bluuebunny/crossref_metadata_2025 huggingface dataset:
The shape of the orientation distribution of carbon nanotubes in aligned arrays
Authors: Vainio Ulla , Schnoor Thea , Koyiloth Vayalil Sarathlal , Schulte Karl , Müller Martin , Lilleodden Erica
Published: November 2015

Recent simulations of vertically aligned carbon nanotube arrays have shown that the shape of the orientation distribution of nanotubes within the array has a drastic effect on the electrical properties of the array. Orienting of shape-anisotropic objects can be carried out in several different ways such as shearing, magnetically steering, or by vibrating the objects. Nevertheless, perfect orientation is difficult if not impossible to achieve. In the case of the growth of carbon nanotube arrays, self-confinement can occur affecting the resultant orientation distribution. Yet so far the shape of the orientation distribution has not been quantified in great detail and it has been mostly assumed to be Gaussian or Lorentzian. In the present work, multi-walled carbon nanotube arrays were grown via aerosol-assisted chemical vapour deposition with iron catalyst and investigated using small-angle X-ray scattering, a method perfectly suited to characterizing the orientation of carbon nanotubes. Using a microfocused X-ray beam of 24 μm x 17 μm in size at beamline P03 of the PETRA III synchrotron storage ring in Hamburg, we determined the orientation distribution of the vertically aligned carbon nanotubes along the film height. Remarkably, the packing density of the carbon nanotubes seems to correlate not only with the width of the distribution but also its shape. The shape of the orientation distribution was then compared to that from different oriented systems. These findings indicate that by using alignment methods that are based on steric interaction between particles, such as shearing or self-confinement during particle growth, the system will reach an alignment with an orientation distribution closer to the Laplace distribution than to the normal distribution. Such a finding has profound implications for simulation studies of mechanical, electrical and other properties of many hierarchical materials.
Structural and Morphogenetic Complexity of Fluorapatite-Gelatine Nanocomposites
Authors: Rosseeva Elena , Simon Paul , Kniep Rüdiger
Published: November 2015

The most fascinating natural examples of nanocomposite materials are represented by so-called biominerals, acting as functional materials in living systems. In particular, apatite-organic (protein) nanocomposites are the main components of bone and teeth hard tissues of vertebrates (including humans) [1]. Biomimetic systems provide an excellent possibility to get deeper insight into the fundamental principles of structuring, organization and formation of biominerals. Therefore, our investigations are focused on biomimetic fluorapatite-gelatine nanocomposites grown by double-diffusion in gelatine gels [2]. In the gelatine gel protein molecules interact with the ions in solution in such a way that they provide nucleation positions for nano apatite and, in this way, give rise to dramatic processes of self-organization and hierarchical composite formation. Numerous experimental observations (by means of XRD, SEM, HRTEM, EH, etc.) together with atomistic computer simulations reveal the material to be best described as a mosaic-dominated nanocomposite superstructure. Furthermore intrinsic electric dipole fields, generated by a non-classical crystallization process of composite nanoboards, cause the integration of a meso/macroscopic pattern of gelatine microfibrils into the superstructure matrix and govern morphogenetic process of fluorapatite-gelatine nanocomposites [3].
Strong stabilization of liquid amorphous calcium carbonate by polymers and proteins
Authors: Natalio Filipe , Corrales Tomas , Dietzsch Michael , Lieberwirth Ingo , Mugnaioli Enrico , Kappl Michael , Panthöfer Martin , Kolb Ute , Butt Hans-Jürgen , Tremel Wolfgang
Published: November 2015

We have studied the effect of bio-inspired polymers and proteins like ovalbumin, lysozyme and silicatein, which are present in the first stage of egg shell formation or in the formation of siliceous spicules of sponges, on the homogeneous formation of the liquid-amorphous calcium carbonate (LACC) precursor, by a combination of complementary methods like in situ WAXS, light scattering, TEM and cryo-TEM. Lysozyme destabilizes the LACC emulsion, whereas ovalbumin extends the lifetime of the emulsified state. We demonstrate that ovalbumin acts as a stabilizer for a polymer-induced liquid precursor (PILP) process. We propose that the liquid amorphous calcium carbonate is affected by polymers by depletion stabilization and de-emulsification rather than induced by acidic proteins and polymers during a polymer-induced liquid precursor process. Thus, the original PILP coating effect appears to be a result of a de-emulsification process of a stabilized LACC phase. Silicatein-α is responsible for the biomineralization of silica in sponges guides the self-assembly of calcite "spicules" similar to the spicules of the calcareous sponge Sycon. The self-assembled spicules, 10-300 µm in length and 5-10 µm in diameter, are composed of aligned calcite nanocrystals. The spicules are initially amorphous but transform into calcite within months, exhibiting unusual growth along [100]. While natural spicules evidence brittle failure, the synthetic spicules show an elastic response which greatly enhances bending strength. Later stages of nucleation have been studied by "trapping" nuclei from solution by shock-freezing of droplets in liquid ethane (cryo-TEM). This yields snapshots of the structure formation process at given point. In a first step the full determination of the structure of vaterite, one of the common CaCO3 polymorphs, was solved on nanometer-sized crystallites by electron crystallography. These results demonstrate that crystals that are too small for single-crystal X-ray diffraction and too difficult to solve by powder diffraction may nevertheless be amenable to accurate structure determination by electron crystallography.
Comparing the dynamics of coordination polyhedra in a metal-cyanide framework
Authors: Phillips Anthony
Published: November 2015

The enormous amount of attention devoted to metal-organic framework materials over the past two decades has yielded substantial synthetic control over these materials, so that specific topologies can be explicitly engineered by carefully selecting metal and ligand "building blocks". The dynamic behaviour of these materials, however, remains far less predictable: yet it is this behaviour that is the key to understanding the highly anomalous thermodynamic properties of many framework materials. When studying these compounds crystallographically it is important to acknowledge the limitations of Bragg scattering, which by revealing only a space- and time-averaged structure can give an incomplete or even actively misleading picture of the material's dynamic behaviour. For this reason, complementary techniques, such as XAFS, that are sensitive to the local structure of materials are vitally important. We have studied the behaviour of a prototypical framework material exhibiting near-zero thermal expansion, tetramethylammonium copper(I) zinc(II) cyanide, by X-ray absorption spectroscopy at the Cu and Zn K edges in combination with total neutron and X-ray scattering, supported by reverse Monte Carlo and density-functional theory calculations, thus simultaneously modelling the long-range and local structure of this material. Our results resolve for the first time the individual flexibility of the copper and zinc coordination tetrahedra, suggesting substantially higher flexibility of both types of polyhedra than was previously thought. These results shed new light on the atomic origins of this material's flexibility, and explain the mobility of guest molecules through the framework structure. More generally, this methodology points the way to being able to choose framework components for their dynamic properties, and hence to the rational synthesis of flexible framework materials with targeted thermodynamic properties.
Advances in Synchrotron XRPD for the characterization of pharmaceuticals
Authors: Gozzo Fabia
Published: November 2015

X-Ray Powder Diffraction (XRPD) directly provides structural and microstructural characterization of materials. Considered the gold standard method in the field of pharmaceutical powders for the identification of solid forms (i.e. polymorphs, solvates, hydrates, salts, co-crystals, amorphous), when combined with a synchrotron X-ray beam, XRPD becomes a truly mighty analytical tool for the characterization of pharmaceuticals. Ultra-high FWHM and d-spacing resolutions, accurate 2theta angle assignment, high signal-to-background and signal-to-noise ratios distinguish synchrotron XRPD patterns from conventional XRPD, whereas the combination of the synchrotron properties with new outstanding single-photon-counting detection systems drastically reduces the measurements times to milliseconds allowing in-situ study of the kinetic of transformations and radiation-damage-free high-resolution diffraction patterns. Advances in instrumentation, calibration and data collection procedures leading to detection limits of contaminating crystalline phases better than 0.05% wt% as well as subtle structural details are described.
Insights into minor pseudopilin complexes of the Type II secretion system
Authors: Zhang Yichen , Faucher Frederick , Jia Zongchao
Published: November 2015

The type II secretion system (T2SS) is sophisticated multiprotein machinery that enables Gram-negative pathogens to secrete a wide range of exoproteins, named virulence factors, into the extracellular environments. In Pseudomonas aeruginosa, the Xcp T2SS is responsible for secreting many virulence factors that induce severe infections. In T2SS, the recognition and binding of secreted exoproteins are conducted by a structure called the pseudopilius tip, which is formed by four minor pseudopilins, including XcpU, XcpV, XcpW and XcpX. These minor pseudopilins form a quaternary complex, which is also involved in the initiation and regulation of the pseudopilus assembly. Although individual structures of these four pseudopilins have been revealed in different organisms, the substrate recognition and binding mechanisms have not been clearly elucidated due to the lack of systematic studies on the whole structures of several complexes formed by these pseudopilins. As a result, the understanding of the structures of these protein complexes will provide useful information for unveiling the mystery of the recognition and binding mechanisms. The establishment of the substrate binding model requires the preparation of stable complex(es) of substrates and certain minor pseudopilin(s). In this work, we aim to gradually elucidate the secretion mechanisms by assembling each component to build up the whole architecture. The structure of XcpV in complex with XcpW has been determined, and other complexes, especially the XcpU-containing binary and ternary complexes, have been stably established and purified. The identification of these complex structures will significantly promote our understandings of the type II secretion mechanisms.
Structural and functional studies of Salmonella effector proteins
Authors: Xu Caishuang , Boniecki Michal , Cherney Maia , Shi Rong , Cygler Miroslaw
Published: November 2015

Gram-negative bacteria of the Salmonella enterica species are ubiquitous facultative intracellular pathogens one of the most infective in humans, causing diseases from gastroenteritis to typhoid fever. Salmonella secretes a range of proteins called effectors to gain entry and colonize the host cell. These effectors are secreted by type 3 secretion system. Upon endocytic internalization by the host cell the bacterium resides in a membrane-bound compartment – the Salmonella containing vacuole (SCV). The effector proteins prevent conversion of SCV into lysosomes and promote bacterial survival and replication within this compartment. The function of effectors varies from interfering protein synthesis and host cell signaling pathways, mediating vesicle traffic to rearranging actin cytoskeleton. We have undertaken studies of several effectors from Salmonella enterica serovar Typhimurium, such as SopD2, GtgE and SpvB, to understand their mechanism of action at the molecular level. We have expressed and purified these proteins and undertaken their crystallization. We will present our most recent results.
Structural perspectives on bacterial secretion machines
Authors: Lea Susan
Published: November 2015

For any cellular secretion mechanisms the key questions that need to be understood center on the processes that ensure how secretion is achieved without disruption of the membrane barrier, how the process is energized and how substrates are selected. We are pursuing structural studies of two very different bacterial secretion systems that take almost opposite approaches to this but where structures are beginning to give insight into mechanism. Recent work will be presented contrasting the Twin Arginine Transport (or Tat) system, a relatively simple 2 or 3 component system that manages to transport a wide range of fully-folded protein substrates, of very different size, shape and charge without promoting leakage from the cell with the Type Three Secretion System (or T3SS) a protein nano-machine constructed of more than 15 proteins that secretes fully unfolded substrates directly into a pathogen's host cells. Comparing the two systems yet again demonstrates how very different mechanisms and architectures can be used to achieve much more similar biological effects. The difficulties presented for structural studies of by these systems will also be highlighted as will the use of mixed structural methods to extend our understanding.
Pilus biogenesis at the outer membrane of bacterial pathogens
Authors: Waksman Gabriel
Published: November 2015

Gram-negative pathogens commonly exhibit adhesive pili on their surface that mediate specific attachment to the host. A major class of pili is assembled via the chaperone/usher (CU) pathway. Type 1 and P pili have served as model systems for the elucidation of the CU biosynthetic pathway. Pilus assembly requires a periplasmic chaperone (FimC and PapD for type 1 and P pili, respectively) and an outer-membrane assembly platform termed "usher" (FiimD and PapC for type 1 and P pili, respectively). CU pilus subunits are produced in the cytoplasm, translocated to the periplasm by the Sec translocation machinery, and then taken up by a chaperone to cross the periplasmic space to reach the outer-membrane. At the outer-membrane, chaperone-subunit complexes are recruited to an outer-membrane assembly platform, the usher, which orchestrates recruitment and polymerization of subunits. Previous work has elucidated the molecular basis of chaperone function. Recent progress has shed light into the mechanism of pilus subunit assembly at the usher, leading to the elucidation of the entire cycle of pilus subunit incorporation.
Intact structure determination of a highly radiation sensitive protein at SACLA
Authors: Ago Hideo , Hirata Kunio , Shinzawa-Itoh Kyoko , Yano Naomine , Tsukihara Tomitake , Yamashita Eiki , Ueno Go , Murakami Hironori , Yoshikawa Shinya , Yamamoto Masaki
Published: November 2015

X-ray irradiation on a protein crystal can cause some subtle structural modification on the protein structure even if the radiation dose is much smaller than a dose used for a common crystal structure determination. In some case such structural modification increases ambiguity of structural inspection, and eventually could be an obstacle on the elucidation of structure basis of protein function. Bovine heart cytochrome c oxidase (CcO) is one of such proteins having some problem caused by the radiation damage. The proton pumping of CcO is coupled with O2 reduction at the O2 reduction site, thus accurate structure determination of bound ligand as well as CcO itself is very important. Whereas accurate structure determination was impeded by the immediate photolysis of the peroxide ligand upon X-ray irradiation even at a cryogenic temperature[1]. We developed a goniometer based data collection system for the femtosecond crystallography at SACLA (SPring-8 Angstrom Compact free-electron LAser). The femtosecond crystallography is expected to have an advantage in high-resolution and radiation damage free structure determination of very large protein by combined usage of large crystal and femtosecond intense X-ray pulse. In this presentation we are going to show the result of the femtosecond crystallography on the crystal of CcO having large unit cell dimensions. The close inspection of the electron density map calculated at 1.9 Å resolution showed the femtosecond crystallography worked fine for the high resolution and radiation damage free crystal structure determination of CcO.
De novo phasing of protein crystallography data from a free-electron laser
Authors: Barends Thomas , Foucar Lutz , Botha Sabine , Doak R. Bruce , Shoeman Robert , Nass Karol , Koglin Jason , Williams Garth , Boutet Sebastien , Messerschmidt Marc , Schlichting Ilme
Published: November 2015

Free-electron lasers (FELs) are pushing back the limits of possibility in protein crystallography. Using the high-intensity, femtosecond duration pulses afforded by FELs allow data collection from micrometer-sized crystals while outrunning radiation damage. Moreover, FELs may be used for pump-probe experiments with unprecedented time resolution. However, the intricacies of FEL data collection pose specific challenges: as every FEL pulse destroys the sample, data are mostly collected from a stream of microcrystals and averaged to remove the variations in crystal size and quality as well as shot-to-shot variations in beam parameters. This technique is called serial femtosecond crystallography (SFX). In SFX, several tens of thousands of images typically need to be averaged to obtain reasonably accurate structure factor amplitudes. We previously showed that SFX yields structure factor amplitudes accurate enough to detect the weak anomalous signal of endogenous sulfur atoms. Now we show that SFX can be used to collect data accurate enough for de-novo phasing of a protein structure[1]. Using a model system (gadolinium-derivatized lysozyme) we collected ~60,000 diffraction images and obtained structure factor amplitudes that allowed phasing by single-wavelength anomalous diffraction. This first demonstration of de novo phasing from FEL data leads us to anticipate that FEL-based crystallography will become an important tool for the structure determination of proteins that are extremely radiation sensitive or that are difficult to crystallize, such as membrane proteins.
Putting variable-sized alkanes into fixed-size hydrogen-bonded molecular flasks
Authors: Van Der Lee Arie , Dumitrescu Dan , Legrand Yves-Marie , Petit Eddy , Barboiu Mihail
Published: November 2015

Confined alkanes within molecular capsules are an intriguing research area which were studied until now only by spectroscopic techniques, but never by single-crystal X-ray techniques [1-2]. We report here an extremely simple molecular flask made up by hydrogen-bonded tectons, which is used as a container for diammonium alkane chains of variable sizes. It was obtained in aqueous solution as well as in the crystalline state by mixing commercially available components: 1,3,5,8-pyrenetetrasulfonate (PTS), guanidinium (G) and 1,ω-diammonium-alkanes (Figure A). 1,10-diammoniumdecane 1 fits perfectly inside the capsule, while the 1,11-diammonium-undecane 2 and 1,12-diammonium-dodecane 3 chains are progressively compressed. Furthermore, it was observed that the compressed conformers may be stabilized by short dihydrogen contacts (Figure B).
Influence of steric crowding on hydrogen bonding in anti-cancer quinols
Authors: Schwalbe Carl , Wells Geoffrey , Stevens Malcolm
Published: November 2015

The quinol 4-(1-benzenesulfonyl-1H-6-fluoroindol-2-yl)-4-hydroxycyclohexa-2,5-dienone (1) is strongly active against cancer cells [1]. Two "Michael acceptor" electrophilic β-carbons on the quinol ring are believed necessary for optimal antitumor activity, and disruption of thioredoxin signaling is a possible mechanism of action. As a model for the possible product, the adduct (2) with two molecules of ethanethiol was prepared. These molecules have just one classical hydrogen bond (HB) donor group, the quinol OH, but a surfeit of acceptors, namely one C=O and two SO2oxygen atoms (designated O15, O17 and O18) as well as O14, the OH itself. In (1) paired molecules form a R22(14) ring by O14-H...O17 HB with H...O distance 2.15 Å and O-H...O angle 156°. In (2) the two EtS groups on the same side of the quinol ring as O14 interfere with this motif. Instead, a C(7) chain is formed by less optimal O14-H...O17 HB (2.34 Å and 134°). In apparent compensation, an intramolecular C-H...O HB to O17 is shorter and straighter in (2). In both structures all O atoms accept C-H...O HB. The unit cell dimensions are dissimilar, but a motif persists: one phenyl CH and one indole CH group bite onto the same O atom, O15 in (1) but O18 in (2).
Core level crystallography: Probing H-bonding through nitrogen XPS and NEXAFS
Authors: Stevens Joanna , Byard Stephan , Newton Lauren , Jaye Cherno , Seaton Colin , Sadiq Ghazala , Fischer Daniel , Davey Roger , Schroeder Sven
Published: November 2015

Determining the location of hydrogen is not always straightforward, despite its potential for wide-reaching effects, such as altering physicochemical properties and biological/chemical processes. Proton transfer can be considered a simple chemical reaction, with a continuum from neutral to protonated states, and short, strong H-bonds (SSHB) and disordered systems between the two extremes. X-ray Photoelectron Spectroscopy (XPS) and Near Edge X-ray Absorption Fine Structure (NEXAFS) intrinsically probe the local environment, with sensitivity to the chemical state of the atom and, importantly, nature of the local chemical and bonding environment. Organic molecular crystals have been studied by nitrogen XPS and NEXAFS, offering an alternative to X-ray and neutron diffraction. Strong chemical shifts occur with proton transfer to nitrogen (+N-H---O vs. N---H-O), unambiguously characterizing protonated and H-bonded systems,[1] leading to direct observation of an unusual solid-state colour change for 4,4'-bipyridine/squaric acid with heating[2] involving proton transfer to nitrogen with temperature-dependent measurements. Correlation between H-bond lengths and chemical shifts indicates potential for predicting H-bond lengths. SSHBs provide an interesting case, as hydrogen can reside midway between donor and acceptor, having a 3-centre, 4-electron bond with quasi-covalent character and atypical properties. Intermediate chemical shifts are found with hydrogen midway between donor and acceptor in 3,5-pyridinedicarboxylic acid, with increased peak width representative of hydrogen's broadened single minimum potential well.[3] This contrasts with conventional 2-site hydrogen disorder, in which signals from both donor and acceptor environments result in 2 peaks reflecting the % occupancy. Valuable electronic and structural information is obtained from the variety of organic systems investigated, with XPS clearly distinguishing different types of crystallographic materials (Fig 1).
Odd-Even Effect in the Elastic Modulii of α,ω-Alkanedicarboxylic Acids
Authors: Mishra Manish , Varughese Sunil , Ramamurty Upadrasta , Desiraju Gautam
Published: November 2015

Nanoindentation is a probe used to quantitatively assess mechanical behavior of small volume materials. In this technique, load applied vs. the depth of penetration of the indenter into the specimen are measured simultaneously and with high precision and resolution. By analyzing the data, one can obtain the elastic modulus and hardness of crystals. Though this technique has been extensively used to characterize inorganic and engineering materials, we have recently extended its utility to study weak interactions and to establish structure-property relationships in molecular crystals. Being able to assess the relative strength of weak interactions such a technique has become relevant to the subject of crystal engineering which is concerned with the design of molecular solids with desired properties and functions. In our recent studies through nanoindentation on the alkanedicarboxylic acids reveals that the elastic modulus shows similar alternation property as the melting point alternation. Our results are endorsing the strained molecular conformations hypothesis for the melting point alternation of diacids, proposed by Thalladi et al. These results support the development of crystal engineering because nanoindentation may be used as a direct measure of molecular and crystal energies of molecular crystals.
The Only N-H...O Hydrogen Bond - Two Ways to Build a Structure of Dimethylglycine
Authors: Kapustin Eugene , Minkov Vasily , Boldyreva Elena
Published: November 2015

Crystalline amino acids are considered to mimic important interactions in peptides, therefore the studies of the structure-forming factors in these systems attract much attention. N,N-dimethylglycine is an interesting model compound that was used to test the role of the N-H...O H-bonds in forming the head-to-tail chains – the main structural unit in the crystals of amino acids. It was hypothesized previously that additional side N-H...O H-bonds play an important role in forming the head-to-tail chains of amino acid zwitterions linked via N-H...O H-bonds between the charged -NH3 and -COO terminal groups. Twice methylated amino group of N,N-dimethylglycine is able to form only one N-H...O H-bond in the crystal structure, so that this hypothesis could be tested. There are two polymorphs of N,N-dimethylglycine, in which the zwitterions are packed in two different ways. In one polymorph (orthorhombic, Pbca) they form finite four member ring motifs not linked to each other via any H-bonds, but only by weak van der Waals interactions. However, in the second polymorph (monoclinic, P21/n) the zwitterions do form infinite head-to-tail chains though the N-H...O H-bond is the only one and is not assisted via any additional H-bonds. The effect of cooling on the two crystal structures was followed by single-crystal X-ray diffraction combined with polarized Raman spectroscopy of oriented single crystals, in order to compare the response of the N-H...O H-bonds to temperature variations. The crystal structure of the monoclinic polymorph compresses anisotropically on cooling, whereas that of the orthorhombic polymorph undergoes a reversible single-crystal to single-crystal phase transition at ~200 K accompanied by non-merohedral twinning, reducing the space symmetry to monoclinic (P21/b), and doubling the asymmetric unit from 2 to 4 molecules. This phase transition could not be detected by Raman spectroscopy and DSC because of the subtle related changes in intermolecular energies.
Molecular Swiss Cheese: new complexes and conformations of p-sulphonato[8]arene
Authors: Lesniewska Barbara , Suwinska Kinga , Coleman Anthony
Published: November 2015

"The crystal structures of the salts of para-sulphonatocalix[8]arene with two flexible guest molecules 1,2-bis(4-pyridyl)-ethane (BPE) and 1,3-bis(4-pyridyl)-propane (BPP) are presented. para-Sulphonatocalix[8]arene molecule adopts new types of conformations: ""double facing cone"" in BPP complex and "up-flat-down" in BPE complex. Although the difference between BPE and BPP is only a presence or absence of a single carbon atom in the central bridge, the structures of their complexes with para-sulphonatocalix[8]arene are remarkably different. While the salt with BPE shows true porosity and can be compared to that of an extremely complex zeolite or to a solid state molecular Swiss Cheese, the second structure with BPP shows no porosity and is of the type of organic clay firstly observed for the sodium salt of para-sulphonato-calix[4]arene [1], and can be compared to a Gruyere Cheese. The structure of the para-sulphonatocalix[8]arene with BPE salt (Figure 1) shows a complex network of interconnecting channels of variable size, one of which contains a BPE cation effectively blocking this channel, the others contain water and solvents and are thus accessible. A total of six different channels are observed in this structure. Gas take-up has been demonstrated, to show the porous nature of the solid. The effect of a single carbon atom between the cations on the complexity of the Supramolecular Organic Framework (SOF), is remarkable. Work is currently underway to study other complexes of para-sulphonatocalix[8]arene with rigid and flexible organic cations and to open up the way to novel SOFs. Figure 1. Solvent accessible surface in para-sulphonatocalix[8]arene and 1,2-bis(4-pyridyl)-ethane complex: view along [001] axis."
Influence on Crystallisation Process of Amino Acids from Solution
Authors: Kupka Anna , Gies Hermann , Merz Klaus
Published: November 2015

The famous Miller experiment to model the primordial soup demonstrated that amino acids can form spontaneously as the essential building blocks of life in solutions. It is, however, still an open question how self-recognition processes influence the transformation of these spontaneously formed amino acids in solvents into higher ordered structures in the solid state, thereby creating chiral materials and catalytically competent structures. The understanding of the first steps of molecular self-assembly processes in such environments will thus give important clues towards the understanding of biological evolution. Most of intermolecular interactions are not very strong and their formation is related to and affected by small changes in the molecular structure and the crystallisation conditions. Continuing our investigations on aggregation of substituted aromatic molecules in the solid state, we studied the influence and boundaries of weak directing substituents like deuterium on the aggregation of small molecules. Hydrogen/deuterium (H/D)-exchange, the smallest possible modification of a molecule, is generally seen as a non dominating parameter in the formation of crystal structures of chemical compounds. On the other hand, it could already be shown that the aggregation of molecules in the solid state of polymorphic N-heterocycle systems like pyridine-N-oxide or acridine can be very sensitive to small changes of the isotopic substitution pattern of the selected molecules. Within our project, the molecular aggregation of amino acids in solution with the formation of molecular aggregates and pre-nucleation clusters in deuterated and non-deuterated systems, and in particular the role of the solvent in these processes, will be studied in both experiment and theory.
Hydrogen bonding structure and polymorphism in agrochemicals
Authors: Di Pumpo Antonietta , Weller Mark , Mason Sax , Lemée-Cailleau Marie-Hélène
Published: November 2015

Polymorphism of crystals, crystal habit and crystal growth are important factors that must be controlled for any commercial crystallization process. Pharmaceuticals and agrochemicals are two of the most industrially-important, active-molecule systems for which the physical properties are strongly correlated to their crystal structure. While pharmaceuticals have attracted more academic interest to date, the market for agrochemicals is also very considerable, amounting to $15 bn annually. Given the potential significant toxicity of some agrochemicals, the ability to control physical properties such as solubility and dissolution rates, which depend on the crystal structure of the agrochemical itself, represents a way of optimizing the ratio between the amount of product used and its efficiency, improving its function and reducing its environmental impact. Hydrogen bonds play a crucial role in the spatial arrangement of the active molecules and the crystallization process. However, high accuracy and precision of the hydrogen atom positions can only be achieved through single crystal neutron diffraction (SND). SND experiments have been performed on three herbicides - isoproturon (IPU), pendimethalin (PDM), and diflufenican (DFF) - and the fungicide cyprodinil (CYP) [1][2]. All four structure refinements show a ten-time improvement in precision in the hydrogen atom positions compared to SXD with accurately determined nuclear positions. For cyprodinil, which crystallises as two polymorphs, A and B, differences in the hydrogen bonding network have been determined. Form A is governed by single, linear hydrogen bonds between two molecules, while the B form is characterized by the presence of dimers linked through pairs of hydrogen bonds, leading to a stable 8-membered ring. These differences in structure are reflected in the physical properties of the two polymorphs such as melting point and the observed slow inter-conversion that takes place during storage.
An X-ray study of new hybrid systems of Fe(III) and Cu(II) based anions
Authors: Bouacida Sofiane , Bouchene Rafika , Khadri Amina
Published: November 2015

Organic-inorganic hybrid compounds represent one of the most important developments in materials chemistry in recent years [1]. The role of weak intermolecular interactions in the stabilization of these hybrid systems is one of the main targets of our investigation in crystal engineering study. In continuation of our research on N-aromatic heterocyclic-metal halide salts, the X-ray crystal structures of 4-dimethylaminopyridinium (HDMAP) cation with tetrachlorocuprate (II) (1) and tetrachloroferrate (III) (2) anions is reported [2,3]. In (1), Cu(II) is situated on a twofold rotation axis (4 e). The [CuCl4]2- ions are highly distorted with a mean trans angle of 141.02(1)0as a result of hydrogen bonding interactions with two nearly planar HDMAP cations (0.0295 Å mean deviation). The crystal structure of (1) is stabilized by N–H...Cl and C–H...Cl hydrogen bonds. In the three dimensional network, cations and anions pack in the lattice so as to generate chains of [CuCl4]2- anions separated by two orientations of cation layers, which are interlocked through π–π tacking contacts between pairs of pyridine rings, with centroid–centroid distances of 3.7874 (7) Å. In (2), the protonoted 4-(dimethylamino) pyridine cation is essentially planar (the r.m.s deviation for all non-H atoms being 0.004 Å). The packing of the ionic entities is realized by alternating layers of cations and [FeCl4]- anions parallel to (010) whereby the cations are oriented in a zig-zag fashion. The crystal packing is stabilized by N–H...Cl and C–H...Cl hydrogen bonds forming a three-dimensional network.
A Persistent N-H...N Ribbon Motif in the Crystal Structures of Triazine Herbicides
Authors: Bhadbhade Mohan , Gao Jiabin , Marjo Christopher , Hook James
Published: November 2015

Triazines have been used for many years as herbicides, but we now report for the first time the crystal structures of two ubiquitous exemplars, Simazine 1 (R = ethyl) and Atrazine 2 (R = i-propyl, 2 polymorphs), which were possible only with the Synchrotron diffraction measurements. Analysis of the crystal structures reveals infinite molecular ribbons (I) comprising centrosymmetric N-H..N hydrogen bonds, with weaker secondary C-H...Cl interactions. The hydrogen bonding constrains each molecule into a very specific conformation, yet the ribbon is conserved across 1 and both polymorphs of 2. Accommodation of the ribbon in each of the crystal structures results in changes in space group and some out-of-plane buckling in the ribbon. A search through the Cambridge Crystallographic Data showed N-H..N synthon is present in other members of the chlorotriazine family, forming a ribbon whenever the alkyl/aryl R groups can "solve" the packing problem to produce a hydrophobic domain parallel to the hydrogen bonds1. Such is the dominance of this ribbon motif that it may persist across a large range of chlorotriazines yet to be analyzed or synthesized.
Hydrogen bond order/disorder in a polar one-dimensional confined ice
Authors: Adamson Jasper , Funnell Nicholas , Thompson Amber , Goodwin Andrew
Published: November 2015

Ice is one of the most well-studied substances yet forming a polar, bulk phase, where the water molecule dipoles are all aligned, has proved to be challenging. One approach is to confine the water in nanotubes, such that the molecules are restricted in orientation [1], however this hinders their use as ferroelectric devices – the primary application of polar ices. An alternative is to exploit the voids in nanoporous crystalline hosts but there are, as yet, no reported confined ice systems where the water molecules are able to switch between paraelectric and ferroelectric states whilst retaining a crystalline structure. One such porous system is 2,3,6,7,10,11-hexahydroxytriphenylene (HHTP) tetrahydrate, where columnar stacks of the HHTP molecules are arranged in a pseudo-square arrangement and the water molecules occupy the pores, forming one-dimensional, meso-helical chains. The structure, determined previously [2], crystallises in Pbcn, however this places inversion centres within the water chains leading to unphysical intermolecular H...H contacts. A variable-temperature single-crystal X-ray diffraction investigation is described where careful consideration of the data shows how long-range dipole ordering within and between the water chains is induced, by varying temperature, transforming the crystal structure to the polar Pna21 space group [3]. Subsequent reassessment of the ambient temperature structure reveals a superposition of opposing polarisation states.
H-bonds and Protons in Molecular Crystals: Insight from Combined XPS/ssNMR/XRD
Authors: Stevens Joanna , Byard Stephen , Seaton Colin , Sadiq Ghazala , Davey Roger , Schroeder Sven
Published: November 2015

Physicochemical properties of molecular crystals are significantly influenced by non-covalent interactions and proton transfer. A well known application is the tuning of solubility, bioavailability and stability of pharmaceutical actives through co-crystal (hydrogen-bonding) or salt (ionic, Brønsted acceptors) formation. X-ray Photoelectron Spectroscopy (XPS) is an intrinsically local structural probe, providing information on the chemical state and chemical environment of atoms in molecules and crystals through the photoemission of core level electrons. We have recently studied a wide range of acid-base complexes in molecular crystals and found that analyzing the chemical shifts of N1s core level binding energies provides a facile route for characterizing the chemical and structural changes at functional groups involved in hydrogen bonding and proton transfer [1]. Very importantly, XPS unequivocally distinguishes protonated (salt) from hydrogen-bonded (co-crystal) nitrogen moieties. We have complemented our results for nitrogen species with 15N Solid-State Nuclear Magnetic Resonance (ssNMR) chemical shifts, which reveal low frequency shifts with protonation, but the magnitude of these shifts is additionally influenced by the wider chemical environment [2]. When crystallographic structure information is available, ssNMR shifts can be computationally predicted and thereby related to H-bond lengths, giving a measure of H-bond strength (NMR crystallography). The wide variety of donor/acceptor systems we have investigated has covered a large range of pKa values and demonstrates the generic nature of taking an XPS/ssNMR/XRD approach to organic molecule crystallography (Fig 1). The excellent agreement between the conclusions drawn by XPS and combined ssNMR/CASTEP investigations opens up a reliable avenue for local structure characterization in molecular systems even in the absence of crystal structure information, for example with non-crystalline or amorphous matter.
Intra-molecular Interactions in Porous Covalent Organic Frameworks
Authors: Banerjee Rahul
Published: November 2015

A new strategy of intramolecular hydrogen bonding in 2D covalent organic framework as an extra stabilizing factor has been introduced, which helps to improve the crystallinity, porosity and chemical stability of the COF. Using this concept, highly stable porphyrin containing covalent organic frameworks have been synthesized using the Schiff base reaction. The stability of the COFs mainly arises due to the strong intramolecular O-H...N=C hydrogen bonding. Validation of this postulate was cross-checked by synthesizing methoxy (OCH3) substituted COF in which no hyrogen bonding exists. It was found that methoxy substituted COF have a low crystallinity, porosity and chemical stability as compared to hydrogen bonded COF.
Hydrogen Bonds and Self-Assembly to Direct Reactivity in the Solid State
Authors: MacGillivray Leonard
Published: November 2015

In this presentation, we will describe our efforts to develop a general method to control chemical reactivity in the organic solid state. We use the method to provide access to complex organic molecules such as ladderanes and cyclophanes. In our method, we exploit hydrogen-bond-directed self-assembly with the use of small-molecule templates to assemble and preorganize olefins for intermolecular [2+2] photodimerizations. The templates assemble the olefins within discrete supramolecular assemblies for single and multiple photoreactions. By assembling the olefins within discrete assemblies, we overcome problems of long-range packing that have frustrated previous attempts to control the dimerization. We will also demonstrate how the approach provides a unique form of supamolecular catalysis that exploits fundamentals of mechanochemistry.
Random point processes and tilings arising from Gaussian analytic functions
Authors: Baake Michael , Koesters Holger , Moody Robert
Published: November 2015

Getting a grasp of what aperiodic order really entails is going to require collecting and understanding many diverse examples. Aperiodic crystals are at the top of the largely unknown iceberg beneath. Here we present a recently studied form of random point process in the (complex) plane which arises as the sets of zeros of a specific class of analytic functions given by power series with randomly chosen coefficients: Gaussian analytic functions (GAF). These point sets differ from Poisson processes by having a sort of built in repulsion between points, though the resulting sets almost surely fail both conditions of the Delone property. Remarkably the point sets that arise as the zeros of GAFs determine a random point process which is, in distribution, invariant under rotation and translation. In addition, there is a logarithmic potential function for which the zeros are the attractors, and the resulting basins of attraction produce tilings of the plane by tiles which are, almost surely, all of the same area. We discuss GAFs along with their tilings and diffraction, and as well note briefly their relationship to determinantal point processes, which are also of physical interest.
Mathematical Diffraction Theory
Authors: Strungaru Nicolae
Published: November 2015

In this talk we will review some of the recent progress in Diffraction Theory. We will start by introducing some general structures which give rise to Bragg peak diffraction, and we will discuss the connection between these structures and the concept of almost periodicity for measures. We will explain why almost periodicity is a very helpful tool in the study of Meyer sets, but yields weaker results outside this class. We will complete our talk by looking at the diffraction of some interesting examples which do not fall into the class of Meyer sets.
Double antisymmetry in magnetic structures
Authors: VanLeeuwen Brian , Huang Mantao , Litvin Daniel , Gopalan Venkatraman
Published: November 2015

This work follows from the recent introduction of the rotation-reversal operation intended to be analogous to the time-reversal operation used to describe the symmetry of magnetic structures. As a second independent antisymmetry operation, this operation "doubles" the antisymmetry of the magnetic space groups, hence the term double antisymmetry. Supposing the consideration of both rotation-reversal and time-reversal symmetry, it was found that there are 17,803 types of symmetry that a crystal could exhibit; the 1,651 magnetic space group types being a subset of these, just as the 230 crystallographic space group types are a subset of the magnetic space group types. In addition to discussing the methods applied to determine these types, describing their properties, and listing their symmetry diagrams (available online), the implications for symmetry constraints in magnetic structure determination will be explored.
Coexistence of magnetic and atomic position modulations in CaMn7O12
Authors: Przeniosło Radosław , Sławiński Wojciech , Wardecki Dariusz , Sosnowska Izabela , Keller Lukas , Bieringer Mario
Published: November 2015

The rhombohedral CaMn7O12 manganite is an important material which shows magnetoelectrioc coupling with very high values of the electric polarization [1]. These outstanding properties motivated many experimental studies and also theoretical analysis. The mechanism which leads to these extraordinary properties has not been explained up to now. A fundamental information needed for such studies is the crystal structure and the magnetic ordering. CaMn7O12 has a complex structure with a magnetic moments modulation below TN=90K [1,2], a modulation of the atomic positions below TC=250K [2] and also orbital ordering. The magnetic modulation propagation vector qm is related with the atomic positions modulation vector qp by the relation qp=2qm [2]. This 2:1 relation is valid across a large range of temperatures and show the importance of spin-lattice coupling. The crystal and magnetic structure of CaMn7O12 was studied by neutron powder diffraction at the instrument DMC at SINQ [3]. The magnetic and atomic position modulations are described by using the superspace group formalism. This approach is especially important for description of both modulations with the same model [2]. The resulting magnetic ordering model obtained in [3] is more precise as compared with earlier works [1,2]. The present results [3] differ from those published by other authors [1]. The important difference is that in the present studies the angle, Phi, between Mn3+ and Mn4+ magnetic moments located in the same (001) planes (Phi = 0.99(2)Pi), i.e. the moments are antiparallel, whereas Johnson et al. [1] determined this angle as Phi=0.84(4) Pi. This angle is an important parameter of the model Hamiltonians describing the electronic and magnetic properties of CaMn7O12.