of growth-temperature on the morphology and orientation of SnS films deposited by thermal evaporation technique. While increasing the growth-temperature, the morphology of SnS films changed from flakes-like nanocrystals to regular cubes, whereas their orientation shifted from <111> to <040> direction. The chemical composition of SnS films gradually changed from sulfur-rich to tin-rich with the increase of growth-temperature. The structural analyzes reveal that the crystal structure of SnS films probably changes from orthorhombic to tetragonal at the growth-temperature of about 410 degrees C. Raman studies show that SnS films grown at all temperatures consist of purely SnS phase, whereas the optical studies reveal that the direct optical bandgap of SnS films decreased with the increase of growth-temperature. From these results it has been emphasized that the morphology and orientation along with electrical and optical properties of nearly stoichiometric SnS films strongly depend on their growth-temperature.

Factors influencing stick-slip motion: effect of hardness, crystal structure and surface texture

In the present investigation, efforts were made to study the different frictional responses of materials with varying crystal structure and hardness during sliding against a relatively harder material of different surface textures and roughness. In the experiments, pins were made of pure metals and alloys with significantly different hardness values. Pure metals were selected based on different class of crystal structures, such as face centered cubic (FCC), body centered cubic (BCC), body centered tetragonal (BCT) and hexagonal close packed (HCP) structures. The surface textures with varying roughness were generated on the counterpart plate which was made of H-11 die steel. The experiments were conducted under dry and lubricated conditions using an inclined pin-on-plate sliding tester for various normal loads at ambient environment. In the experiments, it was found that the coefficient of friction is controlled by the surface texture of the harder mating surfaces. Further, two kinds of frictional response, namely steady-state and stick-slip, were observed during sliding. More specifically, stead-state frictional response was observed for the FCC metals, alloys and materials with higher hardness. Stick-slip frictional response was observed for the metals which have limited number of slip systems such as BCT and HCP. In addition, the stick-slip frictional response was dependent on the normal load, lubrication, hardness and surface texture of the counterpart material. However, for a given kind of surface texture, the roughness of the surface affects neither the average coefficient of friction nor the amplitude of stick-slip oscillation significantly.

Deformation behaviour at macro- and nano-length scales: The development of orientation gradients

The deformation behaviour of macrocrystalline and nanocrystalline nickel shows a striking similarity in terms of higher intragranular misorientation and a texture with dominant Brass component on rolling. This is in contrast to microcrystalline nickel, with lower intragranular misorientation and typical Copper type texture. This has been attributed to the free surfaces in macrocrystalline sample and grain boundaries in nanocrystalline sample. Experimental evidence of `Grain Boundary Affected Zone' (GBAZ) showing multi-slip in contrast to limited slip in the grain interiors has been provided. The similarity in evolution of texture and intragranular misorientation is explained on the basis of reduced contribution from the GBAZ at the two extreme length scales.

Crystal engineering: from molecule to crystal

How do molecules aggregate in solution, and how do these aggregates consolidate themselves in crystals? What is the relationship between the structure of a molecule and the structure of the crystal it forms? Why do some molecules adopt more than one crystal structure? Why do some crystal structures contain solvent? How does one design a crystal structure with a specified topology of molecules, or a specified coordination of molecules and/or ions, or with a specified property? What are the relationships between crystal structures and properties for molecular crystals? These are some of the questions that are being addressed today by the crystal engineering community, a group that draws from the larger communities of organic, inorganic, and physical chemists, crystallographers, and solid state scientists. This Perspective provides a brief historical introduction to crystal engineering itself and an assessment of the importance and utility of the supramolecular synthon, which is one of the most important concepts in the practical use and implementation of crystal design. It also provides a look to the future from the viewpoint of the author, and indicates some directions in which this field might be moving.

Crystal growth and nonlinear optical properties of sodium D-isoascorbate monohydrate

Optical quality single crystals of sodium D-isoascorbate monohydrate were grown by a slow cooling technique. The crystal possesses a bulky prismatic morphology. Thermal analyses indicate that the crystals are stable up to 125 degrees C. The optical transmission window ranges from 307 nm to 1450 nm. The principal refractive indices have been measured employing Brewster's angle method. The crystallographic and the principal dielectric axes coincide with each other such that a lies along Z, b along X and c along Y. The optic axis is oriented 58 degrees (at 532 nm) to the crystallographic a axis in the XZ plane and the crystal is negative biaxial. Type 1 and type 2 phase matching curves are generated and experimentally verified. No polarization dependence of the light absorption was observed confirming the validity of Kleinman's symmetry conjecture, leading to a single nonvanishing nonlinear tensor component. According to Hobden's classification the crystal belongs to class 3. The crystal also exhibits second order noncollinear conic sections. The single shot and multiple shot surface laser damage thresholds are determined to be 32.7 GW cm(-2) and 6.5 GW cm(-2) respectively for 1064 nm radiation.

A new 3D cadmium(II) coordination polymer having mu(4)-oxalato, mu-aquo and mu-chlorido bridges: crystal structure, solid state fluorescence and thermal behavior

A new 3D cadmium(II) coordination polymer, Cd(C2O4)(0.5)Cl(H2O)](n) (1) has been synthesized from a mixture of CdCl2. H2O and (NH4)(2)C2O4 in a slightly acidic pH. Its molecular structure was determined by single crystal X-ray diffraction which reveals that the new polymeric structure consists of simultaneous mu(4)-oxalato, mu-aquo, and mu-chlorido bridges between the metal centers, embedded in distorted pentagonal bipyramidal geometries. On thermal analysis compound exhibits high thermal stability up to 330 degrees C. Compound 1 also exhibits strong fluorescent emission. (c) 2013 Elsevier B.V. All rights reserved.

Photovoltaic structures using thermally evaporated SnS and CdS thin films

Polycrystalline tin sulfide thin films were prepared by thermal evaporation technique. The films grown at substrate temperature of 300 degrees C had an orthorhombic crystal structure with strong preferred orientation along (111) plane. Electrical resistivity of the deposited films was about 32.5 Omega cm with a direct optical band gap of 1.33 eV. Carrier concentration and mobility of charge carriers estimated from the Hall measurement were found to be 6.24 x 10(15) cm(-3) and 30.7 cm(2)V(-1) s(-1) respectively. Heterojunction solar cells were fabricated in superstrate configuration using thermally evaporated SnS as an absorber layer and CdS, In: CdS as window layer. The resistivity of pure CdS thin film of a thickness of 320 nm was about 1-2 Omega cm and was reduced to 40 x 10(-3) Omega cm upon indium doping. The fabricated solar cells were characterized using solar simulator. The solar cells with indium doped CdS window layer showed improved performance as compared to pure CdS window layer. The best device had a conversion efficiency of 0.4% and a fill factor of 33.5%. (C) 2013 Elsevier B.V. All rights reserved.

Understanding the role of domain-domain linkers in the spatial orientation of domains in multi-domain proteins

Inter-domain linkers (IDLs)' bridge flanking domains and support inter-domain communication in multi-domain proteins. Their sequence and conformational preferences enable them to carry out varied functions. They also provide sufficient flexibility to facilitate domain motions and, in conjunction with the interacting interfaces, they also regulate the inter-domain geometry (IDG). In spite of the basic intuitive understanding of the inter-domain orientations with respect to linker conformations and interfaces, we still do not entirely understand the precise relationship among the three. We show that IDG is evolutionarily well conserved and is constrained by the domain-domain interface interactions. The IDLs modulate the interactions by varying their lengths, conformations and local structure, thereby affecting the overall IDG. Results of our analysis provide guidelines in modelling of multi-domain proteins from the tertiary structures of constituent domain components.

The Role of Weak Interactions in the Phase Transition and Distinct Mechanical Behavior of Two Structurally Similar Caffeine Co-crystal Polymorphs Studied by Nanoindentation

Although weak interactions, such as C-H center dot center dot center dot O and pi-stacking, are generally considered to be insignificant, it is their reorganization that holds the key for many a solid-state phenomenon, such as phase transitions, plastic deformation, elastic flexibility, and mechanochromic luminescence in solid-state fluorophores. Despite this, the role of weak interactions in these dynamic phenomena is poorly understood. In this study, we investigate two co-crystal polymorphs of caffeine:4-chloro-3-nitrobenzoic acid, which have close structural similarity (2D layered structures), but surprisingly show distinct mechanical behavior. Form I is brittle, but shows shear-induced phase instability and, upon grinding, converts to Form II, which is soft and plastically shearable. This observation is in contrast to those reported in earlier studies on aspirin, wherein the metastable drug forms are softer and convert to stable and harder forms upon stressing To establish a molecular level understanding, have investigated the two co-crystal polymorphs I and II by single crystal X-ray diffraction, nanoindentation to quantify mechanical properties, and theoretical calculations. The lower hardness (from nanoindentation) and smooth potential surfaces (from theoretical studies) for shearing of layers in Form II allowed us to rationalize the role of stronger intralayer (sp(2))C-H center dot center dot center dot O and nonspecific interlayer pi-stacking interactions in the structure of II. Although the Form I also possesses the same type of interactions, its strength is clearly opposite, that is, weaker intralayer (sp(3))C-H center dot center dot center dot O and specific interlayer pi-stacking interactions. Hence, Form I is harder than Form IL Theoretical calculations and indentation on (111) of Form I suggested the low resistance of this face to mechanical stress; thus, Form I converts to II upon mechanical action. Hence, our approach demonstrates the usefulness of multiple techniques for establishing the role of weak noncovalent interactions in solid-state dynamic phenomena, such as stress induced phase transformation, and hence is important in the context of solid-state pharmaceutical chemistry and crystal engineering.

Crystal structures of SCP2-thiolases of Trypanosomatidae, human pathogens causing widespread tropical diseases: the importance for catalysis of the cysteine of the unique HDCF loop

Thiolases are essential CoA-dependent enzymes in lipid metabolism. In the present study we report the crystal structures of trypanosomal and leishmanial SCP2 (sterol carrier protein, type-2)-thiolases. Trypanosomatidae cause various widespread devastating (sub)-tropical diseases, for which adequate treatment is lacking. The structures reveal the unique geometry of the active site of this poorly characterized subfamily of thiolases. The key catalytic residues of the classical thiolases are two cysteine residues, functioning as a nucleophile and an acid/base respectively. The latter cysteine residue is part of a CxG motif. Interestingly, this cysteine residue is not conserved in SCP2-thiolases. The structural comparisons now show that in SCP2-thiolases the catalytic acid/base is provided by the cysteine residue of the HDCF motif, which is unique for this thiolase subfamily. This HDCF cysteine residue is spatially equivalent to the CxG cysteine residue of classical thiolases. The HDCF cysteine residue is activated for acid/base catalysis by two main chain NH-atoms, instead of two water molecules, as present in the CxG active site. The structural results have been complemented with enzyme activity data, confirming the importance of the HDCF cysteine residue for catalysis. The data obtained suggest that these trypanosomatid SCP2-thiolases are biosynthetic thiolases. These findings provide promise for drug discovery as biosynthetic thiolases catalyse the first step of the sterol biosynthesis pathway that is essential in several of these parasites.

Nanostructured CexZn1-xO thin films: Influence of Ce doping on the structural, optical and electrical properties

Thin films of CexZn1-xO thin films were deposited on glass substrates at 400 degrees C by nebulizer spray pyrolysis technique. Ce doping concentration (x) was varied from 0 to 10%, in steps of 2.5%. X-ray diffraction reveals that all the films have polycrystalline nature with hexagonal crystal structure and high preferential orientation along (002) plane. Optical parameters such as; transmittance, band gap energy, refractive index (n), extinction coefficient (k), complex dielectric constants (epsilon(r), epsilon(i)) and optical conductivity (sigma(r), sigma(i)) have been determined and discussed with respect to Ce concentration. All the films exhibit transmittance above 80% in the wavelength range from 330 to 2500 nm. Optical transmission measurements indicate the decrease of direct band gap energy from 3.26 to 3.12 eV with the increase of Ce concentration. Photoluminescence spectra show strong near band edge emission centered similar to 398 nm and green emission centered similar to 528 nm with excitation wavelength similar to 350 nm. High resolution scanning electron micrographs indicate the formation of vertical nano-rod like structures on the film surface with average diameter similar to 41 nm. Electrical properties of the Ce doped ZnO film have been studied using ac impedance spectroscopy in the frequency range from 100 Hz-1 MHz at different temperatures. (C) 2013 Elsevier B.V. All rights reserved.

Role of Crystal Field in Mixed Alkali Metal Effect: Electron Paramagnetic Resonance Study of Mixed Alkali Metal Oxyfluoro Vanadate Glasses

The mixed alkali metal effect is a long-standing problem in glasses. Electron paramagnetic resonance (EPR) is used by several researchers to study the mixed alkali metal effect, but a detailed analysis of the nearest neighbor environment of the glass former using spin-Hamiltonian parameters was elusive. In this study we have prepared a series of vanadate glasses having general formula (mol %) 40 V2O5-30BaF(2)-(30 - x)LiF-xRbF with x = 5, 10, 15, 20, 25, and 30. Spin-Hamiltonian parameters of V4+ ions were extracted by simulating and fitting to the experimental spectra using EasySpin. From the analysis of these parameters it is observed that the replacement of lithium ions by rubidium ions follows a ``preferential substitution model''. Using this proposed model, we were able to account for the observed variation in the ratio of the g parameter, which goes through a maximum. This reflects an asymmetric to symmetric changeover of. the alkali metal ion environment around the vanadium site. Further, this model also accounts for the variation in oxidation state of vanadium ion, which was confirmed from the variation in signal intensity of EPR spectra.

Kinematic and Mechanical Profile of the Self-Actuation of Thermosalient Crystal Twins of 1,2,4,5-Tetrabromobenzene: A Molecular Crystalline Analogue of a Bimetallic Strip

A paradigm shift from hard to flexible, organic-based optoelectronics requires fast and reversible mechanical response from actuating materials that are used for conversion of heat or light into mechanical motion. As the limits in the response times of polymer-based actuating materials are reached, which are inherent to the less-than-optimal coupling between the light/heat and mechanical energy in them, 1 a conceptually new approach to mechanical actuation is required to leapfrog the performance of organic actuators. Herein, we explore single crystals of 1,2,4,5-tetrabromobenzene (TBB) as actuating elements and establish relations between their kinematic profile and mechanical properties. Centimeter-size acicular crystals of TBB are the only naturally twinned crystals out of about a dozen known materials that exhibit the thermosalient effect-an extremely rare and visually impressive crystal locomotion. When taken over a phase transition, crystals of this material store mechanical strain and are rapidly self-actuated to sudden jumps to release the internal strain, leaping up to several centimeters. To establish the structural basis for this colossal crystal motility, we investigated the mechanical profile of the crystals from macroscale, in response to externally induced deformation under microscope, to nanoscale, by using nanoindentation. Kinematic analysis based on high-speed recordings of over 200 twinned TBB crystals exposed to directional or nondirectional heating unraveled that the crystal locomotion is a kinematically complex phenomenon that includes at least six kinematic effects. The nanoscale tests confirm the highly elastic nature, with an elastic deformation recovery (60%) that is far superior to those of molecular crystals reported earlier. This property appears to be critical for accumulation of stress required for crystal jumping. Twinned crystals of TBB exposed to moderate directional heating behave as all-organic analogue of a bimetallic `strip, where the lattice misfit between the two crystal components drives reveriible deformation of the crystal.

mu-Oxamido binuclear copper (II) complexes: Synthesis, crystal structure, DNA interaction and antibacterial studies

Four binuclear copper (II) complexes Cu(oxpn)Cu(B)](2+) (2-5) bridged by N, N'-bis3-(methylamino) propyl] oxamide (oxpn), where, B is N, N-donor heterocyclic bases (viz. 2,2'-bipyridine (bpy, 2), 1,10-phenathroline (phen, 3), dipyrido3,2-d:2',3'-f]quinoxaline (dpq, 4) and dipyrido3,2-a:2',3'-c]phenazine (dppz, 5) are synthesized, characterized by different spectroscopic and single crystal X-ray data technique. The phen (3) and dpq (4) complexes were structurally characterized by X-ray data analysis. Their DNA binding, oxidative cleavage and antibactirial activities were studied. The dpq (4) and dppz (5) complexes are avid binders to the Calf thymus DNA (CT-DNA). The phen (3), dpq (4) and dppz (5) complexes show efficient oxidative cleavage of supercoiled DNA (SC DNA) through hydroxyl radical ((OH)-O-center dot) pathway in the presence of Mercaptopropionic acid (MPA). (C) 2013 Elsevier Ltd. All rights reserved.