bluuebunny/crossref_metadata_2025 huggingface dataset:
Preferred Orientation, PDF and Debye Equation
Authors: Neder Reinhard
Published: November 2015

The effect of preferred orientation is currently neglected in the Debye Equation and PDF calculations. This is to a large extend justified, especially for the PDF, as the scattering by large sample volumes is detected by an area detector. The integration of powder rings reduces the effects of preferred orientation. As more laboratory PDF measurements become available that use linear position sensitive detectors or single counter detectors, preferred orientation needs to be reconsidered. A Rietveld calculation treats preferred orientation by multiplying the Bragg intensity by a factor that depends on the angle between the reciprocal space vector and the preferred orientation axis. The powder intensity I(Q) is thus multiplied by a complex function that depends at each Q on the degree of preferred orientation, the lattice parameters, reflection multiplicity etc. The effect on the PDF is therefore the convolution by the Fourier transform of this complex function. The Debye equation is derived from a spherical average of the scattering intensity of a finite object. Thus completely random orientation of the powder grains is implicitly assumed. Both, the Debye algorithm and the PDF algorithm calculate the powder pattern, respectively the PDF from a histogram of interatomic distances, which correspond to a spherical average of all interatomic distance vectors. This histogram does not allow for a Rietveld preferred orientation correction. The effects of preferred orientation on the PDF will be presented on the basis of simulated diffraction pattern. An algorithm to describe the changes in the PDF and the inverse sine Fourier transform as a convenient tool to calculate the powder diffraction pattern will be introduced. This is a good alternative to the Debye equation and allows to take preferred orientation into account both for the PDF and the calculated powder.
A method to obtain all geometric ambiguities in powder indexing
Authors: Oishi-Tomiyasu Ryoko , Tamura Satoshi , Ishikawa Yoshihisa , Torii Shuki , Yonemura Masao , Kamiyama Takashi
Published: November 2015

It is known that different unit cells can have the same computed lines in some cases (Figure). The phenomenon was first called geometrical ambiguity and studied in [1]. In all the high-symmetric cases provided in [1], such unit cells correspond to derivative lattices of each other. Although this is not true in general for 3-dimensional lattices, this has been assumed in methods to search for geometrical ambiguities (e.g., [2]). Thus, a method to obtain all the geometrical ambiguities in very short time for a given unit cell parameters is provided. Because such a method has not been used for powder indexing, it will have impact in the following sense: firstly, it is useful for checking powder indexing solutions promptly. Some powder auto-indexing methods cannot obtain all the geometrical ambiguities. Even for the software including Conograph which can gain all the ambiguities, it is not straightforward to search for them from many indexing solutions using the figures of merit which are sometimes not reliable [3]. Secondly, the new method indicates that powder indexing has only finitely many solutions at least if peak search succeeds in obtaining all (but a few) diffraction peaks with q-values smaller than some calculated value. (Note that infinitely many solutions may exist for lattices of dimension more than 4.) The result seems to provide a foundation of automatic powder crystal structure analysis, because it is possible to obtain all the ambiguities by computation. The introduced method was implemented in the newest version of Conograph, which will be distributed on the web (http://research.kek.jp/people/rtomi/ConographGUI/web_page.html) by IUCr2014. ACKNOWLEDGEMENT: this research was partly supported by a JSPS KAKENHI grant (No.22740077) and by Ibaraki Prefecture (J-PARC-23D06).
Combining X-ray scattering and spectroscopy as structure resolving tool
Authors: Haas Sylvio , Plivelic Thomás , Dicko Cedric
Published: November 2015

Modern applications and basic research in medicine, biotechnology and materials are often concerned with hybrid (organic-inorganic) and synergetic systems. In other words, systems that brings enhanced properties and performances. The challenge is now in the understanding of the complex interactions leading to their assembly and operation. Due to their inherent chemical and structural complexities a combination of several techniques is necessary to determine unambiguously the molecular mechanisms of assembly and operation. [1, 2] To address this need, we have implemented a simultaneous measurement platform called SURF [3] that consists of SAXS, UV-Vis, Raman and fluorescence techniques. The SURF platform provides simultaneous measurements on the same sample volume and a multivariate framework to associate the spectroscopic and X-ray scattering information. Convex constraint analysis (CCA) and two dimensional correlation analyses (2DCOS and 2DHCOS) had been introduced to enhance the interpretation and integration of the data from the different techniques producing self-consistent models and resolving complex behaviour details (structure and chemistry). Additional benefits of the SURF are sample quality control and "on line" diagnostics. In this contribution, we illustrate the benefits of the SURF approach on selected examples. Acknowledgements: The SURF set-up has been mainly financial supported by MAX IV laboratory. S. Haas has a postdoctoral grant of MAX IV lab. S Canton and Q. Zhu are acknowledged for fruitful discussions.
Cryo-EM structure of the actin/myosin/tropomyosin complex
Authors: Raunser Stefan
Published: November 2015

Our cryo-EM structure of the actin-tropomyosin-myosin complex provides novel insights into the interaction between actin, myosin and tropomyosin. The pseudo-atomic model of the complex obtained from fitting crystal structures into the map defines the large actin-myosin-tropomyosin interface and the molecular interactions between the proteins in detail. It indicates that the N-terminus of actin is involved in this interaction. Our data suggest that tropomyosin is stabilized by electrostatic interactions with myosin and likely slides rather than rolls on F-actin when moving from the blocked to the myosin-bound state [1].
Light-induced Helix Movements in Channelrhodopsin-2
Authors: Mueller Maria
Published: November 2015

Electron crystallography has the unique advantage of visualizing membrane proteins in a native-like lipid environment, which likely favors the native conformation. In addition, it allows for the protein to undergo conformational changes in response to their activating signals. We used 2D crystals of channelrhodopsin-2, a cation-selective light-gated channel from Chlamydomonas reinhardtii (Nagel et al., 2003) to study light-induced conformational changes of this intriguing channel, which is currently a powerful tool in optogenetics. Therefore, 2D crystals of the slow photocycling C128T ChR2 mutant were exposed to 473 nm light and rapidly frozen to trap the open state. Projection difference maps at 6 Å resolution show the location, extent and direction of light-induced conformational changes in ChR2 during the transition from the closed state to the ion-conducting open state. Difference peaks indicate that transmembrane helices (TMHs) 2, 6, and 7 reorient or rearrange during the photocycle. No major differences were found near TMH3 and 4 at the dimer interface. While conformational changes in TMH6 and 7 are known from other microbial-type rhodopsins, our results indicate that TMH2 has a key role in light-induced channel opening and closing in ChR2.
Preparation of single-layered enzyme 2D crystals for electron crystallography
Authors: Johnson Matthew , Uddin Yusuf , Metcalfe Maureen , Schmidt-Krey Ingeborg
Published: November 2015

Electron crystallography allows for a wide range of membrane proteins to be studied once conditions for two-dimensional (2D) crystallization have been identified. Two-dimensional crystallization is most frequently achieved via the dialysis approach, where the detergent-solubilized membrane protein is reconstituted into a lipid bilayer [1]. Vesicles, planar-tubular crystals, and sheets are the three most common 2D crystal morphologies. Vesicle and planar-tubular morphologies are observed for the largest percentage of 2D crystals of membrane proteins. Upon negative stain as well as electron cryo-microscopy (cryo-EM) grid preparation, each planar-tubular and vesicle 2D crystal will result in two ordered bilayers that can be analyzed separately by image processing. If any of these morphologies, however, contains a larger number of stacked crystals, data of tilted crystal stacks in particular can currently not be analyzed. Sheets constitute the most desirable morphology, allowing for the preparation of very flat samples for cryo-EM [2]. This is at present the only type of morphology that may be amenable to collection and analysis of electron diffraction data of highly ordered samples [3]. We could reproducibly induce single-layered sheet formation in the large majority of 2D crystals of two different enzyme samples and are working towards a general protocol applicable to other membrane protein 2D crystals.
MicroED: Three Dimensional Electron Crystallography of Protein Micro-Crystals
Authors: Gonen Tamir
Published: November 2015

We demonstrate that it is feasible to determine high-resolution protein structures by electron crystallography of three-dimensional crystals in an electron cryo-microscope (CryoEM). Lysozyme microcrystals were frozen on an electron microscopy grid, and electron diffraction data collected to 1.7Å resolution. We developed a data collection protocol to collect a full-tilt series in electron diffraction to atomic resolution. A single tilt series contains up to 90 individual diffraction patterns collected from a single crystal with tilt angle increment of 0.1 - 10and a total accumulated electron dose less than 10 electrons per angstrom squared. We indexed the data from three crystals and used them for structure determination of lysozyme by molecular replacement followed by crystallographic refinement to 2.9Å resolution. In this seminar I will present our initial proof of principle study and highlight the major advances since the first publication.
Crystal Structure of the Carbon-Phosphorus Lyase Complex from Escherichia coli
Authors: Seweryn Paulina , Van Lan , Kjeldgaard Morten , Hove-Jensen Bjarne , Jochimsen Bjarne , Brodersen Ditlev
Published: November 2015

Phosphorus is an essential element for all living cells and is usually taken up in the form of phosphate. A number of microorganisms, however, are capable of extracting phosphorous from organic phosphonate compounds, which are characterized by a stable carbon-phosphorus (C-P) bond (1). The metabolic pathway responsible for phosphonate degradation is still poorly understood, but the process is known to involve two reactions before the actual C-P bond cleavage, which has been proposed to take place via a radical mechanism. A key component in the process is C-P lyase, an enzyme encoded by phnJ within the phn operon (2). To get a better insight into the mechanism of this complex degradation pathway, we have determined the crystal structure of the core of a multi-subunit enzymatic complex including the C-P lyase component with a total molecular mass of 220 kDa (3). The structure reveals the overall architecture of the C-P lyase and has important implications for our understanding of enzyme mechanism and catalysis.
Crystal structure analysis of dipeptidyl amino peptidase from P. mexicana WO24.
Authors: Roppongi Saori , Tateoka Chika , Suzuki Yoshiyuki , Fujimoto Mayu , Morisawa Saori , Iizuka Ippei , Ogasawara Wataru , Tanaka Nobutada , Sakamoto Yasumitsu , Nonaka Takamasa
Published: November 2015

Dipeptidyl aminopeptidase (DAP or DPP, EC 3.4.14) catalyses the removal of dipeptides from the amino termini of peptides and proteins. In microorganisms, we have reported the identification, purification, and characterization of DAP BI, DAP BII, DAP BIII, and DAP IV (bacterial DPP4), POP fromPseudoxanthomonas mexicanaWO24, and demonstrated that DAP BI, DAP BIII, DAP IV and POP belong to the POP family and they are classified into the clan SC, family S9 in the MEROPS database. On the basis of the enzymological data we obtained, we proposed that bacterial DAPs should be classified in a manner different from that of mammalian DPPs, except for the DAP IV. The DAP IV liberates dipeptides from the free amino terminus and has a specificity for both proline and hydroxyproline residues in the penultimate position of peptides. Here, we report the first structure of the bacterial DPP IV (P. mexicanaWO24 DAP IV) complexed with an inhibitor at 2.2 Å resolution. The subunit structure is composed of two domains, the N-terminal eight-bladed β-propeller domain and the C-terminal alpha/beta/alpha sandwich catalytic domain. These structural features are conserved with clan SC S9 family. However, the N-terminal domain contains a unique helix region that extends over the active site acting as a lid, gating substrate or product access. Based upon the structural data, as well as molecular modeling, a model suggesting that the unique helix region is conserved in some kind of bacterial DPP4s except for mammalian DPP4s and some bacterial DPP4s. Some asaccharolytic and anaerobic bacteria can be used protein or peptides as an energy source. Therefore, these bacteria secrete many types of proteases and peptidases. Especially, the elucidation of degradation mechanisms of collagen, including proline and hydroxyproline, are very important from the point of view of host tissue breakdown in pathogens. Our findings suggest that different ligand recognition mechanisms from the bacterial DPP IV to mammalian DPP4 raise the possibility of an antimicrobial development targeting DPP IV from bacteria.
NaD1 forms oligomeric complexes with phosphatidylinositol to lyse cell membranes
Authors: Kvansakul Marc , Poon Ivan , Baxter Amy , Lay Fung , Mills Grant , Adda Christopher , Payne Jennifer , Phan Thanh , Ryan Gemma , Veneer Prem , van der Weerden Nicole , Anderson Marilyn , Hulett Mark
Published: November 2015

Cationic antimicrobial peptides (CAPs) are innate defense molecules produced by essentially all living species and represent a rich source of novel therapeutic molecules for the treatment of human diseases including cancer. Although several CAPs (mainly from amphibians and vertebrates) have been shown to exhibit direct toxicity against tumor cells, the underlying molecular mechanisms are not well understood. Nicotiana alata (ornamental tobacco) defensin 1, NaD1, is a Class II solanaceous plant defensin in the CAP family that exhibits antifungal activities. We have identified NaD1 as a potent molecule in killing mammalian tumour cells. Microscopy analyses have revealed that NaD1 induces cytolysis of tumor cells via the formation of large plasma membrane blebs. NaD1 was demonstrated to bind directly to phosphatidylinositol 4,5-bisphosphate (PtdIns(4,5)P2 or PIP2) resulting in disruption of cytoskeleton-membrane interactions and subsequent plasma membrane blebbing. To define the molecular basis of the interaction between NaD1 and PIP2, we determined the crystal structure of a NaD1:PIP2 complex. Strikingly, NaD1 forms a unique arch-shaped oligomer comprised of seven NaD1 dimers and 14 PIP2. The structure of the protein:lipid complex indicates that the presence of PIP2 is critical for oligomerisation of NaD1. Formation of NaD1:PIP2 oligomers was further confirmed by protein-protein crosslinking and transmission electron microscopy. Based on these data we propose that NaD1 is an innate pattern recognition molecule for PIP2 and forms a unique protein-lipid oligomeric complex that mediates permeabilisation of both microbes and tumour cells.
Structure and function of an Antiporter
Authors: Wöhlert David , Kühlbrandt Werner , Yildiz Özkan
Published: November 2015

Membrane proteins are essential to transport molecules across biological membranes. This gateway task makes them important drug targets. About 60% of all approved drugs target membrane proteins. Transport of ions across membranes is essential for every cell to maintain physiological salt concentrations and to keep pH homeostasis. In the past years X-Ray structures of various secondary transporters have provided insight into the mechanisms of membrane transport. However, difficulties in expression, purification and crystallization of membrane proteins still restrict the number of available structures. For well-characterized secondary transporters such as LeuT (1), BetP (2) and Ca2+/H+-exchangers (3) crystal structures in different conformations and substrate binding states have been obtained. However, for many important classes of transport proteins, detailed structures are urgently needed to understand their mechanism of action and to guide drug development. We report crystal structures of 2 homologues of a new secondary transporter in different states, with or without substrate bound. These structures shed light on the transport mechanism of this important class of membrane transport proteins.
Crystallography history, a tool for science education
Authors: Desenfant Anthony , Pierre Girardeau Alexandre Bily , Mathieu Bertrand Pierre Schefler , Nicolas Ruty David Riassetto , David Thibaud , Cornuejols Dominique , Vauquois Francoise , Jeany Jean-Baptiste , De-Boissieu Marc , Guinebretiere Rene , Durand Claudie , Sophie Cersoy Sabine Douillet , Hodeau Jean-Louis
Published: November 2015

To introduce Crystallography to the Public, we have organized the crystallography exhibition "Journey into the crystal" in 2009, a "Laue Symposium" in 2012 and a "Bragg symposium, Crystallography for life" in 2013. For the IYCr2014 we have created a set of multilingual hands-on travelling exhibitions to be used in different communities and particularly in emerging countries (in Africa, South America, Asia,...). In addition, we create a set of multilingual tools and other educational material like games to come with these exhibition presentations. A voyage of discovery: Based on this travelling exhibition, we can take visitors on a journey of discovery of matter, but also on a journey through time to the beginnings of crystallography. The public discover why crystal puzzles people so much, why it is so useful to science and why it plays such an important role in our daily lives. With crystallography the public can discover, for example: -1- The myths surrounding diamonds including the surprising fact that diamonds will burn like graphite. Thanks to crystallography, the answer lies in the structure of their chemical bonds. -2- How, in the 18th and 19th centuries, scientists still managed to imagine the architecture of crystals, even though they could not use X-rays to see inside them. -3- Here, use a laser as a source of the light to explain `diffraction and learn how the 1895 discovery of the mysterious "X-Rays" inspired the work of Laue and the Braggs, father and son, making it possible to "journey" into the heart of a crystal. -4- The discovery of DNA and the use of crystallography to understand the biological world and thus the secret of life. This knowledge has greatly contributed to the development of new drugs and thus to the expansion of the pharmaceutical industry. -5- Play with card games or mosaics to understand easily the concepts of periodicity and atomic order and see the explanation of crystal's shape and symmetry. -6- Cultivate crystals,... the specific qualities of crystals make them key materials in many applications and we must take our time to make large crystals...
Crystallization Competition in the School: An innovative teaching/outreach tool
Authors: García-Caballero Alfonso , Lahoz Fernando , Cuevas-Diarte Miquel Àngel , García-Granda Santiago , Gómez-Sal Pilar , Esteve-Cano Vicente , Pasán Jorge , López de Andrés Sol , García-Ruiz Juan Manuel
Published: November 2015

The Crystallization Competition in the School is an innovative contest on Crystallography and Crystallization for young students aged 12-16, successfully tried in five yearly editions. During the 2013/2014 school year, the Competition is coordinated by the Specialized Spanish Group of Crystallography and Crystal Growth throughout Spain in seven hosting areas, culminating in a National Final with a selection of the best crystallization projects. Objectives: a) To stimulate scientific vocations amongst secondary school pupils through an enjoyable and enriching activity; b) To explain basic concepts of Crystallography and Crystallization taking advantage of the natural attraction of crystal growth; c) To communicate how researchers work and compete in a scientific environment; d) To bridge the gap between science and society by conveying the importance of Crystallography in everyday life. Development: 1. Training of secondary school teachers (October-November 2013). A number of workshops entitled `Crystallography in the School' are organised to provide school teachers with specific training in Crystallography and Crystallization; 2. Laboratory work and experimental follow-up (December 2013-March 2014). The students grow spectacular large crystals using an innovative crystallization kit of ADP under the guidance of their teachers, while developing a solid understanding of the concepts involved: solubility, supersaturation, nucleation and crystal growth. Students may also develop other crystallization projects related to the formation of geodes, common salt crystallization in its different habits, and crystallization in gels; 3. Intermediate/Regional Finals (April 2014). The best crystallization projects nationwide are selected to present their crystallization projects at the National Final in Madrid; 4. National Final (10 May 2014, headquarters of CSIC). The format is similar to a `Scientific Congress', where the students have to present a crystal model and a poster of their work. * Organized by: GE3C, CSIC and The Crystallization Factory. * Sponsored by: FECYT, MINECO and Triana Science & Technology.
PR with colourful paintings from colourless crystals
Authors: Griesser Ulrich
Published: November 2015

Documentation in crystallographic science provides not only abstract information and data, but offers a particularly high a potential for aesthetical creations. This potential is evident by in the colourful cover images of some top crystallographic journals as well as the illustrations in the individual scientific articles. Those crystallographers who use polarized microscopic techniques in their daily research know about the fascinating and sometimes surprisingly aesthetic images in microscopic preparations of crystalline materials. The investigation of a vast number of organic compounds with hot stage microscopy over decades in our laboratories resulted in a collection of thousands of microphotographs. Although these images were recorded with the scientific purpose to document the morphology, textures, phase transitions etc. of crystalline phases, there are a many strikingly aesthetic pictures among this collection that would attract the attention of everyone. Therefore, we decided to make this material visible to the public and we started to produce high quality prints for back illuminated wall pictures and lampshades. On our opinion, one can "transform" practically every crystalline substance to appealing "paintings" with some scientific knowledge and preparation skills. This will be demonstrated with pictures produced from the products of an agrochemical company, which now decorate the walls of their building. The positive feedback and interest in the phenomena behind the colourful pictures allowed us to make our scientific work more visible to the public and to convey some understanding for the nature and properties of crystalline materials. The aim of this presentation is to report about past activities, our experience in public relations with crystal images and to inspire colleagues in crystallography to utilize the available potential for such purposes.
Chirality control of the Quadruple helixes of the metal strings
Authors: Yu Chung-Han , Kuo Min-Shiang , Chuang Ching-Yi , Lee Gene-Hsiang , Jin Bih-Yaw , Peng Shie-Ming
Published: November 2015

Novel chiral pentadentate ligands with naphthyridine and camphorsulfonyl groups have been designed and used to control the chirality of quadruple helixes of metal strings directly:Δ-Ni5((-)camnpda)4 (1) and Λ-Ni5((+)camnpda)4 (2). Compound 1 is a Δ form metal string complex with H2(-)camnpda and 2 is Λ form one with H2(+)camnpda. By X-ray single-crystal diffraction, The structures of the compound 1 and 2 are both 2,2-trans form in the same monoclinic space group C2 and have the similar unit cell. Further, it demonstrates that two metal strings are chiral isomers each other by CD spectra. In theoretical computation, the local minimum (Λ-Ni5((+)camnpda)4 with the Δ form) becomes energetically unfavourable by about 100 kcal/mol due to the strong steric repulsion introduced by the camphor groups. Finally, the racemic crystal is obtained with a 1:1 mixture of compounds 1 and 2 in triclinic space group P-1. Both the external dinickel distance in 1 and 2, about 2.280 Å, and the SQUID experiment reveal mixed valence [Ni2]3+ characters and the magnetic behaviors are anti-ferromagnetic (J = -55.0 cm-1 for 1 and -63.3 cm-1 for 2). In the electrochemistry, the three reversible oxidation waves in 1 and 2 are -0.13, 0.20 and 0.97 V.
Applications of the Twinning CIF Dictionary 1.0 for Twinned Crystals
Authors: Young Victor , Hester James , Brown Ian
Published: November 2015

Version 1.0 of the Twinning CIF Dictionary was posted on the IUCr web site in February 2014.[1] The purpose of this presentation is to illustrate the application of these definitions in many common situations relevant to chemical crystallography. Within these definitions are tools to describe all known twin types as defined by the monograph by Nespolo.[2] Tools are available to describe a single twin law or combinations of unrelated twin laws. These definitions were developed mindful that experimental data should have a set format for deposition and validation through future developments of the web-based IUCr CheckCIF software. Several examples of twins will be presented to illustrate the functionality of these definitions.
Growth and structure of K2CoxNi(1-x)(SO4)2·6H2O mixed single crystals
Authors: Vasilyeva Natalie , Grigorieva Marina , Antipin Alexander , Sorokina Natalia , Voloshin Alexey
Published: November 2015

To date, crystals of Tutton salts with the general formula (M+)2M2+(SO4)2*6N2O (where M+- alkali metal or ammonium, M2+ - bivalent metal - Co2+, Ni2+) are used as a materials for ultraviolet (UV) filters. Only in recent year effort of ternary crystal growth has been taken. The main problem of mixed crystal growth from liquid solution is high level of the crystal inhomogeneity, which leads to generation of the elastic stress, inclusion trapping and micro- and macrocrack formation in the bulk crystal. For the first time the optically homogeneous mixed K2CoxNi(1 – x)(SO4)2 · 6H2O (KCNSH) large single crystals have been grown from solutions of different compositions by the temperature-reduction technique. Precise X-ray experiment of three mixed crystals was carried out by four-circle diffractometer CAD-4F and XcaliburS diffractometer with two-dimensional CCD detector at the room temperature. KCNSH crystals belong to the monoclinic space group P2(1)/c. Each Co2+ or Ni2+ ion is coordinated with six H2O molecules, forming a distorted octahedral (Co(H2O)6)2+ and (Ni(H2O)6)2+ unit. With increasing content of nickel ions in the crystal, the octahedral unit is narrowed and the unit cell volume is decreased. Chemical formulas refined using diffraction data are K2Co0.657Ni0.343(SO4)2·6H2O, K2Co0.226Ni0.774(SO4)2·6H2O and K2Co0.216Ni0.784(SO4)2·6H2O. Ratios of isomorphic cobalt and nickel components in the mixed crystals are conformed to data obtained by atomic emission spectroscopy. Effect of the Co2+ and Ni2+ ion ratio in KCNSH single crystal to crystal quality is considered.
Cocrystallization of acetaminophen and glutaric acid with different coformers
Authors: Timofeeva Tatiana , Antal Sofia , Draguta Sergiu , Ordonez Karla , Castaneda Raul , Leonova Evgeniya
Published: November 2015

Recently cocrystallization became a popular tool for crystal engineering that allows, for instance, improving properties of pharmaceutical materials, creating new materials for nonlinear optical applications and solar cell technologies. To attract students to crystallographic studies we carried out project that included crystal growth of two series of cocrystals with acetaminophen and with dicarbonic glutaric acid. We attempted cocrystallization of acetaminophen with more than ten different coformers which gave no cocrystals or salts. However, as a result of cocrystallization we obtained new polymorph modification of hydroxyquinoline. On the contrary, cocrystallization of glutaric acid with basic organic compounds gave several new salts. Interesting examples among them are systems of glutaric acid with 2-pyridinamine and with 6-methyl-2-pyridinamine. In spite of the presence of the same substituents that are prone to H-bond formation, cocrystals have different H-bonding systems and even different molecular conformation of glutaric acid. Details of physical properties, such as spectral characteristics and melting points, of obtained multicomponent materials are discussed.
Molecular architectures of new inorganic lamivudine salts, an anti-HIV drug.
Authors: Tenorio Juan , Ellena Javier
Published: November 2015

One of the currently goals of the crystal engineering is the improvement of pharmaceutical properties of Active Pharmaceutical Ingredients. Herein is discussed the design of new solid forms of the Lamivudine (3TC), one of the most used and marketed anti-HIV drug. The crystalline forms herein presented correspond to inorganic acid salts: Lamivudine hydrobromide (3TCH+-Br-), hydrogen difluoride (3TCH+-F-HF) and nitrate (3TCH+-NO3-). These new salts crystallized in non-centrossymetric space group P21. The halogenated salts (3TCH+-Br-and 3TCH+-F-HF) exhibited isostructural supramolecular assemblies, similar to the anhydrous salt of lamivudine hydrochloride (3TCH+-Cl-) reported by our research group, and whose equilibrium solubility showed an increase when compared with 3TC pharmaceutical form. [1,2] The main feature of the salt crystalline assemblies is related to the supramolecular ordering of the 3TCH+cationic units, by observing the formation of vacancies between them generated in the [100] direction due to the helical symmetry, so, the anions are localized into the interstices of these vacancies, stabilizing the crystalline assemblies. Meanwhile, the 3TCH+NO3-salt showed a different conformational and supramolecular behavior from that observed in the halogenated ones. Here is observed the formation of helical strands along the b axis, which will be engaging by translational symmetry in the horizontal direction in the [10-1] plane. Therefore, they form zigzag molecular planes which will subsequently be architected in parallel with the [10-1] direction. In addition, it was used for this study X-ray powder diffraction (XRDP), vibrational analysis: Infrared (IR) and Raman spectroscopy, and thermal analysis: differential scanning calorimetry (DSC), thermogravimetry (TG) and hot-stage microscopy. Comparison of the structural properties of these salts with some forms already reported (e.g. 3TCH+-Cl-) allows to infer some possible pharmaceutical properties.
Structural features of metal dodecahydro-closo-dodecaborates
Authors: Stavila Vitalie
Published: November 2015

Metal dodecahydro-closo-dodecaborates have been recently explored as materials for hydrogen storage and as promising ionic conductors. However, their utility as hydrogen storage media is impeded by their high thermal stability, kinetic limitations, and side reactions. The high thermal and chemical stability of these materials makes them interesting for solid battery membrane applications, however more work is needed to understand the complicated phase transitions which occur in many metal dodecahydro-closo-dodecaborates. Recent literature suggests that dodecahydro-closo-dodecaborate species are formed as stable intermediates during the dehydrogenation of metal borohydrides [1]. This hypothesis is especially intriguing in the context of high thermal stability reported for compounds containing icosahedral dodecahydro-closo-dodecaborate anions in the presence of hydrogen gas [2]. Here, a series of multi-component alkali, alkaline-earth and transition metal [B12H12]2- compounds were isolated and characterized by single-crystal and powder X-ray diffraction techniques. Attempts to rehydrogenate M2B12H12 and MB12H12 (where M= alkali or alkaline-earth metal) in the presence of the metal hydrides we made, and several compounds were found to be susceptible to dehydrogenation/rehydrogenation reactions. In addition, selected M2B12H12 compounds were found to display high-temperature phases with increased values of alkali metal ionic conductivity.
Salts and Co-Crystals of Agomelatine
Authors: Skorepova Eliska , Husak Michal , Ridvan Ludek , Cejka Jan
Published: November 2015

Salts and co-crystal are multicomponent solids but in different ionization states. In salts, there is a proton transfer between the molecular components, making it contain cations and anions. On the other hand, co-crystals are made up from neutral molecules held together by non-bonded interactions. Agomelatine is an active pharmaceutical ingredient (API) used as an antidepressant. Because the search for new solid forms of an API is an important step in a drug development, our aim was to prepare novel co-crystals of agomelatine. Phase analysis was done by powder X-ray diffraction and the structures were solved from single-crystal X-ray diffraction data. Further analyses were done by infrared and Raman spectroscopy and solid state NMR. For agomelatine, several co-crystals have been prepared, namely with citric acid, maleic acid, oxalic acid, 4-hydroxybenzoic acid and isonicotinamide. Agomelatine is an amidic compound and, since amides are considered very neutral, it was quite a surprise, when agomelatine in the combination with benzensulphonic, hydrobromic and hydroiodic acids produced salts. Structural comparison of all the solid phases in the respect of ΔpKA, amidic group bond lengths, conformation and packing of agomelatine and position of the guest molecule in the crystal lattice is also given. For pharmaceuticals, the determination whether the material is a salt or a co-crystal is interesting not only academically, but also from the regulatory point of view. Therefore, our findings may play a crucial role in the future development of the multicomponent solid phases of agomelatine. This work was supported by the Grant Agency of Czech Republic, Grant No. 106/14/03636S and the specific university research, Grant No. A2-FCHT-2014-081.
Interplay of Packing, Proton Transfer and Hydrogen Bonding on Crystal Properties
Authors: Seaton Colin , Munshi Tasnim , Scowen Ian
Published: November 2015

The designed creation of crystalline materials with desired physical properties is a key objective of crystal engineering. Currently the development of multi-component crystals such as salts and co-crystals as a route for the modification of physicochemical properties has been a major focus within the field. However, while the creation of such materials has been repeatedly demonstrated, understanding the structure-property relationships between the component molecules and the final crystal form is great challenge, so limiting the ability to design new materials. Controlling the proton transfer process is vital for the designed creation of protonic conductive materials but also important in other fields as the proton location alters the physical properties of other systems such as pharmaceutical or photochromic materials. The interaction between chemical structure and local crystallographic environment has been shown to alter the energy landscape of the proton transfer process [1,2] This presentation will report on work investigating the relationships between changes in molecular and crystal structure on proton transfer processes in multi-component materials. Both experimental crystal growth and computational modelling have been used to study proton transfer in binary and ternary systems based on the carboxylic acid...pyridine hydrogen bond. Understanding the interplay between packing forces and proton transfer in controlling the observed photochromism in bipy/rac-mandelic acid system and how this can be used to design new material based on these concepts.
A New Look at Organic Hydrates: Chemistry, Crystal Structure and Bioactivity
Authors: Oliveira Mark , Wood Peter , Hickey Magali , Almarsson Orn , Alvarez Juan , Feeder Neil , Galek Peter , Moustakas Demetri
Published: November 2015

Crystalline organic hydrates in the Cambridge Structural Database have been surveyed to better understand water coordination environments and hydration likelihood. Particular emphasis has been paid to the subsets of bioactive organic hydrates and five classes of compound that are important in terms of pharmaceutical activity. Bioactive compounds are found to exhibit a greater hydration likelihood than general small organic compounds, but the distribution of environments remains the same, with the most common by far being where water accepts once and donates twice (DDA, 49.8%).
Alexdrandrite Effects and Pseudosymmetry in Aluminum Oxalates
Authors: Nimthong Ruthairat , Zeller Matthias , Sungnoi Patimaporn , Wongnawa Sumpun , Pakawatchai Chaveng
Published: November 2015

Three chromium doped potassium aluminum oxalates, (K3[Al0.95Cr0.05(C2O4)3]·3H2O) "Blue", (K2/3Na7/3[Al0.95Cr0.05(C2O4)3]·4H2O) "RedCubic", and (K18{Na[Al0.964Cr0.036(C2O4)3]6}Cl·18H2O) "Red-Hexagonal" were prepared from aqueous solutions of K3[Cr(C2O4)3]·3H2O, K3[Al(C2O4)3]·3H2O and NaCl, and their solid state and solution properties were rationalized from their crystal structures, analysis data and solid state and solution UV-vis spectra. Crystals of "RedCubic" are characterized by a metrically cubic I-centered unit cell, but do have actual tetragonal symmetry derived by ordering of sodium and potassium ions not compatible with the apparent cubic symmetry. Results of 13C-NMR, EPMA/EDX, SC-XRD, and UV-Vis spectroscopies are discussed in relation to the compound's structures and color behavior. In aqueous solution RedCubic and Blue show the same greenish purple color and identical electronic absorption peaks. In the solid state, they have different colors and show slightly different absorption peaks. Their color behavior as well as the Alexandrite color-change effect observed in the two Red crystals are rationalized based on the compounds' absorption peaks.
Kinetics and Selectivity in Host-Guest Chemistry
Authors: Nassimbeni Luigi
Published: November 2015

A bulky substituted binaphthyl diol host has been employed in the separation of picolines. The selectivity profiles for pairs of picolines and for all three picolines, have been determined. The results are correlated with measurements of thermal stability and structure. The solid-vapour kinetics of a xanthenol host with volatile guests have been studied. Both the enclathration and the decomposition reactions were analysed. The kinetic laws, rate constants and activation energies were derived. Special balances which were constructed for the kinetics of enclathration will be described. The single crystal to single crystal reaction of a xanthenol host, in which the chlorobenzene guest was exchanged with toluene, was followed at the molecular level by repeated crystal structure analyses.
Furosemide solvates: can they serve as precursors to different polymorphs?
Authors: Minkov Vasily , Beloborodova Alina , Drebushchak Valeri , Boldyreva Elena
Published: November 2015

The importance of polymorphism of molecular crystals is hard to overestimate, especially when dealing with compounds used as materials or drugs. Different polymorphs of a drug substance may have different properties related to their manufacturing, therapeutic usage, or storage (density, hygroscopicity, melting points, thermal stability, solubility, rate of dissolution, surface free energy, toxicity, bioavailability, tabletting, etc.). Different polymorphs, solvates, and co-crystals can be patented, and this opens the way for a competition with brand drugs. Since the energies of different polymorphs are sometimes very close, producing desirable crystalline forms is quite a challenge and can also be complicated by the phenomena of concomitant polymorphism (when several polymorphs crystallize simultaneously from the same batch), or erratic and poorly reproducible (when crystallization gives different polymorphs even at seemingly identical experimental conditions). The aim of the present study was to crystallize various solvates of furosemide, to check whether these solvates can be used as precursors for producing different polymorphs of pure furosemide on their subsequent decomposition upon heating, and to search any correlation between the crystal structures of the solvates and on the furosemide polymorphs produced by desolvation. Four solvates of furosemide with tetrahydrofuran, dioxane, dimethylformamide, and dimethylsulfoxide were crystallized. The detailed structural analysis of furosemide-containing crystal structures showed that the molecule of furosemide has a high conformational lability because of the rotations of the sulfamoyl and furanylmethylamino fragments. Some of the furosemide conformations were shown to be stabilized by the intramolecular N–H···Cl H-bond. Desolvation of the four solvates was studied by TG and X-ray diffraction and was shown to give different products depending on the precursor and particle size.
Modified Phenyl Groups on Pyrazin Groups to Synthesized Cobalt String Complexes
Authors: Lin Geng-Min , Yeh Chen-Yu , Lee Gene-Hsiang , Peng Shie-Ming
Published: November 2015

In the literature, ligand such as oligo-α-pyridylamines and oligo-naphthyridylamine are usually used in the linear metal string complex. In addition to all of the above, another series of ligand is synthesized by mixing two types of ligands. In other words, the type of ligand contains pyridyl and naphthyridyl groups. Permuting the possible permutation, we can find that symmetrical and the shortest ligand is 2,7-bis(α-pyridylamino)-1,8-naphthyridine (H2bpyany). Complexes contain bpyany2-, hexa-nickel or hexa-cobalt, axial ligands such as chloride and thiocyanate, and anions such as hexafluorophosphate and tetrafluoroborate were published1, 2. Another similar ligand that H2bpyany replaces pyridyl groups by pyrimidyl group is 2,7-bis(α-pyrimidylamino)-1,8-naphthyridine (H2bpmany). Hexanickel complexes with bpmany2- were also published3. According to the above, if we replace pyridyl group by pyrazin group, properties of complexes such as magnetic property, CV and resistance make a change. 2,7-bis(α-pyrazinamino)-1,8-naphthyridine (H2bpzany) and nickel or cobalt ions were reacted. We can get the signal in MALDI, but we cannot isolate the target. Because of this, we modified phenyl groups on pyrazin groups. By 2,7-bis(5-phenyl)-α-pyrazinamino-1,8-naphthyridine (H2bphpzany), [Co5(bphpzany)4(NCS)2] (1), [Co6(bphpzany)4(NCS)2](PF6)n (n=1 (2), n=2 (3)) have been synthesized and the crystal structures for complex 1–3 have been determined by X-ray crystallography. Three complexes are the similar component of four ligands, five or six cobalt ions, two thiocyanates as axial ligands, and hexafluorophosphate as counterions. The structural characterization is that the cobalt chain is helically wrapped by four bphpzany2–. Complex 1–3 have Co510+, Co612+ configurations, and all are air-stable.
Pseudo-polymorphism of Halogen Substituted Tetraaza[14]annulene Complexes
Authors: Ichimura Shuhei , Saeki Masahiro , Tamaki Yoshinori , Miyamura Kazuo
Published: November 2015

6,8,15,17-tetramethyldibenzo-5,9,14,18-tetraazacyclotetradecinatonickel (II) (tmtaa) bears strain within its 14-membered ring and is known to adopt saddle-shaped structure. As a consequence, tmtaa has an asymmetric apical coordination sites at both sides of the saddle. Our previous study revealed that the chlorine substituted complex, [Ni(tmtaa-4Cl)] shown in Figure (X = Cl), exhibited pseudo-polymorphism with dichloromethane and chloroform. This behaviour is due to the good affinity between halogen substituents and halomethane solvent. In this study, we grew single crystals of [Ni(tmtaa-4Br)] using various halomethane solvent as crystallization solvents and elucidated the role of the solvents related to the generation of pseudo-polymorprhism. We have succeeded in obtaining two kinds of single crystals 1 and 2 from the same vial container using bromoform. From X-ray structural analysis, 1 and 2 formed twist dimer as with previous report, and are found to include bromoform in their crystal structure. Note that these complexes adopted more distorted saddle-shaped structure than normal tmtaa complexes. The Ni-N4 planes were not planar. The difference of 1 and 2 was the degree of distortion around Ni-N4 plane, and 1 was more distorted than 2. The space group of these complexes were Aba2 and C2/c respectively. The interactions that led to the difference in packing of dimers were CH...π interaction in 1 and π...π interaction in 2.
Single-crystal guest exchange and phase transformations in a porous metallocycle
Authors: du Plessis Marike , Smith Vincent , Barbour Leonard
Published: November 2015

One of the target architectures for porous crystals investigated by our group is the "doughnut-shaped" metallocycle. The "doughnut" shape of the metallocycles prevents them from packing efficiently and results in the formation of crevices, cavities or channels in the packing arrangement. Naturally, owing to close-packing requirements the occurrence of empty space in the crystal structure is energetically unfavourable and therefore the available "space" is usually occupied by solvent molecules. Ideally, the porous phase can be obtained by removing the solvent molecules from the channels without disrupting the host framework. In this regard we have conducted a further investigation of the porous metallocycle previously reported by Barbour et al.[1] Single crystals of a previously reported porous metallocycle [Ag2L2](BF4)2·2CH3CN (1) were grown from acetonitrile and immersed in different organic solvents. The crystals thus treated were subjected to single-crystal X-ray diffraction analysis, which revealed that the acetonitrile guest molecules had been replaced by the solvent that the compound was exposed to, yielding five different solvates: [Ag2L2](BF4)2·2(CH3)2CO (2), [Ag2L2](BF4)2·2CHCl3 (3), [Ag2L2](BF4)2·C6H6 (4), [Ag2L2](BF4)2·C6H4F2 (5), [Ag2L2](BF4)2·C7H8 (6). Thermogravimetric analysis supports these findings.