bluuebunny/crossref_metadata_2025 huggingface dataset:
3D printing of crystallographic models and open access databases
Authors: Kaminsky Werner , Snyder Trevor , Moeck Peter
Published: November 2015

Although introduced 30 years ago, cost and performance improvements have only recently made 3D printing affordable. The industry wide input file format for 3D printers incorporates explicit mesh - `STL' data. Molecules and crystal structures, when including symmetry, crystal morphologies, or crystal defects are encoded in the parametrical `CIF' syntax. Free software for converting directly CIF data to STL files has just been developed, available online [1]. First examples of printed 3D models from STL-files created with these programs include molecules of sucrose, herapathite [2a], caffeine, humulone [2b], an alpha-quartz crystal and its Japanese {112} twin or a brilliant cut diamond. Far more CIF encoded models are available, even open access. The Crystallography Open Database (COD) features over 245,000 entries and has recently developed into the world's premier open-access source for structures of small to medium unit cell-sized inorganic and molecular crystals [3a], complementing the well-established open-access Worldwide Protein Data Bank [3b]. The Cambridge Crystallographic Data Centre in the United Kingdom provides crystal structure data of small (organic) molecules free for bona fide research [3c]. Structural data on inorganic crystals, metals and alloys can be obtained free of charge from the Inorganic Material Database (AtomWork) [3d]. Related to the COD, the crystallographic open-access databases [3e] ("COD offspring") provide CIF data for interdisciplinary college education. With this basic infrastructure in place, any interested college educator may print out her or his favorite crystallographic structure model in 3D and use it in hands on class room demonstrations [3f].
CrisDi School: disseminating crystallography in Piedmont, Italy
Authors: Marabello Domenica , Agostino Angelo , Benna Piera , Dinardo Giovanna , Lamberti Carlo , Cámara Fernando
Published: November 2015

The Interdepartmental Research Centre for the Development of Crystallography (CrisDi) aims to be an institution of reference for researchers at the University of Turin interested on the field of diffraction (X-rays, neutrons and electrons), to promote the knowledge and dissemination of crystallography, and to facilitate the access to available laboratory instrumentation (diffractometers and TEM) and to large scale facilities (synchrotron and neutron sources). CrisDi hosts scientists with interest in the fields of solid state chemistry and physics, organic, inorganic, organometallic and theoretical chemistry, mineralogy, biology, pharmaceutical and agricultural sciences. The Centre encourages the design and the development of new methodologies and applications, and supports the enhancement of the available instruments. The submission of proposals at large scale instruments is encouraged specially for young researchers and PhD students. The cultural and scientific interchange among crystallographers coming from different disciplines is strongly encouraged by CrisDi. A main task of the CrisDi is the annual organization of a post-grade level School with a series of courses dedicated to: (i) basic level crystallography (symmetry, theory of diffraction, crystal-chemistry), diffraction techniques (single crystal and powder X-ray diffraction, neutron and electron scattering); (ii) advanced level (high temperature and high pressure structural studies, macromolecular crystallography, time resolved crystallography and kinetic studies); (iii) spectroscopic approaches (XAFS, XANES, XES and NMR) in crystallography. The school, which is held every year in May for about 20 ECTS equivalent, has no tuition fees and is also open to non-academia people.
The International School of Crystallography: an example of continuing education
Authors: Guerri Annalisa , Scapin Giovanna , Spadon Paola
Published: November 2015

2014 has been declared by UNESCO the International Year of Crystallography. Following the declaration, many initiatives have flourished with the intent of spreading the science and culture of crystallography, since among the major objectives of the IYCr2014 are increase of public awareness on the science of crystallography, promotion of education and research in all fields of crystallography and fostering of international collaborations. The International School of Crystallography is an internationally recognized meeting that was started in 1974 by Prof. Riva di Sanseverino, with the similar goals of promoting high level crystallographic education, scientific exchanges and collaborations. In 2014 the school celebrates its 40th year of activity. During these forty years, courses have been held on many different topics addressing all aspects of crystallography, from crystal growth theory to practical applications in drug discovery to the use of cutting edge technologies; students and teachers have been brought together in an environment that fostered high level scientific discussions as well as unique interpersonal relationships. Many of the students moved on to become well known personality in the crystallographic community, while retaining collaborations and friendships started during the School. Through these years the School teaching methods have also evolved, taking advantage of the fast technological progress of the past 10 years or so. The School offers both traditional lectures and practical computer-based workshops, to guarantee the students not only a theoretical background, but also hands-on experiences on applied crystallography. The dedication of the organizers and lecturers, the unconditioned support of the local staff, and the unique location of the School have made it a great success and a very popular meeting for generations of crystallographers.
Virtual X-Ray Laboratory for Teaching Crystallography and Other Courses
Authors: Cherner Yakov , Kukla Maija , Bunina Olga , Hobbs Linn
Published: November 2015

Contemporary research equipment is not only extremely complex and very expensive, it is typically fully computerized and most tasks are executed without student participation. This creates a number of substantial educational drawbacks and limitations. The paper presents a virtual multifunctional X-ray laboratory (v-Lab) that helps overcome the above mentioned problems, addresses the demands of distance and blended education and meets learning habits of today's students. The v-Lab enables students to practice concepts, tasks, and equipment operations in a manner that can't be achieved on actual equipment. It employs virtual X-ray equipment that realistically imitates the functionality and design of actual equipment and also includes educational analytical software. Virtual data can be exported to popular software as well. Highly interactive online experiments using virtual equipment have been created for undergraduate students to learn fundamental principles underlying the analytical x-ray methods and become familiar with the design and operation of the X-ray equipment. A variety of visual, audio and traditional learning and assessment resources were integrated with virtual experiments to provide students with "just-in-time" learning opportunities. The virtual equipment has also been used for preparing undergraduate and graduate students to perform various research studies including but not limited to: X-Ray diffraction study of phase transitions in ferroelectric ceramics and nanoscale thin films, qualitative phase analysis of various compounds, nanostructured materials and human kidney stones, etc. Examples of virtual experiments used for teaching crystallography and other science and engineering courses at several US and Russian universities are presented and discussed. An easy-to-use authoring tool enables instructors to customize existing virtual experiments, and create new ones, as well as to add their own samples into the sample collection.
The human intellect is the source of its own problems: Ligands of fancy
Authors: Rupp Bernhard
Published: November 2015

Fundamental scientific epistemology requires that a strong claim is supported by strong and convincing proof. As an example, the proposition of a ligand bound to a target protein in a precise conformation and pose presents a very strong claim, and confirming (positive omit difference) electron density will provide the correspondingly strong experimental evidence. A survey of ligand structure models has revealed that in an unexpectedly large number of ligand structures, the required electron density is not present or does not sufficiently support the proposed ligand pose. Upon detailed analysis, it emerged that the origin of such fanciful models lies in the simple neglect of the most basic fundamentals of scientific epistemology, which appears not to be formally taught in some science curricula. A brief introduction into the importance of evidence and its balance with prior expectations in a Bayesian system of empirical reasoning on hand of protein-ligand complex structure examples is therefore provided for young and aspiring scientists. It particular affects early career researchers when fictitious models intended to support bio-medically relevant hypotheses delay the progress of science by unsupported claims: grants cannot be funded when they contradict models believed to be true, and valuable taxpayer money can be squandered trying to pursue science based on false premises. Poor and at minimum self-deceptive work threatens to become systemic and accepted over the course of time unless young researches take full ownership and responsibility for their exciting and important work and resist any postmodern relativism threatening to erode the credibility of their profession.
When good ligands go bad
Authors: Merritt Ethan
Published: November 2015

"Tools for validating structural models of proteins are relatively mature and widely implemented. New protein crystallographers are introduced early on to the importance of monitoring conformance with expected φ/ψ values, favored rotamers, and local stereochemistry. The protein model is validated by the PDB at the time of deposition using criteria that are also available in the standard software packages used to refine the model being deposited. By contrast, crystallographers are typically much less familiar with procedures to validate key non-protein components of the model – cofactors, substrates, inhibitors, etc. It has been estimated that as many as a third of all ligands in the PDB exhibit preventable errors of some sort, ranging from minor deviations in expected bond angles to wholly implausible placement in the binding pocket. Following recommendations from the wwPDB Validation Task Force, the PDB recently began validating ligand geometry as an integral part of deposition processing. This means that many crystallographers will soon receive for the first time a ""grade"" on the quality of ligands in the structure they have just deposited. Some will be surprised, as I was following my first PDB deposition of 2014, at how easily bad ligand geometry can slip through the cracks in supposedly robust structure refinement protocols that their lab has used for many years. I will illustrate use of current tools for generating ligand restraints to guide model refinement. One is the jligand+coot+cprodrg pipeline integrated into the CCP4 suite. Another is the Grade web server provided as a community resource by Global Phasing Ltd. Furthermore I will show examples from recent in-house refinements of how things can still go wrong even if you do use these tools, and how we recovered. The new PDB deposition checks may expose errors in your ligand descriptions after the fact. This presentation may help you avoid introducing those errors in the first place."
Crystallography Education for Non-Science College Students
Authors: Nazarenko Alexander
Published: November 2015

New applications of crystallographic methods made it necessary to teach crystallography to students with limited background in physics and chemistry. In this case, classic approach to crystallography with mandatory study of space group and physics of X-ray diffraction is not feasible. We suggest an alternative direction: (1) introduction to experimental procedures and data collection for polycrystalline and (possibly) monocrystalline samples, (2) raw data processing and use of databases for identification of known crystalline materials. Instead of establishing a crystal structure of a new compound, our goal is limited to reliable identification of known one. With this approach, X-ray diffractometer appears to be one of many tools in analytical laboratory, and crystallographic data can be combined with results coming from multiple techniques such as Raman, IR, NMR, and mass-spectroscopy. Possible modifications of data collection and data processing procedures will be discussed. This presentation is based our experience with teaching various instrumental methods (including X-ray Crystallography) for Forensic and art conservation students at SUNY College at Buffalo.
Structure-properties relationship in Borinic Systems at high and normal pressure
Authors: Wesela-Bauman Grzegorz , Parsons Simon , Luliński Sergiusz , Serwatowski Janusz , Woźniak Krzysztof
Published: November 2015

Recently we were focused on the synthetic, physicochemical and theoretical evaluation of the properties of borinic 8-oxyquinolinates.[1,2] Such systems are of interest of many groups in the world, as borinic derivatives are promising materials for the preparation of luminescent layers in organic light emitting diodes (OLEDs).[3] Our aim is to trace the impact of structure on properties of the system. Hence we have conducted polymorph screening for highly strain aromatic heteroleptic borinic system. As a result, we are presenting, the very first examples of polymorphism in the group of aromatic borinic 8-oxyquinolinate complexes [(2-fluoro-3-pyridyl) (2,2`-biphenyl)borinic 8-oxyquinolinate)]. We wanted to extend our investigations on high-pressure crystallography. These investigations were prompted by results obtained by other groups which analysed crystal structures of AlQ3, GaQ3 and InQ3 under low and high pressure. Such studies helped to trace a connection between the motifs present in the crystal phases and optical properties of these complexes as a consequence of orbital interactions. On this basis we were interested in investigation of the influence of high pressure on the packing of synthesized and characterized (2-fluoro-3-pyridyl) (4-iodophenyl)borinic 8-oxyquinolinate.
New terpyridine-(β-diketonate)-copper(II) complex. Structure and magnetism
Authors: Toledo Dominique , Moreno Yanko , Peña Octavio , Baggio Ricardo , Vega Andrés
Published: November 2015

Over the last decade the design and synthesis of metal-organic compounds with fascinating structural properties and potential applications as functional materials has been a major challenge in various fields of research.1Strategies for preparing these compounds are based on the careful selection of the constituent building blocks. 4'-(substituted)-4,2':6',4''-terpyridine ligands are considered versatile building blocks for the assembly of coordination polymers and networks with useful solid-state properties, such as magnetism, luminescence, redox activity, etc.2The divergent arrangements of N-donor atoms and the attachment of aryl substituents into the 4'-position of 4,2':6',4''-terpyridine allow to bridge two or more metal centers, giving rise to molecular assemblies of 1, 2 or 3 dimensions.3Our line of interest is the obtainment of compounds with emergent magnetic properties. Herein we present a copper complex surveying the new 4'-(quinolin-4-yl)-4,2':6',4''-terpyridine ligand (L), and formulated as [Cu(C5H1F6O2)2(C25H16N4·CHCl3)]n which was produced from the reaction of two equivalents of L with Cu(hfac)2, (hfac=hexafluoroacetylacetonate). The copper ion in trans-{CuN2(hfac)2} has an octahedral environment. The nitrogen atoms of the terminal pyridine rings coordinate to the paramagnetic centres, while the central ring remains uncoordinated. The linkage of the resulting polyhedra gives raise to an undulating 1D polymeric structure. Within these chains there are two main non-covalent interactions: π-stacking between the quinoline substituents and the pyridine rings and CH···F interactions due to CF3group of the hfac ligand. There are also weak CH···N, CH···π and π-π intermolecular interactions linking the L and CHCl3groups, which give stability to the crystal structure. Finally, we performed magnetic measurements, in order to determine the magnetic behaviour of our system. Acknowledgments: FONDECYT 1130433 project, CIPA of University of Concepción, LIA-MIF 836
Study of a 2D coordination polymer of Zn(II) with 5-aminoisophtalic as ligand.
Authors: Rosa Iara , Pinheiro Carlos , Doriguetto Antonio
Published: November 2015

The design, synthesis and characterization of infinite one-, two- and three dimensional coordination polymers have attracted increasing attention in chemistry and material science research due to their potential applications as drug deliver, magnetic and optical sensors [1]. In particular, a series metal-organic frameworks MOFs - (a coordination polymer subclass) with different topological nets such as honey-comb, brick wall, ladder, herringbone, diamondoid and rectangular grids have been comprehensively discussed by Yaghi, Kitagawa and their co-workers [2] and it was observed that the type of metal ion and organic bridge ligand determines the dimensionality and the topology of the network. In this work we report a new 2D coordination polymer obtained by from ZnSO4.7H2O and 5-aminoisophtalic acid (5AIF), using the base diffusion method (DMSO as solvent). The crystal structure was determined from single crystal X-ray diffraction data collect in a Gemini-Oxford diffractometer. The Zn atom is tetrahedrally coordinated with two oxygen and one nitrogen from three different 5AIF molecules and one oxygen from DMSO molecules. The molecular packing indicates the formation of a 2D parallel to (010) forming hydrophilic cavities along [001]. The 2D network is stabilized by intermolecular hydrogen bonds involving the donor hydroxyl group (O3-H3) and the acceptor nitrogen atom (N1). The geometrical features of this new 2D coordination polymer were are all in agreement with similar fragments deposited in CSD [3].
HP-induced penetration of guest molecules in high-Si mordenite
Authors: Quartieri Simona , Leardini Lara , Arletti Rossella , Vezzalini Giovanna
Published: November 2015

A high-Si mordenite (HS-MOR, SiO2/Al2O3 ~ 200, s.g. Cmcm) was investigated by in-situ synchrotron XRPD under HP using silicone oil (s.o.) as non-penetrating pressure transmitting medium (PTM), and the following penetrating PTM: (16:3:1) methanol: ethanol:water (m.e.w), (3:1) water:ethanol (w:e), ethylene glycol (e.g.) and resorcinol (res). The experiments were performed in DAC at SNBL1 (ESRF, Grenoble). The evolution of the structural features was followed by full profile Rietveld refinements. In the Pamb-1.2 GPa range, the volume contraction of HS-MOR compressed in s.o. (Tab. 1) is the highest found among the HS zeolites studied up to now in the same P range [1-2]. Above this P value, a rapid and irreversible loss of long range order is observed in the diffraction patterns. These findings suggest a gradual P-induced amorphization. The main results of the experiments with penetrating PTM are the following (Tab. 1 and Fig. 1): i) no complete X-ray amorphization and phase transitions achieved up to the highest investigated P; ii) penetration of additional guest species into the channels, even at very low P; iii) lower cell-volume reduction with respect to that found in s.o. in the same P range; iv) partial reversibility of the P-induced effects upon decompression. The lower compressibility of HS-MOR in penetrating PTM with respect to s.o. is due to the entrapping of additional guest molecules, which contributes to sustaining the mordenite framework and stiffening the material.
Indium Based Metal-Organic Frameworks: The Search for a powerful Green Catalyst
Authors: Aguirre-Diaz Lina , Iglesias Marta , Snejko Natalia , Gutierrez-Puebla Enrique , Monge Angeles
Published: November 2015

The reduction in negative environment impact is a primary goal in the chemical industry. For these reasons several authors, looking for a "green chemistry", highlighted the special interest in using indium for its diverse physical properties and its stability in air.[1] Our interest is focused on indium MOFs constructed with benzene multicarboxylate ligands, which have been found to be useful building blocks in construction of MOF materials. This approach has allowed the assembly of indium based structures with catalytic activity toward nitroaromatics reduction, sulfide oxidation, aldehydes acetalization and aldehydes cyanosilylation.[2-3] In this way, we have synthesized, purified and characterized five new indium based MOFs using 4,4'-hexafluoroisopropylidene-bis-(benzoic acid) (H2hfipbb) as bent organic linker together with N-donor ancillary ligands, which gave rise to materials with the composition [In(OH)(hfipbb)] (1), [In2(hfipbb)3(1,10-phen)2]·2H2O (2), [In2(hfipbb)3(2,2'-bipy)2]·2H2O (3), [In2(hfipbb)3(4,4'-bipy)] (4) and [In4(OH)4(hfipbb)4(4,4'-bipy)] (5). Taking to account the Lewis acidity properties that these compounds could present, 1-5 were tested in the cyanosilylation reaction (CSR) of aldehydes and ketones.
The crystallochemical role of malonate ions in coordination polymers
Authors: Medvedkov Yakov , Serezhkina Larisa , Pushkin Denis , Serezhkin Viktor
Published: November 2015

All compounds that contain malonate dianions C3H2O42-(mal2-) and atoms of d- or f-metals were analyzed. Dianions mal2-in structures of examined compounds reveal 17 topological types of coordination against metal atoms. Available data shows that mal2-more often form six-membered metal cycles which is the most abundant case for all 570 crystallographic sorts of analyzed mal2-(80%). For those mal2-which form six-membered metal cycles the average observed valence angle SSS is equal to 1200. Results of regression analysis of all mal2-showed linear dependence of ∠SSS on dihedral angel (φ) between planes which go through oxygen and carbon atoms of different carboxyl groups of one anion. For the equation ∠SSS = 124.9 – 0.207φ, correlation coefficient is -0.90. Discovered that in structures of crystals when φ < 600mal2-necessarily form six-membered metal cycles. Structural slackness of mal2-influence on characteristics of six-membered metal cycles formed by them. Those metal cycles usually have bath conformation. Coordination polymers with fixed type of metal atom and identical type of coordination of mal2-can have different dimension even in the absence of other linkers. This effect is evident on the example of [UO2(mal)(L)]·nH2O compounds. Reportedly [1], change of composition and structure of ligand L lead to changes in the system of intramolecular hydrogen bonds which influence on conformation of six-membered metal cycles. The change of conformation of this cycles lead to different relative spatial distribution of the three uranium atoms, connected with one mal2-. Although of the same stoichiometric composition and crystallochemical role of uranium atoms and coordinated ligand resulting polymeric groups [UO2(mal)(L)] in crystals have different dimension: 3D, 2D or 1D respectively for L – carbamide, water or dimethylacetamide. This work was supported by the base part of the government mandate of the Ministry of Education and Science of the Russian Federation.
Silver coordination metallacycles assembled into microporous materials
Authors: Marchio' Luciano , Bassanetti Irene , Atzeri Corrado , Comotti Angiolina , Sozzani Piero
Published: November 2015

Porous solid materials represent one of the most intense areas of study for chemists, physicists, and materials scientists [1]. These systems have found a large number of applications in many fields, such as adsorption, separation and purification, as well as catalysis [2]. We have previously shown that when using the pre-organized thioether functionalized bispyrazolylmethane ligand (LSPh) and silver(I), hexameric metallacycles are formed in solution. In the solid state the role of the counteranion (BF4-, PF6-, NO3-, and CF3SO3-) is of fundamental importance in the way the metallacycles self-assembled into a diversity of 3D supramolecular architectures and cavities. In particular, highly symmetric BF4-and PF6-favours the formation of crystals with permanent porosity as demonstrated by gas adsorption measurements. In order to modulate the porous properties of these silver coordination polymer (CP), we synthesised a series of differently functionalized bis(pyrazolyl)methane ligands (Figure). The silver complexes were prepared with two types of anions (PF6-and CF3SO3-) to investigate their role in the supramolecular arrangements. The structural features and gas sorption properties (CO2, CH4and N2) of the new silver complexes will be presented. Solid state NMR was employed to investigate the localization of CO2within the cavities.
Fructose calcium chloride MOFs for NLO applications
Authors: Marabello Domenica , Antoniotti Paola , Benzi Paola , Canepa Carlo , Diana Eliano , Operti Lorenza , Mortati Leonardo , Sassi Maria Paola
Published: November 2015

Non-centrosymmetric Metal Organic Frameworks (MOF) based on coordination of carbohydrates on alkaline metal ion represent an ideal category of compounds to plan functional materials with interesting second-order non-linear optics properties. Two MOFs obtained from fructose and calcium chloride, [Ca(C6H12O6)(H2O)2]Cl2 (1) and [Ca(C6H12O6)2(H2O)2]Cl2·H2O (2), have been synthetized in ethanol and by solid-solid interactions and have been characterized with X-ray diffraction and IR and RAMAN spectroscopy. The two compounds have also been studied with DFT theoretical calculations to investigate their relative stability and foresee their optical properties. Finally, the second harmonic generation (SHG) properties have been evaluated by SHG microscopy. It has been demonstrated that the coordination of fructose on the calcium ion causes an improvement of the SHG intensity with respect to the fructose itself and that there is a strictly correlation between the calculated dipole moment and the first static hyperpolarizability values and intensity of the SHG signal. Furthermore, the remarkable difference in the SHG intensity of the two compounds studied, suggests that this physical property can be "controlled" not only by tuning the composition of the system, but also by the disposition of the MOF's building units in the crystal. The metal-carbohydrate based MOFs analyzed in this work have a favorable combination of thermal and chemical stability, transparency, and second-order optical non-linearity and are thus potential candidates for applications in electro-optic devices.
Coordination variability of Copper(I) in multidonor heterocyclic thioamides.
Authors: Lobana Tarlok , Kaur Amanpreet
Published: November 2015

The chemistry of copper(I) with scarcely studied heterocyclic thioamides, namely, 2,4,6-trimercaptotriazine, purine-6-thione, 2,4-dithiouracil, 2-thiouracil and pyrimidine-2-thione is described. The interaction of 2,4,6-trimercaptotriazine (tmtH3) with [Cu(CH3COO)(PPh3)2] gave rise to a pair of bond isomers : [Cu(κ1N-tmtH2)(PPh3)2] (6a), [Cu(κ1N,κ1S-tmtH2)(PPh3)2] (6b) and with copper(I) bromide and PPh3, it has formed a trinuclear complex, [Cu3Br2(κ1N,κ1S,κ2S-tmtH2)(PPh3)6] (7) with anionic tmtH2- in these complexes. The 2,4-dithiouracil with copper halides (CuCl, CuBr) and PPh3 yielded dinuclear complexes: [Cu2(κ2Cl)(κ1S,κ1S-dtucH)(PPh3)4] (4) and [Cu2(κ2Br)(κ1S,κ1S-dtucH)(PPh3)4] (5) with unusual eight membered metallacyclic rings. Pyrimidine-2-thione (pymSH) coordinated to CuI as N,S-chelated anion yielding mononuclear complex, [Cu(κ1N,κ1S-pymS)(PPh3)2] (1), while 2-thiouracil (tucH2) with copper(I) chloride and PPh3 yielded a tetrahedral complex, [CuCl(κ1S-tucH2)(PPh3)2] (3). Purine-6-thione (purSH2) coordinated to CuI in two different modes yielding mono- and di-nuclear complexes, [Cu(κ1N,κ1S-purS)(PPh3)2].CH3OH (2a) and [Cu2(κ1N,κ2S-purS)2(PPh3)2] (2b). The existence of bond isomers (6a and 6b), synthesis of novel dinuclear ( 4 and 5) and rare trinuclear (7) complexes with unusual bonding patterns and uncommon chelation to CuI by pymS- in 1 are the novel features of the present study. Complexes have shown intense emission bands in the visible region, λmax 490 to 495 nm.
Coordination of a neutral thiazyl radical to Co(II) tetraphenylporphyrin
Authors: Haynes Delia , Munro Orde , van Laeren Laura , de Villiers Katherine
Published: November 2015

The 1,2,3,5-dithiadiazolyl radicals (R-CNSSN) are of considerable interest due to their potential as building blocks for materials with interesting magnetic or conducting properties. The behaviour of these neutral radicals as ligands has also been investigated [1]. Reactions with Pt(0) and Pd(0) have been shown to yield complexes where coordination to the metal is through sulfur, and the S-S bond in the radical is broken [2]. More recent work has shown that coordination through the radical nitrogen is possible with 2'-pyridyl-substituted dithiadiazolyl in combination with strongly electron-withdrawing ligands. Several of these complexes show magnetic coupling between the radical and the metal centre [3]. We have recently begun investigating the coordination of dithiadiazolyls to metalloporphyrins. The crystal structure of a coordination polymer formed between 4-(4'-pyridyl)-1,2,3,5-dithiadiazolyl and cobalt(II) tetraphenylporphyrin has been determined. The radical in this complex is coordinated through one sulfur atom, a coordination mode for dithiadiazolyls that has not previously been observed. Formation of the complex in solution has been investigated using EPR and UV-vis. Irradiation of a solution of the diamagnetic complex with intense white light leads to homolysis of the radical-ligand bond, observed by EPR. Our investigations of complex formation involving other dithiadiazolyl derivatives with a series of metalloporphyrins will also be presented.
Synthesis, structure and water sorption in Zr metal-organic frameworks
Authors: Gándara Felipe , Furukawa Hiroyasu , Yue-Biao Zhang , Jiang Juncong , Queen Wendy , Hudson Matthew , Yaghi Omar
Published: November 2015

Metal-organic frameworks (MOFs) based on zirconium secondary building units (SBUs) have proven to have great thermal and chemical stability,[1,2] which make them ideal for their use in different applications. We have prepared a series of six new MOFs made from the Zr6O4(OH)4(-CO2)nsecondary building units (n = 6, 8, 10, or 12) and variously shaped carboxyl organic linkers to make extended porous frameworks, with the aim of studying their performance as water adsorbents. Thus, we have evaluated the water adsorption properties of these new MOFs and other reported porous materials to identify the compounds with the most promising materials for use in applications such as thermal batteries or delivery of drinking water in remote areas. An X-ray single-crystal and a powder neutron diffraction study reveal the position of the water adsorption sites in one of the best performing materials, and highlight the importance of the intermolecular interactions between adsorbed water molecules within the pores.
Synthesis, spectroscopic and structural analysis of a melamine copper complex
Authors: Direm Amani , Dadda Noureddine , Falek Wahiba , Boutobba Zina , Benali-Cherif Nourredine
Published: November 2015

Owing to its multiple sites acting as H-bonds' donors, melamine and its derivatives are considered as excellent building blocks for the construction of various crystalline supramolecular architectures based on phosphate, sulfate, chloride and carboxylic anions [1-10] on one hand and chlorometallate anions on the other hand [11-13]. In our contribution, we will discuss the synthesis, FTIR spectra and the structural investigation using the single crystal X-ray diffraction of (H2Melamine) [CuCl5]Cl, (I). The structural analysis of (I) revealed that it consists of alternating negative and positive layers running through the a-axis direction. The negative layers are built up of alternatively CuCl53- and discrete non-coordination Cl- anions, whereas the positive sheets are formed of [H2melamine2+]2 Hydrogen-bonded dimers. The N-H...N and N-H...Cl interactions are assembled to build three-dimensional H-bond patterns which insure the cohesion within the lattice (Fig. 01). A previous work showed that (I) exhibits antiferromagnetic properties [14]
Structural studies of a flexible 2D layer spin crossover coordination polymer
Authors: Chuang Yu-Chun , Chang Chung-Kai , Kao Ching-Che , Lee Jey-Jau , Wang Chih-Chieh
Published: November 2015

The first coordination sphere of spin crossover material has been comprehended to play a dominant role to its magnetic property. However, the intermolecular interactions, such as π···π interaction and hydrogen bonding, also play a crucial factor. The contents of the solvent in a 2D layer structure, Fe (μ-atrz)(μ-pyz)(NCS)2·nH2O where n=4, 2 and 0, has been reported to be able to affect the spin transition behavior dramatically.[1] As loss of solvent molecules, the inter-layer distance becomes shorter and the transition temperature shifts to lower temperature and accompanies a larger hysteresis loop. To further understand the correlation between the inter-layer distance and magnetic property, the guest ab/desorption and pressure-induced synchrotron powder diffraction experiments were performed at BL01C2 in NSRRC. Based on the cyclic TGA measurements, the guest molecules, H2O, MeOH and EtOH, all can be removed and retaken repeatedly. The pressure-induced PXRD experiment was performed using a Boehler-Almax design diamond anvil cell (DAC). The detail structural studies attempt to understand not only the spin state changes from HS (high spin state) to LS (low spin state) but also the cooperative effect through the inter-layer distance.
Coordination polymers of benzenediseleninate, the seleno analog of terephthalate
Authors: Burrow Robert , Belmonte Giancarlo
Published: November 2015

The proligand para-benzenediseleninic acid, (HO2SeC6H4SeO2H) (Figure), is the seleno analog to the commonly used MOF spacer proligand, terephthalic acid. Novel coordination polymers based on this proligand, and Mn(II), Fe(II), Co(II), Ni(II), Cu(II) or Zn(II) metal centers containing auxiliary water molecules, [M(O2SeC6H4SeO2)2(H2O)n], were synthesized. Depending on the reaction conditions, different pure or mixed phases can be produced. Crystal to crystal transformations of the novel coordination polymers were studied with powder X ray diffraction, infrared spectral analysis and thermal gravimetric analysis. These coordination polymers can be dehydrated with subsequent formation of new anhydrous coordination polymer phases. Some of these phases can be rehydrated to lead back to the crystalline starting materials or to new crystalline hydrated phases. We are working on the complete structural characterization of the phases.
Solvent and Anion Dependent Packing and Properties of Supramolecular Nanoballs
Authors: Batten Stuart
Published: November 2015

We have synthesised large (2.7 nm) spherical metallosupramolecules (`nanoballs') with interesting properties [1-3]. Metal ions can be varied with retention of overall structure and crystal packing. The molecular packing creates cavities within the solid state, and the crystals readily absorb solvents such as methanol, acetonitrile or acetone (which also changes the magnetic properties), and absorb significant amounts of hydrogen and carbon dioxide (but not methane), pointing to a new class of porous materials. Other properties include switching between two magnetic spin states (spin crossover) upon change in temperature or irradiation of light, and size-selective catalysis. New packing arrangements of the nanoballs can then be achieved through variation of the counteranions or nitrile solvent, leading to new phases with different physical properties.
Synthesis and post-synthetic modification of metal-organic frameworks
Authors: Burrows Andrew
Published: November 2015

Metal-organic frameworks (MOFs) are currently attracting considerable interest due to their porosity, and the exploitation of this in a wide range of applications as diverse as hydrogen storage, carbon capture, catalysis and drug delivery. Here we present our recent work on the preparation of functionalised MOFs through two post-synthetic modification protocols. We have used a range of organic transformations including oxidations and tandem modifications involving either diazonium salt formation or reductive amination to undertake covalent modifications of reactive 'tag' groups on the linkers.[1] In addition, we have used a post-synthetic exchange approach to substitute one linker with another. We have compared the MOFs prepared post-synthetically with those that can be accessed by direct combination of metal salt and functionalised linker. We also report on the synthesis and structure of mixed-component MOFs, in which two or more linking ligands have the same structural role.[2] We reveal the role of solubility in the uneven distribution of the ligands in the crystals, and illustrate how the ratio of ligands used in the synthesis can affect the pore structure. Finally we present recent developments in the synthesis of MOFs containing the biologically active molecule deferiprone, and show how this can be released from MOF.[3] This illustrates the potential of MOFs to act as reservoirs for drug molecules.
Neutron diffraction study to elucidate reaction mechanism of RNase A
Authors: Kusaka Katsuhiro , Yamada Taro , Tomoyori Katsuaki , Hosoya Takaaki , Ohhara Takashi , Tanaka Ichiro , Niimura Nobuo
Published: November 2015

Ribonuclease A (RNase A) is a pyrimidine-specific endoribonuclease that claves and hydrolyzes single-stranded RNA in two distinct steps. The mechanism of the cleavage reaction catalyzed by RNase A involves two key histidine residues, His12 and His119. It is important to know the protonation states of them in order to understand the hydrolysis mechanism of RNase A. Neutron protein crystallography is a powerful technique for solving the problems. In previous reports, the protonation states of them for RNase A complexed with phosphate ion, uridine vanadate and phosphate free one have been investigated by neutron diffraction analysis [1-3]. In this study, neutron diffraction analysis of phosphate free RNase A has been carried out with high resolution and completeness data set in order to clarify the protonation states of two active site histidine residues, and to elucidate the detailed mechanism of the cleavage reaction. Neutron diffraction data of bovine pancreatic RNase A were collected by IBARAKI biological crystal diffractometer iBIX in J-PARC. The structure was determined by joint neutron and X-ray structure refinement. The final values of Rcryst and Rfree were 19.5% and 22.0%, respectively, for completeness of 86.7% to a resolution of 1.4Å. The structure with high reliability and good data statistics could be obtained by comparing with the already-reported one [3]. We calculated |Fo|-|Fc| neutron scattering length density map after omitting Dδ1 and Dε2 of His12 and His119 in order to confirm the protonation states of them. These omit maps indicated that His12 is completely singly protonated and Hi119 is doubly protonated. The protonation states of them are consistent with those in the first step of the putative mechanism of catalysis by RNase A. We could also observed a D atom of water molecule which is hydrogen bonded to Nε2 of His12.
Perdeuteration: Vital to visualising solvent in neutron crystallography?
Authors: Fisher Stuart , Blakeley Matthew , Howard Eduardo , Petit-Haertlein Isabelle , Haertlein Michael , Mitschler Andre , Cousido- Siah Alexandra , Salvaya Andre , Popov Alexandre , Muller- Dieckmann Christoph , Petrovah Tatiana , Podjarny Alberto
Published: November 2015

Early neutron crystallography studies replaced hydrogen with deuterium by soaking the crystal in heavy water prior to data collection, which exchanged labile hydrogen atoms (OH, NH, and SH) and solvent molecules only. Carbon bonded hydrogen atoms were not replaced, and their negative scattering density resulted in cancellation in nuclear density maps with resolution worse than 1.8 Å. Furthermore complications arise due to partial exchange, where deuterium is present in some unit cells and hydrogen in others. More recently it has become possible to completely replace hydrogen with deuterium through expression in a deuterated medium, using facilities such as the Deuteration Laboratory (DLAB) in Grenoble. As this is a complex and expensive task, the question arises as to the importance of its use. As well as allowing the study of radically smaller crystals (<0.05mm3), it also has the possibility to avoid the cancellation problems discussed above. We have obtained data from high quality crystals of partially hydrogenated type III antifreeze protein, where methyl protonated valine and leucine residues were incorporated into the perdeuterated protein. This provides an excellent opportunity to assess the effects of negative scattering from hydrogen atoms not only on the visibility of neighbouring carbon atoms but also on water molecules in close vicinity. The observation of these cancellation effects gives a further reason to use full deuteration in neutron protein crystallography.
Ultra-high resolution neutron and X-ray crystallography: structure of crambin
Authors: Chen Julian , Hanson Bryant , Fisher S , Langan Paul , Kovalevsky Andrey , Ginell Stephan , Rosenbaum Gerold , Joachimiak Andrzej
Published: November 2015

Neutron diffraction data to 1.1 Å was collected on a crystal of the small protein crambin at the Protein Crystallography Station (PCS) at Los Alamos, the highest resolution neutron structure of a protein to date, and a technical benchmark for the instrument. 95 % of the hydrogen atoms in the protein structure were resolved. The data allowed for the refinement of anisotropic temperature factors for selected deuterium atoms within the protein. Hydrogen bonding networks ambiguous in room temperature, ultra-high resolution (0.84 Å) electron density maps are clarified in the nuclear density maps. The ultra-high resolution data also reveals unusual H/D exchange patterns and novel chemistry in the side chains and protein backbone. Complementary X-ray diffraction data was collected at 19-ID at the Advanced Photon Source, with extensive re-configuration of the beamline to allow for operation at higher energy settings.
Combining neutron crystallography, high-performance computing for enzyme design
Authors: Kovalevsky Andrey , Wymore Troy , Sangha Amandeep , Challacombe Matt , Mason Sax , Forsyth Trevor , Parks Jerry , Keen David , Graham David , Langan Paul
Published: November 2015

Enzymes continue to expand their role in industry as a "green" option for the synthesis of value-added products. They are targeted for the design of drugs in pharmaceutical applications and also for protein engineering in industry to improve their efficiency, stability, and specificity. Knowledge of the exact mechanisms of enzymatic reactions may provide essential information for more effective drug design and enzyme engineering. For the first time, we are employing a joint X-ray/neutron (XN) protein crystallographic technique in combination with high-performance computing, including QM and QM/MM calculations, MD and Rosetta simulations, to investigate the mechanisms of several enzymes that are important to renewable energy and chemical synthesis. D-xylose isomerase (XI) is an enzyme which can be used to increase the production of biofuels from lignocellulosic biomass and also to synthesize rare sugars for pharmaceutical industry. XI catalyzes the reversible multi-stage sugar inter-conversion reaction facilitated by the presence of two divalent metal cations in its active site. It primarily catalyzes the isomerization of the aldo-sugar D-xylose to the keto-isomer D-xylulose, but can also epimerize L-arabinose into L-ribose, albeit much less efficiently. The reaction involves moving hydrogen atoms between the protein residues, sugar and water molecules, and can only be understood if hydrogen atoms are visualized at each reaction stage. We have obtained a number of joint XN structures of XI complexes representing snapshots along the reaction path with D-glucose, D-xylose and L-arabinose. The suggested reaction mechanism has been verified by QM calculations using the novel O(N) methodology. We are using this structural and mechanistic information to re-design XI to be more efficient on D-xylose and L-arabinose for biofuels and biomedical applications by employing QM/MM, MD, and Rosetta methodologies.
Evaluation of pKa of Amino Acid Residue in Proteins by Neutron Crystallography
Authors: Niimura Nobuo
Published: November 2015

The pKa values of isolated amino acids in solution are tabulated in standard textbooks. However, the protonation state of a given amino-acid side chain in a protein cannot be estimated from standard pKa values measured from isolated amino acids in solution, because inside a protein it may vary significantly depending on the local environment. The electrically charged states of the amino-acid residues are very important in understanding the physiological function of the protein, the interaction between ligands and proteins, molecular recognition, structural stability, and so on. Neutron Protein Crystallography (NPC) is the unique method to provide the definite protonation states of the amino acid residue in proteins because neutron can identify not only hydrogen atoms but also protons. (N.Niimura & R. Bau: Acta Cryst. A64, 12 (2008); N.Niimura & A. Podjarny: IUCr Monographs on Crystallography 25 (2011)) Biological mechanism such as enzymatic reactions is well understood by studying protonation states of the catalytic polar amino acid residues, which can be identified by NPC. It is proposed that the protonation states should be systematically discussed from the view point of the pKa values of the amino acid residues in proteins. Several examples of the protonation states of the catalytic residues determined by NPC, such as serine proteases (trypsin, elastase, thrombin, & acromabacter), insulin, hen egg white lysozyme, RNase A, and HIV-1 protease will be introduced and discussed on the basis of the pKa values.