High Proton Mobility, Solvent Induced Single Crystal to Single Crystal Structural Transformation, and Related Studies on a Family of Compounds Formed from Mn-3 Oxo-Clusters

The reaction between 4,4'-sulfonyldibenzoic acid (H(2)SDBA) and manganese under mild conditions resulted in the isolation of two new three-dimensional compounds, Mn-4(C14H8O6S)(4)(DMA)(2)]center dot 3DMA, I, and Mn-3(C14H8O6S)(3)(DMA)(2)(MeOH)]center dot DMA, IIa. Both structures have Mn-3 trimer oxo cluster units. While the Mn-3 oxoclusters are connected through octahedral manganese forming one-dimensional Mn-O-Mn chains in I, the Mn-3 units are isolated in IIa. The SDBA units connect the Mn-O-Mn chains and the Mn-3 clusters giving rise to the three-dimensional structure. Both compounds have coordinated and free solvent molecules. In IIa, two different solvent molecules are coordinated, of which one solvent can be reversibly exchanged by a variety of other similar solvents via a solvent-mediated single crystal to single crystal (SCSC) transformation. The free lattice DMA solvent molecules in I can be exchanged by water molecules resulting in hydrophilic channels. Proton conductivity studies on I reveals a high proton mobility with conductivity values of similar to 0.87 x 10(-3) Omega(-1) cm(-1) at 34 degrees C and 98% RH, which is comparable to some of the good proton conductivity values observed in inorganic coordination polymers. We have also shown structural transformation of I to IIa through a possible dissolution and recrystallization pathway. In addition, both I and IIa appear to transform to two other manganese compounds H3O]Mn-3(mu(3)-OH)(C14H8O6S)(3)(H2O)](DMF)(5) and H3O](2)Mn-7(mu 3-OH)(4)(C14H8O6S)(6)(H2O)(4)](H2O)(2)(DMF)(8) under suitable reaction conditions. We have partially substituted Co in place of Mn in the Mn-3 trimer clusters forming CoMn2(C14H8O6S)(3)(DMA)(2)(EtOH)]center dot DMA, III, a structure that is closely related to IIa. All the compounds reveal antiferromagnetic behavior. On heating, the cobalt substituted phase (compound III) forms a CoMn2O4 spinel phase with particle sizes in the nanometer range.

Composition dependent non-ideality in aqueous binary mixtures as a signature of avoided spinodal decomposition

We explore the potential energy landscape of structure breaking binary mixtures (SBBM) where two constituents dislike each other, yet remain macroscopically homogeneous at intermediate to high temperatures. Interestingly, we find that the origin of strong composition dependent non-ideal behaviour lies in its phase separated inherent structure. The inherent structure (IS) of SBBM exhibits bi-continuous phase as is usually formed during spinodal decomposition. We draw analogy of this correlation between non-ideality and phase separation in IS to explain observation of non-ideality in real aqueous mixtures of small amphiphilic solutes, containing both hydrophilic and hydrophobic groups. Although we have not been able to obtain IS of these liquids, we find that even at room temperature these liquids sustain formation of fluctuating, transient bi-continuous phase, with limited lifetime (tau less than or similar to 20 ps). While in the model (A, B) binary mixture, the non-ideal composition dependence can be considered as a fluctuation from a phase separated state, a similar scenario is expected to be responsible for the unusually strong non-ideality in these aqueous binary mixtures.

Lizards of the Thar Desert - Resource partitioning and community composition

How similar species co-exist in nature is a fundamental question in community ecology. Resource partitioning has been studied in desert lizard communities across four continents, but data from South Asia is lacking. We used area-constrained visual encounter surveys to study community composition and spatial and temporal resource partitioning in a lizard community during summer in the Thar Desert, western India, addressing an important biogeographic gap in knowledge. Twelve one-hectare grids divided into 25 m x 25 m plots were placed across four habitats barren dunes, stabilized dunes, grassland, and rocky hills. We recorded 1039 sightings of 12 species during 84 sampling sessions. Lizard abundance decreased in the order stabilized dunes > grassland > barren dunes > rocky hills; richness was in roughly the opposite order. Resource partitioning was examined for the seven commonest species. Overall spatial overlap was low (<0.6) between species pairs. Overlap was higher within habitats, but species showed finer separation through use of different microhabitat categories and specific spatial resources, as well as by positioning at different distances to vegetation. Diurnal species were also separated by peak time of activity. Space appears to be an important resource dimension facilitating coexistence in this desert lizard community. (C) 2015 Elsevier Ltd. All rights reserved.

Crystal Structure and Prediction

The notion of structure is central to the subject of chemistry. This review traces the development of the idea of crystal structure since the time when a crystal structure could be determined from a three-dimensional diffraction pattern and assesses the feasibility of computationally predicting an unknown crystal structure of a given molecule. Crystal structure prediction is of considerable fundamental and applied importance, and its successful execution is by no means a solved problem. The ease of crystal structure determination today has resulted in the availability of large numbers of crystal structures of higher-energy polymorphs and pseudopolymorphs. These structural libraries lead to the concept of a crystal structure landscape. A crystal structure of a compound may accordingly be taken as a data point in such a landscape.

Doping effect of Ag+, Mn2+ ions on Structural and Optical Properties of ZnO nanoparticles

Pure ZnO and co-doped (Mn, Ag) ZnO nanoparticles have been successfully prepared by chemical co-precipitation method without using a capping agent. X-ray diffraction (XRD) studies confirms the presence of wurtzite (hexagonal) crystal structure similar to undoped ZnO, suggesting that doped Mn, Ag ions are substituted to the regular Zn sites. The morphology of the samples were studied by scanning electron microscopy (SEM). The chemical composition of pure and co-doped ZnO nanoparticles were characterized by energy dispersive X-ray analysis spectroscopy (EDAX). Optical absorption properties were determined by UV-vis Diffuse Reflectance Spectrophotometer. The incorporation of Ag+, Mn2+ in the place of Zn2+ provoked to decrease the size of nanocrystals as compared to pure ZnO. Optical absorption measurements indicates blue shift in the absorption band edge upon Ag, Mn ions doped ZnO nanoparticles.

Structural characterization of folded and extended conformations in peptides containing gamma amino acids with proteinogenic side chains: crystal structures of gamma(n), (alpha gamma)(n) and gamma gamma delta gamma sequences

The crystal structures of nine peptides containing gamma(4)Val and gamma(4)Leu are described. The short sequences Boc-gamma(4)(R)Val](2)-OMe 1, Boc-gamma(4)(R)Val](3)-NHMe 2 and Boc-gamma(4)(S)Val-gamma(4)(R)Val-OMe 3 adopt extended apolar, sheet like structures. The tetrapeptide Boc-gamma(4)(R)Val](4)-OMe 4 adopts an extended conformation, in contrast to the folded C-14 helical structure determined previously for Boc-gamma(4)(R)Leu](4)-OMe. The hybrid alpha gamma sequence Boc-Ala-gamma(4)(R)Leu](2)-OMe 5 adopts an S-shaped structure devoid of intramolecular hydrogen bonds, with both alpha residues adopting local helical conformations. In sharp contrast, the tetrapeptides Boc-Aib-gamma(4)(S)Leu](2)-OMe 6 and Boc-Leu-gamma(4)(R)Leu](2)-OMe 7 adopt folded structures stabilized by two successive C-12 hydrogen bonds. gamma(4)Val residues have also been incorporated into the strand segments of a crystalline octapeptide, Boc-Leu-gamma(4)(R)Val-Val-(D)Pro-Gly-Leu-gamma(4)(R)Val-Val-OMe 8. The gamma gamma delta gamma tetrapeptide containing gamma(4)Val and delta(5)Leu residues adopts an extended sheet like structure. The hydrogen bonding pattern at gamma residues corresponds to an apolar sheet, while a polar sheet is observed at the lone delta residue. The transition between folded and extended structures at gamma residues involves a change of the torsion angle from the gauche to the trans conformation about the C-beta-C-alpha bond.

Spatial modulation of the composition of a binary liquid near a repulsive wall

When a binary liquid is confined by a strongly repulsive wall, the local density is depleted near the wall and an interface similar to that between the liquid and its vapor is formed. This analogy suggests that the composition of the binary liquid near this interface should exhibit spatial modulation similar to that near a liquid-vapor interface even if the interactions of the wall with the two components of the liquid are the same. The Guggenheim adsorption relation quantifies the concentrations of two components of a binary mixture near a liquid-vapor interface and qualitatively states that the majority (minority) component enriches the interface for negative (positive) mixing energy if the surface tensions of the two components are not very different. From molecular dynamics simulations of binary mixtures with different compositions and interactions we find that the Guggenheim relation is qualitatively satisfied at wall-induced interfaces for systems with negative mixing energy at all state points considered. For systems with positive mixing energy, this relation is found to be qualitatively valid at low densities, while it is violated at state points with high density where correlations in the liquid are strong. This observation is validated by a calculation of the density profiles of the two components of the mixture using density functional theory with the Ramakrishnan-Yussouff free-energy functional. Possible reasons for the violation of the Guggenheim relation are discussed.

Functional characterization of heat-shock protein 90 from Oryza sativa and crystal structure of its N-terminal domain

Heat-shock protein 90 (Hsp90) is an ATP-dependent molecular chaperone that is essential for the normal functioning of eukaryotic cells. It plays crucial roles in cell signalling, cell-cycle control and in maintaining proteome integrity and protein homeostasis. In plants, Hsp90s are required for normal plant growth and development. Hsp90s are observed to be upregulated in response to various abiotic and biotic stresses and are also involved in immune responses in plants. Although there are several studies elucidating the physiological role of Hsp90s in plants, their molecular mechanism of action is still unclear. In this study, biochemical characterization of an Hsp90 protein from rice (Oryza sativa; OsHsp90) has been performed and the crystal structure of its N-terminal domain (OsHsp90-NTD) was determined. The binding of OsHsp90 to its substrate ATP and the inhibitor 17-AAG was studied by fluorescence spectroscopy. The protein also exhibited a weak ATPase activity. The crystal structure of OsHsp90-NTD was solved in complex with the nonhydrolyzable ATP analogue AMPPCP at 3.1 angstrom resolution. The domain was crystallized by cross-seeding with crystals of the N-terminal domain of Hsp90 from Dictyostelium discoideum, which shares 70% sequence identity with OsHsp90-NTD. This is the second reported structure of a domain of Hsp90 from a plant source.

Building upon Supramolecular Synthons: Some Aspects of Crystal Engineering

It has been 20 years since the concept of supramolecular synthon was introduced with the purpose of rational supramolecular synthesis. While this concept has been greatly successful in employing a retrosynthetic approach in crystal engineering, the past few years have seen a continuous evolution of supramolecular synthons from being a synthetic subunit to a basic unit for understanding the dynamics of crystallization. This review attempts to give a glimpse of such developments.

The crystal structure of a lectin from Butea monosperma: Insight into its glycosylation and binding of ligands

Crystal structure of a lectin purified from Butea monosperma seeds was determined by Molecular Replacement method. Its primary structure was determined by Tandem Mass Spectroscopy and electron density maps from X-ray diffraction data. Its quaternary structure was tetrameric, formed of two monomers, alpha and beta, beta appearing as truncated alpha. The occurrence of two tetramers in the asymmetric unit of the crystal might be a consequence of asymmetric contacts due to difference in glycosylation and variable loops structures, to form an `octamer-structure'. The crystal structure showed binding pockets for gamma Abu, having a proposed role in plant defense, at the interface of canonical dimer-partners. Hemagglutination studies, enzyme kinetics, isothermal titration calorimetry and molecular dynamics showed that the lectin is specific to N-acetyl D-galactosamine, galactose and lactose in decreasing order, and alpha-amylase inhibitor. (C) 2014 Elsevier B.V. All rights reserved.

Variation of Electrical Resistivity with High Pressure in Ge-Te-Sn Glasses: A Composition Dependent Study

The variation of normalized electrical resistivity in the system of glasses Ge15Te85-xSnx with (1 <= x <= 5) has been studied as a function of high pressure for pressures up to 9.5 GPa. It is found that with the increase in pressure, the resistivity decreases initially and shows an abrupt fall at a particular pressure, indicating the phase transition from semiconductor to near metallic at these pressures, which lie in the range 1.5-2.5 GPa, and then continues being metallic up to 9.5 GPa. This transition pressure is seen to decrease with the increase in the percentage content of tin due to increasing metallicity of tin. The semiconductor to near metallic transition is exactly reversible and may have its origin in a reduction of the band gap due to high pressure.

Crystal landscape in the orcinol:4,4 `-bipyridine system: synthon modularity, polymorphism and transferability of multipole charge density parameters

Polymorphism in the orcinol: 4,4'-bipyridine cocrystal system is analyzed in terms of a robust convergent modular phenol...pyridine supramolecular synthon. Employing the Synthon Based Fragments Approach (SBFA) to transfer the multipole charge density parameters, it is demonstrated that the crystal landscape can be quantified in terms of intermolecular interaction energies in the five crystal forms so far isolated in this complex system. There are five crystal forms. The first has an open, divergent O-H...N based structure with alternating orcinol and bipyridine molecules. The other four polymorphs have different three-dimensional packing but all of them are similar at an interaction level, and are based on a modular O-H...N mediated supramolecular synthon that consists of two orcinol and two bipyridine molecules in a closed, convergent structure. The SBFA method, which depends on the modularity of synthons, provides good agreement between experiment and theory because it takes into account the supramolecular contribution to charge density. The existence of five crystal forms in this system shows that polymorphism in cocrystals need not be considered to be an unusual phenomenon. Studies of the crystal landscape could lead to an understanding of the kinetic pathways that control the crystallization processes, in other words the valleys in the landscape. These pathways are traditionally not considered in exercises pertaining to computational crystal structure prediction, which rather monitors the thermodynamics of the various stable forms in the system, in other words the peaks in the landscape.

Halogen bonds in some dihalogenated phenols: applications to crystal engineering

3,4-Dichlorophenol (1) crystallizes in the tetragonal space group I4(1)/a with a short axis of 3.7926 (9) angstrom. The structure is unique in that both type I and type II Cl.....Cl interactions are present, these contact types being distinguished by the angle ranges of the respective C-Cl....Cl angles. The present study shows that these two types of contacts are utterly different. The crystal structures of 4-bromo-3-chlorophenol (2) and 3-bromo-4-chlorophenol (3) have been determined. The crystal structure of (2) is isomorphous to that of (1) with the Br atom in the 4-position participating in a type II interaction. However, the monoclinic P2(1)/c packing of compound (3) is different; while the structure still has O-H....O hydrogen bonds, the tetramer O-H.....O synthon seen in (1) and (2) is not seen. Rather than a type I Br....Br interaction which would have been mandated if (3) were isomorphous to (1) and (2), Br forms a Br....O contact wherein its electrophilic character is clearly evident. Crystal structures of the related compounds 4-chloro-3-iodophenol (4) and 3,5-dibromophenol (5) were also determined. A computational survey of the structural landscape was undertaken for (1), (2) and (3), using a crystal structure prediction protocol in space groups P2(1)/c and I4(1)/a with the COMPASS26 force field. While both tetragonal and monoclinic structures are energetically reasonable for all compounds, the fact that (3) takes the latter structure indicates that Br prefers type II over type I contacts. In order to differentiate further between type I and type II halogen contacts, which being chemically distinct are expected to have different distance fall-off properties, a variable-temperature crystallography study was performed on compounds (1), (2) and (4). Length variations with temperature are greater for type II contacts compared with type I. The type II Br....Br interaction in (2) is stronger than the corresponding type II Cl....Cl interaction in (1), leading to elastic bending of the former upon application of mechanical stress, which contrasts with the plastic deformation of (1). The observation of elastic deformation in (2) is noteworthy; in that it finds an explanation based on the strengths of the respective halogen bonds, it could also be taken as a good starting model for future property design. Cl/Br isostructurality is studied with the Cambridge Structural Database and it is indicated that this isostructurality is based on shape and size similarity of Cl and Br, rather than arising from any chemical resemblance.

Electric field induced short range to long range structural ordering and its influence on the Eu+3 photoluminescence in the lead-free ferroelectric Na1/2Bi1/2TiO3

Eu+3 was incorporated into the lattice of a lead-free ferroelectric Na1/2Bi1/2TiO3 (NBT) as per the nominal formula Na0.5Bi0.5-xEuxTiO3. This system was investigated with regard to the Eu+3 photoluminescence (PL) and structural behaviour as a function of composition and electric field. Electric field was found to irreversibly change the features in the PL spectra and also in the x-ray diffraction patterns below the critical composition x = 0.025. Detailed analysis revealed that below the critical composition, electric field irreversibly suppresses the structural heterogeneity inherent of the host matrix NBT and brings about a long range ferroelectric state with rhombohedral (R3c) distortion. It is shown that the structural disorder on the nano-scale opens a new channel for radiative transition which manifests as a new emission line branching off from the main D-5(0)-> F-7(0) line along with a concomitant change in the relative intensity of the other crystal field induced Stark lines with different J values. The study suggests that Eu+3 luminescence can be used to probe the relative degree of field induced structural ordering in relaxor ferroelectrics and also in high performance piezoelectric alloys where electric field couples very strongly with the lattice and structural degrees of freedom. (C) 2015 AIP Publishing LLC.