bluuebunny/crossref_metadata_2025 huggingface dataset:
Multiple magnetic interactions in ordered perovskite-structure oxides
Authors: Shimakawa Yuichi
Published: November 2015

Cation ordering in transition-metal oxides often drastically modifies their properties. We focus on A-and-B-site-ordered quadruple perovskite-structure oxides AA'3B2B'2O12, in which transition-metal ions are included at the A', B, and B' sites in an ordered manner. In such compounds A'-A', A'-B, A'-B', and B-B' interactions compete with each other and play important role in giving rise to unusual properties. The A-and-B-site-ordered quadruple perovskite CaCu3Fe2Sb2O12with magnetic Fe3+at the B site and nonmagnetic Sb5+at the B' site was successfully synthesized under a high-pressure and high-temperature condition. The B-site Fe3+spin sublattice adapts a tetrahedral framework and the Fe3+-Fe3+antiferromagnetic interaction causes geometrical spin frustration as seen in the double perovskite Ca2FeSbO6. With the introduction of Cu2+into the A' site, the frustration is relieved by strong antiferromagnetic A'(Cu2+)-B(Fe3+) interaction, leading to a ferrimagnetic ordering below 160 K. When B'-site Sb5+was replaced with Re5+, another A-and-B-site-ordered quadruple perovskite CaCu3Fe2Re2O12was synthesized by a high-pressure technique. The compound contains magnetic Fe3+at the B site and Re5+at the B' sites, and strong antiferromagnetic A'(Cu2+)-B'(Re5+) interaction overcomes the A'(Cu2+)-B(Fe3+) interaction, leading to a ferrimagnetism with the ferromagnetic A'(Cu2+)-B(Fe3+) spin arrangement below 550 K. More importantly, the electronic structure of CaCu3Fe2Re2O12is half metallic and the compound shows large magnetoresistance by the spin-dependent transport.
Crystal Chemistry and Symmetry based approaches to multiferroics.
Authors: Claridge John
Published: November 2015

The area of improper ferroelectrics and potentially multiferroics has recently received significant attention do the prediction that a combination of a–a–c+ tilting and layered ordering of the A site cations along [001]perov in perovskite ABX3 systems or in the even n Ruddlesden Popper (RP) phases (An+1BnX3n+1), leads to non-centrosymmetric structures which are predicted to have significant switchable polarisations. Two practical examples will be discussed: (i) Suitable doping of the RP phase SrLn2Fe2O7 can induce a polar tilted ground state where weak ferromagnetism and magnetocelecricity are induced by the appearance of the polar tilted state. The transition temperatures and phase sucession is dependant on the degree of doping. (ii) The oxide heterostructure [(YFeO3)5(LaFeO3)5]40,which is magnetically ordered and piezoelectric at room temperature, has been constructed from two weak ferromagnetic AFeO3 perovskites with different A cations using RHEED-monitored pulsed laser deposition.1 Here we elaborate a superspace description of cation ordering in tilted perovskites that allows the prediction of the symmetry of arbitrary cation ordered superlattices, along <100>perov, <110>perov and <111>perov and ordering of both A and B cations, of the various tilted perovskites, which also rationalizes the observed domain structures. This approach is expaned to include magnetic symmetry and the potential for finding other suitable structural distortions in non-perovskite systems will be discussed.
Experimental charge density studies of silver (I) complex
Authors: Owczarzak Anita , Kubicki Maciej , Kyros Lucas , Banti Christina , Hadjikakou Sotiris , Kucińska Małgorzata , Murias Marek
Published: November 2015

The antimicrobial [1] as well as antitumor activity of silver(I) complexes has been attributed to their interactions with nucleic acids, in the latter case preferentially with the bases rather than the phosphate groups [2]. The ability of silver(I) complexes to adopt structural diverse geometries with variable nuclearities , on the other hand, makes the study of silver(I) chemistry very attractive [1]. In the course of our studies of silver complexes with thioamide ligands we have determined the experimental charge density distribution in new silver(I) bromide complex with 2-mercaptobenzothiazole (mbztH) and triphenylphosphine (tpp) [AgBr(tpp)2(mbztH)], which allowed us to study e.g. the transfer of electron density to the bonding regions and the detailed analysis of different intra- and intermolecular interactions. In view of strong anticancer activity for MCF-7 (IC50 1.7510.25 μM) [3] of (1) and its sulfur containing ligand, this structure can be very interesting. Moreover the structure of (1) contains two independent complex molecules in asymmetric part of the unit cell, which together with the charge density description of mbztH and tpp allowed us to study different transferability approaches.
Charge Density Studies on Anti-Alzheimer Agents
Authors: Luger Peter , Mebs Stefan , Weber Manuela , Dittrich Birger
Published: November 2015

The average age of people is increasing continuously thanks to the progress in the medicinal sciences and further social advances. As a consequence, however, diseases which affect people more likely at a higher age also increase. In this course Alzheimer's disease (AD) and related brain disorders distribute rapidly and have to be taken more serious. One of the most frequently applied drugs against AD is donepezil®. Its function is a reversible inhibition of acetylcholinesterase (AChE), thereby reducing the deficit of acetylcholine associated with the occurrence of AD. As one result from the charge density (CD) of the small-molecule structure containing the donepezilium cation comparable electronic interactions were identified as in the macromolecular TcAChE-donepezil complex which were made visible by electrostatic potential and Hirshfeld surfaces.[1] Two newer developments of Alzheimer agents are bexarotene and methylene blue. For the first one a therapeutic effect on AD in a mouse model was recently reported. From a comparative CD study on bexarotene and its disila analogue differences in the electrostatic potentials were identified, while the spherical structures showed no significant differences. The second one, methylene blue, targets the abnormal tangle type tau protein aggregation inside the nerve cells in the brain and stops its spread. The molecule is positively charged with various counterions. From the CD an answer to the not yet understood question is expected whether the formal positive charge is localized or delocalized.
Charge density studies of nucleobase analogues - the case of DAP and isocytosine
Authors: Budniak Urszula , Jarzembska Katarzyna , Dominiak Paulina
Published: November 2015

Nucleobases belong to purine and pyrimidine family and constitute a biologically crucial group of compounds thank to their relation to nucleic acids. Specific interactions between these moieties are responsible for maintaining a proper structure of DNA, namely: hydrogen bonding and π-π stacking interactions (between aromatic ring fragments). Furthermore, many modifications of natural nucleobases serve as drugs, but some could be extremely harmful. In view of the above, investigating the properties of analogues of nucleobases may contribute to our knowledge about nucleic acid properties in general and give an opportunity to find novel ligands binding to DNA, what is essential for drug design. Within this project two modified nucleobases were examined: 2,6-diaminopurine (DAP) and isocytosine (iC). DAP is a derivative of the adenine and iC is an isomer of cytosine. These compounds do not appear naturally in nucleic acids, however, can be used to compare Watson-Crick pairing in DNA and pairing of alternative bases. High resolution X-ray diffraction experiments were carried out to obtain appropriate data for charge density analysis. A comprehensive study of crystal packing and energetic features of the analysed systems was conducted. The nature of intermolecular interactions, structural motifs and crystal packing was analysed via Hirshfeld surface analysis [1], charge density distribution examination, QTAIM (Quantum Theory of Atoms in Molecules) [2] and theoretical calculations (gas phase dimers and periodic). Implications of the observed interactions for biological systems are discussed. This study was supported by the Polish Ministry of Science and Higher Education within the Diamond Grant No DI 2011012441.
Drug target interaction by KEM of Quantum Crystallography
Authors: Massa Lou , Huang Lulu , Matta Cherif
Published: November 2015

It is possible to use the full power of ab initio quantum mechanics in application to the interaction of drugs and their molecular targets. Two things advance this perspective: (i) the use of parallel supercomputers, and (ii) the discovery of a quantum formalism called quantum crystallography and the use of quantum kernels, a method that is well suited for parallel computation. The calculations are simplified by adopting an acceptable approximation that allows a full biological molecule to be represented by smaller "kernels"of atoms. The KEM is suggestive that problems in the rational design of drugs, may be illuminated by quantum mechanical analysis. The general case is illustrated by specific examples.
New Ligands and New Insights for Vitamin D Receptor from Charge Density
Authors: Malińska Maura , Kutner Andrzej , Woźniak Krzysztof
Published: November 2015

Vitamin D protective effects result from its role as a nuclear transcription factor that regulates cell growth, differentiation, and a wide range of cellular mechanisms crucial to the development and progression of cancer.[1] Many academic investigators and pharmaceutical companies try to develop calcitriol analogs that exhibit equal or even increased anti-proliferative activity while exhibiting a reduced tendency to cause hypercalcemia. Analysis of 24 Vitamin D analogs bearing similar molecular structures with a complex of a Vitamin D Receptor (VDR) enabled the design of new agonists (TB1, TB2, TB3 and TB4). Undertaken approach was to minimize the electrostatic interaction energies available after the reconstruction of charge density with the aid of the pseudoatom databank (UBDB[2]). Comprehensive studies revealed 29 residues crucial for agonist binding. Trp286, which is specific to VDR among the representatives of the Nuclear Receptor Family, plays the crucial role of positioning the ligand forming dispersive interactions, mostly C-H...π, with an average strength of -4 kcal mol-1. The ligand binding pocket is primarily composed of hydrophobic residues, however there are 6 hydrogen bonds characteristic for all the ligands. They electrostatic interaction energies strongly contribute to the total interaction energy, with an average strength of -8, -19, -11 and -12 kcal mol-1 for hydrogen bonds to Ser237, Arg274, Ser278 and Tyr143. The aliphatic chain of the Vitamin D analogs adopt an extended conformation and the 25-hydroxyl group is hydrogen bonded to His305 and His397 with electrostatic interaction energies of -13 and -11 kcal mol-1. The geometries of complexes of the proposed ligand with VDR were obtained by the docking procedure implemented in Autodock4.3[3]. New agonsits form all mentioned before interactions with VDR. The final results of electrostatic interaction energy for TB1 and TB2 are -153 and -120 kcal mol-1, and this results are the smallest among all studied Vitamin D analogs.
Light-Atom Structures: Absolute Configuration Determination and Beyond
Authors: Graf Jürgen , Ruf Michael , Ott Holger , Noll Bruce , Freisz Séverine , Gerisch Alexander , Dittrich Birger , Kleine Andreas , Michaelsen Carsten
Published: November 2015

The determination of the absolute configuration for light-atom structures is central to research in pharmaceuticals and natural-product synthesis [1]. In the absence of elements heavier than silicon, it is often problematic to make a significant assignment of absolute configuration. Traditionally, heavy-atom derivatives were prepared which have a stronger anomalous signal compared to the native compound. However, this is not always feasible. The assignment of the absolute structure of pure organic compounds has become somewhat easier with the advent of high-intensity microfocus sources [2], as the increased flux density improves the anomalous signal through improvements in counting statistics. In order to maximize the anomalous signal, X-ray sources with Cu anodes are usually used for the absolute structure determination. However, these data are usually limited to a maximum resolution of about 0.80 Å. High-brilliance microfocus X-ray sources with Mo targets enable the collection of high quality data beyond 0.40 Å within a reasonable amount of time. This allows not only a more accurate modelling of the electron density by using aspherical scattering factors, but also enables a reliable determination of the absolute structure, despite the significantly lower anomalous signal obtained with Mo Kα radiation. With the recently introduced liquid-Gallium-jet X-ray source unprecedented beam intensities can be achieved [3]. The shorter wavelength of Ga Kα compared to Cu Kα slightly weakens the anomalous signal of a typical light-atom structure. However, due to the shorter wavelength, the highest resolution for the liquid metal-jet source is typically at about 0.70 Å, compared to about 0.80 Å for Cu Kα. Hence, about 50% more unique reflections can be recorded. This clearly improves the structural model and the quality of the Flack parameter. Selected results on the absolute structure and charge density determinations for light-atom structures will be presented.
An XAFS Investigation of static and thermal disorder above the Nickel K-edge
Authors: Tantau Lachlan , Chantler Christopher , Islam Md , Bourke Jay
Published: November 2015

We present recent experimental X-ray Absorption Fine Structure (XAFS) data of the Nickel K-edge, measured at temperatures of 15, 70 and 140 K. This study has taken elements of the X-ray Extended Range Technique (XERT) and for the first time, applied them to a cryostat cold cell system. These measurements permit critical tests of XAFS theory, with emphasis on quantification of the Debye-Waller factor and static vs. thermal disorder. X-ray Absorption Fine Structure contains vital information about the surrounding system of an absorbing atom including crystal structure, bond distances and coordination number. It is crucial that we understand all processes that may affect the measured XAFS spectra. The aim of this study is to investigate thermal effects and quantify thermal and static disorder [1]. The XERT is an experimental technique developed by our group, capable of measuring X-ray mass attenuation coefficients on an absolute scale with accuracies down to 0.02% [2]. This study has taken crucial elements from the XERT and applied them to complex experimental systems. This includes, but is not limited to high accuracy energy calibration [3], quantification and correction of beam harmonics and fluorescence. Our robust technique allows us to take the high accuracy data required to determine fundamental structural and crystallographic properties. These developments give great insight into our understanding of more complex systems such as organometallic molecules and biological systems.
EXAFS and DFT studies on iridium catalysts for SABRE
Authors: Feiters Martin , Engwerda A. , van Weerdenburg B. , Eshuis N. , Tessari M. , Longo A. , Banerjee D. , Fonseca Guerra C. , Bickelhaupt F. M. , Rutjes F.
Published: November 2015

Since it was first developed, Nuclear Magnetic Resonance (NMR) has become a powerful analytical tool that is now used widely in the fields of chemistry, materials science, and medicine. One way to overcome the intrinsic insensitivity of NMR is to use hyperpolarization techniques to produce non-Boltzmann spin-state distributions. One of these techniques is Signal Amplification By Reversible Exchange (SABRE),[1] in which hyperpolarization is achieved by the temporary association of parahydrogen and a substrate in the coordination sphere of a transition metal. The polarization can be transferred from the parahydrogen-derived hydride ligands to the bound substrate via scalar coupling, followed by dissociation of the hyperpolarized substrate into the bulk solution. We have investigated the efficiency of various iridium NHC complexes with aliphatic and aromatic R groups as SABRE catalysts.[2] The used metal centre is a six-coordinate iridium N-heterocyclic carbene complex, with three substrates and two hydrides, in which the exchange rate of substrate and parahydrogen at the metal centre determines the efficiency of the hyperpolarization. As solvent molecules compete with pyridine for coordination to iridium, the sensitivity of SABRE can be enhanced by displacement of solvent molecules by cosubstrates, i.e. proton-poor ligands such as methyltriazole.[3] In this exchange process, several mixed iridium complexes can be considered to exist, which were not all observed by NMR. Therefore, Density Functional Theory (DFT) calculations were performed on these complexes to better understand this phenomenon. While NMR itself is the best source of information on protons and dynamic processes involved in SABRE, we have found that Extended X-ray Absorption Fine Structure (EXAFS) studies in organic solutions provide interesting complimentary information on the complexes involved.
Dynamic structure in nanoclusters and its effect on size & shape modeling
Authors: Frenkel Anatoly , Nuzzo Ralph , Rehr John , Henkelman Graeme , Crooks Richard
Published: November 2015

As recently as 10-15 years ago, nanoparticles were described qualitatively: oblate and hemispherical, discs and rafts. Today we discriminate between different faceted nano-architectures with unprecedented accuracy using EXAFS. As an illustration (Fig. 1), we will describe a Pt particle in equilibrium with support and adsorbate. We will show how to resolve analytically metal-support, metal-adsorbate, and support-adsorbate and obtain the size and shape information. We will show new methods for circumventing the main limitation of EXAFS analysis. EXAFS works best for ordered systems while nanoparticles have strong, asymmetric bond length disorder. They also have nonbulklike dynamics: the surface bonds are soft, while the interior bonds are stiff, resulting in a bimodal distributions of bonds. This heterogeneity, if not accounted for, results in smaller coordination numbers and, hence, in smaller particle sizes compared to the actual ones [1]. Conventional EXAFS analysis, based on the solution of "inverse problem" where experimental spectra is an input, and the unknown cluster architecture is an output, is unstable for systems with strong and asymmetric disorder. We will present a new methodology for the analysis of nm-scale clusters based on solving "direct problem". The starting point is the model system investigated using DFT-MD simulations to produce theoretical EXAFS signals that could be directly compared to the experimental results. The information that is learned from theory can be compared with traditional EXAFS fitting results to identify and rationalize any errors in the experimental fit. Our study, using both supported [2] and unsupported [3] clusters, demonstrates that DFT-MD simulations accurately depict complex experimental systems, and shows the advantages of using a combined experimental/theoretical approach over standard EXAFS fitting methodologies for determining the structural and dynamic parameters of metallic nanoparticles.
Carbonate contamination in nitrate and organic hydrotalcites by XRPD/TGA-GC-MS
Authors: Viterbo Davide , Conterosito Eleonora , Croce Gianluca , Palin Luca , Antonioli Diego , Favaro Giada , Perioli Luana , Milanesio Marco , Gianotti Valentina
Published: November 2015

Layered double hydroxides are versatile materials used for intercalating bioactive molecules, both in pharmaceutical and cosmetic fields, with the purpose of protecting them from degradation, enhancing their water solubility to increase bioavailability, and/or obtaining modified release properties. The crystal chemistry of hydrotalcite-like compounds is investigated by X-ray powder diffraction (XRPD) and hyphenated TGA-GC-MS to shed light on the mechanisms involved in ion exchange and absorption of contaminants, mainly carbonate anions. XRPD demonstrated that the presence of carbonate is able to drive the intercalation of organic molecules into LDH, since CO3 contaminated samples tend to assume d-spacing roughly multiple of LDH-CO3 d-spacing. TGA-GC-MS allowed distinguishing and quantifying intercalated and surface adsorbed organic molecules, confirming the presence and amount of carbonate, especially at low (ppm) concentrations and separating the different types and strength of adsorption, in relation with the temperature of elimination. Also the importance of the intercalation method on the carbonate absorption was examined. This is probably due to the fact that the larger molecules leave some voids in the packing and the carbonate can occupy these voids during the intercalation. Finally the presence of adsorbed and not intercalated organic guest was quantified by TGA-GC-MS.
Characterization of a diffraction profile using the fourth cumulant
Authors: Dasgupta Prabal , Mitra Girija
Published: November 2015

In this study, line broadening in a diffraction intensity profile of powder crystalline materials due to particle size and lattice strain has been characterized by a new function- the fourth cumulant of the diffraction profile. Diffraction intensity profile is usually characterized in terms of half intensity width (FWHM), Fourier Transforms, second and fourth restricted moments etc. The cumulants, with addtional property of additivity[1], can be used to de-convolute the contribution of several effects such as crystallite size, lattice strain, stacking fault, dislocation, etc., to the line broadening. Since the first three cumulants are the same as the corresponding moments, we investigate the fourth cumulant, which is a function of fourth and second moments. Here, line broadening has only been due to particle size and lattice strain. Previous reports [1] showed that fourth cumulant of a Gaussian was zero, where as we now show that for Cauchy, Voigt and pseudo-Voigt distributions, the fourth cumulant is non-zero. Hence, the fourth cumulant of functions describing particle size and lattice strain for the latter types of distribution has been derived, as well as those for crystalline and para-crystalline materials. For crystalline materials, it was shown that fourth cumulant for particle size and strain (jointly) is the simple sum of the 4th cumulant for particle size and that of strain individually- thus proving the additivity of the fourth cumulant. This work illustrates the advantages of considering the fourth cumulant for characterizing line broadening in terms of particle size and strain.
Application of synchrotron powder diffraction to research and issues in mining
Authors: Reid Joel
Published: November 2015

Powder diffraction (PXRD) is an important tool for synergistic synchrotron studies of mining issues. Quantitative phase analysis with powder diffraction often provides basic information required to guide additional studies such as X-ray absorption (XAS) or micro-diffraction (μ-XRD). Elemental speciation in dilute and complex mineralogical systems with X-ray absorption near edge structure (XANES) spectroscopy is critically dependent on high quality phase pure standards, which are generally appraised using PXRD. This talk will examine the powder diffraction capabilities at the CLS, and discuss application of PXRD to mining issues as part of a combined synchrotron approach using examples.
Sandwich-like flat freestanding silicon nanocrystals
Authors: Aslanov Leonid , Zakharov Valery , Yatsenko Alexandr
Published: November 2015

For the first time we have obtained the sandwich-like flat freestanding silicon nanocrystals (nc-Si) as a result of synthetic procedure in colloidal solution: the outer layers are formed by the perfluorophenyl ligands and flat silicon nanocrystal is located between two ligand layers. The fact of binding of the perfluorophenyl ligands to the surface of silicon nanoparticles is supported by FTIR, EDS and XPS spectroscopy. Concentrations of the elements observed on the surface of samples were calculated for the separate lines appeared to be as follows: Si 11.0, O 17.0, F 3.2, Morphology and structure of the synthesized Si-nanoparticles were studied by Transmission Electron Microscopy (TEM). The samples comprise two types of nanoparticles: spherical and flat (2D structures). The average diameter of spherical particles is 4.010.5 nm. Electron diffraction pattern (DP) demonstrates that spherical Si-nanoparticles are amorphous. Along with halo-like DP from spherical particles, the spot diffraction patterns from some areas are observed for flat nanoparticles which have the crystalline structure. The experimental DP is in a good agreement with the simulated diffraction pattern for cubic Si phase. analysis of electron diffraction data indicates that thickness of these particles is less than 10 nm. The size of these particles can reach 50 nm.The thickness of flat nanocrystals was evaluated by Atomic Force Microscopy (AFM) also: it appeared to be close to 3.3 nm in average what is thrice smaller than that determined by TEM. This difference will be discussed. Lamellar nanocrystals are possibly formed at the stage of replacement of the bromide ligands by perfluorophenyl groups and are the products of aggregation of spherical silicon nanoparticles in flat plates. Growth of the plates is caused by C...F specific interactions between the ligands, which result in formation of layers of the perfluorophenyl ligands due to their self-assembly in fluorophobic media.
High-entropy alloys in light transition metal systems
Authors: Kozak Roksolana , Steurer Walter
Published: November 2015

High-entropy alloys (HEAs) are a new class of alloys designed with the approach of maximization of configurational mixing entropy by increasing the number of constituents [1,2]. Alloys produced in such a way are reported for a variety of promising properties (high hardness and strength, wear resistance, magnetism etc.) [3]. However, origin of these properties (microstructure, phase content, element composition, thermal history) is not always clear. High mixing entropy in HEAs favours the formation of single-phase substitutional solid solutions at elevated temperatures with approximately equiatomic compositions and simple average crystal structures of either the cF4-Cu (fcc) or the cI2-W (bcc). Nevertheless, only a few element combinations produce truly single-phase materials. In order to search for new HEAs compositions samples in the systems Cr-Fe-Co-Ni-Al and Cr-Fe-Co-Ni-Mn were synthesized by arc melting and homogenized in tantalum ampoules at 1100 and 1300 °C for 2 weeks. DTA, X-ray diffraction and electron microscopy measurements were performed. Only samples with small Al content (~ 5 at.%) showed the single-phase microstructure. Their local atomic structure is under investigation.
Thermal expansion in isomorphic Me5Si3(Me=transition metal) compounds
Authors: Suzuki Paulo , Rodrigues Geovani , Nunes Carlos , Coelho Gilberto
Published: November 2015

Transition metal silicides have been investigated due to the applications in several fields, such as: structural materials, electronic devices, nuclear industry. The physical properties including mechanic, electric, magnetic, thermal, optical, etc. of these compounds are strongly dependent of the metallic atoms and their atomic bonds. The family of silicon-based compounds of Me5Si3stoichiometry, known as Nowotny phases, where Me is a IV, V or IV transition metal element crystallize in three different structures: 1) Ti5Si3, Zr5Si3and Hf5Si3compounds crystallize in a hexagonal structure obeying P6/mcm symmetry and (Me: 4d and 6g, Si: 6g) Wyckoff positions; 2) Compounds such as V5Si3, Cr5Si3, Mo5Si3, W5Si3, βNb5Si3and βTa5Si3crystallize in so-called T1structure with I4/mcm space group and (Me: 4b and 16k, Si: 4a and 8h) Wyckoff positions and 3) Compounds such as αNb5Si3and αTa5Si3crystallize also in a tetragonal structure, called T2, in same I4/mcm space group but different Wyckoff positions (Me: 4c and 16l, Si: 4a and 8h). The measurement of the thermal expansion coefficients of these compounds by high temperature X-ray diffraction shown that they are strongly dependent of the metallic atoms. Since these compounds crystallize in hexagonal or tetragonal symmetry, the thermal expansion is anistropic. The anisotropy of the thermal expansion in these materials have been controlled by the following ways: 1) by partial substitution of the metallic atom by another metallic atom to promote the formation of solid solutions, or 2) by formation of ternary compounds, by partial substitution of silicon by boron in the structures, for example. Since these compounds present high melting temperatures, they are prepared in polycristalline form by arc-melting process followed by heat-treatment at temperatures above 1400 K. The thermal expansion coefficients of Me5Si3compounds have been analyzed taking into account the crystal structure of these compounds.
25 years of crystallographic studies related to HIV/AIDS
Authors: Wlodawer Alexander
Published: November 2015

This year we celebrate 25 years since the first crystal structures of HIV-encoded proteins became available. The structure of HIV protease, the first one to be determined, immediately became a guide for designing drugs directed at this enzyme crucial to viral maturation, with several drugs gaining approval in a record time of 6 years. The structures of the other HIV enzymes (reverse transcriptase, RNase H, and integrase) followed and all were immediately useful to drug developers. Other HIV-encoded proteins that control membrane fusion, viral entry, and regulatory processes were also pursued, together with host proteins that are involved in maintaining viral life-cycle. This large body of structural knowledge was crucial to the development of multi-drug therapy that changed the face of the AIDS epidemic from an irrevocably mortal disease to a manageable infection. The history of these 25 years of world-wide crystallographic efforts is worth recounting.
Protein crystallography in the 1970s: starting from scratch in a remote outpost
Authors: Baker Edward
Published: November 2015

A conversation with Dorothy Hodgkin on a long bus trip, just before I returned to New Zealand in 1970, left me full of determination and optimism. This presentation will recount my experience in starting a protein crystallography lab with only a sealed-source generator and a precession camera for equipment. Crystals had to be large (0.5 - 1.0 mm on edge) and X-ray data, collected at room temperature on a borrowed small-molecule diffractometer, accumulated very slowly. We corrected for absorption and decay and scaled data sets rather crudely. It was very much a do-it-yourself environment. With no CCP4, software had to be borrowed or adapted or written oneself; methods papers in Acta Cryst. were like gold as I pored through them trying to understand. Communications with friends, by airmail, were vital. An electron density map for the cysteine protease actinidin, at 2.8 Å, was immediately interpretable thanks to excellent data and phases from more derivatives than were really necessary. An R factor of 42% to 2.0 Å, for a model built in a Richards box, was really quite astonishing. Later FFT-based least squares refinement at the University of York in 1978 was even more astonishing as the R factor rocketed down [1]. No computer graphics, but the difference electron density told the story – in retrospect there was even evidence that the crystals (prepared from kiwifruit bought at the local shop) contained several genetic variants of the protein! It may not have been the most exciting protein in the world (except to me!) but what a way to learn protein crystallography and protein structure.
Virus crystallography from its beginnings until 1978
Authors: Harrison Stephen
Published: November 2015

Viruses, first crystallized in the 1930's, were for many years the only exemplars of large macromolecular assemblies accessible to x-ray crystallography. The talk will outline the most interesting biological questions these structures posed, review some of the early technical challenges, and describe some of the specific history that led to the first published virus crystal structure in 1978.
Electron and X-ray diffraction – two worlds united
Authors: Kolb Ute , Krysiak Yasar , Gorelik Tatiana , Mugnaioli Enrico
Published: November 2015

Small crystals structure solution usually done with X-ray powder diffraction (XRPD) provides bulk information and is powerful for in-situ investigations. Peak overlap in the one-dimensional data causes problems e.g. for polyphasic or impure samples and large cell parameters thus peak indexing and intensity extraction are the main issues where x-ray powder data may be supported by extra information. Electrons sample smaller volumes but strong coulombic interaction cause multiple scattering effects changing intensities often so strong that a structure solution is becoming impossible. Nevertheless, oriented electron diffraction patterns may provide sufficient information to support indexing or the assignment of impurity peaks in the case of low quality x-ray powder pattern. Reciprocal space tomography [1] uses a series of non-oriented diffraction patterns for which dynamical effects are significantly reduced and an enhanced amount of independent reflections sampled allows "ab-initio" crystal structure solution using established X-ray structure solution packages. Although structure refinement based on kinematical intensities is stable, achievable R values of 10-30% are high and final refinement may be performed based on X-ray powder data. Scanning transmission electron microscopy (STEM) for crystal tracking and nano electron diffraction (NED) is suitable for beam sensitive material, agglomerated particles, twins or intergrown phases on crystals down to 30nm size [2, 3]. Interesting properties of nanocrystalline materials are driven mainly by twinning, defects, disorder in one or two dimensions down to the amorphous state. Here low data completeness or uncertain intensity determination causes problems in structure solution. Here a mean structure may be determinable serving as a basis for disorder description and being used as a starting model being refined onto X-ray powder data maybe supported by a combination of the diffraction methods or by adding extra information.
Heterolytic Cleavage of H2 Revealed by Neutron Single Crystal Diffraction
Authors: Wang Xiaoping , Liu Tianbiao , Bullock R. Morris , Hoffmann Christina
Published: November 2015

Synthetic biologically inspired complexes exhibiting reactivity similar to hydrogenase enzymes have provided evidence of hydride transfer to the metal and proton transfer to an amine, but key structural information about the intermediate is not readily discernible with X-rays. The greater sensitivity of neutron to hydrogen makes it ideal for studying the structure and dynamics of catalytic materials. The newly commissioned TOPAZ neutron single crystal diffractometer at the SNS is capable of continuous 3D diffraction space mapping from a small stationary crystal, permitting detailed structural study at atomic resolution. The structure measured on TOPAZ for an Fe-based mononuclear electrocatalyst confirms that reaction of [CpFeN-L)](BARF) (1) with H2 under mild conditions leads to heterolytic cleavage of the H-H bond into a proton and hydride[1]. The precise location of H atoms in [Fe-H···H-N]+ reveals an unconventional H-bonding interaction, where the ferrous hydridic site {Fe(II)-H-} acts as the H-bond acceptor and the nitrogen of the protic pendant amine {L-N-H+} as the H-bond donor. The neutron structure provides clear evidence of a crucial intermediate involving an Fe-H···H-N interaction in the oxidation of H2. The result clarifies the key role of the pendant amine in the iron complex and provides insights into the design of synthetic electrocatalysts sought as cost-effective alternatives to platinum in fuel cells. The reaction is also a critical step in homogeneous catalysts for hydrogenation of C=O and C=N bonds. A preliminary result from TOPAZ measurement shows that 1 undergoes further single-crystal to single-crystal chemical reaction with moisture in the air, leading to a Fe(H2O)+ complex. Abbreviations: Cp = pentafluoropyridylcyclopentadienide; N-L= 1, 5-di(tert-butyl)-3,7-di(benzyl)-1,5-diaza-3,7-diphospha-cyclooctane; BARF = [B[3,5-(CF3)2C6H3]4]–
Structure and stability of solid oligoglycines
Authors: Smith Aaron , Ali Farukh , Soldatov Dmitriy
Published: November 2015

Although peptides have been extensively studied within many disciplines, their solid state chemistry is not sufficiently explored. Crystalline peptide materials could present new opportunities in solid state organic synthesis as well as pharmaceutical, cosmetic and food industries. In order to facilitate these future applications, a better understanding of the relationship between the solid state structure and chemical reactivity in peptide crystals is required. In this work, a series of linear glycine oligomers was studied to see how their crystal structure and thermal reactivity changes with the chains growth. Single crystals of tetra- and pentaglycines were grown from aqueous solutions and investigated with XRD analysis (see Figure for pentaglycine). The newly collected data together with those reported previously reveal general trends likely present throughout all glycine oligomers. An antiparallel, hydrogen bound, β-sheet-like structure exists throughout the whole series and is the most stable polymorphic form in higher oligomers. Further, the thermal reactivity of this series was studied using gas chromatography – mass spectrometry (GC-MS), thermal gravimetric analysis (TGA) coupled with IR spectroscopy, differential scanning calorimetry (DSC) and bulk oven heating regimes. Finally 1H and 13C NMR and XRD analysis were used to identify key components of the thermal decomposition pathways as well as new products discovered during the thermal treatment. The results from all these studies suggest that the thermal stability of the oligomers increases with the chain length, but the decomposition pathways for the series are similar. In all cases, 2,5-diketopiperazine was formed through either condensation reactions (glycine and diglycine[1]) or depolymerisation of the peptide chain[2] in parallel with competing decomposition mechanisms. 2,5-Diketopiperazine and its derivatives are important biologically active molecules, and if this trend holds for other peptide oligomers, this solid state reaction could form a new, widely applicable synthetic method.
Cooperativity in the Reaction of 9-Methylanthracene With a 1,4-Dithiin Molecule
Authors: Khorasani Sanaz , Fernandes Manuel
Published: November 2015

Solid-state chemistry involves the manipulation of molecules and materials through photochemical, thermal, or mechanical reaction methods. Single-crystal-to-single-crystal (SCSC) reactions are rare, but offer the opportunity to study reaction mechanisms and molecular motions in the solid state at the atomic level using single crystal X-ray diffraction. This allows the effect of the surrounding molecules, and hence the reaction cavity, on the reacting molecules to be examined which may ultimately lead to postcrystallization methods for creating new materials or reaction products that cannot easily be obtained via solution. SCSC reactions involving two different molecules are relatively uncommon. A convenient system that allows the study of such reactions is the [4+2] Diels-Alder reaction of 1,4-dithiintetracarboxylic type compounds with anthracene derivatives. In the work reported here, electron donor to acceptor interactions between 9-Methylanthracene and bis(N-cyclobutylimino)-1,4-dithiin lead to the formation of chiral charge transfer (CT) crystals [1]. These undergo a topochemical thermal SCSC [4 + 2] Diels-Alder reaction in the solid state. CT crystals were reacted at 400C, their structures determined by X-ray diffraction at various degrees of conversion, and examined using Hirshfeld surfaces and lattice energy calculations to find evidence of reaction cooperativity and feedback mechanisms. In this case, a maximum reaction conversion of around 96% was obtained indicating that the reaction is non-random within the charge transfer stacks, with close contacts between product molecules in the reacted crystal also providing some evidence for reaction cooperativity along the b axis perpendicular to the CT stacking axis.
Solid state intramolecular cyclization of leucyl-alanine and alanyl-leucine
Authors: Ali Farukh , Soldatov Dmitriy
Published: November 2015

Solid state organic synthesis is a future alternative to traditional, solution-based laboratory and industrial synthetic procedures. Solvent-free synthetic methods allow for quantitative yields, high stereospecificity, need no solvent, and are easy to conduct. They may contribute to green economy by reducing pollution, cutting the consumption of energy, and lowering the cost of production of various organic compounds. Although solid state reactions have been reported for almost all main classes of organic compounds and reaction types[1], the reactivity of peptides in the solid state has not been well explored. One potential product of the solid state transformation of dipeptides is 2,5-diketopiperazines (DKPs), the cyclic forms of dipeptides. They have attracted attention due to their high biological activity and use in medicinal chemistry[2,3]. In this study, we investigated the thermally induced intramolecular cyclization of leucyl-alanine and alanyl-leucine in the solid state. The reaction was conducted in a range of experimental conditions using thermogravimetric analyzer (TGA), differential scanning calorimeter (DSC), and gas chromatograph - mass spectrometer (GC-MS). The progress of the reaction was observed in situ through monitoring the release of water (mass loss and infra-red spectra) as well as the characterization of the solid residue (1H and 13C NMR, powder and single crystal XRD). The scalability of the reaction was tested with larger samples using a ventilation oven, and a microwave reactor. We found that the both dipeptides easily undergo the cyclization reaction upon mild heating, to give a stereospecific product with ~100% yield. However, the study was complicated with polymorphism displayed by the cyclic product. The solid state reaction yielded an orthorhombic form of the cyclic dipeptide, while its recrystallization produced a triclinic polymorph. The crystal structure and relative stability of the forms were investigated with XRD and DSC techniques. When the solid-state reaction was conducted at higher temperature, partial racemization and distereomerization were observed which led to new crystal structures. The degree of racemization was evaluated by a polarimeter and the NMR analysis.
Mechanical Effects in Molecular Crystals – A Revival
Authors: Naumov Panče , Panda Manas , Sahoo Subash , Nath Naba , Husain Ahmad , Nauha Elisa
Published: November 2015

"The classical perception of single crystals of molecular materials as rigid and brittle entities has downsized the research interest in mechanical effects that had been initiated and was active back in the 1980s. More recently, the modern analytical techniques for mechanical, electron-microscopic, structural, spectroscopic and kinematic characterization have contributed to accumulate compelling evidence that under certain circumstances, even some seemingly rigid single crystals can deform, bend, twist, hop, wiggle or perform other ""acrobatics"" that are atypical for non-soft matter. These examples contribute to a paradigm shift in our understanding of the elasticity of molecular crystals and also provide direct mechanistic insight into the structural perturbations at the limits of the susceptibility of ordered matter to internal and external mechanical force. As the relevance of motility and reshaping of molecular crystals is being recognized by the crystal research community as a demonstration of a very basic concept–conversion of thermal or light energy into work–a new and exciting crystal chemistry around mechanically responsive single crystals rapidly unfolds."
Reactive Species Unveiled by Ab Initio Powder Structure Analysis
Authors: Kawano Masaki
Published: November 2015

Porous coordination network has been the subject of explosive development because of their fascinating properties. However, there is still an unexplored research field in self-assembly of porous materials. There are many metastable states before reaching the thermally most stable state. By controlling the weak intermolecular interactions, we can trap various metastable coordination networks which will not be obtained by conventional thermodynamic control. Kinetically trapped metastable networks were not paid much attention, because firstly it is very difficult to analyze crystal structures. We demonstrated that it is possible to perform ab initio powder structure determination of porous coordination networks using low resolution data; totally different coordination networks can be selectively prepared from the same starting materials by thermodynamic and kinetic control; a robust porous coordination network can be prepared from the kinetic product which can be prepared instantly and in a large scale.[1] We also demonstrated that a pore in porous networks can be used as a crystalline molecular flask.[2] The robust networks maintain crystallinity and enable direct observation of reactive species by X-ray diffraction. It is still challenging to observe reactive species in a pore with clear structural evidence. In this talk, we will report ab initio powder structure analysis of reactive species trapped in a porous coordination network and their unique chemistry.[3]
Tuning Polymorphs using Pressure-Transmitting Media
Authors: Hutchison Ian , Delori Amit , Marshall William , Oswald Iain
Published: November 2015

The role of pressure-transmitting media is to ensure that uniaxial pressure is translated into a hydrostatic pressure. Many of these media are useful to high-pressure scientists for a limited pressure regimen out with which the media becomes non-hydrostatic in nature. For most pressure studies the role of the media is purely to apply the pressure however in recent years the media has been used to dissolve compounds of interest before precipitating these out by the application of pressure. Previous work of Fabbiani et al gave a wonderful example of how changing the concentration of the solution and hence the pressure of precipitation can isolate new polymorphs of the pharmaceutical material, piracetam.[1] It is known that the structural changes that occur in a material may depend on the pressure that is applied i.e. phase transition may not occur under hydrostatic regime whereas they will if put under non-hydrostatic environments. Our present studies have been exploring the role of pressure in the polymerisation reaction of simple systems and structurally characterising the materials preceding these events.[2] These studies have provided extra structural insight into the previous Raman studies.[3] We present here a case study where the role of the pressure-transmitting medium extends beyond just application of pressure but where, depending on the medium chosen, new phases can be observed. This work has been conducted at the Pearl beamline at ISIS Neutron Facility in UK.