bluuebunny/crossref_metadata_2025 huggingface dataset:
Supramolecular Stark Effect in Host-Guest Complexes via Charge Density Analysis
Authors: Thomas Sajesh , Fuller Rebecca , Sobolev Alexandre , Schauer Philip , Grabowsky Simon , Koutsantonis George , Spackman Mark
Published: November 2015

The effect of an electric field on the vibrational spectra, the Vibrational Stark Effect (VSE), has been utilized extensively to probe the local electric field in the active sites of enzymes [1, 2]. For this reason, the electric field and consequent polarization effects induced by a supramolecular host system upon its guest molecules attain special interest due to the implications for various biological processes. Although the host-guest chemistry of crown ether complexes and clathrates is of fundamental importance in supramolecular chemistry, many of these multicomponent systems have yet to be explored in detail using modern techniques [3]. In this direction, the electrostatic features associated with the host-guest interactions in the inclusion complexes of halogenated acetonitriles and formamide with 18-crown-6 host molecules have been analyzed in terms of their experimental charge density distribution. The charge density models provide estimates of the molecular dipole moment enhancements which correlate with the simulated values of dipole moments under electric field. The accurate electron density mapping using the multipole formalism also enable the estimation of the electric field experienced by the guest molecules. The electric field vectors thus obtained were utilized to estimate the vibrational stark effect in the nitrile (-C≡N) and carbonyl (C=O) stretching frequencies of the guest molecules via quantum chemical calculations in gas phase. The results of these calculations indicate remarkable elongation of C≡N and C=O bonds due to the electric fields. The electronic polarization in these covalent bonds induced by the field manifests as notable red shifts in their characteristic vibrational frequencies. These results derived from the charge densities are further supported by FT-IR experiments and thus establish the significance of a phenomenon that could be termed as the "supramolecular Stark effect" in crystal environment.
Guest-induced fluorescence property of macrocyclic boronic ester
Authors: Sugiyama Haruki , Johmoto Kohei , Uekusa Hidehiro , Kikuchi Yuji , Takahagi Hiroki , Ono Kosuke , Iwasawa Nobuharu
Published: November 2015

Macrocyclic boronic esters (1) are obtained as a self-assembled molecule by condensation reaction between rac-tetrol (2) and 1,4-naphthalenediboronic acid (3) in the presence of toluene molecule [1]. In the crystal, this macrocyclic molecules form a charasteristic one dimensional channel structure that accommodates various small molecules. Interestingly, reversible desorption / absorption phenomena of guest molecules is observed without significant crystal packing change, meaning this crystal may have guest storage, separation, and catalytic abilities. In the course of exploring further functional aspects of the molecule, we give fluorescence property to this crystal by inclusion of acene molecules into this robust one dimensional channel structure. Naphthalene inclusion crystal was obtained by the diffusion method. The crystal structure is isostructural to known crystals, that is, a naphthalene molecule is included in a channel and sandwiched by two naphthalene moieties of the macrocyclic molecule (inter planar distance is about 3.6 angstrom). Under UV light, a blue color fluorescence observed in this crystal, suggesting the guest naphthalene molecule contributes the fluorescence property. After heating by 200 degrees C, the naphthalene was released to leave isostructural apohost crystal without fluorescence property. However, by naphthalene vapor exposure to the apohost crystal, the fluorescence property was recovered, which means naphthalene desorption and absorption are possible in crystalline state. Moreover Anthracene and Tetracene inclusion crystal were obtained, and they also showed light blue and yellow color fluorescence under UV light, respectively. Thus, the fluorescence function was successfully realized by inclusion of acene molecule in the one dimensional channel of the crystals, and furthermore the fluorescent color can be controlled by changing acene molecules.
Vapochromism of Organic Cocrystal Induced by Crystalline Solvent Exchange
Authors: Sakon Aya , Sekine Akiko , Uekusa Hidehiro
Published: November 2015

Vapochromic materials, which show color change induced by vapors, are expected to be applied to the sensing of volatile organic compounds or humidity. As for the metal complex crystals, many vapochromic crystals are reported, however, vapochromic organic crystals are not common. Therefore, it is important to find vapochromic organic crystals and to reveal the mechanistic aspects of structure transformations and color change based on the crystal structures. Pale brown Enoxacin-3,5-Diaminobenzoic Acid (ENO-3,5DABA) dihydrate cocrystal changed to yellow on exposure to four kinds of alcohol solvent vapors (methanol, ethanol, 1-propanol, 2-propanol), and these yellow crystals returned to pale brown dihydrate crystal by humidity, which is called vapochromism. The single crystals recrystallized from water (pale brown) and methanol (yellow) are equal to the dihydrate and the methanol vapor applied forms, respectively, and their crystal structure determination revealed that the cocrystals are 1:1 salt of ENO and 3,5DABA. Surprisingly, in the methanol vapor applied from, the crystalline solvent was changed to 0.5-methanol-0.5-water solvate (composition is ENO:3,5DABA:MeOH:H2O=2:2:1:1). Thus the dihydrate cocrystal undergoes solvent exchange transformation on exposure to methanol vapor and the color changes from pale brown to yellow. Because the XRD patterns of the yellow 0.5-methanol-0.5-water solvate cocrystal and the forms exposed to other alcohol solvent vapors shows high similarity, they are isostructure crystals. The color change is caused by the π...π interaction formation between the ENO molecule and 3,5DABA molecule in alcohol solvate form via solvent exchange transformations.
New polymorphs of tiphenyltin(IV) halides
Authors: Reuter Hans , Ye Fei , Reichelt Martin , Schwidtke Sandra , Vages Johanna , Osthaar Susanne , Reuter Amane , Mundt Frederike
Published: November 2015

Triphenyltin(IV) halides, Ph3SnHal with Hal = Cl, Br, and I, are white, low melting solids soluble in many indifferent organic solvents like chloroform or toluene. In these solutions as well as in solid they consist of isolated, tetrahedral molecules which intermolecular interactions restricted to van-der Waals ones. These molecules are characterized through the three aromatic phenyl rings attached at a certain pitch angle around the shaft of the tin-halide bond giving them a propeller-like shape accompanied by molecular chirality as the normal vectors of the blades can be oriented clock-wise or anti-clock-wise with respect to the tin-halide bond. In the past, a lot of different polymorphs of triphenyltin(IV) halides with up to 24 molecules in the unit cell have been described, all crystallizing in centrosymmetric space groups, implying that both chiral molecules are present. From a structural point of view there are still several questions of general interest: (i) how are both enantiomers distributed in these polymorphs, (ii) how are the molecular dipole moments arranged, and (iii) how are the different polymorphs related to each other. During various studies on the syntheses and reactivity of triphenyltin(IV) halides we found four additional polymorphs, which constitute new structure types in case of δ-Ph3SnI (Z = 8, monoclinic, P21/c), and ε-Ph3SnI (Z = 12, monoclinic, P21/c) or complete the already existing α-Ph3SnCl structure type (Z = 24, rhomboedric, R-3) in case of β-Ph3SnBr and ζ-Ph3SnI. Analysing the new and already known polymorphs with respect to the three questions mentioned above points out (i) the influence of crystal symmetry elements (screw axes and glide planes) as well as (ii) the importance of the formation of supramolecular dimers composed of both enantiomers with an antiparallel orientation of the two molecular dipole moments, on the different structure types formed and their relation among each other.
New Ag(I) Coordination Complexes Based on Bis(1-isoquinolinecarboxamide)ethane.
Authors: Parra Nicole , Belmar Julio , Jiménez Claudio , Pasán Jorge , Ruiz-Pérez Catalina
Published: November 2015

Crystal Engineering is an interdisciplinary research area that involves chemists, physicists, biologists and materials scientists.1It is an important field inside Supramolecular Chemistry which has been considered as a new form of synthesis, named Supramolecular Synthesis.2It is known that important properties in molecular solids are closely related with the way that molecules are aggregated in the condensed phase. Consequently, the ability to control the molecular association in the crystal packing could offer control over specific properties and potential applications. Because of that, the main goal of Crystal Engineering is the rational design and synthesis of functional materials using the nature of the intermolecular forces as a toolkit. Our strategy is the systematic study of non-covalent forces in homologous series.3In this work our interest is focused on the study of crystal packing of two homologous ligands N,N'-bis(1-isoquinolinecarboxamide)-1,2-ethane (1) and N,N'-dimethyl-N,N'-bis(1-isoquinolinecarboxamide)-1,2-ethane (2) and their Ag(I) coordination complexes. The compound 1 consists of two isoquinoline rings and one ethylene bridge linked by amide functional groups. Compound 2 is the result of the N-methylation of 1. The main difference in the molecular structures is that while 1 present a gauche conformation in the 1,2-ethanediamine bridge (600) 2 present a staggered conformation (1800). Curiously, in spite of this fact, the Ag(I) complexes in both cases present a small torsion angle of 4501-Ag(I) and 6502-Ag(I). These orientations allow the torsion of the isoquinoline moiety and the formation of homonuclear 0D coordination complexes, over the 1D coordination polymer expected. The main intermolecular interaction in 1 is the amide-to-amide hydrogen bond that is replaced by a weak CH··O interaction in 2 On the other hand, both Ag(I) complexes use the nitrate counteranion to build a chain using NH··O(nitrate) in 1 and CH(quinoline)··O(nitrate) in 2.Acknowledgment: Grant DIUC 212.023.049-1.0
Optical Properties of Three Crystal Modifications of a 2,3-Dicyanopyrazine Dye
Authors: Okada Naoya , Eto Ryohei , Horiguchi-Babamoto Emi , Matsumoto Shinya
Published: November 2015

Some pyrazine dyes are known to display strong fluorescence not only in solution but also in the solid-state. 5-t-Butyl-2,3-dicyano-6-[4-(dimethylamino)styryl]pyrazine (1) is a 2,3-dicyanopyrazine dye synthesized for an examination of substituent effects on thin-film growth [1]. Dye 1 was found to exhibit three crystal modifications with different color appearance (I: red, II: black, III: reddish purple). Modification I is a solvate crystal including one chloroform per one dye molecule [2], and modifications II and III are polymorphs. In this work, optical properties of these three modifications were interpreted on the basis of their crystal structures. The absorption spectra of the modifications were measured using optical waveguide spectroscopy. The absorption maxima of modifications I, II and III were found at 559 nm, 462 nm and 571 nm, respectively. A bathochromic absorption shift of reddish modifications I and III from that of 1 in toluene was 79 nm (-2944 cm-1) and 91 nm (-3320 cm-1), respectively. On the other hand, a hypsochromic absorption shift of 18 nm (812 cm-1) was observed in modification II. The fluorescence maxima of modifications I, II and III were found at 619 nm, 734 nm and 668 nm, respectively. The energy displacement corresponding to the observed spectral shifts was characterized in terms of an exciton interaction. The exciton interaction for a dimer was estimated using the extended dipole model, and the nearest-neighbor approximation was applied for evaluating a total energy displacement due to crystallization. The calculation results were qualitatively in good agreement with the observed spectral shifts. The result also revealed that molecular pairs in two-dimensional stacking structure in these modifications play a significant role in the total energy displacement.
The Effect of the Methanol Molecule in the Stabilization of C18H18O4Chalcone
Authors: Napolitano Hamilton , Sallum Lóide , Carvalho-Jr Paulo , Silva Valter Henrique , Aquino Gilberto , Camargo Ademir
Published: November 2015

The (E)-3-(4-hydroxy-3,5-dimethoxyphenyl)-1-p-tolylprop-2-en-1-one crystallizes in the triclinic centrossymetric P1 ¯ space group as a solvate structure (Figure 1). The asymmetric unit is described by a 2[(C18H18O4).(CH3OH)] molecular complex, in which each independent C18H18O4 molecules is bonded to a specific methanol molecule (R1 = 0.1237, wR2 = 0.1869 to all data). The presence of methanol in this crystal lattice results in a unit cell with Z' > 1 which two molecules of methanol and chalcone (alpha molecule and beta molecule) forming a stable molecular complex. With the aim of understanding the process of crystal lattice stabilization, a combination of technique has been used including X-ray diffraction (XRPD), computational molecular modeling and a molecular dynamic. The results show: alpha molecule and beta molecule are sterically barred to form direct hydrogen bond each other. On the another hand, the presence of methanol molecule stabilizes the crystal structure by bifurcated O-H...O interaction acting as a bridge between them. The theoretical thermodynamic parameter and the rigid potential energy surface scan comprise the role of methanol in the energetic stabilization of the crystal. The absence the methanol compound in the asymmetric unit destabilizes the crystalline structure, turning the formation process of the asymmetric unit not spontaneous. The energy difference between alpha and beta molecules is around 0.80 kcal/mol, indicating that both are stable and are equally possible in the crystal lattice. The analyze of the energetic profile of the C14 – O2...H1 – O3 and O2 – H1...O3 – C17 torsion angles in the packing crystal show that the alpha and beta molecules are confined in the stable potential region, in agreement with the two conformer in the asymmetric unit. The MEP show that the methanol have no steric effect that avoid small motion around the torsions angles. The authors would like to acknowledge the Brazilian agencies for financial support: Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq), Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) and Fundação de Amparo Pesquisa do Estado de Goias (FAPEG).
Electronic interactions in 1D-π-assemblies from TLS analysis of thermal motion
Authors: Lindeman Sergey , Talipov Marat , Wadumethrige Shriya , Dolomanov Oleg , Rathore Rajendra
Published: November 2015

Advanced features of TLS analysis within Olex2 program package allow for a detailed analysis of electronic redistribution in supramolecular systems. Particularly, the possibility of calculating TLS tensors in user-defined coordinate systems along with qualitative graphical representation of difference thermal motion are especially useful for analysis of atomic asphericity and intra- and inter-molecular electron redistribution. In addition, these features allow for a directional dynamic analysis of intermolecular motions from variable-temperature experiments. We explored the exciting new possibilities analyzing supramolecular assemblies closely resembling modern electronic materials for a series of electron donor-acceptor complexes and ion-radical salts based on aromatic octamethyl-anthracene and anti-aromatic octamethyl-biphenylene substrates. The difference TLS analysis revealed intimate details of chemical bond polarization and electronic shell expansion for acceptor components along with electronic shell contraction for donor components of the complexes indicative of intra- and intermolecular charge transfer. Also, the variable-temperature analysis of relative thermal motion of the complex components in the crystals revealed some widening of the potential-energy minima in direction of the electronic overlap as a result of intermolecular pi-orbital coupling both in charge-transfer and charge-resonance supramolecular assemblies. A theoretical interpretation of the observed peculiarities was undertaken supported by respective spectroscopic data.
Comparative study of two oxalate isomers with different dimensionalities
Authors: Kherfi Hamza , Hamadène Malika , Guehria-Laidoudi Achoura , Dahaoui Slimane , Lecomte Claude
Published: November 2015

We report here two bimetallic oxalate isomers with the same chemical formula [RbCr(C2O4)2(H2O)2], which have been synthesized respectively by a slow evaporation method at room temperature (compound I) [1], and under hydrothermal conditions (compound II) [2] with the same starting salts. Their structures show a several discrepancies, due probably to the synthetic conditions. Indeed, the compound I crystallizes in space group C2/m with the Cr, Rb atoms and one oxygen from water molecule lying on special positions. Moreover, the unique oxalate ligand forms a bridge between metal centers. The Cr atom is coordinated to 2 bidentate-chelating oxalates and 2 aqua ligands in a trans-conformation and any water molecule has been found around the 8-coordinated Rb atom, leading to a layered structure consists of alternating Rb and Cr polyhedra connected via the unique organic ligand. Whereas, the compound II crystallizes in space group P21/n, with all atoms located on general positions. Furthermore, two independent oxalato ligands exhibit different configurations, which one is pentadentate and the other is hexadentate with two different chelating modes. The very slightly distorted Cr octahedra consists of 2 bidentate-chelating oxalato ligands and 2 water molecules in a cis-conformation, while the alkali metal is surrounded by seven O atoms from oxalate groups, completed with two H2O molecules which are bridging the Cr and Rb polyhedra by one common edge. This results in the formation of three different chains of alternating edge- and vertex-shared polyhedra through oxalates groups and aqua ligands, running along the three space directions to build a three dimensional framework. These two compounds can be considered as supramolecular isomers [3].
Bonding in Group 1 Citrate Salts
Authors: Kaduk James , Rammohan Alagappa
Published: November 2015

Computational studies of > 15 new crystal structures and the 10 previously-reported structures of alkali metal citrates provide insight into why the atoms are where they are. The metal-citrate bonding is predominantly ionic, with very little covalent character, which decreases as the cation size increases. Bond valence calculations indicate that most cations are crowded, and that the crowding decreases as the cation size increases. Although most oxygen atoms coordinate to the metals, a few do not, and they tend to be the least-negative oxygens. Both the citrate hydroxyl groups and water molecules tend to bridge two cations, and the carboxylate coordination is more varied. The solid state energy differences are dominated by differences in van der Waals and electrostatic energy contributions. In the Li and Na salts, the citrate anion occurs predominantly in a higher-energy "kinked" conformation, rather than the extended lowest-energy conformation observed in salts of the larger cations. Detailed conformational analysis of the citrate anions enables quantification of the conformational energy costs in these solids. Hydrogen bonding is important to the stability of these salts. The Mulliken overlap population in the hydrogen bonds provides a quantitative measure of their strength, and permits identification of long (weak) interactions which are significant in some of these compounds. Patterns in both the local environments of the hydrogen bonds and the more-extended features (graph sets) are noted. Polymorphs and sets of isostructural compounds permit more-detailed analysis of the structures and energetics in these compounds. The order of ionization of the three carboxylic acid groups is in general central/terminal/terminal, but there are two exceptions. While we have concentrated on salts containing a single alkali metal cation (and hydrogen), the structures of NaK2C6H5O7 and NaKHC6H5O7 provide an exciting window on a larger universe of mixed salts.
Halogen Bonding with Sulfur Functional Groups
Authors: Eccles Kevin , Morrison Robin , Sinha Abhijeet , Maguire Anita , Lawrence Simon
Published: November 2015

Crystal engineering has been defined as "the understanding of intermolecular interactions in the context of crystal packing and the utilisation of such understanding in the design of new solids with desired physical and chemical properties".[1] Halogen bonding is a significant type of intermolecular interaction involving a halogen atom with neutral or anionic components which has recently been exploited for the formation of multicomponent crystalline materials. Sulfur can exist in a variety of different oxidation states, giving rise to a wide variety of different functional groups that are potentially available for halogen bonding. We have recently reported our investigations with sulfoxide,[2] sulfone[2] and sulfinamide functional groups.[3] Herein we extend this work to include the thioamide functional group and compare it with its more extensively studied amide analogue. Investigation into the propensity for primary aromatic thioamides to form halogen interactions through the thiocarbonyl (C=S) functional group. A range of substituent aromatic primary thioamides containing different electronic substituents on the aromatic ring were synthesized and investigated for cocrystallisation. These cocrystals are held together by a combination of weak hydrogen bonding (N–H···S=C) and strong halogen interactions (C–X···S=C).
Polyhalides as scaffolds for supramolecular, ion-conducting crown ether stacks
Authors: Fromm Katharina , Crochet Aurélien , Dagri Cyrille , Chérémond Yvens
Published: November 2015

"Crown ethers, such as dibenzo-18-crown-6 (DB18C6) are in principle perfect building blocks to be stacked on top of each other for one-dimensional (1D) channel formation. However, in the more than 1000 publications on crown ethers in the solid state, only one case was of channel formation described, but not as main focus of research.[1] We now present a way to systematically induce the stacking of DB18C6 with the help of polyhalides, which play the roles of scaffolds via halogen bonding.[2] These compounds can be considered as ""supramolecular straws"". Using for example potassium as couter ion for triiodide for example, we obtained a solid which contains three differently filled, parallel channels in the solid state, which are arranged between the polyhalide anions. Exchanging potassium with sodium by immersion of a single crystal into NaOH solution leads to a single-crystal-to-single-crystal transformation into a compound with two channel types. This transition from a system crystallizing initially in the P2-space group to yield a compound in Pccn is only possible under these very special conditions. We will further present how the ion transport through these channels can be quantified and which process is involved in ion exchange. The role of the polyhalide anions, which cannot be replaced by other linear anions, will be emphasized as well. "
Assembly with Multinuclear Silver-Ethynediide/-Ethynide Supramolecular Synthons
Authors: Mak Thomas
Published: November 2015

Over the past 15 years, our group has conducted a systematic investigation on the synthesis and structural characterization of a series of silver(I) double and multiple salts containing silver carbide Ag2C2n (n = 1, 2), in which the all-carbon dianion ethynediide C22-is generally capsulated inside a polyhedral Agm (m = 6-10) cage, whereas C42-exhibits variable coordination modes involving each terminal triple-bond and a Agm (m = 3-5) basket. Recently we reported the first successful synthesis of their unstable higher homologues Ag2C6and Ag2C8, which were characterized through X-ray structure determination of their crystalline double salts Ag2C6·8AgCF3CO2·6H2O (3), 4(Ag2C6)·16AgCF3CO2·14.5DMSO and 2.5(Ag2C8)·10AgCF3CO2·10DMSO (Figure 1).[1] Our concomitant research program focused on silver(I) coordination and supramolecular network assembly based on multinuclear aggregates containing various kinds of carbon-rich ethynide ligands has established the robustness of multinuclear metal-ligand silver-ethynide supramolecular synthons symbolized as C2@Agn (n = 5-10), Ag4⊂C≡C–C≡C⊃Ag4, Agn⊂C6H4(n = 7-9), Agn⊂C≡C–R–C≡C⊃Agn (R = o-, m-, p-C6H4; n = 4, 5) and R–C≡C⊃Agn (R = aryl, alkyl, heterocycle,...; n = 4, 5), which function as versatile structural building units for the construction of a variety of discrete molecules, high-nuclearity clusters,[2] as well as 1D-3D coordination and supramolecular architectures.[3] In the absence of a definitive theoretical study, an empirical bonding model involving ionic, covalent and argentophilic interactions that consolidate the above-mentioned supramolecular synthons is proposed, which can account for the fact that analogous synthons have not been found for copper(I) and gold(I). This work is supported by Hong Kong Research Grants Council GRF CUHK 402710
Functional properties ensue from cooperation of different interactions
Authors: Resnati Giuseppe , Metrangolo Pierangelo , Terraneo Giancarlo , Cavallo Gabriella
Published: November 2015

According to the definition recommended by IUPAC [1], a halogen bond (XB) occurs when there is evidence of a net attractive interaction between an electrophilic region in a halogen atom and a nucleophilic region in another atom. The halogen bond has many similarities with the hydrogen bond (HB) and here we discuss the specific profile of the two interactions. We also show how the cooperation between the two interactions afford crystalline systems possessing unique and useful properties. For instance, the diiodide, dibromide, and dichloride salts of the 1,6-bis(trimethylammonium)hexane cation (hexamethonium, HMET2+, cation) react with two equivalents of diiodine in a solid-gas reaction and the corresponding bis-trihalides (halogen bonded adducts) are formed [2]. No cavities are present in the starting dihalides and the observed behavior reveals the dynamically porous character of bis(trimethylammonium)alkane dihalides. In the obtained bis-trihalides a net of X-···H-C HBs (X=Cl, Br, I) plays a decisive role in controlling the crystal packing: Four cationic columns embrace an anionic twin column formed by stacking of trihalide dimers. When heated, these bis-trihalides lose one diiodine molecule and the virtually unknown tetrahalide dianions [I4]2-, [I2Br2] 2-, and [I2Cl2]2-are formed. These dianions are the product of the double pinning of a diiodine molecule by two halide anions via strong XBs. The last two tetrahalides were never obtained in solution. The confined environment of dynamically porous materials clearly confers useful synthetic opportunities relative to solution-state processes. Other cases are described wherein XB and HB cooperate in driving self-assembly processes which afford solid materials endowed with useful properties. For instance, we will discuss the formation of two-component supramolecular gels [3] wherein a bis-urea and a diiodoarene self-assemble via cooperative XB and HB.
Twin Tandem Bicycle Pedal Motion - Using X-rays to Resolve Disorder Thermodynamic Parameters
Authors: Vande Velde Christophe , Collas Alain , Zeller Matthias , Blockhuys Frank
Published: November 2015

During our research into polar crystals for organic electronic applications, we synthesized E,E-1-[2-(4-nitrophenyl)ethenyl]-4-[2-(2,4-dimethoxyphenyl)ethenyl]benzene, which has a polar crystal structure (space group Pc) and displays the typical bicycle pedal motion, as studied in detail by Harada and Ogawa [1], in one of its ethenylic links. A van `t Hoff plot of the logarithm of the population ratio versus 1/T, however, showed a kink instead of being a straight line, which led us to conclude that an unusual phase transition was occurring in this material [2]. In the mean time we have crystallized the same material in a second, centrosymmetric polymorph (space group P-1). There, the asymmetric unit consists of two complete molecules, and they display the same kind of bicycle pedal motion, but this time in all four different ethenylic linkers. Every one of these population differences increases with temperature, so that four van `t Hoff plots can be constructed for this structure. Two of these behave normally, the other two display a kink, just like the van `t Hoff plot of the pedaling ethenylic link in the other polymorph of this molecule. This is, to the best of our knowledge, the first instance of a structure where four different dynamic equilibria can be resolved simultaneously, and only the second example in which van `t Hoff plots for the thermodynamics of dynamic disorder are not linear, indicating an unusual type of phase transition linked only to the dynamics of the molecules in the crystal.
Diffuse scattering in the polymorphs of p(N-methylbenzylidene)-p-methylaniline
Authors: Hudspeth Jessica , Goossens Darren , Welberry Richard
Published: November 2015

Polymorphism refers to the ability of a solid to exist in more than one crystal structure. Apart from being of scientific interest, it is of practical importance in the pharmaceutical and chemical manufacturing industries. In pharmaceuticals the polymorphic form of the substance can affect the ease of manufacture or the rate of uptake by the human body [1]. There is consequently a great need to be able to understand, predict and control polymorphism. This work is part of a larger study using diffuse scattering methods to investigate the role of molecular flexibility and disorder in polymorphism. Diffuse scattering is sensitive to two-body correlations so can provide information about the intermolecular interactions that cannot be obtained from the Bragg peaks, such as how the displacement or orientation of a molecule is correlated with that of its neighbours. p-(N-methylbenzylidene)-p-methylaniline (MeMe) is a model system for studying polymorphic behaviour. The system is trimorphic with all three polymorphs exhibiting highly structured diffuse scattering patterns [2]. The short-range order has been modelled using the program ZMC in which the molecules are allowed to interact via Hooke's law springs and brought to thermal equilibrium using a Monte Carlo algorithm [3]. Here we present a comparison of the diffuse scattering in the different forms of MeMe and assess how successfully different models for the intermolecular interactions reproduce the observed diffuse scattering data.
Modeling of SAPO-18/34 intergrowth crystal structure
Authors: Slawinski Wojciech , Wragg David , Akporiaye Duncan , Fjellvag Helmer
Published: November 2015

"Aluminophosphate framework structures have been widely studied because of their many technological applications. The most significant application of aluminophosphate type framework catalysts is in the methanol-to-olefin (MTO) conversion process [1], catalysed by SAPO-34 (the silicoaluminophosphate form of the chabazite (CHA) zeolite framework with silicon substituted into its structure). The effectiveness of SAPO-34 in the MTO process is due to both the shape selective properties of the framework and the concentration and strengths of the acid sites created by silicon substitution [2]. Another aluminophosphate framework MTO catalyst is SAPO-18 (zeolite framework type (AEI)), which has a very closely related structure to SAPO-34 and can form intergrowths with it. It has been suggested that the level of intergrowth can affect the efficiency of the MTO process [3], however, assessment of the level of intergrowth has remained difficult. We present a consistent model of the crystal structure of SAPO-18/34 family members which can accurately determine the level of intergrowth. The model utilises two types of stacking fault: Displacement and Growth which have significantly different effects on the diffraction pattern. A series of powder diffraction patterns is calculated using the Discus software package. Changes in the level of intergrowth and stacking fault type strongly affect the calculated pattern. A series of patterns has been calculated to illustrate this. The structure of an intergrown SAPO-34 sample with 4.8% Si content is modelled and refined using Displacement stacking faults. An example of ""defect-free"" AlPO-18 (0% Si content) is then presented. Refinement of the model shows that even this contains a small amount of stacking faults. Finally, a simple method for defect level estimation is proposed based on FWHM (Full Width at Half Maximum) ratios for selected Bragg reflections."
Do Fullerene Superconductors Belong to the High-Tc Superconductivity Universe?
Authors: Prassides Kosmas
Published: November 2015

A3C60 (A = alkali metal) superconductors were known to adopt face-centred cubic (fcc) structures with their superconducting Tc increasing monotonically with increasing interfullerene spacing, reaching a 33 K maximum for RbCs2C60 – this physical picture had remained unaltered since 1992. Trace superconductivity (s/c fraction<0.1%) at 40 K under pressure was also reported in 1995 in multiphase samples with nominal composition Cs3C60. Despite numerous attempts by many groups worldwide, this remained unconfirmed and the structure and composition of the material responsible for superconductivity unidentified. Thus the possibility of enhancing fulleride superconductivity and understanding the structures and properties of these archetypal molecular solids had remained elusive. Here I will present our recent progress in this field in accessing high-symmetry hyperexpanded alkali fullerides in the vicinity of the Mott-Hubbard metal-insulator boundary and at previously inaccessible intermolecular separations. The physical picture that emerges for the alkali fullerides is that, contrary to long-held beliefs, they are the simplest members of the high-Tc superconductivity family. We demonstrated this by showing that in the two hyperexpanded Cs3C60 polymorphs (fcc- and A15-structured) [1-3], superconductivity emerges upon applied pressure out of an antiferromagnetic insulating state and displays an unconventional behaviour – a superconductivity dome – explicable by the prominent role of strong electron correlations.
Optimization in S-SAD phasing - difference between solved and unsolved structure
Authors: Stránský Jan , Kovaľ Tomáš , Østergaard Lars , Dušková Jarmila , Skálová Tereza , Hašek Jindřich , Kolenko Petr , Fejfarová Karla , Dohnálek Jan
Published: November 2015

Development of X-ray diffraction technologies have made de novo phasing of protein structures by single-wavelength anomalous dispersion by sulphur (S-SAD) more common. As anomalous differences in the sulphur atomic factors are in the order of errors of measurement, careful intensity reading and data processing are crucial. S-SAD was used for de novo phasing of a small 12 kDa protein with 4 sulphur atoms per molecule at 2.3 Å, where the data did not enable a straightforward structure solution. Data processing was performed using XDS [1] and scaling using XSCALE. The sulphur substructure was determined by SHELXD [2] and phases were obtained from SHELXE [2]. Both algorithms strongly depend on input parameters and default values did not lead to the correct phases. Therefore a systematic search of optimal values of several parameters was used to find a solution. This method helped to confirm sulphur substructure and to differentiate the handedness of the solutions. Moreover, a script for comfortable conversion of SHELX outputs to MTZ format was developed, using programmes included in the CCP4 package [3]. The previously unsolvable protein structure was successfully resolved with the described procedure. This work was supported by the Grant Agency of the Czech Technical University in Prague, (SGS13/219/OHK4/3T/14), the Czech Science Foundation (P302/11/0855), project BIOCEV CZ.1.05/1.1.00/02.0109 from the ERDF.
Metal Speciation in Macromolecules Using Anomalous Diffraction Method
Authors: Jakoncic Jean
Published: November 2015

Metals play vitally important roles in biological processes and are present in a large fraction of macromolecules. In proteins, the metal species is usually known from previous work or can be assigned using X-ray absorption spectroscopy. The metal can also be assigned looking at the local environment using coordination properties. Several methods exist to determine which metal is present in a given sample, but there is no method that can locally pin point the type of metal in a protein crystal. Anomalous scattering method was used to generate element specific 3D maps for a model protein. The method, that allows to scan for a wide range of metals with minimum X-ray dose will be described and qualitative as well as quantitative results will be presented. The experiment was performed in the 7-10 keV range but the full potential will be achieved with a broader energy range, i.e. 2-10 keV giving access to the absorption K edges of most of the key metals for life science.
Low Multiplicity Sulfur SAD Phasing in the Home lab
Authors: Freisz Severine , Graf Juergen , Benning Matthew , Smith Vernon
Published: November 2015

Advances in crystallographic hardware and software are enabling structural biologists to investigate more challenging projects. Recent developments in hardware and software are greatly increasing the capabilities of in-house diffraction systems making it more routine to obtain de novo structural information in the home lab. Single-wavelength anomalous diffraction (SAD) techniques with Cu Ka or Ga Ka radiation are now widely used for structure solution even in cases involving weak anomalous scatterers, like sulfur. We have now introduced the D8 Venture solution for structural biology with the PHOTON 100 detector featuring the first CMOS active pixel sensor for X-ray crystallography. Our new microfocus source, the METALJET delivers beam intensity exceeding those of typical bending-magnet beamlines. The very high intensity, the small beam focus and the lower air scatter produced by Gallium Kα radiation help to greatly reduce the background scatter. This provides greater signal to noise essential to identify weak anomalous signal. Due to the very weak anomalous scattering of S, data multiplicities in the order of 40 are typically necessary to obtain phases by S-SAD. Collecting high-multiplicity data minimizes systematic experimental errors to measure with very high accuracy the minute intensity difference between Friedel Pairs (1.0 – 1.5 %) [1]. This requires software which optimizes the collection strategy, for example with respect to overall data collection time to minimize radiation damage. The combination of a brighter, more stable X-ray source with a high sensitivity low noise detector have greatly improved the quality of data collected in-house. The high quality allows successful SAD measurements far away from the absorption edge. Here we present a low multiplicity sulfur-SAD phasing experiment on a small Thaumatin crystal showing the high quality of the data collected on the D8 VENTURE with the METALJET.
Experimenting S-SAD on BM14-2 at the ESRF
Authors: Belrhali Hassan , Khadrouche Akim , Manjasetty Babu , Mairs Trevor
Published: November 2015

Bending Magnet beamline 14 (BM14) at the European Synchrotron Radiation Facility (ESRF, Grenoble, France) is dedicated to macromolecular crystallography (MX). This experimental station has been designed specifically to produce MX diffraction data using the methods of Single- or Multiple-wavelength Anomalous Diffraction (SAD or MAD) (www.bm14.eu). From 1994 to 2000, BM14 operated as an ESRF public beamline. Then from 2001 to 2009 the beamline was acquired and operated as an UK Medical Research Council Collaborative Research Group beamline. Since 2010, it is now back an ESRF beamline operated by a consortium between the ESRF, the EMBL Grenoble Outstation and the Indian Department of Biotechnology for the benefit of both the European and Indian MX communities. During 2011 and 2012, the beamline optics' hutch was fully upgraded (hence the new denomination BM14-2). As a consequence the upgrade produced a four-time increase in beam brilliance with the concomitant reduction in average exposure time (~5 s today versus 20 s for BM14), leading to a substantial gain in the beamline screening capacity and in scientific productivity. Moreover, in addition to the new optical elements, the new channel-cut crystal was equipped with a second crystal pusher to reject high-energy harmonics. This latter device turned to be crucial for sulphur-SAD experiment success rate as it is very efficient in "cleaning up" the spectral purity of the low energy beams. We will illustrate the benefit of rejecting harmonics in terms of data quality and phasing power, critical for S-SAD experiments. We will also explicit our multiple-kappa orientation approach to enhance multiplicity as well as to optimise scaling protocols, both also very important for the success rate of these very low anomalous signal experiments. Nota Bene: European users may apply for direct access to the beamline via the Biostruct-X European program (www.biostruct-x.eu). Users from India are encouraged to apply from http://process.mbu.iisc.ernet.in/BM14/index.jsp
Sulfur-SAD phasing and UV-RIP analysis on a single Cysteine bridge protein
Authors: Gorgel Manuela , Ulstrup Jakob , Bøggild Andreas , Weiss Manfred , Mueller Uwe , Nissen Poul , Boesen Thomas
Published: November 2015

The advantage of using the anomalous signal of sulfur for phase determination is that only a single, well-diffracting crystal is needed and that a native structure will be obtained. Using long-wavelength S-SAD to a resolution of 1.9 Å we have determined the novel structure of an 89 residue protein with only 2 Cysteines fixed in a disulfide bridge. To the best of our knowledge, the Bijvoet ratio in our example is one of the smallest for which a successful structure solution by S-SAD has been reported. Data were collected on 3 different volumes of a single crystal at beamline 14.1. at BESSY II, Berlin [1], at a wavelength of 1.8 Å. At this wavelength the maximum resolution obtainable was 1.9 Å. The data were processed in space group I222 with a low resolution R-factor of 3.2% and a multiplicity of 17. Based on an anomalous correlation coefficient cut off at 30% the signal extends to 2.6 Å. The sulfur substructure was determined using AutoSol/HYSS [2] showing a total of four clear sulfur positions in the asymmetric unit with a resulting FOM of 0.27 and a BAYES Coefficient of 0.36. The crystal has a solvent content of 62% and the structure reveals a dimer and large solvent channels. Density modification lead to well-defined electron density maps for the protein and associated solvent molecules. This example demonstrates that S-SAD phase determination can work with as little as one S-atom per 45 amino acid residues. Additionally, we performed a UV-RIP (ultraviolet radiation damage-induced phasing) experiment in which a dataset was collected before and after irradiating the crystal with a hard UV laser. An isomorphous difference map shows the clear disruption of both disulfide bridges and we are currently working on combined phasing using both anomalous and isomorphous differences based on the S-SAD and UV-RIP data.
Advancing Native-SAD Phasing at Synchrotron with 13 Real-life Case Studies
Authors: Wang Meitian
Published: November 2015

The key step in elucidating de novo 3D X-ray structures relies on the incorporation of heavy elements into proteins or crystals. Selenomethionine incorporation or heavy metal derivatization are however not always possible and require additional efforts. Exploiting anomalous signals from intrinsically present elements like S, P, and Ca2+ from proteins and nucleic acids, as well as Cl-, SO42-, and PO42- from crystallization solutions, is therefore an appealing alternative. Such a method has been shown to be valid by collecting data from several crystals and combining them(1). Recent developments at macromolecular crystallography beamlines are however pushing the limits of what could be obtained out of a single crystal. Here we introduce a novel data collection routine for native-SAD phasing, which distributes tolerable X-ray life-doses to very high multiplicity X-ray diffraction data sets measured at 6 keV energy and at different crystal orientations on a single crystal. This allows the extraction of weak anomalous signals reliably by reducing both systematic and random measurement errors. The data collection method has been applied successfully to thirteen real-life examples including membrane proteins, a protein/DNA complex, and a large protein complex. In addition to de novo structure determination, we advocate such a data collection protocol for molecular replacement solvable structures where unbiased phase information is crucial in objective map interpretation and model building, especially for medium and low-resolution cases.
Measuring the specific surface area of mesoporous silica using x-ray scattering
Authors: Cambedouzou Julien , Diat Olivier
Published: November 2015

The development of porous silica or carbon material with high specific surface area raises a high interest in the field of materials science given their potential interest in a wide range of applications including catalysis, water treatment or drug delivery. Among these mesoporous structures, those consisting of one-dimensional pores aligned along a compact hexagonal packing are of prime importance and can be referred to as "hexagonal mesoporous materials" (HMPM). The most famous silica structures of this kind are MCM-41 and SBA-15. The same symmetry can be found in carbon mesoporous materials, for example in FDU-15 structures. The precise characterization of HMPM is necessary for most of the applications envisioned for these materials (pore size, pore density, specific surface and sometimes thickness of the functionalization layer). Small angle X-ray scattering techniques offer the opportunity to determine the mean structural parameters of HMPM. Although different approaches can be found in the literature in order to numerically reproduce the experimental data obtained on HMPM or hexagonal liquid crystals, when the sample is a powder, fitting the experimental data in absolute scale with numerical models becomes necessary. However, with a large scattering contribution of grain at low q vector as well as short range correlation contribution at large q, the analysis is not so simple. In this paper, we propose a comprehensive study [1] devoted to the quantitative interpretation of small-angle scattering patterns of HMPM in terms of structure and specific surface estimation based on the formalism proposed by Spalla et al. [2]. In the case of two real samples, namely a SBA-15 and a MCM-41 powder, the specific surface area of the mesopores is estimated and is discussed in the light of gas adsorption measurements.