XIX Congress and General Assembly
Reports continued from Volume 10#4
Amorphous materials and glasses
Speakers at the microsymposium on amorphous materials and glasses demonstrated that, despite not being able to use many of the powerful tools of crystallography, it is possible to gain new, useful and important insights into the structure of non-crystalline materials.
E. Bychkov (France) discussed the change in the structure of silica glass when subjected to laser irradiation. High energy x-ray diffraction and SANS measurements reveal that laser irradiation induces a permanent 2-3% densification.
S. Kohara (Japan) described how high energy x-ray diffraction at SPring8 can provide 'neutron-like' data. High real-space resolution data were presented for SiO2, GeO2 and GeS2 glasses, and the results were simulated using the Reverse Monte Carlo (RMC) technique. Evidence was found for three-membered rings in SiO2 and GeO2, and for an edge-sharing pair plus near neighbour configuration in GeS2.
A. Hannon (UK) showed neutron diffraction data for lead gallate, thallium containing bismuth gallate and calcium aluminate glasses, and recommended that expanded use be made of information from chemical crystallography in examining glass diffraction results. The concepts of electrostatic bond strength and bond-valence are both of great value in making sense of diffraction studies of glass structure.
L. Pusztai (Hungary) discussed how RMC techniques can be used to assess the quality of non-crystalline diffraction data. A RMC simulation of earlier neutron diffraction data on D2O deviated from the experimental result, but was subsequently found to be consistent with later more reliable measurements. RMC analysis was shown to be much more resilient to a lack of high momentum transfer information than is the direct Fourier transform analysis.Alex C. Hannon
Non-ambient diffraction and kinetic studies
The microsymposium emphasized the range of timescales, materials, and problems being addressed using non-ambient crystallography. Applications described ranged from proteins to glasses and ceramics, studied at timescales from milliseconds to hours, using both constant wavelength and white beam synchrotron and neutron diffraction methods.
P. Barnes (UK) showed a range of elegant experimental set-ups to study ZrO2 formation, reduction of metal oxides, zeolite dehydration, diffusion of environmentally relevant species into minerals and spatial resolution of the growth of zeolites in gels and on substrates.
E. Kisi (Australia) then gave a fascinating talk on how the new generation of high-flux neutron diffractometers (here D20 at the ILL) can allow the kinetics of even extremely rapid combustion syntheses to be followed, with Rietveld-quality data being collected in time slices down to 0.38 seconds.
J. Wright (France) described high resolution powder x-ray studies using synchrotron diffractometers that have revealed a number of new phase transitions observed on cooling myoglobin. He gave a thoughtful assessment of both the potential benefits and inevitable difficulties of studying such complex, though hugely important, samples by powder methods. C. Benmore (USA) showed how extremes of temperature (~2000°C) can be achieved on levitated droplets of liquid oxides allowing complementary x-ray and neutron scattering studies to be performed.
C. Howard (Australia) presented a detailed ('the final word'?) study of the many high temperature phases of WO3 and their symmetry relationships. This elegant methodology prompted an enthusiastic general debate about the group theoretical aspects of phase transitions. The presence of the likes of J. Jorgensen, T. Hahn, H. Stokes and M. Glazer in the session ensured that firm opinions were expressed, and discussions spilled over into Palexpo’s corridors when we were forced to vacate the hall for the next meeting.John Evans
Free electron lasers and other pulsed sources
3rd Generation Light Sources (3GLS) presently dominate synchrotron radiation science. Taking prospective demands into account, we perceive a serious limit in storage-ring-based sources where the typical pulse length of SR is in picoseconds, much longer than that of short pulse lasers currently available. SR is obtained when electrons move in the magnetic field. This emission process is the origin of long pulse characteristic of SR. Generally, SR increases the bunch length, energy spread and emittance of electron beam. Therefore, we need so called 4th Generation Light Sources (4GLS) based on special accelerators without any SR emission. This was the main topic of the microsymposium.
T. Shintake (Japan) gave a tutorial on SASE FEL, one of 4GLSs. He described an operation mechanism of SASE FEL and special characteristics of the x-ray beam available from it, and showed Japanese activities in this field, especially on the new soft x-ray SASE FEL project at SPring-8. S. Gruner (USA) gave a tutorial on Energy Recovery Linacs, the other kind of 4GLSs, which allows the production of SR beams of exceptional brilliance and flux with very short x-ray bursts. T. Moeller (Germany) described the first scientific results obtained by using the TTF Free Electron Laser at DESY and demonstrated that the high intensity radiation from FELs allows the study of multiphoton processes. J. Arthur (USA) presented a scientific program to be performed in the Sub-Picosecond Photon Source project (SPPS) as well as in the Linac Coherent Light Source project (LCLS), including expected capabilities for performing experiments in various scientific fields. D. Boschetto (France) presented femtosecond x-ray diffraction applications based on x-ray laser-plasma sources, and proposed a new x-ray geometry compatible with the features of 4GLSs.Hideo Kitamura
Methods for the characterization of layered structures
This microsymposium focused on experimental techniques and theoretical approaches used to investigate the structure, microstructural properties, and chemical composition of low-dimensional systems. V. Holy (Czech Republic) showed how surface/interface sensitive x-ray methods (grazing-incidence small angle scattering and diffraction) can be used to investigate shape, position, and chemical composition of buried nanostructured species. Q. Shen (USA) spoke about applications of high-resolution x-ray diffraction for the determination of elastic strain tensor and strain gradients in quantum structures. A. Boulle (France) documented the capability of reciprocal space mapping and diffraction pattern modeling for studies of structural faulting, mosaicity, and strain gradients in highly mismatched oxide thin films. S. Zheludeva (Russia) reported on the generation of standing waves by multilayers, combining high structure sensitivity from x-ray scattering with spectroscopic selectivity. A. Belger (Germany) emphasized a complementarity of several methods for studies of structural and mechanical properties of hard multilayers, and reported on observed superlattice hardening at nanoscale levels upon heat treatment.Davor Balzar and David Rafaja
Novel materials and physical properties at high pressure
Due to scientific and technical advances, high pressure variablity is becoming increasingly important in the study of amorphous materials and the synthesis and design of new technological materials. This interdisciplinary session opened with a presentation by J. Tse (Canada) on the role of computational studies to predict and understand new and hypothetical high-pressure structures and physical phenomena. T. Sekine (Japan) described the latest shock-wave methods for high-throughput synthesis of high-pressure nitride and oxynitride spinels and N. Serebryanaya (Russia) presented studies of new super-hard carbon materials based on high pressure-high temperature treatment of fullerenes and C-nanotubes. K. Shimizu (Japan) showed the latest techniques for electrical and magnetic properties measurements under high-P and cryogenic conditions, and showed that the 'superconducting periodic table' now extends to all classes of elements under megabar pressures. C. Bull (UK) described results of 'pressure-tuning' IR absorption properties of electronic perovskites, and M. Somayazulu (USA) gave new insights into the comparative 'mineralogical' structural chemistry of CO2 and N2O/NO2 solids. A. Zerr (Germany) ended the session describing the structure and physical properties of the newly-discovered family of high-pressure nitride spinels and post-spinel materials.Paul F. McMillan
Liquids and amorphous materials at high pressure
C. Tulk (USA) gave a lively introduction to the session on the fundamental complexities of the phase diagram of ice. He presented neutron and x-ray results clearly showing the formation of several new distinct meta-stable amorphous forms of ice at ambient pressure, between the well known high and low density forms. These were obtained by annealing and subsequent relaxation of the high density form. S. Klotz (France) continued the high density ice theme with high quality in-situ neutron diffraction data at 2.2GPa that was interpreted using the EPSR Monte Carlo technique to reveal the collapse of the second nearest neighbour shell. Klotz suggested that the local structure resembled that of crystalline ice VII. S. Sampath (USA) presented neutron and high energy x-ray diffraction data on permanently densified GeO2 glass (recovered from 10GPa). The two measurements were combined to extract detailed structural information. The next nearest neighbour oxygen atoms determine the high pressure phase of the glass, which appeared as a rotation and distortion of the GeO4 tetrahedra. T. Hattori (Japan) discussed the structure of liquid group III-V compounds measured using synchrotron techniques. InSb was studied up to 20GPa and temperatures up to 1300°C, and showed a clear discontinuity at around 10GPa. The data appeared to be a mixture of two configurations (beta-tin and the bcc phase) which was most stable in equal proportions. P. McMillian (UK) gave an inspirational talk on amorphous Si, negative melting slopes and enthalpic signatures. Above 6GPa he showed a high density amorphous form of Silicon which relaxes on decompression, and suggested this amorphous-amorphous phase transition may be linked to an underlying phase transition in the liquid state.Chris Benmore
The papers presented in this session reflected the great diversity of different systems and types of disorder and diffuse scattering that are of current interest. The topics discussed included measurement of phonon dispersion curves from thermal diffuse scattering in silicon and niobium (with possible future application to plutonium!); diffuse scattering due to stacking faults in the zeolite mordenite; diffuse scattering associated with phase transitions in relaxor ferroelectric materials; magnetic diffuse scattering in icosahedral quasicrystals; magnetic diffuse scattering in CMR manganite materials and diffuse scattering due to orientational ordering in C70 single crystals.
It is clear that with increasing use of synchrotron radiation and area detectors many more people are seeing diffuse scattering and there appears to be a burgeoning interest in the field.Richard Welberry
Crystals for pharmaceutical applications: high-throughput and combinatorial techniques
The pharmaceutical industry is concerned with reliable and reproducible crystallization methods to guarantee consistent production of a specific solid forms. In addition to monitoring many crystallization parameters during scale-up and production particular emphasis is put towards discovery of polymorphs, with the ultimate aim to know all polymorphs of a given drug. The empirical nature of the phenomenon of polymorphism enforces a systematic search via crystallization experiments in order to discover as many polymorphs as possible. These prerequisites render the combinatorial high throughput approach extremely suitable for polymorph discovery.
R. Storey (UK) illustrated the knowledge-based approach followed by Pfizer UK. High throughput crystallization together with adequate characterization methods were given equal importance to detailed studies of individual polymorphs using various physical chemistry and theoretical techniques. C.W. Lehmann (Germany) presented a development from the non-industrial sector, which focuses on the problem of x-ray diffractometric analysis of potentially different polymorphs, crystallized in a multi-well plate. A fully automated solution, including computational design of the crystallization library, crystallization experiments using robotics, characterization the solids with different analytical techniques, and the statistical analysis of crystal forms versus experimental conditions, was offered by P. Desrosiers (USA). A. van Langevelde (Netherlands) described a proprietary crystallization plate and x-ray diffraction system used for statistical evaluation and single crystal structure elucidation. A completely different experimental approach developed at Solid State Characterization Services was presented by P. Stahly (USA). Crystals of meta-stable forms are grown in capillaries, either from the melt or from highly concentrated solutions, whereby supersaturations exceeding those of larger volume experiments by at least an order of magnitude are achieved. Direct XRD analysis of the capillaries is possible and yields a unique characterization.
Lively discussion followed the talks, this was a rare opportunity for those involved in polymorph discovery to collect information about the state of the art.C. W. Lehmann
Hot structures I
The papers in the Hot Structures Microsymposia give a snapshot of exciting new macromolecular structures across the whole breadth of biological crystallography. Although it is perhaps unfair to single out any one contribution as the highlight of a fascinating session, D. Vassylyev’s (Japan) presentation of the structure of a bacterial RNA polymerase, complete with its bound sigma factor snaking its way over and through the core enzyme represented a spectacular crystallographic achievement on an enzyme of extreme biological importance. Also focused on transcription, A. Roll-Mecak (USA) described the intriguing chalice-shaped structure of the translation initiation factor IF2/eIF5B, which facilitates the Met-tRNA binding to ribosomes, and in which a small conformational change is translated and amplified over 90 Å. Also on the theme of transcription, X. Cheng (USA) described the structures of enzymes from a family of methyltransferases that modify lysine and arginine side chains and are critically important in the role of histones in regulating access to chromatin during transcription. Surprisingly, these enzymes have a completely different fold from other SAM-dependent methyltransferases. Other cellular processes were not forgotten. T. Garrett (Australia) presented structures of the extracellular regions of two members of the EGF receptor family, mutations which are associated with many cancers. The structures revealed elongated, multidomain molecules in which ligand binding and dimerisation are linked by quite novel mechanisms. P. Haebel (Switzerland) described a complex that is critical to correct disulfide bond formation and folding in the bacterial periplasm. In this complex, in which redox state is vital, a modified Ig domain from a membrane-bound electron transporter DsbD binds to the Y-shaped dimer of the periplasmic isomerase DsbC. Finally J. Emsley (UK) described another use for leucine-rich repeat proteins, with the beautiful structure of the LRR domain from the platelet receptor GPIb, leading to a model for the way in which this protein may mediate the aggregation of platelets at sites of vascular damage.Ted Baker and Andrea Mattevi
Twins, disorders and other demons
There is a growing awareness that twinned crystals and structural disorders occur frequently and present major obstacles to the correct determination of crystal structures. The microsymposium centered on twinning according to the classical twin laws, and on planar polytypic disorder as a frequently encountered mechanism of disorder. S. Parsons (UK) presented his program ROTAX which proposes possible twin orientations by examining poorly fitting data after refinement of the structure. From zones showing a systematic tendency of |Fobs|2 > |Fcalc|2, twin matrices are proposed which often give dramatically improved refinement results. Use of the program is highly recommended. R. D. Gilardi (USA) presented several case studies of difficult structures of multiple polymorphs in energetic organic materials. Vastly improved results were obtained once a structure was recognized to be twinned. One compound presented six polymorphs with asymmetric units containing between 3 and 18 molecules; the figures presented may suggest different stacking variants of a planar structure. H. Birkedal (Switzerland) presented heavily stacking faulted structures of orange HgI2 and of an organic molecule assembling in hexagonal layers, both exhibiting rods of diffuse intensity. He showed for both compounds, that two very different stacking sequences result in exactly the same observable intensities, even in the limit where the stacking faults result in equi-volume macroscopic twinning. A.D. Rae (Australia) uses the symmetry of the so-called parent structure, defined by a subset of structure factors, e.g. those of a polytypic family invariant of the stacking order, to enumerate the symmetries of the possible ordered structures agreeing with observed unit cells. He also desymmetrizes parent structures by interpreting superstructure reflections as commensurate modulations. E. Estevez-Rams (Cuba and Germany) quantitatively derives from x-ray powder patterns pair correlation functions between layers of polytypic structures, e.g. RE2Co17. From this, the depth of interaction between layers may be derived. Stacking-faulted layer structures occur very frequently, and clearer presentations on some aspects ought to be foreseen for future meetings.Dieter Schwarzenbach
Macromolecular neutron scattering and sources
The development of the neutron imaging plate (NIP) produced a breakthrough in neutron protein crystallography. The first application of the NIP was realized on the Laue type diffractometer, LADI at ILL. In Japan the NIP has been constructed on high-resolution neutron diffractometers that use a monochromatized neutron beam and are dedicated to biological macromolecules (BIX-type). Hydrogens and hydration in Myoglobin, Rubredoxin (wild type and mutant) are observed by a BIX-type diffractometer at 1.5 Å resolution, and those in Lysozyme, Pyrophosphatase and Endothiapepsin have been observed by LADI. Neutron diffractometers equipped with NIPs open a new field of structural biology that will include locating hydrogen atoms and water of hydration.Nobuo Niimura
With the advent of high brilliance 3rd generation synchrotron sources and progress in x-ray focusing optics, very intense small x-ray beams in the micron and submicron range are now routinely produced at synchrotron beamlines around the world. While very small monochromatic beams are extensively used for imaging techniques such as x-ray microscopy and tomography, x-ray microdiffraction using either monochromatic or white beam is expected to become an increasingly important tool with many applications in soft material physics, thin film mechanics and earth sciences. It allows for the structure determination from very small crystals, and texture studies of fiber only a few micrometers in diameter (C. Riekel, France). Combined with other microprobe techniques, such as scanning x-ray microfluorescence and micro-EXAFS, it becomes a powerful tool to study the speciation of trace elements in soils (A. Manceau, USA). Orientation imaging and strain/stress mapping obtained by white beam scanning x-ray microdiffraction allows the study of thin film mechanical properties at a granular and subgranular level (R. Spolenak, USA). The development of 3D x-ray microdiffraction using either monochromatic (H. Poulsen, France) or white radiation (B. Larson, USA) allows dynamical studies of grain deformation and plasticity in polycrystalline bulk materials during in-situ loading conditions.Nobumichi Tamura
Visualization of macromolecules
The microsymposium concerned algorithms, software development, and novel user interfaces. H. Bernstein (USA) discussed advances in the widely used molecular visualization program RasMol. He described his approach to displaying molecular surface representations with adequate performance on computers that do not necessarily have the power of today’s hardware.
C. Bajaj, (USA) discussed new algorithms useful for the display and analysis of molecular properties, including rapid interactive recontouring of volumetric data sets such as electron density maps or electrostatic potential maps, techniques for finding the most informative contour levels for visualization and an extension to conventional volume rendering, for visualizing functions in 4, 5 or higher dimensions. Much of his software is available at his website (www.cs.utexas.edu/users/bajaj/).
M. Sanner, (USA), discussed his strategy for design and implementation of software for biomolecular visualization and analysis, including the Python programming language to develop re-useable software components to enable rapid evolution of useful molecular modelling tools, Viper a visual programming network editor, for developing new applications without the need for writing new code, the Bajaj rapid isocontouring algorithm, and a graphically programmable symmetry generation network.
A. Olson (USA) described 'Tangible Interfaces for Molecular Biology.' He discussed the evolution of computer graphics from physical models to computer graphics, and now back to physical models produced as 'solid prints' by computer autofabrication, including output from his new full color solid printer, a Zcorp 406. Using Augmented Reality technologies, the physical model can be tracked by a video camera, and computer graphics representations and other computer stored data can be superimposed on the physical model using video see-through glasses. He showed an example of manipulating a drug molecule into the active site of an enzyme, using physical models combined with computer graphics.Arthur J. Olson
Structures and phase transitions at high pressure
E. Gregoryanz (France) described recent work on the high pressure phase diagram of nitrogen. Over the past 2 years he and co-workers at the Geophysical Lab of the Carnegie Inst. of Washington have discovered remarkable complexity in the megabar region including the first evidence for the long-sought after non-molecular phase. J. Chen (USA) described a translating image plate detector and its use for real time kinetic studies of olivine to spinel phase transition. P. McGregor (UK) discussed high-pressure structures of alcohols illustrating the structural complexity which can now be handled at high pressure and the remarkable range of conformations which the pressure variable can produce.
S. Redfern (UK) described the development of a high-temperature/high-pressure cell for neutron diffraction and recent experiments in structural studies of hydrous minerals and of order-disorder phase transitions. N. Ashcroft (USA) explored the implications of the complex structures recently discovered in elemental metals at high pressure. These high density metallic systems have a very different balance of length-scales from that which operates in 'normal' metals at ambient pressure and offer new insights into the general problem of electrons in metals.John Loveday and Serge Desgreniers