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  • International Union of Crystallography (IUCr)  (52,383)
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  • 1
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    International Union of Crystallography (IUCr) | Wiley-Blackwell - STM
    Online: 53.1997 – 66.2010
    Formerly as: Crystal Structure Communications  (1972–1982)
    Publisher: International Union of Crystallography (IUCr) , Wiley-Blackwell - STM
    Corporation: International Union of Crystallography, IUCr
    Print ISSN: 0108-2701 , 2053-2296
    Electronic ISSN: 1600-5759 , 2053-2296
    Topics: Chemistry and Pharmacology , Geosciences , Physics
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  • 2
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    International Union of Crystallography (IUCr)
    Online: 1.1948 – 23.1967
    Publisher: International Union of Crystallography (IUCr)
    Print ISSN: 0365-110X
    Electronic ISSN: 1600-8642
    Topics: Geosciences
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  • 3
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    International Union of Crystallography (IUCr) | Wiley-Blackwell - STM
    Online: 53.1997 – 66.2010
    Formerly as: Acta Crystallographica  (1948–1967)
    Publisher: International Union of Crystallography (IUCr) , Wiley-Blackwell - STM
    Corporation: International Union of Crystallography, IUCr
    Print ISSN: 0108-7681 , 0567-7408 , 2052-5192
    Electronic ISSN: 1600-5740 , 1600-8650 , 2052-5206
    Topics: Chemistry and Pharmacology , Geosciences , Physics
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  • 4
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    International Union of Crystallography (IUCr)
    Online: 64.2008 –
    Publisher: International Union of Crystallography (IUCr)
    Corporation: International Union of Crystallography, IUCr
    Electronic ISSN: 1600-5368 , 2056-9890
    Topics: Chemistry and Pharmacology , Geosciences
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  • 5
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    International Union of Crystallography (IUCr)
    Online: 4.1996 –
    Publisher: International Union of Crystallography (IUCr)
    Print ISSN: 1067-0696
    Electronic ISSN: 1945-0834
    Topics: Geosciences , Physics
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  • 6
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    International Union of Crystallography (IUCr)
    Online: 1(1).2014 –
    Publisher: International Union of Crystallography (IUCr)
    Electronic ISSN: 2052-2525
    Topics: Geosciences , Physics
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  • 7
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    Wiley-Blackwell - STM | International Union of Crystallography (IUCr)
    Online: 1.1968 – 42.2009
    Print: 26.1993 – 30.1997 (Location: A17, Archiv, Magazin, 30/5)
    Publisher: Wiley-Blackwell - STM , International Union of Crystallography (IUCr)
    Print ISSN: 0021-8898
    Electronic ISSN: 1600-5767
    Topics: Geosciences , Physics
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  • 8
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    International Union of Crystallography (IUCr) | Wiley-Blackwell
    Online: 57.2001 – 63.2007
    Publisher: International Union of Crystallography (IUCr) , Wiley-Blackwell
    Corporation: International Union of Crystallography, IUCr
    Electronic ISSN: 1600-5368
    Topics: Chemistry and Pharmacology , Geosciences , Physics
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  • 9
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    International Union of Crystallography (IUCr)
    Online: 61.2005 –
    Publisher: International Union of Crystallography (IUCr)
    Electronic ISSN: 1744-3091
    Topics: Chemistry and Pharmacology , Physics
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  • 10
    Formerly as: Acta Crystallographica  (1948–1967)
    Publisher: International Union of Crystallography (IUCr) , Wiley-Blackwell - STM
    Corporation: International Union of Crystallography, IUCr
    Print ISSN: 0108-7673 , 0567-7394
    Electronic ISSN: 1600-5724 , 1600-8596 , 2053-2733
    Topics: Chemistry and Pharmacology , Geosciences , Physics
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  • 11
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    International Union of Crystallography (IUCr) | Wiley-Blackwell - STM
    Online: 53.1997 – 66.2010
    Publisher: International Union of Crystallography (IUCr) , Wiley-Blackwell - STM
    Corporation: International Union of Crystallography, IUCr
    Print ISSN: 0907-4449
    Electronic ISSN: 1399-0047 , 2059-7983
    Topics: Chemistry and Pharmacology , Geosciences , Physics
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  • 12
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    International Union of Crystallography (IUCr) | Wiley-Blackwell - STM
    Online: 61.2005 – 66.2010
    Publisher: International Union of Crystallography (IUCr) , Wiley-Blackwell - STM
    Print ISSN: 1744-3091
    Electronic ISSN: 2053-230X
    Topics: Biology , Chemistry and Pharmacology , Geosciences , Physics
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  • 13
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    Wiley-Blackwell - STM | International Union of Crystallography (IUCr)
    Online: 1.1994 – 17.2010
    Publisher: Wiley-Blackwell - STM , International Union of Crystallography (IUCr)
    Print ISSN: 0909-0495
    Electronic ISSN: 1600-5775
    Topics: Geosciences , Physics
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  • 14
    Publication Date: 2015-04-23
    Description: New opportunities for studying (sub)microcrystalline materials with small unit cells, both organic and inorganic, will open up when the X-ray free electron laser (XFEL) presently being constructed in Switzerland (SwissFEL) comes online in 2017. Our synchrotron-based experiments mimicking the 4%-energy-bandpass mode of the SwissFEL beam show that it will be possible to record a diffraction pattern of up to 10 randomly oriented crystals in a single snapshot, to index the resulting reflections, and to extract their intensities reliably. The crystals are destroyed with each XFEL pulse, but by combining snapshots from several sets of crystals, a complete set of data can be assembled, and crystal structures of materials that are difficult to analyze otherwise will become accessible. Even with a single shot, at least a partial analysis of the crystal structure will be possible, and with 10–50 femtosecond pulses, this offers tantalizing possibilities for time-resolved studies.
    Keywords: serial snapshot crystallographymulti-microcrystal diffractionindexingbroad-bandpass beamXFEL
    Electronic ISSN: 2052-2525
    Topics: Geosciences , Physics
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  • 15
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    International Union of Crystallography (IUCr)
    In: IUCrJ
    Publication Date: 2015-05-02
    Description: The design of novel supramolecular synthons for functional groups relevant to drugs is an essential prerequisite for applying crystal engineering in the development of novel pharmaceutical cocrystals. It has been convincingly shown over the past decade that molecular level control and modulation can influence the physicochemical properties of drug cocrystals. Whereas considerable advances have been reported on the design of cocrystals for carboxylic acids and carboxamide functional groups, the sulfonamide group, which is a cornerstone of sulfa drugs, is relatively unexplored for reproducible heterosynthon-directed crystal engineering. The occurrence of synthons and isostructurality in sulfonamide–lactam cocrystals (SO2NH2...CONH hydrogen bonding) is analyzed to define a strategy for amide-type GRAS (generally recognized as safe) coformers with sulfonamides. Three types of supramolecular synthons are identified for the N—H donor of sulfonamide hydrogen bonding to the C=O acceptor of amide. Synthon 1: catemer synthon C21(4) chain motif, synthon 2: dimer–cyclic ring synthon R22(8)R42(8) motifs, and synthon 3: dimer–catemer synthon of R22(8)C11(4)D notation. These heterosynthons of the cocrystals observed in this study are compared with the N—H...O dimer R22(8) ring and C(4) chain motifs of the individual sulfonamide structures. The X-ray crystal structures of sulfonamide–lactam cocrystals exhibit interesting isostructurality trends with the same synthon being present. One-dimensional, two-dimensional and three-dimensional isostructurality in crystal structures is associated with isosynthons and due to their recurrence, novel heterosynthons for sulfonamide cocrystals are added to the crystal engineer's toolkit. With the predominance of sulfa drugs in medicine, these new synthons provide rational strategies for the design of binary and potentially ternary cocrystals of sulfonamides.
    Keywords: crystal engineeringsupramolecular synthonspharmaceutical cocrystalsisostructurality
    Electronic ISSN: 2052-2525
    Topics: Geosciences , Physics
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  • 16
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    International Union of Crystallography (IUCr)
    In: IUCrJ
    Publication Date: 2015-03-21
    Description: Second harmonic generation (SHG) is a well known non-linear optical phenomena which can be observed only in non-centrosymmetric crystals due to non-zero hyperpolarizability. In the current work we observed SHG from a Zn(II) complex which was originally thought to have crystallized in the centrosymmetric space group C2/c. This has been attributed to the unequal antiparallel packing of the metal complexes in the non-symmetric space group Cc or residual non-centrosymmetry in C2/c giving rise to polarizability leading to strong SHG. The enhancement of SHG by UV light has been attributed to the increase in non-centrosymmetry and hence polarity of packing due to strain induced in the crystals. The SHG signals measured from these crystals were as large as potassium dihydrogen phosphate crystals, KH2PO4 (KDP), and showed temperature dependence. The highest SHG efficiency was observed at 50 K. The SHG phenomenon was observed at broad wavelengths ranging from visible to below-red in these crystals.
    Keywords: second harmonic generationcentrosymmetric crystals
    Electronic ISSN: 2052-2525
    Topics: Geosciences , Physics
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  • 17
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    International Union of Crystallography (IUCr)
    In: IUCrJ
    Publication Date: 2015-03-21
    Description: Serial femtosecond crystallography (SFX) is capable of collecting three-dimensional single-crystal diffraction data using polycrystalline samples. This may dramatically enhance the power of X-ray powder diffraction. In this paper a test has been performed using simulated diffraction patterns. The test sample is a mixture of two zeolites with crystal grain sizes from 100 to 300 nm. X-ray diffraction snapshots by SFX were simulated and processed using the program suite CrystFEL. Identification according to the primitive unit-cell volume determined from individual snapshots was able to separate the whole set of snapshots into two subsets, which correspond to the two zeolites in the sample. Monte Carlo integration in CrystFEL was then applied to them separately. This led to two sets of three-dimensional single-crystal diffraction intensities, based on which crystal structures of the two zeolites were solved easily by direct methods implemented in the program SHELXD.
    Keywords: serial crystallographyX-ray powder diffractionphase identificationstructure solution
    Electronic ISSN: 2052-2525
    Topics: Geosciences , Physics
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  • 18
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    International Union of Crystallography (IUCr)
    In: IUCrJ
    Publication Date: 2015-04-23
    Description: The likelihood of occurrence of intermolecular contacts in crystals of halogenated organic compounds has been analysed statistically using tools based on the Hirshfeld surface. Several families of small halogenated molecules (containing organic F, Cl, Br or I atoms) were analysed, based on chemical composition and aromatic or aliphatic character. The behaviour of crystal contacts was also probed for molecules containing O or N. So-called halogen bonding (a halogen making short interactions with O or N, or a π interaction with C) is generally disfavoured, except when H is scarce on the molecular surface. Similarly, halogen...halogen contacts are more rare than expected, except for molecules that are poor in H. In general, the H atom is found to be the preferred partner of organic halogen atoms in crystal structures. On the other hand, C...C interactions in parallel π-stacking have a high propensity to occur in halogenated aromatic molecules. The behaviour of the four different halogen species (F, Cl, Br, I) is compared in several chemical composition contexts. The analysis tool can be refined by distinguishing several types for a given chemical species, such as H atoms bound to O or C. Such distinction shows, for instance, that C—H...Cl and O—H...O are the preferred interactions in compounds containing both O and Cl.
    Keywords: intermolecular contactshalogenated organic compoundshalogen bondingπ-stacking interactionscrystal packingHirshfeld surface analysisenrichment ratio
    Electronic ISSN: 2052-2525
    Topics: Geosciences , Physics
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  • 19
    Publication Date: 2015-04-23
    Description: Carboxylic acids, amides and imides are key organic systems which provide understanding of molecular recognition and binding phenomena important in biological and pharmaceutical settings. In this context, studies of their mutual interactions and compatibility through co-crystallization may pave the way for greater understanding and new applications of their combinations. Extensive co-crystallization studies are available for carboxylic acid/amide combinations, but only a few examples of carboxylic acid/imide co-crystals are currently observed in the literature. The non-formation of co-crystals for carboxylic acid/imide combinations has previously been rationalized, based on steric and computed stability factors. In the light of the growing awareness of eutectic mixtures as an alternative outcome in co-crystallization experiments, the nature of various benzoic acid/cyclic imide combinations is established in this paper. Since an additional functional group can provide sites for new intermolecular interactions and, potentially, promote supramolecular growth into a co-crystal, benzoic acids decorated with one or more hydroxyl groups have been systematically screened for co-crystallization with one unsaturated and two saturated cyclic imides. The facile formation of an abundant number of hydroxybenzoic acid/cyclic carboximide co-crystals is reported, including polymorphic and variable stoichiometry co-crystals. In the cases where co-crystals did not form, the combinations are shown invariably to result in eutectics. The presence or absence and geometric disposition of hydroxyl functionality on benzoic acid is thus found to drive the formation of co-crystals or eutectics for the studied carboxylic acid/imide combinations.
    Keywords: crystal structurecarboxylic acidscarboximidesco-crystalseutectics
    Electronic ISSN: 2052-2525
    Topics: Geosciences , Physics
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  • 20
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    International Union of Crystallography (IUCr)
    In: IUCrJ
    Publication Date: 2015-04-23
    Description: Current trends for X-ray imaging detectors based on hybrid and monolithic detector technologies are reviewed. Hybrid detectors with photon-counting pixels have proven to be very powerful tools at synchrotrons. Recent developments continue to improve their performance, especially for higher spatial resolution at higher count rates with higher frame rates. Recent developments for X-ray free-electron laser (XFEL) experiments provide high-frame-rate integrating detectors with both high sensitivity and high peak signal. Similar performance improvements are sought in monolithic detectors. The monolithic approach also offers a lower noise floor, which is required for the detection of soft X-ray photons. The link between technology development and detector performance is described briefly in the context of potential future capabilities for X-ray imaging detectors.
    Keywords: X-ray imaging detectorshybrid detectorsmonolithic detectorsrecent detector developments
    Electronic ISSN: 2052-2525
    Topics: Geosciences , Physics
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  • 21
    Publication Date: 2015-04-23
    Description: Small-angle X-ray and neutron scattering (SAXS and SANS) experiments on solutions provide rapidly decaying scattering curves, often with a poor signal-to-noise ratio, especially at higher angles. On modern instruments, the noise is partially compensated for by oversampling, thanks to the fact that the angular increment in the data is small compared with that needed to describe adequately the local behaviour and features of the scattering curve. Given a (noisy) experimental data set, an important question arises as to which part of the data still contains useful information and should be taken into account for the interpretation and model building. Here, it is demonstrated that, for monodisperse systems, the useful experimental data range is defined by the number of meaningful Shannon channels that can be determined from the data set. An algorithm to determine this number and thus the data range is developed, and it is tested on a number of simulated data sets with various noise levels and with different degrees of oversampling, corresponding to typical SAXS/SANS experiments. The method is implemented in a computer program and examples of its application to analyse the experimental data recorded under various conditions are presented. The program can be employed to discard experimental data containing no useful information in automated pipelines, in modelling procedures, and for data deposition or publication. The software is freely accessible to academic users.
    Keywords: small-angle scatteringWAXSSAXSsolution scatteringprotein structureShanum
    Electronic ISSN: 2052-2525
    Topics: Geosciences , Physics
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  • 22
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    International Union of Crystallography (IUCr)
    In: IUCrJ
    Publication Date: 2015-03-21
    Description: X-ray scattering images collected on timescales shorter than rotation diffusion times using a (partially) coherent beam result in a significant increase in information content in the scattered data. These measurements, named fluctuation X-ray scattering (FXS), are typically performed on an X-ray free-electron laser (XFEL) and can provide fundamental insights into the structure of biological molecules, engineered nanoparticles or energy-related mesoscopic materials beyond what can be obtained with standard X-ray scattering techniques. In order to understand, use and validate experimental FXS data, the availability of basic data characteristics and operational properties is essential, but has been absent up to this point. In this communication, an intuitive view of the nature of FXS data and their properties is provided, the effect of FXS data on the derived structural models is highlighted, and generalizations of the Guinier and Porod laws that can ultimately be used to plan experiments and assess the quality of experimental data are presented.
    Keywords: fluctuation X-ray scatteringXFELSbiological moleculesnanoparticlesmesoscopic materials
    Electronic ISSN: 2052-2525
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  • 23
    Publication Date: 2015-02-12
    Description: Phase identification and structure determination are important and widely used techniques in chemistry, physics and materials science. Recently, two methods for automated three-dimensional electron diffraction (ED) data collection, namely automated diffraction tomography (ADT) and rotation electron diffraction (RED), have been developed. Compared with X-ray diffraction (XRD) and two-dimensional zonal ED, three-dimensional ED methods have many advantages in identifying phases and determining unknown structures. Almost complete three-dimensional ED data can be collected using the ADT and RED methods. Since each ED pattern is usually measured off the zone axes by three-dimensional ED methods, dynamic effects are much reduced compared with zonal ED patterns. Data collection is easy and fast, and can start at any arbitrary orientation of the crystal, which facilitates automation. Three-dimensional ED is a powerful technique for structure identification and structure solution from individual nano- or micron-sized particles, while powder X-ray diffraction (PXRD) provides information from all phases present in a sample. ED suffers from dynamic scattering, while PXRD data are kinematic. Three-dimensional ED methods and PXRD are complementary and their combinations are promising for studying multiphase samples and complicated crystal structures. Here, two three-dimensional ED methods, ADT and RED, are described. Examples are given of combinations of three-dimensional ED methods and PXRD for phase identification and structure determination over a large number of different materials, from Ni–Se–O–Cl crystals, zeolites, germanates, metal–organic frameworks and organic compounds to intermetallics with modulated structures. It is shown that three-dimensional ED is now as feasible as X-ray diffraction for phase identification and structure solution, but still needs further development in order to be as accurate as X-ray diffraction. It is expected that three-dimensional ED methods will become crucially important in the near future.
    Keywords: three-dimensional electron diffractionpowder X-ray diffractionphase identificationstructure determination
    Electronic ISSN: 2052-2525
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  • 24
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    International Union of Crystallography (IUCr)
    In: IUCrJ
    Publication Date: 2015-02-27
    Keywords: biological crystallographyfree electron laserseditorialIUCrJ
    Electronic ISSN: 2052-2525
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  • 25
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    International Union of Crystallography (IUCr)
    In: IUCrJ
    Publication Date: 2015-02-27
    Keywords: intermolecular atom–atom bondscrystal binding
    Electronic ISSN: 2052-2525
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  • 26
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    International Union of Crystallography (IUCr)
    In: IUCrJ
    Publication Date: 2015-02-27
    Keywords: crystalsintermolecular atom–atom bonds
    Electronic ISSN: 2052-2525
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  • 27
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    International Union of Crystallography (IUCr)
    In: IUCrJ
    Publication Date: 2015-02-27
    Keywords: coordination polymerstopochemical controlsolid–gas reactions
    Electronic ISSN: 2052-2525
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  • 28
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    International Union of Crystallography (IUCr)
    In: IUCrJ
    Publication Date: 2015-02-27
    Description: Professor Dunitz questions the usefulness of ascribing crystalline structural stability to individual atom–atom intermolecular interactions viewed as bonding (hence stabilizing) whenever linked by a bond path. An alternative view is expressed in the present essay that articulates the validity and usefulness of the bond path concept in a crystallographic and crystal engineering context.
    Keywords: bond paths in crystalscrystal bindingcrystal stabilityelectron densityquantum theory of atoms in molecules (QTAIM)high-resolution X-ray diffractionsynthons
    Electronic ISSN: 2052-2525
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  • 29
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    International Union of Crystallography (IUCr)
    In: IUCrJ
    Publication Date: 2015-02-27
    Keywords: molecular replacementab initio modelingcoiled-coil proteins
    Electronic ISSN: 2052-2525
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  • 30
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    International Union of Crystallography (IUCr)
    In: IUCrJ
    Publication Date: 2015-02-27
    Description: Coiled-coil protein folds are among the most abundant in nature. These folds consist of long wound α-helices and are architecturally simple, but paradoxically their crystallographic structures are notoriously difficult to solve with molecular-replacement techniques. The program AMPLE can solve crystal structures by molecular replacement using ab initio search models in the absence of an existent homologous protein structure. AMPLE has been benchmarked on a large and diverse test set of coiled-coil crystal structures and has been found to solve 80% of all cases. Successes included structures with chain lengths of up to 253 residues and resolutions down to 2.9 Å, considerably extending the limits on size and resolution that are typically tractable by ab initio methodologies. The structures of two macromolecular complexes, one including DNA, were also successfully solved using their coiled-coil components. It is demonstrated that both the ab initio modelling and the use of ensemble search models contribute to the success of AMPLE by comparison with phasing attempts using single structures or ideal polyalanine helices. These successes suggest that molecular replacement with AMPLE should be the method of choice for the crystallographic elucidation of a coiled-coil structure. Furthermore, AMPLE may be able to exploit the presence of a coiled coil in a complex to provide a convenient route for phasing.
    Keywords: molecular replacementab initio modellingcoiled-coil proteinssearch-model ensemblesmacromolecular complexes
    Electronic ISSN: 2052-2525
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  • 31
    Publication Date: 2015-02-27
    Description: A family of one-dimensional coordination polymers, [Ag4(O2C(CF2)2CF3)4(phenazine)2(arene)n]·m(arene), 1 (arene = toluene or xylene), have been synthesized and crystallographically characterized. Arene guest loss invokes structural transformations to yield a pair of polymorphic coordination polymers [Ag4(O2C(CF2)2CF3)4(phenazine)2], 2a and/or 2b, with one- and two-dimensional architectures, respectively. The role of pre-organization of the polymer chains of 1 in the selectivity for formation of either polymorph is explored, and the templating effect of toluene and p-xylene over o-xylene or m-xylene in the formation of arene-containing architecture 1 is also demonstrated. The formation of arene-free phase 2b, not accessible in a phase-pure form through other means, is shown to be the sole product of loss of toluene from 1-tol·tol [Ag4(O2C(CF2)2CF3)4(phenazine)2(toluene)]·2(toluene), a phase containing toluene coordinated to Ag(I) in an unusual μ:η1,η1 manner. Solvent-vapour-assisted conversion between the polymorphic coordination polymers and solvent-vapour influence on the conversion of coordination polymers 1 to 2a and 2b is also explored. The transformations have been examined and confirmed by X-ray diffraction, NMR spectroscopy and thermal analyses, including in situ diffraction studies of some transformations.
    Keywords: solid-state transformationcoordination polymerssolvent-vapour-assisted conversion
    Electronic ISSN: 2052-2525
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  • 32
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    International Union of Crystallography (IUCr)
    In: IUCrJ
    Publication Date: 2015-02-27
    Description: Dynamic ensembles of macromolecules mediate essential processes in biology. Understanding the mechanisms driving the function and molecular interactions of `unstructured' and flexible molecules requires alternative approaches to those traditionally employed in structural biology. Small-angle X-ray scattering (SAXS) is an established method for structural characterization of biological macromolecules in solution, and is directly applicable to the study of flexible systems such as intrinsically disordered proteins and multi-domain proteins with unstructured regions. The Ensemble Optimization Method (EOM) [Bernadó et al. (2007). J. Am. Chem. Soc. 129, 5656–5664] was the first approach introducing the concept of ensemble fitting of the SAXS data from flexible systems. In this approach, a large pool of macromolecules covering the available conformational space is generated and a sub-ensemble of conformers coexisting in solution is selected guided by the fit to the experimental SAXS data. This paper presents a series of new developments and advancements to the method, including significantly enhanced functionality and also quantitative metrics for the characterization of the results. Building on the original concept of ensemble optimization, the algorithms for pool generation have been redesigned to allow for the construction of partially or completely symmetric oligomeric models, and the selection procedure was improved to refine the size of the ensemble. Quantitative measures of the flexibility of the system studied, based on the characteristic integral parameters of the selected ensemble, are introduced. These improvements are implemented in the new EOM version 2.0, and the capabilities as well as inherent limitations of the ensemble approach in SAXS, and of EOM 2.0 in particular, are discussed.
    Keywords: small-angle scatteringproteinsmacromolecular dynamicsunstructured biologyhybrid methodssymmetric oligomers
    Electronic ISSN: 2052-2525
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  • 33
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    International Union of Crystallography (IUCr)
    In: IUCrJ
    Publication Date: 2015-02-05
    Description: Protein crystallography using synchrotron radiation sources has had a tremendous impact on biology, having yielded the structures of thousands of proteins and given detailed insight into their mechanisms. However, the technique is limited by the requirement for macroscopic crystals, which can be difficult to obtain, as well as by the often severe radiation damage caused in diffraction experiments, in particular when using tiny crystals. To slow radiation damage, data collection is typically performed at cryogenic temperatures. With the advent of free-electron lasers (FELs) capable of delivering extremely intense femtosecond X-ray pulses, this situation appears to be remedied, allowing the structure determination of undamaged macromolecules using either macroscopic or microscopic crystals. The latter are exposed to the FEL beam in random orientations and their diffraction data are collected at cryogenic or room temperature in a serial fashion, since each crystal is destroyed upon a single exposure. The new approaches required for crystal growth and delivery, and for diffraction data analysis, including de novo phasing, are reviewed. The opportunities and challenges of SFX are described, including applications such as time-resolved measurements and the analysis of radiation damage-prone systems.
    Keywords: serial femtosecond crystallographySFXX-ray lasersFELstime-resolved crystallographymicrocrystalsradiation damage
    Electronic ISSN: 2052-2525
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  • 34
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    International Union of Crystallography (IUCr)
    In: IUCrJ
    Publication Date: 2015-02-05
    Description: Structural studies in general, and crystallography in particular, have benefited and still do benefit dramatically from the use of synchrotron radiation. Low-emittance storage rings of the third generation provide focused beams down to the micrometre range that are sufficiently intense for the investigation of weakly scattering crystals down to the size of several micrometres. Even though the coherent fraction of these sources is below 1%, a number of new imaging techniques have been developed to exploit the partially coherent radiation. However, many techniques in nanoscience are limited by this rather small coherent fraction. On the one hand, this restriction limits the ability to study the structure and dynamics of non-crystalline materials by methods that depend on the coherence properties of the beam, like coherent diffractive imaging and X-ray correlation spectroscopy. On the other hand, the flux in an ultra-small diffraction-limited focus is limited as well for the same reason. Meanwhile, new storage rings with more advanced lattice designs are under construction or under consideration, which will have significantly smaller emittances. These sources are targeted towards the diffraction limit in the X-ray regime and will provide roughly one to two orders of magnitude higher spectral brightness and coherence. They will be especially suited to experiments exploiting the coherence properties of the beams and to ultra-small focal spot sizes in the regime of several nanometres. Although the length of individual X-ray pulses at a storage-ring source is of the order of 100 ps, which is sufficiently short to track structural changes of larger groups, faster processes as they occur during vision or photosynthesis, for example, are not accessible in all details under these conditions. Linear accelerator (linac) driven free-electron laser (FEL) sources with extremely short and intense pulses of very high coherence circumvent some of the limitations of present-day storage-ring sources. It has been demonstrated that their individual pulses are short enough to outrun radiation damage for single-pulse exposures. These ultra-short pulses also enable time-resolved studies 1000 times faster than at standard storage-ring sources. Developments are ongoing at various places for a totally new type of X-ray source combining a linac with a storage ring. These energy-recovery linacs promise to provide pulses almost as short as a FEL, with brilliances and multi-user capabilities comparable with a diffraction-limited storage ring. Altogether, these new X-ray source developments will provide smaller and more intense X-ray beams with a considerably higher coherent fraction, enabling a broad spectrum of new techniques for studying the structure of crystalline and non-crystalline states of matter at atomic length scales. In addition, the short X-ray pulses of FELs will enable the study of fast atomic dynamics and non-equilibrium states of matter.
    Keywords: synchrotron radiationfuture light sourcesFELscoherent radiation
    Electronic ISSN: 2052-2525
    Topics: Geosciences , Physics
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  • 35
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    International Union of Crystallography (IUCr)
    In: IUCrJ
    Publication Date: 2015-02-05
    Description: In situ and in operando studies are commonplace and necessary in functional materials research. This review highlights recent developments in the analysis of functional materials using state-of-the-art in situ and in operando X-ray and neutron scattering and analysis. Examples are given covering a number of important materials areas, alongside a description of the types of information that can be obtained and the experimental setups used to acquire them.
    Keywords: functional materialsX-ray scatteringneutron scatteringmaterials characterization
    Electronic ISSN: 2052-2525
    Topics: Geosciences , Physics
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  • 36
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    International Union of Crystallography (IUCr)
    In: IUCrJ
    Publication Date: 2015-02-05
    Description: A current overview of synchrotron radiation (SR) in macromolecular crystallography (MX) instrumentation, methods and applications is presented. Automation has been and remains a central development in the last decade, as have the rise of remote access and of industrial service provision. Results include a high number of Protein Data Bank depositions, with an increasing emphasis on the successful use of microcrystals. One future emphasis involves pushing the frontiers of using higher and lower photon energies. With the advent of X-ray free-electron lasers, closely linked to SR developments, the use of ever smaller samples such as nanocrystals, nanoclusters and single molecules is anticipated, as well as the opening up of femtosecond time-resolved diffraction structural studies. At SR sources, a very high-throughput assessment for the best crystal samples and the ability to tackle just a few micron and sub-micron crystals will become widespread. With higher speeds and larger detectors, diffraction data volumes are becoming long-term storage and archiving issues; the implications for today and the future are discussed. Together with the rise of the storage ring to its current pre-eminence in MX data provision, the growing tendency of central facility sites to offer other centralized facilities complementary to crystallography, such as cryo-electron microscopy and NMR, is a welcome development.
    Keywords: automationmicrocrystalsstorage-ring upgradesX-ray lasersneutronsindustrial and commercial accessexpanding wavelength rangetime-resolved studiesdynamicsdiffuse scatteringroom-temperature studiesraw data
    Electronic ISSN: 2052-2525
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  • 37
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    International Union of Crystallography (IUCr)
    In: IUCrJ
    Publication Date: 2015-02-12
    Description: Crystallization processes are characterized by activated events and long timescales. These characteristics prevent standard molecular dynamics techniques from being efficiently used for the direct investigation of processes such as nucleation. This short review provides an overview on the use of metadynamics, a state-of-the-art enhanced sampling technique, for the simulation of phase transitions involving the production of a crystalline solid. In particular the principles of metadynamics are outlined, several order parameters are described that have been or could be used in conjunction with metadynamics to sample nucleation events and then an overview is given of recent metadynamics results in the field of crystal nucleation.
    Keywords: crystallizationnucleationmolecular modellingenhanced samplingmetadynamics
    Electronic ISSN: 2052-2525
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  • 38
    Publication Date: 2015-09-24
    Description: Characterization of transverse coherence is one of the most critical themes for advanced X-ray sources and their applications in many fields of science. However, for hard X-ray free-electron laser (XFEL) sources there is very little knowledge available on their transverse coherence characteristics, despite their extreme importance. This is because the unique characteristics of the sources, such as the ultra-intense nature of XFEL radiation and the shot-by-shot fluctuations in the intensity distribution, make it difficult to apply conventional techniques. Here, an extended Young's interference experiment using a stream of bimodal gold particles is shown to achieve a direct measurement of the modulus of the complex degree of coherence of XFEL pulses. The use of interference patterns from two differently sized particles enables analysis of the transverse coherence on a single-shot basis without a priori knowledge of the instantaneous intensity ratio at the particles. For a focused X-ray spot as small as 1.8 µm (horizontal) × 1.3 µm (vertical) with an ultrahigh intensity that exceeds 1018 W cm−2 from the SPring-8 Ångstrom Compact free-electron LAser (SACLA), the coherence lengths were estimated to be 1.7 ± 0.2 µm (horizontal) and 1.3 ± 0.1 µm (vertical). The ratios between the coherence lengths and the focused beam sizes are almost the same in the horizontal and vertical directions, indicating that the transverse coherence properties of unfocused XFEL pulses are isotropic. The experiment presented here enables measurements free from radiation damage and will be readily applicable to the analysis of the transverse coherence of ultra-intense nanometre-sized focused XFEL beams.
    Keywords: X-ray free-electron laserstransverse coherencebeam diagnostics
    Electronic ISSN: 2052-2525
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  • 39
    Publication Date: 2015-10-17
    Description: A new monoclinic polymorph, form II (P21/c, Z = 4), has been isolated for 3,4-dimethoxycinnamic acid (DMCA). Its solid-state 2 + 2 photoreaction to the corresponding α-truxillic acid is different from that of the first polymorph, the triclinic form I (P\bar 1, Z = 4) that was reported in 1984. The crystal structures of the two forms are rather different. The two polymorphs also exhibit different photomechanical properties. Form I exhibits photosalient behavior but this effect is absent in form II. These properties can be explained on the basis of the crystal packing in the two forms. The nanoindentation technique is used to shed further insights into these structure−property relationships. A faster photoreaction in form I and a higher yield in form II are rationalized on the basis of the mechanical properties of the individual crystal forms. It is suggested that both Schmidt-type and Kaupp-type topochemistry are applicable for the solid-state trans-cinnamic acid photodimerization reaction. Form I of DMCA is more plastic and seems to react under Kaupp-type conditions with maximum molecular movements. Form II is more brittle, and its interlocked structure seems to favor Schmidt-type topochemistry with minimum molecular movement.
    Keywords: crystal engineeringcinnamic acidphotosalientnanoindentationpolymorphism
    Electronic ISSN: 2052-2525
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  • 40
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    International Union of Crystallography (IUCr)
    In: IUCrJ
    Publication Date: 2015-10-17
    Description: Protein interactions are essential in all biological processes. The changes brought about in the structure when a free component forms a complex with another molecule need to be characterized for a proper understanding of molecular recognition as well as for the successful implementation of docking algorithms. Here, unbound (U) and bound (B) forms of protein structures from the Protein–Protein Interaction Affinity Database are compared in order to enumerate the changes that occur at the interface atoms/residues in terms of the solvent-accessible surface area (ASA), secondary structure, temperature factors (B factors) and disorder-to-order transitions. It is found that the interface atoms optimize contacts with the atoms in the partner protein, which leads to an increase in their ASA in the bound interface in the majority (69%) of the proteins when compared with the unbound interface, and this is independent of the root-mean-square deviation between the U and B forms. Changes in secondary structure during the transition indicate a likely extension of helices and strands at the expense of turns and coils. A reduction in flexibility during complex formation is reflected in the decrease in B factors of the interface residues on going from the U form to the B form. There is, however, no distinction in flexibility between the interface and the surface in the monomeric structure, thereby highlighting the potential problem of using B factors for the prediction of binding sites in the unbound form for docking another protein. 16% of the proteins have missing (disordered) residues in the U form which are observed (ordered) in the B form, mostly with an irregular conformation; the data set also shows differences in the composition of interface and non-interface residues in the disordered polypeptide segments as well as differences in their surface burial.
    Keywords: protein–protein interactionsprotein flexibilitydisorder–order transitionbound and unbound protein formsinterface areacrystallographic temperature factorsecondary structurebioinformaticsmolecular recognition
    Electronic ISSN: 2052-2525
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  • 41
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    International Union of Crystallography (IUCr)
    In: IUCrJ
    Publication Date: 2015-10-23
    Keywords: integrated computational materials engineeringnondestructive crystal structure mappingstress tensor measurement
    Electronic ISSN: 2052-2525
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  • 42
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    International Union of Crystallography (IUCr)
    In: IUCrJ
    Publication Date: 2015-10-31
    Keywords: cryoEMcrystallographyeditorialGPCRribosomeserial crystallographysynchrotron radiationXFELs
    Electronic ISSN: 2052-2525
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  • 43
    Publication Date: 2015-10-01
    Description: X-ray free-electron lasers (XFELs) show great promise for macromolecular structure determination from sub-micrometre-sized crystals, using the emerging method of serial femtosecond crystallography. The extreme brightness of the XFEL radiation can multiply ionize most, if not all, atoms in a protein, causing their scattering factors to change during the pulse, with a preferential `bleaching' of heavy atoms. This paper investigates the effects of electronic damage on experimental data collected from a Gd derivative of lysozyme microcrystals at different X-ray intensities, and the degree of ionization of Gd atoms is quantified from phased difference Fourier maps. A pattern sorting scheme is proposed to maximize the ionization contrast and the way in which the local electronic damage can be used for a new experimental phasing method is discussed.
    Keywords: serial femtosecond crystallographyhigh-intensity phasingradiation damageelectronic damageX-ray free-electron lasershigh XFEL doses
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  • 44
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    International Union of Crystallography (IUCr)
    In: IUCrJ
    Publication Date: 2015-10-01
    Description: Nondestructive measurements of the full elastic strain and stress tensors from individual dislocation cells distributed along the full extent of a 50 µm-long polycrystalline copper via in Si is reported. Determining all of the components of these tensors from sub-micrometre regions within deformed metals presents considerable challenges. The primary issues are ensuring that different diffraction peaks originate from the same sample volume and that accurate determination is made of the peak positions from plastically deformed samples. For these measurements, three widely separated reflections were examined from selected, individual grains along the via. The lattice spacings and peak positions were measured for multiple dislocation cell interiors within each grain and the cell-interior peaks were sorted out using the measured included angles. A comprehensive uncertainty analysis using a Monte Carlo uncertainty algorithm provided uncertainties for the elastic strain tensor and stress tensor components.
    Keywords: full elastic strainstress tensor measurementcopper through-Si viasmicroelectronics
    Electronic ISSN: 2052-2525
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  • 45
    Publication Date: 2015-08-19
    Description: Rubrene is one of the most studied organic semiconductors to date due to its high charge carrier mobility which makes it a potentially applicable compound in modern electronic devices. Previous electronic device characterizations and first principles theoretical calculations assigned the semiconducting properties of rubrene to the presence of a large overlap of the extended π-conjugated core between molecules. We present here the electron density distribution in rubrene at 20 K and at 100 K obtained using a combination of high-resolution X-ray and neutron diffraction data. The topology of the electron density and energies of intermolecular interactions are studied quantitatively. Specifically, the presence of Cπ...Cπ interactions between neighbouring tetracene backbones of the rubrene molecules is experimentally confirmed from a topological analysis of the electron density, Non-Covalent Interaction (NCI) analysis and the calculated interaction energy of molecular dimers. A significant contribution to the lattice energy of the crystal is provided by H—H interactions. The electron density features of H—H bonding, and the interaction energy of molecular dimers connected by H—H interaction clearly demonstrate an importance of these weak interactions in the stabilization of the crystal structure. The quantitative nature of the intermolecular interactions is virtually unchanged between 20 K and 100 K suggesting that any changes in carrier transport at these low temperatures would have a different origin. The obtained experimental results are further supported by theoretical calculations.
    Keywords: electron densityrubreneorganic semiconductorinteraction energy
    Electronic ISSN: 2052-2525
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  • 46
    Publication Date: 2015-08-19
    Description: The name of one of the authors in the article by Heymann et al. [(2014), IUCrJ, 1, 349–360] is corrected.
    Keywords: protein crystallizationX-ray diffractionserial crystallographymicrofluidic devices
    Electronic ISSN: 2052-2525
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  • 47
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    International Union of Crystallography (IUCr)
    In: IUCrJ
    Publication Date: 2015-08-23
    Keywords: coherent diffractive imagingcryo-CDIthree-dimensional imagingthree-dimensional cellular structurecoherent diffractionX-ray imaging
    Electronic ISSN: 2052-2525
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  • 48
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    International Union of Crystallography (IUCr)
    In: IUCrJ
    Publication Date: 2015-08-23
    Keywords: crystallographyeditorialneutronssynchrotron radiation
    Electronic ISSN: 2052-2525
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  • 49
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    International Union of Crystallography (IUCr)
    In: IUCrJ
    Publication Date: 2015-08-23
    Keywords: doped ceriadisorderpair distribution functionhigh-resolution X-ray powder diffractionpercolationhierarchysolid electrolyteselectron spin resonance
    Electronic ISSN: 2052-2525
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  • 50
    Publication Date: 2015-08-23
    Description: A structural understanding of whole cells in three dimensions at high spatial resolution remains a significant challenge and, in the case of X-rays, has been limited by radiation damage. By alleviating this limitation, cryogenic coherent diffractive imaging (cryo-CDI) can in principle be used to bridge the important resolution gap between optical and electron microscopy in bio-imaging. Here, the first experimental demonstration of cryo-CDI for quantitative three-dimensional imaging of whole frozen-hydrated cells using 8 keV X-rays is reported. As a proof of principle, a tilt series of 72 diffraction patterns was collected from a frozen-hydrated Neospora caninum cell and the three-dimensional mass density of the cell was reconstructed and quantified based on its natural contrast. This three-dimensional reconstruction reveals the surface and internal morphology of the cell, including its complex polarized sub-cellular structure. It is believed that this work represents an experimental milestone towards routine quantitative three-dimensional imaging of whole cells in their natural state with spatial resolutions in the tens of nanometres.
    Keywords: coherent diffractive imagingcryo-CDIthree-dimensional imagingthree-dimensional cellular structurecoherent diffractionX-ray imagingNeospora caninum
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  • 51
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    International Union of Crystallography (IUCr)
    In: IUCrJ
    Publication Date: 2015-08-23
    Description: The crystallization behavior of methylthio- or methylsulfonyl-containing spacer extended Z,Z-bis-ene–yne molecules capped with trimethylsilyl groups obtained by (tandem) thiophene ring fragmentation and of two non-spacer extended analogs were investigated. The rigid and linear molecules generally crystallized in layers whereby the flexibility of the layer interfaces formed by the silyl groups leads to a remarkably rich crystal chemistry. The molecules with benzene and thiophene spacers both crystallized with C2/c symmetry and can be considered as merotypes. Increasing the steric bulk of the core by introduction of ethylenedioxythiophene (EDOT) gave a structure incommensurately modulated in the [010] direction. Further increase of steric demand in the case of a dimethoxythiophene restored periodicity along [010] but resulted in a doubling of the c vector. Two different polytypes were observed, which feature geometrically different layer interfaces (non-OD, order–disorder, polytypes), one with a high stacking fault probability. Oxidation of the methylthio groups of the benzene-based molecule to methylsulfonyl groups led to three polymorphs (two temperature-dependent), which were analyzed by Hirshfeld surface de/di fingerprint plots. The analogously oxidized EDOT-based molecule crystallized as systematic twins owing to its OD polytypism. Shortening of the backbone by removal of the aryl core resulted in an enantiomorphic structure and a further shortening by removal of a methylthio-ene fragment again in a systematically twinned OD polytype.
    Keywords: arene spacersincommensurately modulated structureslayer interfacesorder–disorder polytypesHirshfeld surface fingerprint plots
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  • 52
    Publication Date: 2015-09-21
    Description: The structure and mechanical properties of crystalline materials of three boron difluoride dibenzoylmethane (BF2dbm) derivatives were investigated to examine the correlation, if any, among mechanochromic luminescence (ML) behaviour, solid-state structure, and the mechanical behaviour of single crystals. Qualitative mechanical deformation tests show that the crystals of BF2dbm(tBu)2 can be bent permanently, whereas those of BF2dbm(OMe)2 exhibit an inhomogeneous shearing mode of deformation, and finally BF2dbmOMe crystals are brittle. Quantitative mechanical analysis by nanoindentation on the major facets of the crystals shows that BF2dbm(tBu)2 is soft and compliant with low values of elastic modulus, E, and hardness, H, confirming its superior suceptibility for plastic deformation, which is attributed to the presence of a multitude of slip systems in the crystal structure. In contrast, both BF2dbm(OMe)2 and BF2dbmOMe are considerably stiffer and harder with comparable E and H, which are rationalized through analysis of the structural attributes such as the intermolecular interactions, slip systems and their relative orientation with respect to the indentation direction. As expected from the qualitative mechanical behaviour, prominent ML was observed in BF2dbm(tBu)2, whereas BF2dbm(OMe)2 exhibits only a moderate ML and BF2dbmOMe shows no detectable ML, all examined under identical conditions. These results confirm that the extent of ML in crystalline organic solid-state fluorophore materials can be correlated positively with the extent of plasticity (low recovery). In turn, they offer opportunities to design new and improved efficient ML materials using crystal engineering principles.
    Keywords: crystal engineeringintermolecular interactionsmechanochromismmechanical propertiesnanoindentationorganic solid-state reactionshydrogen bonding
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  • 53
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    International Union of Crystallography (IUCr)
    In: IUCrJ
    Publication Date: 2015-09-21
    Description: In the last few decades, supramolecular chemistry has been at the forefront of chemical research, with the aim of understanding chemistry beyond the covalent bond. Since the long-range periodicity in crystals is a product of the directionally specific short-range intermolecular interactions that are responsible for molecular assembly, analysis of crystalline solids provides a primary means to investigate intermolecular interactions and recognition phenomena. This article discusses some areas of contemporary research involving supramolecular interactions in the solid state. The topics covered are: (1) an overview and historical review of halogen bonding; (2) exploring non-ambient conditions to investigate intermolecular interactions in crystals; (3) the role of intermolecular interactions in morphotropy, being the link between isostructurality and polymorphism; (4) strategic realisation of kinetic coordination polymers by exploiting multi-interactive linker molecules. The discussion touches upon many of the prerequisites for controlled preparation and characterization of crystalline materials.
    Keywords: intermolecular interactionscrystal engineeringself-assemblyhalogen bondingpolymorphismkinetic assemblycoordination polymersnon-ambient conditionsphase transitions
    Electronic ISSN: 2052-2525
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  • 54
    Publication Date: 2015-08-01
    Description: As halogen bonds gain prevalence in supramolecular synthesis and materials chemistry, it has become necessary to examine more closely how such interactions compete with or complement hydrogen bonds whenever both are present within the same system. As hydrogen and halogen bonds have several fundamental features in common, it is often difficult to predict which will be the primary interaction in a supramolecular system, especially as they have comparable strength and geometric requirements. To address this challenge, a series of molecules containing both hydrogen- and halogen-bond donors were co-crystallized with various monotopic, ditopic symmetric and ditopic asymmetric acceptor molecules. The outcome of each reaction was examined using IR spectroscopy and, whenever possible, single-crystal X-ray diffraction. 24 crystal structures were obtained and subsequently analyzed, and the synthon preferences of the competing hydrogen- and halogen-bond donors were rationalized against a background of calculated molecular electrostatic potential values. It has been shown that readily accessible electrostatic potentials can offer useful practical guidelines for predicting the most likely primary synthons in these co-crystals as long as the potential differences are weighted appropriately.
    Keywords: crystal engineeringhydrogen bondshalogen bondssynthonselectrostatic potentials
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  • 55
    Publication Date: 2015-08-01
    Description: A new hierarchical approach is presented for elucidating the structural disorder in Ce1−xGdxO2−x/2 solid solutions on different scale lengths. The primary goal of this investigation is to shed light on the relations between the short-range and the average structure of these materials via an analysis of disorder on the mesocopic scale. Real-space (pair distribution function) and reciprocal-space (Rietveld refinement and microstructure probing) analysis of X-ray powder diffraction data and electron spin resonance (ESR) investigations were carried out following this approach. On the local scale, Gd- and Ce-rich droplets (i.e. small regions a few ångströms wide) form, exhibiting either a distorted fluorite (CeO2) or a C-type (Gd2O3) structure in the whole compositional range. These droplets can then form C-type nanodomains which, for Gd concentrations xGd ≤ 0.25, are embedded in the fluorite matrix. At the site percolation threshold pC for a cubic lattice (xGd = pC ≃ 0.311), C-type nanodomains percolate inside each crystallite and a structural phase transformation is observed. When this occurs, the peak-to-peak ESR line width ΔHpp shows a step-like behaviour, which can be associated with the increase in Gd–Gd dipolar interactions. A general crystallographic rationale is presented to explain the fluorite-to-C-type phase transformation. The approach shown here could be adopted more generally in the analysis of disorder in other highly doped materials.
    Keywords: doped ceriadisorderpair distribution functionhigh-resolution X-ray powder diffractionpercolationhierarchysolid electrolyteselectron spin resonance
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  • 56
    Publication Date: 2015-08-01
    Description: The homologous series of phenyl and pyridyl substituted bis(acrylamido)alkanes have been synthesized with the aim of systematic analysis of their crystal structures and their solid-state [2 + 2] reactivities. The changes in the crystal structures with respect to a small change in the molecular structure, that is by varying alkyl spacers between acrylamides and/or by varying the end groups (phenyl, 2-pyridyl, 3-pyridyl, 4-pyridyl) on the C-terminal of the amide, were analyzed in terms of hydrogen-bonding interference (N—H...Npy versus N—H...O=C) and network geometries. In this series, a greater tendency towards the formation of N—H...O hydrogen bonds (β-sheets and two-dimensional networks) over N—H...N hydrogen bonds was observed. Among all the structures seven structures were found to have the required alignments of double bonds for the [2 + 2] reaction such that the formations of single dimer, double dimer and polymer are facilitated. However, only four structures were found to exhibit such a solid-state [2 + 2] reaction to form a single dimer and polymers. The two-dimensional hydrogen-bonding layer via N—H...O hydrogen bonds was found to promote solid-state [2 + 2] photo-polymerization in a single-crystal-to-single-crystal manner. Such two-dimensional layers were encountered only when the spacer between acryl amide moieties is butyl. Only four out of the 16 derivatives were found to form hydrates, two each from 2-pyridyl and 4-pyridyl derivatives. The water molecules in these structures govern the hydrogen-bonding networks by the formation of an octameric water cluster and one-dimensional zigzag water chains. The trends in the melting points and densities were also analyzed.
    Keywords: homologous serieshydrogen bondssolid-state [2 + 2] reactionorganic polymer
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  • 57
    Publication Date: 2015-08-06
    Description: This study focuses on the effects of the organic ligand 4-ethylresorcinol on the crystal structure of human insulin using powder X-ray crystallography. For this purpose, systematic crystallization experiments have been conducted in the presence of the organic ligand and zinc ions within the pH range 4.50–8.20, while observing crystallization behaviour around the isoelectric point of insulin. High-throughput crystal screening was performed using a laboratory X-ray diffraction system. The most representative samples were selected for synchrotron X-ray diffraction measurements, which took place at the European Synchrotron Radiation Facility (ESRF) and the Swiss Light Source (SLS). Four different crystalline polymorphs have been identified. Among these, two new phases with monoclinic symmetry have been found, which are targets for the future development of microcrystalline insulin drugs.
    Keywords: powder diffractionhuman insulindiabetessynchrotron radiationX-ray diffractionpH variation4-ethylresorcinol
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  • 58
    Publication Date: 2015-08-06
    Description: Serial femtosecond crystallography (SFX) at X-ray free-electron lasers (XFELs) enables high-resolution protein structure determination using micrometre-sized crystals at room temperature with minimal effects from radiation damage. SFX requires a steady supply of microcrystals intersecting the XFEL beam at random orientations. An LCP–SFX method has recently been introduced in which microcrystals of membrane proteins are grown and delivered for SFX data collection inside a gel-like membrane-mimetic matrix, known as lipidic cubic phase (LCP), using a special LCP microextrusion injector. Here, it is demonstrated that LCP can also be used as a suitable carrier medium for microcrystals of soluble proteins, enabling a dramatic reduction in the amount of crystallized protein required for data collection compared with crystals delivered by liquid injectors. High-quality LCP–SFX data sets were collected for two soluble proteins, lysozyme and phycocyanin, using less than 0.1 mg of each protein.
    Keywords: serial femtosecond crystallographyX-ray free-electron laserlipidic cubic phasesoluble protein
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  • 59
    Publication Date: 2015-08-16
    Description: CTB-MPR is a fusion protein between the B subunit of cholera toxin (CTB) and the membrane-proximal region of gp41 (MPR), the transmembrane envelope protein of Human immunodeficiency virus 1 (HIV-1), and has previously been shown to induce the production of anti-HIV-1 antibodies with antiviral functions. To further improve the design of this candidate vaccine, X-ray crystallography experiments were performed to obtain structural information about this fusion protein. Several variants of CTB-MPR were designed, constructed and recombinantly expressed in Escherichia coli. The first variant contained a flexible GPGP linker between CTB and MPR, and yielded crystals that diffracted to a resolution of 2.3 Å, but only the CTB region was detected in the electron-density map. A second variant, in which the CTB was directly attached to MPR, was shown to destabilize pentamer formation. A third construct containing a polyalanine linker between CTB and MPR proved to stabilize the pentameric form of the protein during purification. The purification procedure was shown to produce a homogeneously pure and monodisperse sample for crystallization. Initial crystallization experiments led to pseudo-crystals which were ordered in only two dimensions and were disordered in the third dimension. Nanocrystals obtained using the same precipitant showed promising X-ray diffraction to 5 Å resolution in femtosecond nanocrystallography experiments at the Linac Coherent Light Source at the SLAC National Accelerator Laboratory. The results demonstrate the utility of femtosecond X-ray crystallography to enable structural analysis based on nano/microcrystals of a protein for which no macroscopic crystals ordered in three dimensions have been observed before.
    Keywords: X-ray crystallographyfemtosecond nanocrystallographyHIV-1gp41membrane-proximal regioncholera toxin B subunitcrystallizationfree-electron lasers
    Electronic ISSN: 2052-2525
    Topics: Geosciences , Physics
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  • 60
    Publication Date: 2015-08-16
    Description: An emulsion-based serial crystallographic technology has been developed, in which nanolitre-sized droplets of protein solution are encapsulated in oil and stabilized by surfactant. Once the first crystal in a drop is nucleated, the small volume generates a negative feedback mechanism that lowers the supersaturation. This mechanism is exploited to produce one crystal per drop. Diffraction data are measured, one crystal at a time, from a series of room-temperature crystals stored on an X-ray semi-transparent microfluidic chip, and a 93% complete data set is obtained by merging single diffraction frames taken from different unoriented crystals. As proof of concept, the structure of glucose isomerase was solved to 2.1 Å, demonstrating the feasibility of high-throughput serial X-ray crystallography using synchrotron radiation.
    Keywords: protein crystallizationX-ray diffractionserial crystallographymicrofluidic devices
    Electronic ISSN: 2052-2525
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  • 61
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    International Union of Crystallography (IUCr)
    In: IUCrJ
    Publication Date: 2015-08-16
    Description: Hirshfeld atom refinement (HAR) is a method which determines structural parameters from single-crystal X-ray diffraction data by using an aspherical atom partitioning of tailor-made ab initio quantum mechanical molecular electron densities without any further approximation. Here the original HAR method is extended by implementing an iterative procedure of successive cycles of electron density calculations, Hirshfeld atom scattering factor calculations and structural least-squares refinements, repeated until convergence. The importance of this iterative procedure is illustrated via the example of crystalline ammonia. The new HAR method is then applied to X-ray diffraction data of the dipeptide Gly–l-Ala measured at 12, 50, 100, 150, 220 and 295 K, using Hartree–Fock and BLYP density functional theory electron densities and three different basis sets. All positions and anisotropic displacement parameters (ADPs) are freely refined without constraints or restraints – even those for hydrogen atoms. The results are systematically compared with those from neutron diffraction experiments at the temperatures 12, 50, 150 and 295 K. Although non-hydrogen-atom ADPs differ by up to three combined standard uncertainties (csu's), all other structural parameters agree within less than 2 csu's. Using our best calculations (BLYP/cc-pVTZ, recommended for organic molecules), the accuracy of determining bond lengths involving hydrogen atoms from HAR is better than 0.009 Å for temperatures of 150 K or below; for hydrogen-atom ADPs it is better than 0.006 Å2 as judged from the mean absolute X-ray minus neutron differences. These results are among the best ever obtained. Remarkably, the precision of determining bond lengths and ADPs for the hydrogen atoms from the HAR procedure is comparable with that from the neutron measurements – an outcome which is obtained with a routinely achievable resolution of the X-ray data of 0.65 Å.
    Keywords: aspherical atom partitioningquantum mechanical molecular electron densitiesX-ray structure refinementhydrogen atom modellinganisotropic displacement parameters
    Electronic ISSN: 2052-2525
    Topics: Geosciences , Physics
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  • 62
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    International Union of Crystallography (IUCr)
    In: IUCrJ
    Publication Date: 2015-08-16
    Description: Rv1625c is one of 16 adenylyl cyclases encoded in the genome of Mycobacterium tuberculosis. In solution Rv1625c exists predominantly as a monomer, with a small amount of dimer. It has been shown previously that the monomer is active and the dimeric fraction is inactive. Both fractions of wild-type Rv1625c crystallized as head-to-head inactive domain-swapped dimers as opposed to the head-to-tail dimer seen in other functional adenylyl cyclases. About half of the molecule is involved in extensive domain swapping. The strain created by a serine residue located on a hinge loop and the crystallization condition might have led to this unusual domain swapping. The inactivity of the dimeric form of Rv1625c could be explained by the absence of the required catalytic site in the swapped dimer. A single mutant of the enzyme was also generated by changing a phenylalanine predicted to occur at the functional dimer interface to an arginine. This single mutant exists as a dimer in solution but crystallized as a monomer. Analysis of the structure showed that a salt bridge formed between a glutamate residue in the N-terminal segment and the mutated arginine residue hinders dimer formation by pulling the N-terminal region towards the dimer interface. Both structures reported here show a change in the dimerization-arm region which is involved in formation of the functional dimer. It is concluded that the dimerization arm along with other structural elements such as the N-terminal region and certain loops are vital for determining the oligomeric nature of the enzyme, which in turn dictates its activity.
    Keywords: Rv1625cadenylyl cyclasesMycobacterium tuberculosis
    Electronic ISSN: 2052-2525
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  • 63
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    International Union of Crystallography (IUCr)
    In: IUCrJ
    Publication Date: 2015-08-16
    Keywords: crystallizationring-opening polymerizationcoordination polymers
    Electronic ISSN: 2052-2525
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  • 64
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    International Union of Crystallography (IUCr)
    In: IUCrJ
    Publication Date: 2015-08-16
    Description: The aim of this article is a general description of the so-called Patterson-function direct methods (PFDM), from their origin to their present state. It covers a 20-year period of methodological contributions to crystal structure solution, most of them published in Acta Crystallographica Section A. The common feature of these variants of direct methods is the introduction of the experimental intensities in the form of the Fourier coefficients of origin-free Patterson-type functions, which allows the active use of both strong and weak reflections. The different optimization algorithms are discussed and their performances compared. This review focuses not only on those PFDM applications related to powder diffraction data but also on some recent results obtained with electron diffraction tomography data.
    Keywords: direct methodsPFDMδ recyclingS-FFTS-TFcluster-based DMpowder diffractionab initio structure solutionprecession electron diffractionelectron diffraction tomography
    Electronic ISSN: 2052-2525
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  • 65
    Publication Date: 2015-08-16
    Description: Synchrotron radiation has many compelling advantages over conventional radiation sources in the measurement of accurate Bragg diffraction data. The variable photon energy and much higher flux may help to minimize critical systematic effects such as absorption, extinction and anomalous scattering. Based on a survey of selected published results from the last decade, the benefits of using synchrotron radiation in the determination of X-ray electron densities are discussed, and possible future directions of this field are examined.
    Keywords: electron-density studiessynchrotron radiationX-ray diffraction
    Electronic ISSN: 2052-2525
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  • 66
    Publication Date: 2015-08-16
    Description: A rare example is reported in which discrete Ag2L2 ring and (AgL)∞ chain motifs [L = N,N′-bis(3-imidazol-1-yl-propyl)-pyromellitic diimide] co-crystallize in the same crystal lattice with varying ratios and degrees of disorder. Crystal structures obtained from representative crystals reveal compatible packing arrangements of the cyclic and polymeric isomers within the crystal lattice, which enables them to co-exist within a crystalline solid solution. A feasible pathway for transformation between the isomers is suggested via facile rotation of the coordinating imidazolyl groups. This chemical system could provide a chance for direct observation of ring-opening isomerization at the crystal surface. Mass spectrometry and 1H NMR titration show a dynamic equilibrium between cyclic and oligomeric species in solution, and a potential crystallization process is suggested involving alignment of precursors directed by aromatic stacking interactions between pyromellitic diimide units, followed by ring-opening isomerization at the interface between the solid and the solution. Both cyclic and oligomeric species can act as precursors, with interconversion between them being facile due to a low energy barrier for rotation of the imidazole rings. Thermogravimetric analysis and variable-temperature powder X-ray diffraction indicate a transition to a different crystalline phase around 120°C, which is associated with loss of solvent from the crystal lattice.
    Keywords: crystallizationstructural transformationring-opening isomerismsolid solutiondisorder
    Electronic ISSN: 2052-2525
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  • 67
    Publication Date: 2015-08-16
    Description: Crystal structures are presented for two dihydrate polymorphs (DH-I and DH-II) of the non-steroidal anti-inflammatory drug sodium (S)-naproxen. The structure of DH-I is determined from twinned single crystals obtained by solution crystallization. DH-II is obtained by solid-state routes, and its structure is derived using powder X-ray diffraction, solid-state 13C and 23Na MAS NMR, and molecular modelling. The validity of both structures is supported by dispersion-corrected density functional theory (DFT-D) calculations. The structures of DH-I and DH-II, and in particular their relationships to the monohydrate (MH) and anhydrate (AH) structures, provide a basis to rationalize the observed transformation pathways in the sodium (S)-naproxen anhydrate–hydrate system. All structures contain Na+/carboxylate/H2O sections, alternating with sections containing the naproxen molecules. The structure of DH-I is essentially identical to MH in the naproxen region, containing face-to-face arrangements of the naphthalene rings, whereas the structure of DH-II is comparable to AH in the naproxen region, containing edge-to-face arrangements of the naphthalene rings. This structural similarity permits topotactic transformation between AH and DH-II, and between MH and DH-I, but requires re-organization of the naproxen molecules for transformation between any other pair of structures. The topotactic pathways dominate at room temperature or below, while the non-topotactic pathways become active at higher temperatures. Thermochemical data for the dehydration processes are rationalized in the light of this new structural information.
    Keywords: pharmaceuticalhydrateX-ray diffractionsolid-state NMRDFT-D
    Electronic ISSN: 2052-2525
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  • 68
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    International Union of Crystallography (IUCr)
    In: IUCrJ
    Publication Date: 2015-12-20
    Keywords: Editorialcrystal engineering
    Electronic ISSN: 2052-2525
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  • 69
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    International Union of Crystallography (IUCr)
    In: IUCrJ
    Publication Date: 2015-12-20
    Description: In this overview, we briefly outline recent advances in electron cryomicroscopy (cryoEM) and explain why the journal IUCrJ, published by the International Union of Crystallography, could provide a natural home for publications covering many present and future developments in the cryoEM field.
    Keywords: electron cryomicroscopyelectron tomographysingle particlecryoEMoverview
    Electronic ISSN: 2052-2525
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  • 70
    Publication Date: 2015-12-20
    Description: Single-crystal X-ray diffraction structural results for benzidine dihydrochloride, hydrated and protonated N,N,N,N-peri(dimethylamino)naphthalene chloride, triptycene, dichlorodimethyltriptycene and decamethylferrocene have been analysed. A critical discussion of the dependence of structural and thermal parameters on resolution for these compounds is presented. Results of refinements against X-ray data, cut off to different resolutions from the high-resolution data files, are compared to structural models derived from neutron diffraction experiments. The Independent Atom Model (IAM) and the Transferable Aspherical Atom Model (TAAM) are tested. The average differences between the X-ray and neutron structural parameters (with the exception of valence angles defined by H atoms) decrease with the increasing 2θmax angle. The scale of differences between X-ray and neutron geometrical parameters can be significantly reduced when data are collected to the higher, than commonly used, 2θmax diffraction angles (for Mo Kα 2θmax 〉 65°). The final structural and thermal parameters obtained for the studied compounds using TAAM refinement are in better agreement with the neutron values than the IAM results for all resolutions and all compounds. By using TAAM, it is still possible to obtain accurate results even from low-resolution X-ray data. This is particularly important as TAAM is easy to apply and can routinely be used to improve the quality of structural investigations [Dominiak (2015). LSDB from UBDB. University of Buffalo, USA]. We can recommend that, in order to obtain more adequate (more accurate and precise) structural and displacement parameters during the IAM model refinement, data should be collected up to the larger diffraction angles, at least, for Mo Kα radiation to 2θmax = 65° (sin θmax/λ   65°.
    Keywords: X-ray diffraction resultsprecisionindependent atom modeltransferable aspherical atom modelgeometric parametersTLS analysis
    Electronic ISSN: 2052-2525
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  • 71
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    International Union of Crystallography (IUCr)
    In: IUCrJ
    Publication Date: 2015-12-20
    Keywords: local structure analysispair distribution function analysisperovskitessingle-crystal diffuse scattering
    Electronic ISSN: 2052-2525
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  • 72
    Publication Date: 2016-01-13
    Description: The possibility of using femtosecond pulses from an X-ray free-electron laser to collect diffraction data from protein crystals formed in their native cellular organelle has been explored. X-ray diffraction of submicrometre-sized alcohol oxidase crystals formed in peroxisomes within cells of genetically modified variants of the methylotrophic yeast Hansenula polymorpha is reported and characterized. The observations are supported by synchrotron radiation-based powder diffraction data and electron microscopy. Based on these findings, the concept of in cellulo serial crystallography on protein targets imported into yeast peroxisomes without the need for protein purification as a requirement for subsequent crystallization is outlined.
    Keywords: protein structureX-ray crystallographyfemtosecond studiesnanocrystalsfree-electron laser
    Electronic ISSN: 2052-2525
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  • 73
    Publication Date: 2016-01-13
    Description: A synthetic strategy is outlined whereby a binary cocrystal may be developed in turn into a ternary and finally into a quaternary cocrystal. The strategy hinges on the concept of the long-range synthon Aufbau module (LSAM) which is a large supramolecular synthon containing more than one type of intermolecular interaction. Modulation of these interactions may be possible with the use of additional molecular components so that higher level cocrystals are produced. We report six quaternary cocrystals here. All are obtained as nearly exclusive crystallization products when four appropriate solid compounds are taken together in solution for crystallization.
    Keywords: long-range synthon Aufbau modulecrystal engineeringinermolecular interactionspolymorphismcocrystalscrystal design
    Electronic ISSN: 2052-2525
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  • 74
    Publication Date: 2016-01-13
    Description: A synthetic strategy is described for the co-crystallization of four- and five-component molecular crystals, based on the fact that if any particular chemical constituent of a lower cocrystal is found in two different structural environments, these differences may be exploited to increase the number of components in the solid. 2-Methylresorcinol and tetramethylpyrazine are basic template molecules that allow for further supramolecular homologation. Ten stoichiometric quaternary cocrystals and one quintinary cocrystal with some solid solution character are reported. Cocrystals that do not lend themselves to such homologation are termed synthetic dead ends.
    Keywords: crystal engineeringintermolecular interactionspolymorphismcocrystalscrystal design
    Electronic ISSN: 2052-2525
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  • 75
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    International Union of Crystallography (IUCr)
    In: IUCrJ
    Publication Date: 2015-12-20
    Description: Through X-ray crystallographic fragment screening, 4-bromopyrazole was discovered to be a `magic bullet' that is capable of binding at many of the ligand `hot spots' found in HIV-1 reverse transcriptase (RT). The binding locations can be in pockets that are `hidden' in the unliganded crystal form, allowing rapid identification of these sites for in silico screening. In addition to hot-spot identification, this ubiquitous yet specific binding provides an avenue for X-ray crystallographic phase determination, which can be a significant bottleneck in the determination of the structures of novel proteins. The anomalous signal from 4-bromopyrazole or 4-iodopyrazole was sufficient to determine the structures of three proteins (HIV-1 RT, influenza A endonuclease and proteinase K) by single-wavelength anomalous dispersion (SAD) from single crystals. Both compounds are inexpensive, readily available, safe and very soluble in DMSO or water, allowing efficient soaking into crystals.
    Keywords: phasingdrug discoveryX-ray crystallography
    Electronic ISSN: 2052-2525
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  • 76
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    International Union of Crystallography (IUCr)
    In: IUCrJ
    Publication Date: 2015-10-23
    Description: During the last five years, serial femtosecond crystallography using X-ray laser pulses has been developed into a powerful technique for determining the atomic structures of protein molecules from micrometre- and sub-micrometre-sized crystals. One of the key reasons for this success is the `self-gating' pulse effect, whereby the X-ray laser pulses do not need to outrun all radiation damage processes. Instead, X-ray-induced damage terminates the Bragg diffraction prior to the pulse completing its passage through the sample, as if the Bragg diffraction were generated by a shorter pulse of equal intensity. As a result, serial femtosecond crystallography does not need to be performed with pulses as short as 5–10 fs, but can succeed for pulses 50–100 fs in duration. It is shown here that a similar gating effect applies to single-molecule diffraction with respect to spatially uncorrelated damage processes like ionization and ion diffusion. The effect is clearly seen in calculations of the diffraction contrast, by calculating the diffraction of the average structure separately to the diffraction from statistical fluctuations of the structure due to damage (`damage noise'). The results suggest that sub-nanometre single-molecule imaging with 30–50 fs pulses, like those produced at currently operating facilities, should not yet be ruled out. The theory presented opens up new experimental avenues to measure the impact of damage on single-particle diffraction, which is needed to test damage models and to identify optimal imaging conditions.
    Keywords: coherent diffractive imagingsingle-molecule imagingradiation damage`self-gated' pulsesXFELs
    Electronic ISSN: 2052-2525
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