bluuebunny/crossref_metadata_2025 huggingface dataset:
Computational approaches towards crystal engineering in molecular crystals
Authors: Chopra Deepak , Dey Dhananjay
Published: November 2015

The investigation of a large number of crystal structures has resulted in the development of the area of crystal engineering, which involves the study of intermolecular interactions in crystalline solids [1]. It is now of importance to understand the nature and energetics associated with different interactions [2] which influence the crystal packing. In this regard, different computational approaches (utilizing PIXEL and TURBOMOLE) have been developed which aid in the understanding of intra- and intermolecular interactions (for example, hydrogen and halogen bonding) in molecular crystals. This approach has been successfully applied in different classes of molecules [3]. These approaches can be combined with topological analysis of the electron density using the quantum theory of atoms in molecules (QTAIM) (in absence of high quality crystals for experimental electron density studies). In order to validate the above-mentioned methodology, we have performed a comprehensive analysis of a series of synthesized fluoro-derivatives of N'-phenylbenzimidamide to gain quantitative insights into different interactions which accompany crystal formation. The packing of the molecules has contributions from strong N-H...N, weak N-H...π [Fig 1], C-H...N, C-H...F, and C-H...π intermolecular interactions along with π-π stacking. In addition to that, ubiquitous H...H contacts are also present in the solid state. This methodology can be extended to include cocrystals, polymorphs (including solvates) and protein-ligand interactions at the active site.
From Neutral to Ionic Species: Studies of Li...P(SiMe3)-PtBu2Complexes
Authors: Bombicz Petra , Sattler Ewald , Kovács Ilona , Rothenberger Alexander , Okrut Alexander
Published: November 2015

The alkali and alkaline earth phosphanides have already been intensively studied, nonetheless there are only a few reports on the alkali metal diphosphanides, on their structural properties and their synthetic use as building blocks for the synthesis of phosphorus-rich compounds and, in particular, transition- metal complexes. This study extends the so far small family of lithium diphosphanides with the series of Li(L)nP-(SiMe3)-PtBu2, where L = THF, n = 0–3; L = TMEDA or 12-crown-4, n = 2. The coordination numbers of the Li ions are in the range of two to eight in the investigated compounds. There is a clear correlation between the Li-P distance and the coordination number of the Li atom. The higher the coordination number of the Li atom, the longer the Li–P distance is. Coordination numbers of four or higher lead to ionic structures. The influence of the space requirement of the phosphorus substituents on the Li-P bond length should also be taken into account especially in the case of coordination number two. Eight-membered ring structures are realized when the formation of four-membered rings is prevented by sterically demanding substituents. This work is a contribution to the fine tuning of structures by donor molecules and substituents [1].
Energy-filtered electron diffuse scattering of ferroelectrics PMN and PMN-xPT
Authors: Pacaud Jerome , Saidi Wajdi , Withers Ray , Dkhil Brahim , Zuo Jian-Min
Published: November 2015

PbMb1/3Nb2/3O3 (PMN) and its solid solution (1-x)PbMb1/3Nb2/3O3-(x)PbTiO3 (PMN-xPT) are relaxor ferroelectrics which have attracted attention in the last few decades because of their very interesting dielectric and piezoelectric properties and have since be two of the most extensively studied. All the previous studies emphasized the role of the local structural fluctuations leading to local changes in symmetries [1] due to displacements of ions in the unit-cell. We studied PMN and PMN-xPT by electron diffuse scattering using an in-column energy filter and Imaging-Plates as detector. We found evidences for streaks of intensity along the [110]* direction as previously found in PbZn1/3Nb2/3O3 (PZN) with neutron diffraction [2]. Moreover, weak diffuse scattering sheets can be observed along (111)* reciprocal planes showing the existence of correlations along the [111] directions of the direct lattice. Figure 1 shows a diffraction pattern taken along [02-1] zone axis presenting both diffuse features. This can be related to the displacement of Pb ions along the diagonals of the cube found by simulation [3] but greatly complexify the analysis of the shape of the diffuse intensity. Compared to the neutron, electron diffraction has the advantage of two dimensional recording of diffuse scattering and eventually sensitivity to charge ordering but quantitative analysis is limited due to the complication of multiple scattering and the lack of sufficient energy resolution for the study of inelastic phonon scattering.
Diffuse scattering and local polar correlations in ferroelectric materials
Authors: Paściak Marek , Hlinka Jirka
Published: November 2015

Modern ferroelectric materials (e.g. PbMg1/3Nb2/3O3 - PbTiO3) are often based on ternary and quaternary oxides where disorder constitutes a groundwork for exceptional electromechanical properties. While the basic role of the inhomogeneity (strain and/or local electric field generated by occupational disorder locks and enhances the 'transition state' and thus electromechanical coupling) is widely accepted, precise description of mechanisms governing polar correlations is still lacking. In particular, indicating the role of ferroelectric soft phonon modes, their 'interaction' with inhomogeneous medium and relation to (quasi) static polar state at low temperatures constitutes an intriguing and fundamental problem [1,2]. Diffuse scattering analysis providing information about atomic to mesoscale correlations is a method of choice for studying of these phenomena; the fact that has been proven by an abundance of X-ray, neutron and electron diffraction results for ferroelectric materials in the recent years. At the same time, interpretation has been very often ambiguous, calling for better understanding of how the experimental data should be approached. We address some principal questions related to the diffuse scattering analysis of ferroelectric and related compounds. Can we gain some insight into the local structure treating data 'ab-initio', without assuming any model of polar correlations [3]? Can we separate static and dynamic contributions to the diffuse scattering (e.g. by calculating theoretical phonon-related thermal diffuse scattering)? The study is carried out using atomistic computational methods including reverse Monte Carlo, molecular dynamics and density functional theory based calculations.
Stable Compound of Helium and Sodium at High Pressure
Authors: Saleh Gabriele , Dong Xiao , Oganov Artem , Gatti Carlo , Qian Guang-rui , Zhu Qiang , Zhou Xiang-Feng , Wang Hiu-tian
Published: November 2015

Helium (He) is, on par with Neon, the most inert element in the Periodic Table. Indeed, no conclusive proofs about stable compounds containing chemical bonds with He at ambient conditions have been reported so far. However, pressure significantly affects chemical properties of elements. By using USPEX [1], a software which has been successfully used in the past to predict unexpected high pressure crystal structure [1], we found that above 160 GPa He and Sodium exothermically combine to form the compound Na2He, whose structure is reported in Fig. 1. Quasiharmonic free energy calculations based on computed phonon spectra indicate that the free energy of formation of Na2He is negative and that the latter is barely affected by the temperature (0-800 K range was considered). In order to understand the cause of stability of Na2He, we carried out a thorough study of its electronic structure at various pressures by means of several different approaches including the examination of the band structure and the analysis of real-space descriptors such as the electron density in the framework of the Quantum Theory of Atoms in Molecules [2], the Electron Localization Function [3] and the deformation density. By examining the band structure, we found that such compound is an insulator whose band-gap increases with pressure. Regarding real-space descriptors, two remarkable features of Na2He are the negative charge on He (obtained both using Mulliken and Bader partitioning) and the presence of interstitially localized electrons (i.e. Non-Nuclear Attractors), the latter being detectable in all the analyses above mentioned. In the range 160-350 GPa, the exothermicity associated to the formation of Na2He is mainly due to the volume reduction, while at higher pressures the electronic energy plays a prominent role in the stabilization of this compound. In this contribution we present the results of our study with particular emphasis on the role played by He in the stabilization of Na2He.
New electronic perovskite oxides from beyond high pressure synthesis
Authors: Attfield J
Published: November 2015

Materials synthesised from high pressure (HP) conditions offer a variety of possibilities for the discovery of new electronic and magnetic phenomena. Recovery of a solid to ambient pressure (AP) from its HP thermodynamic stability field effectively introduces a large negative pressure that can drive the material into an unusual electronic ground state; as illustrated by HP structural and property studies of PbRuO3 and BiNiO3. PbRuO3 is synthesised at 10 GPa and shows an orbitally ordered phase at AP and low temperatures that is suppressed at an apparent quantum critical point near 6 GPa [1]. A new structural phase emerges at much higher pressures ~30 GPa. BiNiO3 synthesised at 6 GPa shows an unusual charge order that is suppressed at 3.4 GPa; the transition is associated with a volume collapse leading to colossal negative thermal expansion [2]. Materials recovered from HP are also precursors for 'hard-soft' chemistry, where the instability of a dense precursor from `hard' HP conditions is relieved through `soft' post-synthesis modification. We recently demonstrated this concept for the HP phase SrCrO3 which on reduction gives two new phases SrCrO2.80 and SrCrO2.75 with long period oxygen vacancy, charge and spin ordered superstructures [3]. These studies have been carried out in collaboration with co-authors of the papers below.
S-SAD phasing on SOLEIL Beamline PROXIMA 1
Authors: Gourhant Patrick , Guimaraes Beatriz , Isabet Tatiana , Klinke Sebastian , Legrand Pierre , Rinaldi Jimena , Thompson Andrew
Published: November 2015

"PROXIMA 1, a beamline for macro-molecular crystallography at the 3rd generation synchrotron source SOLEIL, is equipped with a multi-circle goniometer (alpha 50 degrees) as well as a PILATUS 6M detector. These features, along with the extended energy range of the beam line towards the low energies (down to 5.5 keV) and the possibility to adapt the source size to the sample in order to optimize signal to noise ratio, have made the beam line very attractive for S-SAD phasing with more than seven examples of successful de novo phasing achieved over the last two years. The use of low energies has also proved a significant aid in assisting with MODEL building. The technical capabilities of the beam line for low energy data collections will be presented, along with a number of examples of the successful use of low wavelengths on the beam line. The importance of combining data from multiple sample orientations in order to achieve ""true multiplicity"" will be highlighted, as well as the importance of combining data from multiple crystals in order to achieve high multiplicity."
Case studies of sulfur SAD phasing with LigM from Sphingobium sp. SYK-6
Authors: Harada Ayaka , Yamada Yusuke , Liebschner Dorothee , Senda Toshiya
Published: November 2015

Sphingobium sp. SYK-6 grows on a lignin-related biphenyl compound as the sole carbon and energy source and was initially isolated from a pond waste liquor from a kraft pulp mill. In SYK-6, 5-CH3-H4folate is synthesized from aromatic compounds such as a vanillate by a O-demethylase, LigM. The 5-CH3-H4folate is then converted to 5,10-CH2-H4folate, which is utilized for syntheses of DNA, repair DNA, and methylate DNA as well as to act as a cofactor in certain biological reactions, by another enzyme, MetF. In other bacterial speceis, 5,10-CH2-H4folate is directly synthesized by T- and H-proteins that are enzymes in Glycine Cleavage System. It is considered that SYK-6 has evolved to acquire this unique pathway for the 5,10-CH2-H4folate production, in order to survive in extreme environmental condition. To elucidate the molecular mechanisim of this pathway, we have carried out the structural analysis of LigM. LigM was purified by using IMPACT system provided from NEB, which use intein and affinity chitin-binding tag. After crystallization screening, a reservoir solution of 0.2 M Mg acetate, 0.1 M Acetate buffer pH 4.6, and 20 %(w/v) PEG8000 gave a needle crystals with approximate dimensions of 0.3×0.1×0.01 mm3. A diffraction data set was collected with 1.1 Å wavelength at BL1-A in the Photon Factory. However, phasing trials via molecular replacement (using a model with 19% sequence identity) failed. Because LigM is a 53 kDa protein and contains fourteen sulfur atoms, LigM is an interesting candidate for SAD phasing with sulfur (S-SAD). Diffraction data sets of LigM crystals were collected with 1.9 and 2.7 Å wavelengths, reaching a maximum resolution of 2.3Å. Preliminary results are promising for solving the phase problem via S-SAD. This study is also of methodological interest as the phasing capability of two different wavelengths can be compared. A thorough analysis of the diffraction data is in progress.
Native-SAD Phasing at Synchrotrons: A Low-dose and High-redundancy Strategy
Authors: Liu Qun , Hendrickson Wayne
Published: November 2015

Native biological macromolecules contain intrinsic light elements such as sulfur in proteins and phosphorus in nucleic acids. Native-SAD phasing utilizes the anomalous signals from light elements for de novo structure determination: first the substructure of anomalous scatterers is determined; phase evaluation for the entire structure then follows. Synchrotron beamlines are expected to be ideal instruments for native-SAD phasing due to their brilliant and energy-tunable x-rays. However, anomalous signals from light elements are typically very weak at x-ray energies accessible to most synchrotron beamlines. Efforts have been made to promote the utility of synchrotrons for routine native-SAD phasing with no requirement for heavy-atom incorporation. Our strategy is to limit the x-ray dose per crystal and to enhance the signal-to-noise ratio by increasing data redundancy through use of multiple crystals. We have devised a robust procedure and applied it for routine native-SAD analyses on real-life membrane proteins, protein-protein complexes, and recalcitrant proteins. Here we use these real-life case studies to illustrate our procedures in sample preparation, x-ray energy selection, data collection, data analysis and phasing.
Polymolybdates and Peroxomolybdates: Candidates for Catalysts in Industry
Authors: Lasocha Wieslaw , Szymanska Anna , Oszajca Marcin , Appleby Graham , Pamin Katarzyna , Poltowicz Jan
Published: November 2015

Progress in catalysis depends on a full understanding of the role of the individual components of catalytic materials. Crystallographic studies offer insight into crystal structure, which enables the rational selection of reagents and better planning of the syntheses of novel materials and catalysts. In this paper we have studied the process of the oxidation of hydrocarbons and terpenes with oxygen from the air. Processes of this type are important in so-called "Green Chemistry." Their application can reduce the amount of environmentally harmful pollutants formed through conventional oxidation based on nitric acid. While investigating the catalytic activity of peroxo- and polymolybdates(VI) in the oxidation of cycloalkanes, we found a number of intriguing relationships. To explain them, we designed, synthesized and solved the crystal structures of the family of new peroxomolybdates, tri-, octa- and pentamolybdates of amines. Both single crystal and polycrystalline materials were investigated using laboratory as well as synchrotron radiation. Next, we used these compounds as catalysts in certain interesting for industry processes (e.g. oxidation of cyclic hydrocarbons). We have concluded that: – The activity of peroxocompounds is enhanced by the coordination of N-oxide groups to Mo atoms. – The activity of anionic polymeric trimolybdates decreases when `surface of polymeric fiber' is blocked by cations. – The anionic layers of pentamolybdates are separated by cations of variable size. The distance between layers plays a role similar to that of the size of channels in zeolites. Summary: Peroxomolybdates and polyoxomolybdates show great prospects for new industrial uses (besides cracking and desulfurization).
Site-selective analyses of battery reactivities in Li1+xNi1-xO2by powder DAFS
Authors: Kawaguchi Tomoya , Fukuda Katsutoshi , Oishi Masatsugu , Ichitsubo Tetsu , Mizuki Jun'ichiro , Matsubara Eiichiro
Published: November 2015

Deep understanding of a battery reactivity of transition metals in a positive electrode is essential for further development of lithium ion batteries (LIBs). Li1-xNi1+xO2(LNO, 0 < x < 1) is one of the typical positive-electrodes with a layered rock-salt structure. LNO often contains significant antisite defects of Ni at Li site, i.e., interlayer gallery, in addition to Ni site in the host layer. Though a relationship between such structural disorder and capacity fading of the battery has been reported[1], its degradation mechanism is still unclear presumably because of insufficient insight into electrochemical behavior of Ni at each site in LNO. In the present work, powder diffraction anomalous fine structure (P-DAFS)[2] has been applied to LNO to analyze the valence and local structure of Ni at both different symmetric sites for tackling this degradation issue. We prepared pellets of as-synthesized and charged LNOs for P-DAFS measurements. The composition of the samples is [LiyNi0.11]3a[Ni]3b[O2]6c(y = 0.89, 0.40) in R-3m space group. DAFS measurements were carried out at undulator beamline BL28XU, SPring-8 in Japan. The DAFS spectra were measured with use of 003 and 104 diffractions in ~1 keV energy range around Ni K-edge (8.331 keV). The XAFS-like spectra were extracted from DAFS spectra with a priori structural information from Rietveld analyses. Figure 1 shows (a) the DAFS spectra of the as-synthesized sample, XAFS-like spectra of Ni occupying the Ni site (b) and the Li site (c) in the as-synthesized (solid line) and the charged (broken line) samples. The spectrum at the Ni site shows a shift to the higher energy with charging, indicating the oxidation of Ni accompanied with Li extraction. In contrast, Ni at the Li site shows no significant shift with charging. Thus, Ni at the Li site hardly compensates the charge for delithiation, which indicates that the electrochemically inactive Ni occupying the Li sites would cause irreversibility in this system.
Industry and large scale facilitie, a cooperation of mutual benefit
Authors: Wroblewski Thomas
Published: November 2015

Large scale facilities like synchrotron radiation sources offer a variety of techniques for the characterization of materials and processes. These are not only suited to answer academic questions but may also help solving problems of industrial relevance. On the other hand the complexity of industrial products and processes demand sophisticated techniques for their investigation that may go beyond the requirements of pure academic research. The presentation will give examples on how the cooperation of science and industry triggered progress in research for mutual benefit in the field of (in operando) XAFS, diffraction scattering and other techniques. A paramount aspect in this context is the availability of auxiliary (not synchrotron radiation based) techniques, laboratories, equipment and expertise. A non negligible issue is occupational health and safety including radiation and bio hazards. The advanced photon sources at DESY in combination with further laboratories and research institutes on site are an excellent example for an environment enabling the investigation of manifold task of industrial relevance.
Structural studies on the Clostridium perfringens conjugation system
Authors: Torres Von , Wisniewski Jessica , Rood Julian , Whisstock James , Traore Daouda
Published: November 2015

Conjugation is the mechanism by which two bacteria share genetic information. This process relies on the direct transfer of mobile genetic element via a trans-membrane channel between the donor and the recipient. Although this mechanism has been extensively studied in gram-negative organism, very little in known on how this process takes place in their gram-positive counterpart. To address this important question in bacterial evolution, we use the tetracycline resistance plasmid pCW3 from Clostridium perfringens as study model. The pCW3 plasmid encodes 11 proteins necessary for the assembly the C. perfingens conjugation system. Here, I will focus on the relaxosome complex, which is the starting point of DNA transfer. We identified two protein (IntP and TcpK) involved in the processing of the DNA. Sequence analysis revealed that IntP was a potential Tyrosine recombinase and TcpK, directly upstream of IntP was identified a potential accessory protein of the relaxosome. We cloned, expressed and purified IntP and TcpK. These proteins were then subject to biochemical and biophysical characterizations. I will first present why these two proteins are required for efficient conjugative transfer and how they contribute to DNA processing. Then I will present the crystal structure of TcpK and discuss its interaction with IntP and other components of pCW3 apparatus. This study brings a further insight into this important mechanism of DNA transfer in Gram-positive bacteria.
Crystal structures of LsrR complexed with p-AI-2 reveal distinct mechanisms
Authors: Ha Jung-Hye , Kim Eun-Hee , Cheong Hae-Kap , Ryu Kyoung-Seok
Published: November 2015

Quorum sensing (QS) is a cell-to-cell communication system and responsible for a variety of bacterial phenotypes including virulence and biofilm formation. QS is mediated by small molecules, autoinducers (AIs), including AI-2 that is secreted by both Gram (+/–) microbes. LsrR is a key transcriptional regulator that governs the varied downstream processes by perceiving AI-2 signal, but its activation via autoinducer-binding remains poorly understood [1]. The ligand-free crystals of LsrR and complex crystals of LsrR and C-LsrR with 5 mM R5P were grown with reservoir buffer. Complex crystal of C-LsrR/D5P and C-LsrR/D8P were obtainded by soaking the native crystals in the same crystallization buffer (pH 6.5, 0.1 M bis-tris, 9.1% PEG-3350, 10 mM barium chloride dehydrate, 10 mM R5P) containing 0.15mM D5P and 2.0 mM D8P. These crystals were determined its 3-demensional (3D) structure at 3.2 Å ~ 1.9 Å resolution after SAD phasing. The ligand-binding affinities for LsrR protein were measured using fluorescence spectrophotometer and Isothermal titration calorimetry (ITC) while increasing the ligand concentrations. Detailed regulatory mechanism of LsrR from the crystal structures in complexes with the native signal (phospho-AI-2, D5P) and two quorum quenching antagonists (ribose-5-phosphate, R5P; phosphoisobutyl-AI-2, D8P). The bound D5P and D8P molecules are not the diketone forms but rather hydrated, and the hydrated moiety forms important H-bonds with the carboxylate of D243. The D5P-binding flipped out F124 of the binding pocket, and resulted in the disruption of the dimeric interface-1 by unfolding the α7 segment. However, the same movement of F124 by the D8P'-binding did not cause the unfolding of the α7 segment. Although the LsrR-binding affinity of R5P (Kd, ~1 mM) is much lower than those of D5P and D8P (~2.0 and ~0.5 μM), the α-anomeric R5P molecule fits into the binding pocket without any structural perturbation, and thus stabilizes the LsrR tetramer. The binding of D5P, not D8P and R5P, disrupted the tetrameric structure and thus is able to activate LsrR. The detailed structural and mechanistic insights from this study could be useful for facilitating design of new anti-virulence and anti-biofilm agents based on LsrR.
Temperature-dependent structural change of 1D ice, water nanopipe, in crystal
Authors: Wakahara Akio , In Yasuko
Published: November 2015

One-dimensional ice (1D ice) is formed in the single crystal prepared by mixing tryptophan and pyridoxal-5-phosphate in aqueous solution. This ice (diameter=1.649nm at 90K) consists of a hollow-type nanowire, viz., water nanopipe, and the structure is constructed by piling up the cluster unit of 15 water molecules, five independent waters (W1,--W5) of which are arranged around a 3-fold axis. As can be seen from the side view of this nanopipe, a tape structure is made of the continuous chair-type six-membered rings running parallel to the longest crystal axis, and its three tapes arranged around 3-fold axis are linked together via two kinds of hydrogen bonds of W5 (W5-W2 and W5-W4). Thus, the overall structure of this 1D ice could be described as three-square nanometric column. In order to investigate the temperature-dependent structural change of 1D ice, the crystal structure was refined using the X-ray diffraction data measured at different temperature between 90K and 293K. From these results, it was confirmed that the nanopipe structure is stable under 200K, but W5 and W4 disappear at 220K and 273K, respectively, indicating the importance of W5 for the structural stability of 1D ice.
Single crystal synchrotron X-ray diffraction for imaging hydrogen bond evolution
Authors: Saunders Lucy , Nowell Harriott , Thomas Lynne , Raithby Paul , Wilson Chick
Published: November 2015

Hydrogen bonding is a valuable intermolecular interaction in "engineering" solid-state materials. This is because of the directionality and relative strength (1) of these bonds. Hydrogen bonds enable charge and energy transfer, via H-bond evolution, in a range of biological and chemical systems (2). Recent work has demonstrated that single crystal X-ray diffraction can be used to image the evolution of hydrogen bonds, including variable temperature proton migration and proton disorder processes. In particular, in a recent study of the temperature dependent proton disorder in hydrogen bonded 3,5-dinitrobenzoic acid (3,5-DNBA) dimers, the proton disorder deduced from data collected on an X-ray laboratory source is in agreement with that found from neutron data (3). This work focuses on variable temperature single crystal synchrotron X-ray diffraction, for the imaging of evolving hydrogen bonds. The development of appropriate methodology is important here, particularly as previous studies have involved laboratory X-ray sources only. Results will be presented from variable temperature data collections on I19, at the Diamond Light Source, and on beamline 11.3.1, at the Advanced Light Source (ALS), on systems such as 3,5-DNBA and co-crystals of benzimidazole, both exhibiting proton disorder across hydrogen bonding interactions. Synchrotron X-ray diffraction measurements have also been used to follow the change in the position of a proton within an intramolecular [N–H···N]+ hydrogen bond across a range of proton-sponge molecular complexes. Importantly, it has been possible to visualise the evolving hydrogen atom position in Fourier difference electron density maps generated from the synchrotron data. In particular, for the 35-DNBA study, the clearest picture of the evolving hydrogen atom position is observed in those generated from data collected at the ALS; even clearer than that observed in X-ray laboratory and neutron measurements on the same system.
Expanding the Chemical Versatility of Thiostannate Anions.
Authors: Nørby Peter , Overgaard Jacob , Iversen Bo , Johnsen Simon
Published: November 2015

Soluble tin(IV) chalcogenide complexes play a major role in solution processing synthesis of macroelectronic tin(IV) chalcogenide based devices, e.g. thin film transistors (TFTs) and the technological interesting photovoltaic material, Cu2ZnSnS4 (CZTS). The synthesis and study of new soluble thiostannate(IV) complexes without electronic impurity atoms and with low decomposition temperature are of key importance for the further development of tin(IV) chalcogenide based devices. We have from the same aqueous ammonium tin(IV) sulfide solution, synthesized and characterized four new crystal structures with different sized thiostannate(IV) complexes (i.e. monomeric [SnS4]4-, dimeric [Sn2S6]4-, pyramids of [Sn3S9]6- and the linear chain [SnS3]2-). Hirshfeld surface analysis for the anionic dimeric [Sn2S6]4- complex in (NH4)4Sn2S6·3H2O shows that water bound hydrogens interact equally well as the ammonium bound hydrogens with the anionic complex. The elongation of the terminal Sn-S bond depends only on the number of hydrogen atoms which interact with the sulfur atom (regardless of the hydrogen atom is bound in water molecules or in ammonium cations). We present the results for the application of the as-synthesized thiostannate(IV) crystals in solution processing of SnS2 thin films. Crystallographic and electron microscopic methods have established that all films are highly textured with the high mobility ab-plane parallel to the substrate surface. This is ideal for e.g. TFT devices where high mobility is required parallel to the substrate surface.
Supramolecular architectures of 4-hydroxytetraphenylporphyrin with aza-donors
Authors: Nandy Purnendu , Pedireddi V.
Published: November 2015

Molecular adducts of 5,10,15,20-tetrakis(4-hydroxyphenyl)porphyrin (1) with aza-donors like 4,4'-bipyridine (a), 1,2-bis(4-pyridyl)ethane (b), trans-1,2-bis(4-pyridyl)ethylene (c), 4,4'-trimethylene-dipyridine (d), phenazine (e), 1,10-phenanthroline (f), 1,7-phenanthroline (g) and 4,7-phenanthroline (h) have been prepared. All the molecular complexes are crystallized along with the solvent of crystallization, except in the complex with the aza-donor b. Detailed structural analysis of the obtained complexes has been carried out by single crystal X-ray diffraction. The three dimensional structures of the molecular adducts are facilitated by directional hydrogen bonding features of hydroxyl groups with aza donors as well as solvent molecules, leading to the formation of different types of supramolecular architectures like sheets, tapes, host-guest assembly etc. For example, in the complex of 1 and aza donor a, which crystallizes as a hydrate, the porphyrin molecules interact with water and 4,4'-bipyridine through O-H...O and O-H...N hydrogen bonds, which leads to the formation of molecular sheets in two dimensional arrangement. An important noteworthy observation is that the molecular complexes are crystalline even after removal of the solvents by heating, as characterized by thermogravimetric analysis (TGA) and powder X-ray diffraction (PXRD). Further, all the complexes are found to be fluorescence sensitive, perhaps due to the porphyrin molecules.
Triphenylarenes: a New Family of Tunable Porous Organic Crystals
Authors: Lai Holden , Zentner Cassandra , Wiscons Ren , Zeller Matthias , Rowsell Jesse
Published: November 2015

Porous organic molecular crystals are of particular interest to crystal engineers because of their potential applications in small molecule storage, separation and catalysis. Compared to network solids, molecular solids present advantages for processing related to their solubility and ease of derivatization. Our research group recently established the microporosity of a carboxylated triphenylbenzene crystal structure, which retains crystallinity even after solvent evaporation. The extrinsically porous structure of this compound is largely directed by two intermolecular interactions: aromatic stacking, and hydrogen bonding in the familiar R22(8) motif. We have synthesized new derivatives bearing various functional groups to probe their steric and electronic effects on the molecular packing and the surface polarity of the pores. The structures of two solvated quasi-polymorphs of the nitro-substituted derivative have been determined using single-crystal X-ray diffraction methods. These structures provide insight into the interplay between the two important synthons, while exhibiting different catenation modes of hexagonal hydrogen-bonded sheets. In both packings, the nitro functional group points towards the interior of solvent-filled channels, suggesting that the installation of other functional groups at the same position is a viable method for tailoring the interactions between guest molecules and the host framework.
Hydrogen bonding patterns in hydroxyamidine/α-aminonitrone (AMOX) type compounds
Authors: Cibian Mihaela , Derossi Sofia , Spasyuk Denis , Ferreira Janaina , Hanan Garry
Published: November 2015

N,N'-Disubstituted hydroxyamidines/ α-aminonitrones (AMOXs) present high steric and electronic modularity (substituents can be varied on the central C atom and/or on the N atoms) resulting in precise electronic tunability, enhanced by the delocalization on the amidine backbone. They are good chelating ligands, forming stable 5-membered chelate rings with metal ions, and they also present hydrogen bonding capacity. [1] In our research, we exploit these properties by investigating their incorporation into supramolecular assemblies based on coordination chemistry and/ or hydrogen bonding. Herein, we present the synthesis and the structural characterization of different mono- and bis-AMOX type compounds. [2] The analysis of the hydrogen bonding patterns found in each case is highlighted (Figure 1), in an effort to identify factors (e.g. substituent effects: sterics and/ or electronics, other type of supramolecular interactions) that are generating specific hydrogen-bonding patterns. Understanding and rationalizing such a cause – effect relationship is of paramount importance in order to efficiently use hydrogen bonding as a crystal engineering design tool. Figure 1. Type of hydrogen bonding pattern in AMOX type compounds. [3]
Hydrogen Bonding in Inclusion Chemistry and Porous Materials
Authors: Lloyd Gareth
Published: November 2015

Hydrogen bonding played an important role in the development of crystal engineering and cocrystal formation, and continues to do so. Our take on hydrogen bonding will focus on its consequences on the functional properties of a number of materials based on how hydrogen bonding directionality effects porosity design and inclusion chemistry. The design of molecular porous materials has focused on the production of intrinsic porosity within a number of interesting materials where the intrinsic voids are defined by capsules (tetrahedra in our examples) and macrocycles (2X2 metallocycles in our examples). The crystal engineering of the macrocycle packing efficiencies can result in the intrinsic voids spaces being connected into pore networks allowing for diffusion of guest species such as gases. We will show how the hydrogen bonding of these intrinsically porous molecules can result in an increased porosity through the creation of extrinsic void space.[1] The inclusion chemistry we have investigated has looked at gas and vapour sorption where we have determined the guest:framework interaction of a number of porous materials. This includes the inclusion chemistry of a number of persistent organic radicals where the hydrogen bonding and Pi-Pi stacking interactions with the flexible host material results in paramagnetic materials whereas the pure radical materials tend towards being diamagnetic.[2] We will also describe our crystallographic insights into gas:framework interactions, especially that of the hydrogen bonding of Carbon Dioxide.[3]
Beyond Crystals and Plane Waves - Generalizing the von Laue Condition
Authors: Jüstel Dominik , Friesecke Gero , James Richard
Published: November 2015

The success of X-ray crystallography is due to the relationship between the symmetries of plane wave radiation and crystal structure. The resulting sharply peaked diffraction patterns allow to reconstruct translational symmetry information directly via the von Laue condition. A natural question to ask is whether one can design radiation that is in a similar way related to certain non-crystalline structures such as the so-called 'objective structures' whose symmetries were analyzed recently in [1]. Ideas and results surrounding these questions are discussed. It is shown that the use of novel forms of radiation might have the potential to improve the structural analysis of structures such as nanotubes, fullerenes, protein substructures or tails and capsids of certain viruses, which are non-crystalline but highly symmetric.
Aperiodic crystals and beyond
Authors: Grimm Uwe , Baake Michael
Published: November 2015

Following Dan Shechtman's discovery of quasicrystals in 1982, the realm of crystallography has been extended to include structures that lack translational periodicity. While periodic crystals can be modelled as decorations of lattices, aperiodic crystals require more general discrete structures such as point sets or tilings in space for the description of their structure. For a mathematical introduction to the field of aperiodic order, we refer to the recent monograph [1]. Interesting examples are obtained by projections from higher-dimensional lattices, leading to model sets which have pure Bragg diffraction, though the Bragg peaks are, in general, dense in space. All symmetries that have been experimentally observed in quasicrystals can be reproduced in this way, and some of the resulting structures are standard examples of tilings that are frequently used in quasicrystal modelling, such as the famous Penrose tiling. But there exists a plethora of ordered structures beyond cut and project sets, some of which have even weirder properties. After a general introduction to aperiodically ordered structures, a couple of examples of such systems are briefly described, offering a glimpse at the largely unexplored world of order beyond (aperiodic) crystals.
Sheding light on the multiferroicity in Mn1-xCoxWO4using superspace formalism
Authors: Urcelay-Olabarria Irene , Perez-Mato Juan Manuel , García Muñoz José Luis , Ressouche Eric
Published: November 2015

The use of the superspace symmetry formalism allows to rationalize the physical properties induced by an incommensurate magnetic ordering [1]. The incommensurate magnetic structures (ICMS) in Mn1-xCoxWO4 have been studied in the light of this formalism. MnWO4 is a multiferroic material in which the magnetic order of one of its magnetic phases induces ferroelectricity. Like most multiferroic materials MnWO4 is extremely sensitive to small perturbations such as chemical substitution. It turned out that doping with Co2+ is particularly interesting since it strongly stabilizes the multiferroic phase at low temperatures, and moreover, by increasing the cobalt amount in the crystals the orientation of the electric polarization flops from the b axis to the ac plane [2]. This change of orientation is linked to a symmetry change. The ICMS of the x = 0 and x = 0.10 compounds, which exhibit completely different behavior, have been studied thoroughly using superspace formalism. We have found, not only the symmetry of the magnetic structures and their intrinsic restrictions, but also information about the tensor properties of each incommensurate phase, such as ferroelectric and magnetostructural properties [3]: in the paramagnetic state, there is a unique independent magnetic atom in the crystallographic unit cell in both cases, but when the system enters into the multiferroic phase, this is no-longer true. In the multiferroic phase of MnWO4, the two Mn atoms in the unit cell become symmetry independent, whereas in the x = 0.10 substituted compound, they are still symmetry-related. This difference is related to the change of the electric polarization.
Symmetry constraints in frustrated magnets with strong magnetoelastic coupling
Authors: Khalyavin Dmitry
Published: November 2015

Geometrical frustration, related to the specific topology of certain crystal structures, plays a crucial role in forming exotic magnetic ground states. The presence of frustrated spins often leads to the suppression of long-range magnetic ordering and promotes short-range correlations due to fluctuations between nearly or totally degenerate ground states. The well-known structural topologies causing the presence of geometrical frustration are the three-dimensional pyrohlore and two-dimensional Kagome lattices. Compounds whose structural motif embraces these lattices are of great interest as model systems and have been the focus of numerous studies. In some cases, frustration is partially or entirely released by structural distortions through a strong magnetoelastic coupling and long-range magnetic order is established at a finite temperature. In the resulting distorted phases, complex noncollinear or partially disordered spin configurations can be observed. The phase transitions to the ordered state are quite often first order and may involve several irreducible representations of the paramagnetic space group and sometimes, like in the case of ZnCr2O4, even several propagation vectors which do not belong to the same star. The approach to determine magnetic structures in these systems, based on representation theory, should take into account the coupling free-energy invariants relating the magnetic and structural order parameters. Application of magnetic space groups and superspace groups is especially useful and can be efficiently combined with the representation theory. Based on specific examples, I will demonstrate how both approaches can be combined to provide symmetry constraints sufficient to solve complex magnetic structures in some geometrically frustrated systems.
Composite materials based on cerium oxide nanoparticles and graphene
Authors: Zaporozhets Marina , Soloveva Anastasya , Shalyapina Anastasya , Buslaeva Elena , Nikolaichik Vladimir , Gubin Sergey , Avilov Anatoly
Published: November 2015

Deposition of nanoparticles (NPs) onto graphene (G) surface is actively studied now in connection with the prospects of such composites for use in power supply and other areas. In order to increase the energy density of electrochemical capacitors the development of electrode materials consisting of carbon nanostructures and metal oxides such as CeO2, SnO2 and some others is paid attention. Carbon materials typically exhibit excellent stability and reversibility, but their capacity is limited by microstructure. Therefore, if the integration of these two types of materials is realized high capacitance stability can be attained. Synthesis of the composites was carried out in several stages. In the beginning, dispersion of graphene oxide (GO) was prepared by the Hummers's technique. Then, GO surface was precipitated with CeO2 NPs synthesized in aqueous solutions of Ce(NO3)3 and ammonia. Thereafter, the GO/CeO2 system was reduced to the G/CeO2 one in supercritical isopropanol. The obtained composites were characterized by a complex of structural and spectral methods including transmission electron microscopy (TEM), X-ray powder diffraction (XRD) and optical absorption spectroscopy. TEM has revealed that CeO2 NPs in the G/CeO2 composite form associates of a nearly spherical shape. Associates demonstrate a broad size distribution, their average size on G surface is 220 nm. High resolution TEM studies have shown that associates consist of CeO2 NPs of smaller size with an average size of ≍ 12 nm. XRD has shown the presence of two phases: ceria CeO2 with a cubic fluorite structure and graphene. The average size of CeO2 NPs estimated from the region of coherent scattering is ≍11 nm, which agrees well with the TEM data. According to UV-visible spectroscopy, absorption spectra of G/CeO2 dispersion contain an absorption band only in the wavelength range of 280-360 nm typical for CeO2. This work was supported by the grant of the President of the Russian Federation (MK-7155.2013.3).
Processing and characterisation of two-dimensional nanostructures
Authors: Nicolosi Valeria
Published: November 2015

Low-dimensional nanostructured materials such as organic and inorganic nanotubes, nanowires and platelets are potentially useful in a number of areas of nanoscience and nanotechnology due to their remarkable mechanical, electrical and thermal properties. However difficulties associated with their lack of processability have seriously hampered both. In the last few years dispersion and exfoliation methods have been developed and demonstrated to apply universally to 1D and 2D nanostructures of very diverse nature, offering a practical means of processing the nanostructures for a wide range of innovative technologies. Among the first materials to have benefitted most from these advances are carbon nanotubes [6] and more recently graphene. Recently this work has been extended to boron nitride and a wide range of two-dimensional transition metal chalcogenides. These are potentially important because they occur in >40 different types with a wide range of electronic properties, varying from metallic to semiconducting. To make real applications truly feasible, however, it is crucial to fully characterize the nanostructures on the atomic scale and correlate this information with their physical and chemical properties. Advances in aberration-corrected optics in electron microscopy have revolutionised the way to characterise nano-materials, opening new frontiers for materials science. With the recent advances in nanostructure processability, electron microscopes are now revealing the structure of the individual components of nanomaterials, atom by atom. Here we will present an overview of very different low-dimensional materials issues, showing what aberration-corrected electron microscopy can do to answer materials scientists' questions. Particular emphasis will be given to the investigation of hexagonal boron nitride (hBN), molybdenum disulfide (MoS2), and tungsten disulfide (WS2) and the study of their structure, defects, stacking sequence, vacancies and low-atomic number individual adatoms. The analyses of the h-BN data showed that majority of nanosheets retain bulk stacking. However several of the images displayed stacking different from the bulk. Similar, to 2D h-BN, images of MoS2 and WS2 have shown the stacking previously unobserved in the bulk. This novel stacking consists of Mo/W stacked on the top each other in the consecutive layers.
XRD Studies of Synthesized Bi2S3Crystalline Materials
Authors: Patel Ishverbhai , Solanki Sneha
Published: November 2015

Bismuth sulfide preparation and its x-ray diffraction studies are reported in this paper. The author have synthesized Bi2Sx (x = 3.15, 3.45) compound material with different sulfur content by conventional high temperature solid state solvothermal reaction of bismuth and sulfur which conforms that the (121) preferred orientation with crystallite size ~30 nm and splitting of peaks due to orthorhombic structure matches well with the standard data and demonstrate good crystalline quality and structural homogeneity of synthesized powder.This paper also describes the synthesis and x-ray diffraction studies of bismuth sulfide powder via versatile precipitation technique . Bismuth sulfide powder was synthesized using thiourea and sodium dodecyl sulfate or in absence of any surfactant maintained at 800C for 12 h keeping pH of solution constant at 1.4. Synthesized powder was characterized by x-ray diffraction technique which indicates that surfactants play major role in synthesis of bismuth sulfide that conforms the crystallite size ~35 nm. The employed solid state solvothermal technique played an important role to progress the homogeneous reaction and preparation of pure and fine bismuth sulfide powder. The possible application of this material in photovoltaic devices is suggested.