# WILBERT

## Wildauer Bücher+E-Medien Recherche-Tool

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• 1
Unknown
International Union of Crystallography (IUCr)
In: IUCrJ
Publication Date: 2018-05-12
Keywords: protein crystalscrystal lattices
Electronic ISSN: 2052-2525
Topics: Geosciences , Physics
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• 2
Unknown
International Union of Crystallography (IUCr)
In: IUCrJ
Publication Date: 2018-05-12
Description: The availability of dummy-atom modelling programs to determine the shape of monodisperse globular particles from small-angle solution scattering data has led to outstanding scientific advances. However, there is no equivalent procedure that allows modelling of stacked, seemingly endless structures, such as helical systems. This work presents a bead-modelling algorithm that reconstructs the structural motif of helical and rod-like systems. The algorithm is based on a projection scheme': by exploiting the recurrent nature of stacked systems, such as helices, the full structure is reduced to a single building-block motif. This building block is fitted by allowing random dummy-atom movements without an underlying grid. The proposed method is verified using a variety of analytical models, and examples are presented of successful shape reconstruction from experimental data sets. To make the algorithm available to the scientific community, it is implemented in a graphical computer program that encourages user interaction during the fitting process and also includes an option for shape reconstruction of globular particles.
Keywords: SAXSstacked structureshelical structuresshape retrievalSasHelstructure determinationsolution scatteringcomputational modellingstructural biologynanoscience
Electronic ISSN: 2052-2525
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• 3
Unknown
International Union of Crystallography (IUCr)
In: IUCrJ
Publication Date: 2018-05-12
Description: X-ray crystallography and cryo-electron microscopy (cryo-EM) are complementary techniques for structure determination. Crystallography usually reveals more detailed information, while cryo-EM is an extremely useful technique for studying large-sized macromolecules. As the gap between the resolution of crystallography and cryo-EM data narrows, the cryo-EM map of a macromolecule could serve as an initial model to solve the phase problem of crystal diffraction for high-resolution structure determination. FSEARCH is a procedure to utilize the low-resolution molecular shape for crystallographic phasing. The IPCAS (Iterative Protein Crystal structure Automatic Solution) pipeline is an automatic direct-methods-aided dual-space iterative phasing and model-building procedure. When only an electron-density map is available as the starting point, IPCAS is capable of generating a completed model from the phases of the input map automatically, without the requirement of an initial model. In this study, a hybrid method integrating X-ray crystallography with cryo-EM to help with structure determination is presented. With a cryo-EM map as the starting point, the workflow of the method involves three steps. (1) Cryo-EM map replacement: FSEARCH is utilized to find the correct translation and orientation of the cryo-EM map in the crystallographic unit cell and generates the initial low-resolution map. (2) Phase extension: the phases calculated from the correctly placed cryo-EM map are extended to high-resolution X-ray data by non-crystallographic symmetry averaging with phenix.resolve. (3) Model building: IPCAS is used to generate an initial model using the phase-extended map and perform model completion by iteration. Four cases (the lowest cryo-EM map resolution being 6.9 Å) have been tested for the general applicability of the hybrid method, and almost complete models have been generated for all test cases with reasonable Rwork/Rfree. The hybrid method therefore provides an automated tool for X-ray structure determination using a cryo-EM map as the starting point.
Keywords: FSEARCHIPCASiterative phasingcryo-EMmodel buildingstructure determinationcryo-electron microscopyX-ray crystallographyphase problem
Electronic ISSN: 2052-2525
Topics: Geosciences , Physics
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• 4
Unknown
International Union of Crystallography (IUCr)
In: IUCrJ
Publication Date: 2018-05-30
Description: Many important biological processes like amyloid formation, viral assembly etc. can be monitored in vitro. Small-angle X-ray scattering (SAXS) is one of the most effective techniques to structurally characterize these processes in solution. For monodisperse systems and some oligomeric mixtures, low-resolution shapes can be determined ab initio from the SAXS data, but for evolving systems, such analysis is hampered by the presence of multiple species and no direct reconstruction procedures are available. The authors consider a frequently occurring case where the scattering from the initial and final states of the process are known but there exists a major (unknown) intermediate component. A method is presented to directly reconstruct the low-resolution shape of this transient component together with its volume fractions from multiple scattering patterns recorded from an evolving system. The method is implemented in the computer program DAMMIX freely available to academic users and its effectiveness is illustrated in several synthetic and experimental examples.
Keywords: SAXSDAMMIXintermediatesmacromolecular solutionsbiological processes
Electronic ISSN: 2052-2525
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• 5
Unknown
International Union of Crystallography (IUCr)
In: IUCrJ
Publication Date: 2018-06-02
Description: The relationship between crystal structure and physical properties in the ferroelectric Na0.5Bi0.5TiO3 (NBT) has been of interest for the last two decades. Originally, the average structure was held to be of rhombohedral (R3c) symmetry with a fixed polarization direction. This has undergone a series of revisions, however, based on high-resolution X-ray diffraction, total neutron scattering, and optical and electron microscopy. The recent experimental findings suggest that the true average symmetry is monoclinic (space group Cc), which allows for a rotatable spontaneous polarization. Neither polarization rotation nor its potentially important real role in enhanced piezoelectricity is well understood. The present work describes an in situ investigation of the average monoclinic distortion in NBT by time-resolved single-crystal X-ray diffraction under external electric fields. The study presents a high-resolution inspection of the characteristic diffraction features of the monoclinic distortion – splitting of specific Bragg reflections – and their changes under a cyclic electric field. The results favour a model in which there is direct coupling between the shear monoclinic strain and the polarization rotation. This suggests that the angle of polarization rotation under a sub-coercive electric field could be 30° or more.
Keywords: ferroelectricspiezoelectricstime-resolved X-ray diffractionpolarization rotation
Electronic ISSN: 2052-2525
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• 6
Unknown
International Union of Crystallography (IUCr)
In: IUCrJ
Publication Date: 2018-06-07
Description: An experimental procedure for transmission X-ray ghost imaging using synchrotron light is presented. Hard X-rays from an undulator were divided by a beamsplitter to produce two copies of a speckled incident beam. Both beams were simultaneously measured on an indirect pixellated detector and the intensity correlation between the two copies was used to retrieve the ghost image of samples placed in one of the two beams, without measuring the samples directly. Aiming at future practical uses of X-ray ghost imaging, the authors discuss details regarding data acquisition, image reconstruction strategies and measure the point-spread function of the ghost-imaging system. This approach may become relevant for applications of ghost imaging with X-ray sources such as undulators in storage rings, free-electron lasers and lower-coherence laboratory facilities.
Keywords: X-ray imagingX-ray ghost imagingX-ray specklecoherencecomputational X-ray imaginghard X-rayspoint-spread function
Electronic ISSN: 2052-2525
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• 7
Unknown
International Union of Crystallography (IUCr)
In: IUCrJ
Publication Date: 2018-06-09
Description: The high-pressure synthesis and incommensurately modulated structure are reported for the new compound Sr2Pt8−xAs, with x = 0.715 (5). The structure consists of Sr2Pt3As layers alternating with Pt-only corrugated grids. Ab initio calculations predict a metallic character with a dominant role of the Pt d electrons. The electrical resistivity (ρ) and Seebeck coefficient confirm the metallic character, but surprisingly, ρ showed a near-flat temperature dependence. This observation fits the description of the Mooij correlation for electrical resistivity in disordered metals, originally developed for statistically distributed point defects. The discussed material has a long-range crystallographic order, but the high concentration of Pt vacancies, incommensurately ordered, strongly influences the electronic conduction properties. This result extends the range of validity of the Mooij correlation to long-range ordered incommensurately modulated vacancies. Motivated by the layered structure, the resistivity anisotropy was measured in a focused-ion-beam micro-fabricated well oriented single crystal. A low resistivity anisotropy indicates that the layers are electrically coupled and conduction channels along different directions are intermixed.
Keywords: platinum-based metallic compoundsincommensurately modulated structurevacanciesMooij correlationcomposite materialsinorganic materialsdensity functional theory
Electronic ISSN: 2052-2525
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• 8
Unknown
International Union of Crystallography (IUCr)
In: IUCrJ
Publication Date: 2018-06-09
Description: This paper presents experimental charge-density studies of cytosinium chloride, adeninium chloride hemihydrate and guaninium dichloride crystals based on ultra-high-resolution X-ray diffraction data and extensive theoretical calculations. The results confirm that the cohesive energies of the studied systems are dominated by contributions from intermolecular electrostatic interactions, as expected for ionic crystals. Electrostatic interaction energies (Ees) usually constitute 95% of the total interaction energy. The Ees energies in this study were several times larger in absolute value when compared, for example, with dimers of neutral nucleobases. However, they were not as large as some theoretical calculations have predicted. This was because the molecules appeared not to be fully ionized in the studied crystals. Apart from charge transfer from chlorine to the protonated nucleobases, small but visible charge redistribution within the nucleobase cations was observed. Some dimers of singly protonated bases in the studied crystals, namely a cytosinium–cytosinium trans sugar/sugar edge pair and an adeninium–adeninium trans Hoogsteen/Hoogsteen edge pair, exhibited attractive interactions (negative values of Ees) or unusually low repulsion despite identical molecular charges. The pairs are metastable as a result of strong hydrogen bonding between bases which overcompensates the overall cation–cation repulsion, the latter being weakened due to charge transfer and molecular charge-density polarization.
Keywords: charge densitymultipole refinementquantum crystallographyelectrostatic potentialelectrostatic interaction energylike-charged ionsnucleobasescytosineadenineguaninebase pairsintermolecular interactionsspin densitymomentum densityhydrogen bondingpharmaceutical solidsnucleic acid structures
Electronic ISSN: 2052-2525
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• 9
Unknown
International Union of Crystallography (IUCr)
In: IUCrJ
Publication Date: 2018-09-13
Description: This work demonstrates a new method for investigating time-resolved structural changes in protein conformation and oligomerization via photocage-initiated time-resolved X-ray solution scattering by observing the ATP-driven dimerization of the MsbA nucleotide-binding domain. Photocaged small molecules allow the observation of single-turnover reactions of non-naturally photoactivatable proteins. The kinetics of the reaction can be derived from changes in X-ray scattering associated with ATP-binding and subsequent dimerization. This method can be expanded to any small-molecule-driven protein reaction with conformational changes traceable by X-ray scattering where the small molecule can be photocaged.
Keywords: biophysicsX-ray solution scatteringphotocagingstructural biology
Electronic ISSN: 2052-2525
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• 10
Unknown
International Union of Crystallography (IUCr)
In: IUCrJ
Publication Date: 2018-09-15
Description: It is shown that the average signal-to-noise ratio (SNR) in the three-dimensional electron-density distribution of a sample reconstructed by coherent diffractive imaging cannot exceed twice the square root of the ratio of the mean total number of scattered photons detected during the scan and the number of spatially resolved voxels in the reconstructed volume. This result leads to an upper bound on Shannon's information capacity of this imaging method by specifying the maximum number of distinguishable density distributions within the reconstructed volume when the radiation dose delivered to the sample and the spatial resolution are both fixed. If the spatially averaged SNR in the reconstructed electron density is fixed instead, the radiation dose is shown to be proportional to the third or fourth power of the spatial resolution, depending on the sampling of the three-dimensional diffraction space and the scattering power of the sample.
Keywords: coherent diffractive imagingsignal-to-noise ratiospatial resolutioninformation capacity
Electronic ISSN: 2052-2525
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• 11
Unknown
International Union of Crystallography (IUCr)
In: IUCrJ
Publication Date: 2018-09-15
Description: This paper reports on the polymorphism of 2-propyl-1H-benzimidazole (2PrBzIm) induced by temperature change. Upon heating, an irreversible reconstructive-type phase transition at T = 384 K from the ordered form I (P212121) to a new polymorph, form IIHT (Pcam), was observed. The structural transformation between forms I and II involves significant changes in the crystal packing, as well as a key conformational variation around the propyl chain of the molecule. After the first irreversible phase transition, the IIHT form undergoes two further (reversible) phase transitions upon cooling at 361 K (IIRT) and 181 K (IILT). All three phases (forms IIHT, IIRT and IILT) have almost identical crystal packing and, given the reversibility of the conversions as a function of temperature, they are referred to as form II temperature phases. They differ, however, with respect to conformational variations around the propyl chain of 2PrBzIm. Energy calculations of the gas-phase conformational energy landscape of this compound about its flexible bonds allowed us to classify the observed conformational variations of all forms into changes and adjustments of conformers. This reveals that forms I and II are related by conformational change, and that two of the form II phases (HT and RT) are related by conformational adjustment, whilst the other two (RT and LT) are related by conformational change. We introduce the term conformational phases' for different crystal phases with almost identical packing but showing changes in conformation.
Keywords: molecular crystalspolymorphismphase transitionsconformational changesenergy minimization
Electronic ISSN: 2052-2525
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• 12
Unknown
International Union of Crystallography (IUCr)
In: IUCrJ
Publication Date: 2018-09-19
Description: The analysis of a single-particle imaging (SPI) experiment performed at the AMO beamline at LCLS as part of the SPI initiative is presented here. A workflow for the three-dimensional virus reconstruction of the PR772 bacteriophage from measured single-particle data is developed. It consists of several well defined steps including single-hit diffraction data classification, refined filtering of the classified data, reconstruction of three-dimensional scattered intensity from the experimental diffraction patterns by orientation determination and a final three-dimensional reconstruction of the virus electron density without symmetry constraints. The analysis developed here revealed and quantified nanoscale features of the PR772 virus measured in this experiment, with the obtained resolution better than 10 nm, with a clear indication that the structure was compressed in one direction and, as such, deviates from ideal icosahedral symmetry.
Keywords: single-particle imagingthree-dimensional virus reconstructionsXFELs
Electronic ISSN: 2052-2525
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• 13
Unknown
International Union of Crystallography (IUCr)
In: IUCrJ
Publication Date: 2018-10-12
Description: The AMPA receptor GluA2 belongs to the family of ionotropic glutamate receptors, which are responsible for most of the fast excitatory neuronal signalling in the central nervous system. These receptors are important for memory and learning, but have also been associated with brain diseases such as Alzheimer's disease and epilepsy. Today, one drug is on the market for the treatment of epilepsy targeting AMPA receptors, i.e. a negative allosteric modulator of these receptors. Recently, crystal structures and cryo-electron microscopy (cryo-EM) structures of full-length GluA2 in the resting (apo), activated and desensitized states have been reported. Here, solution structures of full-length GluA2 are reported using small-angle neutron scattering (SANS) with a novel, fully matched-out detergent. The GluA2 solution structure was investigated in the resting state as well as in the presence of AMPA and of the negative allosteric modulator GYKI-53655. In solution and at neutral pH, the SANS data clearly indicate that GluA2 is in a compact form in the resting state. The solution structure resembles the crystal structure of GluA2 in the resting state, with an estimated maximum distance (Dmax) of 179 ± 11 Å and a radius of gyration (Rg) of 61.9 ± 0.4 Å. An ab initio model of GluA2 in solution generated using DAMMIF clearly showed the individual domains, i.e. the extracellular N-terminal domains and ligand-binding domains as well as the transmembrane domain. Solution structures revealed that GluA2 remained in a compact form in the presence of AMPA or GYKI-53655. At acidic pH only, GluA2 in the presence of AMPA adopted a more open conformation of the extracellular part (estimated Dmax of 189 ± 5 Å and Rg of 65.2 ± 0.5 Å), resembling the most open, desensitized class 3 cryo-EM structure of GluA2 in the presence of quisqualate. In conclusion, this methodological study may serve as an example for future SANS studies on membrane proteins.
Keywords: ionotropic glutamate receptorsmall-angle neutron scatteringagonistsnegative allosteric modulatorsresting stateAlzheimer's diseaseParkinson's diseaseepilepsy
Electronic ISSN: 2052-2525
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• 14
Unknown
International Union of Crystallography (IUCr)
In: IUCrJ
Publication Date: 2018-10-20
Description: The application of X-ray photon correlation spectroscopy (XPCS) at free-electron laser (FEL) facilities enables, for the first time, the study of dynamics on a (sub-)nanometre scale in an unreached time range between femtoseconds and seconds. For soft-matter materials, radiation damage is a major limitation when going beyond single-shot applications. Here, an XPCS study is presented at a hard X-ray FEL on radiation-sensitive polymeric poly(N-isopropylacrylamide) (PNIPAM) nanoparticles. The dynamics of aqueous suspensions of densely packed silica-PNIPAM core-shell particles and a PNIPAM nanogel below the radiation-damage threshold are determined. The XPCS data indicate non-diffusive behaviour, suggesting ballistic and stress-dominated heterogeneous particle motions. These results demonstrate the feasibility of XPCS experiments on radiation-sensitive soft-matter materials at FEL sources and pave the way for future applications at MHz repetition rates as well as ultrafast modes using split-pulse devices.
Keywords: XPCSFELPNIPAM nanoparticlesSACLAradiation-damage thresholdsoft-matter materials
Electronic ISSN: 2052-2525
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• 15
Unknown
International Union of Crystallography (IUCr)
In: IUCrJ
Publication Date: 2018-10-30
Keywords: crystal engineeringcrystalscrystallography
Electronic ISSN: 2052-2525
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• 16
Unknown
International Union of Crystallography (IUCr)
In: IUCrJ
Publication Date: 2018-10-30
Description: This paper reports a new structured prismatic platelet, self-assembled by an ellipse-like quasi-unit cell, precipitated in Mg–In–Yb and Mg–In–Ca ternary alloys and aged isothermally at 200°C using aberration-corrected high-angle annular dark-field scanning transmission electron microscopy combined with density functional theory computations. The ordered stacking of solute atoms along the [0001]α direction based on elliptically shaped self-adapted clustering leads to the generation of the quasi-unit cell. The bonding of these ellipse-like quasi-unit-cell rods by the Mg atomic columns along the 〈11{\overline 2}0〉α directions formed a two-dimensional planar structure, which has three variants with a {10{\overline 1}0}α habit plane and full coherence with the α-Mg matrix. This finding is important for understanding the clustering and stacking behaviors of solute atoms in condensed matter, and is expected to guide the future design of novel high-strength Mg alloys strengthened by such high-density prismatic platelets.
Keywords: magnesium alloysprecipitationprismatic plateletsquasi-unit-cellsDFTHAADF-STEM
Electronic ISSN: 2052-2525
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• 17
Unknown
International Union of Crystallography (IUCr)
In: IUCrJ
Publication Date: 2018-10-30
Description: A method has been developed to measure the similarity between materials, focusing on specific physical properties. The information obtained can be utilized to understand the underlying mechanisms and support the prediction of the physical properties of materials. The method consists of three steps: variable evaluation based on nonlinear regression, regression-based clustering, and similarity measurement with a committee machine constructed from the clustering results. Three data sets of well characterized crystalline materials represented by critical atomic predicting variables are used as test beds. Herein, the focus is on the formation energy, lattice parameter and Curie temperature of the examined materials. Based on the information obtained on the similarities between the materials, a hierarchical clustering technique is applied to learn the cluster structures of the materials that facilitate interpretation of the mechanism, and an improvement in the regression models is introduced to predict the physical properties of the materials. The experiments show that rational and meaningful group structures can be obtained and that the prediction accuracy of the materials' physical properties can be significantly increased, confirming the rationality of the proposed similarity measure.
Keywords: data miningmaterials informaticsfirst-principles calculationsphysical properties of materialsmachine learningsimilarity
Electronic ISSN: 2052-2525
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• 18
Unknown
International Union of Crystallography (IUCr)
In: IUCrJ
Publication Date: 2018-10-30
Description: Single-particle cryo-electron microscopy (cryo-EM) has recently become a mainstream technique for the structural determination of macromolecules. Typical cryo-EM workflows collect hundreds of thousands of single-particle projections from thousands of micrographs using particle-picking algorithms. However, the number of false positives selected by these algorithms is large, so that a number of different cleaning steps' are necessary to decrease the false-positive ratio. Most commonly employed techniques for the pruning of false-positive particles are time-consuming and require user intervention. In order to overcome these limitations, a deep learning-based algorithm named Deep Consensus is presented in this work. Deep Consensus works by computing a smart consensus over the output of different particle-picking algorithms, resulting in a set of particles with a lower false-positive ratio than the initial set obtained by the pickers. Deep Consensus is based on a deep convolutional neural network that is trained on a semi-automatically generated data set. The performance of Deep Consensus has been assessed on two well known experimental data sets, virtually eliminating user intervention for pruning, and enhances the reproducibility and objectivity of the whole process while achieving precision and recall figures above 90%.
Keywords: cryo-EMdeep learningimage processingparticle pruningthree-dimensional reconstruction
Electronic ISSN: 2052-2525
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• 19
Unknown
International Union of Crystallography (IUCr)
In: IUCrJ
Publication Date: 2018-10-30
Description: The crystal and molecular structure of the pure (S)-enantiomer of the popular analgesic and anti-inflammatory drug ketoprophen (α-ket) is reported. A detailed aspherical charge-density model based on high-resolution X-ray diffraction data has been refined, yielding a high-precision geometric description and classification of the O—H...O interactions as medium strength hydrogen bonds. The crystal structure of the racemic form of ketoprophen (β-ket) was also redetermined at 100 K, at 0.5 Å resolution. A previously unreported disorder (10% occupancy) was discovered. In contrast to the racemic β-ket case, the (S)-enantiomer crystallizes with two independent molecules in the asymmetric unit with two distinct conformations. The major difference between the β-ket and α-ket crystal forms lies in the formation of distinct hydrogen-bonded motifs: a closed ring motif in β-ket versus infinite chains of hydrogen bonds in the chiral α-ket structure. However, the overall crystal packing of both forms is surprisingly similar, with close-packed layers of antiparallel-oriented benzophenone moieties bound by C—H...π interactions. Notably, the most important stabilizing term in the total lattice energies in both instances proved to be the dispersion related to these interactions. Both forms of the title compound (α- and β-ket) were additionally characterized by differential scanning calorimetry and thermogravimetric analysis.
Keywords: ketoprophencharge densitycrystal structurespharmaceuticalsbioinversion
Electronic ISSN: 2052-2525
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• 20
Unknown
International Union of Crystallography (IUCr)
In: IUCrJ
Publication Date: 2018-09-13
Description: Hexaferrites are an important class of magnetic oxides with applications in data storage and electronics. Their crystal structures are highly modular, consisting of Fe- or Ba-rich close-packed blocks that can be stacked in different sequences to form a multitude of unique structures, producing large anisotropic unit cells with lattice parameters typically 〉100 Å along the stacking axis. This has limited atomic-resolution structure solutions to relatively simple examples such as Ba2Zn2Fe12O22, whilst longer stacking sequences have been modelled only in terms of block sequences, with no refinement of individual atomic coordinates or occupancies. This paper describes the growth of a series of complex hexaferrite crystals, their atomic-level structure solution by high-resolution synchrotron X-ray diffraction, electron diffraction and imaging methods, and their physical characterization by magnetometry. The structures include a new hexaferrite stacking sequence, with the longest lattice parameter of any hexaferrite with a fully determined structure.
Keywords: large repeat hexaferritesmixed-layer structural modelspolytypesstacking sequencesdefectsmagnetic properties
Electronic ISSN: 2052-2525
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• 21
Unknown
International Union of Crystallography (IUCr)
In: IUCrJ
Publication Date: 2018-12-05
Description: During screening of the phase space using KOH and 1-methyl-4-aza-1-azoniabicyclo[2.2.2]octane hydroxide (1-methyl-DABCO) under hydrothermal zeolite synthesis conditions, K-paracelsian was synthesized. Scanning electron microscopy, energy dispersive X-ray spectroscopy and ex situ powder X-ray diffraction analysis revealed a material that is compositionally closely related to the mineral microcline and structurally closely related to the mineral paracelsian, both of which are feldspars. In contrast to the feldspars, K-paracelsian contains intrazeolitic water corresponding to one molecule per cage. In the case of K-paracelsian it might be useful to consider it a link between feldspars and zeolites. It was also shown that K-paracelsian can be described as the simplest endmember of a family of dense double-crankshaft zeolite topologies. By applying the identified building principle, a number of known zeolite topologies can be constructed. Furthermore, it facilitates the construction of a range of hypothetical small-pore structures that are crystallo-chemically healthy, but which have not yet been realized experimentally.
Keywords: K-paracelsiandense double-crankshaft zeolite topologiesstructure refinementcrystal engineeringinorganic porous solidsmicroporous materials
Electronic ISSN: 2052-2525
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• 22
Unknown
International Union of Crystallography (IUCr)
In: IUCrJ
Publication Date: 2018-04-20
Description: With the recent developments in microcrystal handling, synchrotron microdiffraction beamline instrumentation and data analysis, microcrystal crystallography with crystal sizes of less than 10 µm is appealing at synchrotrons. However, challenges remain in sample manipulation and data assembly for robust microcrystal synchrotron crystallography. Here, the development of micro-sized polyimide well-mounts for the manipulation of microcrystals of a few micrometres in size and the implementation of a robust data-analysis method for the assembly of rotational microdiffraction data sets from many microcrystals are described. The method demonstrates that microcrystals may be routinely utilized for the acquisition and assembly of complete data sets from synchrotron microdiffraction beamlines.
Keywords: microcrystalsmicrodiffractionradiation damagedata analysismultiple crystalsX-ray crystallographystructural biology
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• 23
Unknown
International Union of Crystallography (IUCr)
In: IUCrJ
Publication Date: 2018-05-01
Description: Ionic scattering factors of atoms that compose biological molecules have been computed by the multi-configuration Dirac–Fock method. These ions are chemically unstable and their scattering factors had not been reported except for O−. Yet these factors are required for the estimation of partial charges in protein molecules and nucleic acids. The electron scattering factors of these ions are particularly important as the electron scattering curves vary considerably between neutral and charged atoms in the spatial-resolution range explored in structural biology. The calculated X-ray and electron scattering factors have then been parameterized for the major scattering curve models used in X-ray and electron protein crystallography and single-particle cryo-EM. The X-ray and electron scattering factors and the fitting parameters are presented for future reference.
Keywords: form factorselectron crystallographysingle-particle cryo-EMstructure refinementX-ray crystallographyimagingstructure determination
Electronic ISSN: 2052-2525
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• 24
Unknown
International Union of Crystallography (IUCr)
In: IUCrJ
Publication Date: 2018-05-01
Description: We report on the self-assembly of gold nanoparticles coated with a soft poly(ethylene glycol) shell studied by X-ray cross-correlation analysis. Depending on the initial concentration of gold nanoparticles used, structurally heterogeneous films were formed. The films feature hot spots of dominating four- and sixfold local order with patch sizes of a few micrometres, containing 104–105 particles. The amplitude of the order parameters suggested that a minimum sample amount was necessary to form well ordered local structures. Furthermore, the increasing variation in order parameters with sample thickness demonstrated a high degree of structural heterogeneity. This wealth of information cannot be obtained by the conventional microscopy techniques that are commonly used to study nanocrystal superstructures, as illustrated by complementary scanning electron microscopy measurements.
Keywords: self-assembled nanoparticle filmsX-ray cross-correlationsXCCAgold nanoparticles
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• 25
Unknown
International Union of Crystallography (IUCr)
In: IUCrJ
Publication Date: 2018-05-12
Keywords: protein crystalscrystal lattices
Electronic ISSN: 2052-2525
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• 26
Unknown
International Union of Crystallography (IUCr)
In: IUCrJ
Publication Date: 2018-03-23
Description: The epoxide hydrolase StEH1 catalyzes the hydrolysis of trans-methylstyrene oxide to 1-phenylpropane-1,2-diol. The (S,S)-epoxide is exclusively transformed into the (1R,2S)-diol, while hydrolysis of the (R,R)-epoxide results in a mixture of product enantiomers. In order to understand the differences in the stereoconfigurations of the products, the reactions were studied kinetically during both the pre-steady-state and steady-state phases. A number of closely related StEH1 variants were analyzed in parallel, and the results were rationalized by structure–activity analysis using the available crystal structures of all tested enzyme variants. Finally, empirical valence-bond simulations were performed in order to provide additional insight into the observed kinetic behaviour and ratios of the diol product enantiomers. These combined data allow us to present a model for the flux through the catalyzed reactions. With the (R,R)-epoxide, ring opening may occur at either C atom and with similar energy barriers for hydrolysis, resulting in a mixture of diol enantiomer products. However, with the (S,S)-epoxide, although either epoxide C atom may react to form the covalent enzyme intermediate, only the pro-(R,S) alkylenzyme is amenable to subsequent hydrolysis. Previously contradictory observations from kinetics experiments as well as product ratios can therefore now be explained for this biocatalytically relevant enzyme.
Keywords: epoxide hydrolasestereoselectivityempirical valence-bond simulationsbiocatalysisreaction fluxtrans-methylstyrene oxide
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• 27
Unknown
International Union of Crystallography (IUCr)
In: IUCrJ
Publication Date: 2018-03-23
Description: High-resolution crystal structures of enzymes in relevant redox states have transformed our understanding of enzyme catalysis. Recent developments have demonstrated that X-rays can be used, via the generation of solvated electrons, to drive reactions in crystals at cryogenic temperatures (100 K) to generate structural movies' of enzyme reactions. However, a serious limitation at these temperatures is that protein conformational motion can be significantly supressed. Here, the recently developed MSOX (multiple serial structures from one crystal) approach has been applied to nitrite-bound copper nitrite reductase at room temperature and at 190 K, close to the glass transition. During both series of multiple structures, nitrite was initially observed in a top-hat' geometry, which was rapidly transformed to a side-on' configuration before conversion to side-on NO, followed by dissociation of NO and substitution by water to reform the resting state. Density functional theory calculations indicate that the top-hat orientation corresponds to the oxidized type 2 copper site, while the side-on orientation is consistent with the reduced state. It is demonstrated that substrate-to-product conversion within the crystal occurs at a lower radiation dose at 190 K, allowing more of the enzyme catalytic cycle to be captured at high resolution than in the previous 100 K experiment. At room temperature the reaction was very rapid, but it remained possible to generate and characterize several structural states. These experiments open up the possibility of obtaining MSOX structural movies at multiple temperatures (MSOX-VT), providing an unparallelled level of structural information during catalysis for redox enzymes.
Keywords: serial crystallographycopper nitrite reductasevariable temperatureradiolysisstructural dynamicsdensity functional theory
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• 28
Unknown
International Union of Crystallography (IUCr)
In: IUCrJ
Publication Date: 2018-03-30
Description: The origin of unknown polymorphic phases within thin films is still not well understood. This work reports on crystals of the molecule terthiophene which were grown by thermal gradient crystallization using glass-plate substrates. The crystalline domains displayed a plate-like morphology with an extended lateral size of about 100 µm, but a thickness of only a few µm. Specular X-ray diffraction patterns confirmed the presence of a new polymorph of terthiophene. Crystal structure solution from a single crystal peeled from the film revealed a structure with an extremely large unit-cell volume containing 42 independent molecules. In contrast to the previously determined crystal structure of terthiophene, a herringbone packing motif was observed where the terminal ends of the molecules are arranged within one plane (i.e. the molecular packing conforms to the flat substrate surface). This type of molecular packing is obtained by 180° flipped molecules combined with partially random (disordered) occupation. A densely packed interface between terthiophene crystallites and the substrate surface is obtained, this confirms that the new packing motif has adapted to the flat substrate surface.
Keywords: molecular crystalssurface-mediated polymorphismthermal gradient crystallizationsingle-crystalline filmsspecular X-ray diffraction
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• 29
Unknown
International Union of Crystallography (IUCr)
In: IUCrJ
Publication Date: 2018-02-23
Description: The Arenaviridae family, together with the Bunyaviridae and Orthomyxoviridae families, is one of the three negative-stranded RNA viral families that encode an endonuclease in their genome. The endonuclease domain is at the N-terminus of the L protein, a multifunctional protein that includes the RNA-dependent RNA polymerase. The synthesis of mRNA in arenaviruses is a process that is primed by capped nucleotides that are stolen' from the cellular mRNA by the endonuclease domain in cooperation with other domains of the L protein. This molecular mechanism has been demonstrated previously for the endonuclease of the prototype Lymphocytic choriomeningitis virus (LCMV). However, the mode of action of this enzyme is not fully understood as the original structure did not contain catalytic metal ions. The pivotal role played by the cap-snatching process in the life cycle of the virus and the highly conserved nature of the endonuclease domain make it a target of choice for the development of novel antiviral therapies. Here, the binding affinities of two diketo-acid (DKA) compounds (DPBA and L-742,001) for the endonuclease domain of LCMV were evaluated using biophysical methods. X-ray structures of the LCMV endonuclease domain with catalytic ions in complex with these two compounds were determined, and their efficacies were assessed in an in vitro endonuclease-activity assay. Based on these data and computational simulation, two new DKAs were synthesized. The LCMV endonuclease domain exhibits a good affinity for these DKAs, making them a good starting point for the design of arenavirus endonuclease inhibitors. In addition to providing the first example of an X-ray structure of an arenavirus endonuclease incorporating a ligand, this study provides a proof of concept that the design of optimized inhibitors against the arenavirus endonuclease is possible.
Keywords: ArenaviridaeendonucleasesLymphocytic choriomeningitis virusLCMVdiketo acidscompound optimizationmetal chelation
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• 30
Unknown
International Union of Crystallography (IUCr)
In: IUCrJ
Publication Date: 2018-06-26
Description: An error in the paper by Pflüger, Soltwisch, Probst, Scholze & Krumrey [IUCrJ (2017), 431–438] is corrected.
Keywords: grazing-incidence small-angle X-ray scatteringGISAXSbeam footprintlithographic inspectiongratings
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• 31
Unknown
International Union of Crystallography (IUCr)
In: IUCrJ
Publication Date: 2018-06-26
Description: Mycobacterium tuberculosis (MTB) caused 10.4 million cases of tuberculosis and 1.7 million deaths in 2016. The incidence of multidrug-resistant and extensively drug-resistant MTB is becoming an increasing threat to public health and the development of novel anti-MTB drugs is urgently needed. Methionyl-tRNA synthetase (MetRS) is considered to be a valuable drug target. However, structural characterization of M. tuberculosis MetRS (MtMetRS) was lacking for decades, thus hampering drug design. Here, two high-resolution crystal structures of MtMetRS are reported: the free-state structure (apo form; 1.9 Å resolution) and a structure with the intermediate product methionyl-adenylate (Met-AMP) bound (2.4 Å resolution). It was found that free-state MtMetRS adopts a previously unseen conformation that has never been observed in other MetRS homologues. The pockets for methionine and AMP are not formed in free-state MtMetRS, suggesting that it is in a nonproductive conformation. Combining these findings suggests that MtMetRS employs an induced-fit mechanism in ligand binding. By comparison with the structure of human cytosolic MetRS, additional pockets specific to MtMetRS that could be used for anti-MTB drug design were located.
Keywords: Mycobacterium tuberculosismethionyl-tRNA synthetasecrystal structureinduced fitantituberculosis drugs
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• 32
Unknown
International Union of Crystallography (IUCr)
In: IUCrJ
Publication Date: 2018-06-26
Description: Synchrotron single-crystal X-ray diffraction has revealed diffuse scattering alongside sharp satellite reflections for different samples of mullite (Al4+2xSi2−2xO10−x). Structural models have been developed in (3+1)-dimensional superspace that account for vacancy ordering and Al/Si ordering based on harmonic modulation functions. A constraint scheme is presented which explains the crystal-chemical relationships between the split sites of the average structure. The modulation amplitudes of the refinements differ significantly by a factor of ∼3, which is explained in terms of different degrees of ordering, i.e. vacancies follow the same ordering principle in all samples but to different extents. A new approach is applied for the first time to determine Al/Si ordering by combining density functional theory with the modulated volumes of the tetrahedra. The presence of Si–Si diclusters indicates that the mineral classification of mullite needs to be reviewed. A description of the crystal structure of mullite must consider both the chemical composition and the degree of ordering. This is of particular importance for applications such as advanced ceramics, because the physical properties depend on the intrinsic structure of mullite.
Keywords: Al/Si orderingvacancy orderingceramicssuperspaceincommensurate structures
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• 33
Unknown
International Union of Crystallography (IUCr)
In: IUCrJ
Publication Date: 2018-06-26
Description: There are few cases where tyrosine has been shown to be involved in catalysis or the control of catalysis despite its ability to carry out chemistry at much higher potentials (1 V versus NHE). Here, it is shown that a tyrosine that blocks the hydrophobic substrate-entry channel in copper-haem nitrite reductases can be activated like a switch by the treatment of crystals of Ralstonia pickettii nitrite reductase (RpNiR) with nitric oxide (NO) (−0.8 ± 0.2 V). Treatment with NO results in an opening of the channel originating from the rotation of Tyr323 away from AspCAT97. Remarkably, the structure of a catalytic copper-deficient enzyme also shows Tyr323 in the closed position despite the absence of type 2 copper (T2Cu), clearly demonstrating that the status of Tyr323 is not controlled by T2Cu or its redox chemistry. It is also shown that the activation by NO is not through binding to haem. It is proposed that activation of the Tyr323 switch is controlled by NO through proton abstraction from tyrosine and the formation of HNO. The insight gained here for the use of tyrosine as a switch in catalysis has wider implications for catalysis in biology.
Keywords: catalysisredox biologystructural biologyenzyme mechanismdenitrificationnitrogen cyclecopper-haem nitrite reductasesRalstonia pickettii
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• 34
Unknown
International Union of Crystallography (IUCr)
In: IUCrJ
Publication Date: 2018-06-26
Description: Halogen bonds have emerged as noncovalent forces that govern the assembly of molecules in organic solids with a degree of reliability akin to hydrogen bonds. Although the structure-directing roles of halogen bonds are often compared to hydrogen bonds, general knowledge concerning the fundamental structural behavior of halogen bonds has had limited opportunity to develop. Following an investigation of solid-state reactions involving organic syntheses and the development of photoresponsive materials, this work demonstrates the ability of the components of intermolecular N...I halogen bonding – a workhorse' interaction for the crystal engineer – to support a single-crystal-to-single-crystal [2+2] photodimerization. A comparison is provided of the geometric changes experienced by the halogen-bonded components in the single-crystal reaction to the current crystal landscape of N...I halogen bonds, as derived from the Cambridge Structural Database. Specifically, a linear-to-bent type of deformation of the halogen-bonded components was observed, which is expected to support the development of functional halogen-bonded materials containing molecules that can undergo movements in close-packed crystal environments.
Keywords: solid-state reactivityhalogen bondsphotodimerizationsupramolecular chemistrysingle-crystal-to-single-crystal reactioncrystal engineeringco-crystalsorganic solid-state reactionsframework-structured solids and amorphous materialsmolecular crystals
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• 35
Unknown
International Union of Crystallography (IUCr)
In: IUCrJ
Publication Date: 2018-07-28
Description: The hypothesis that H/D exchange affects the structural formation of organic compounds in the solid state is supported by a deeper understanding of the altering polymorphism of ROY (a substance striking for its high number of polymorphic forms) through deuteration. Therefore, ROY was deuterated at its amine function, which leads to a seemingly small yet effective modification of the hydrogen-bond strength. In contrast to the crystallization of the non-deuterated ROY in methanol or ethanol, which leads to the simultaneous formation of two forms (OP and Y polymorphs), so-called concomitant polymorphs, the crystallization of d1-ROY leads to the selective formation of the Y polymorph exclusively. The preferred aggregation behavior of the Y form of d1-ROY is assigned to the weakening of an intramolecular hydrogen bond and a consequently strengthened intermolecular hydrogen bond after deuteration.
Keywords: concomitant polymorphsdeuterationhydrogen bondsROYcrystal engineeringH/D exchange
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• 36
Unknown
International Union of Crystallography (IUCr)
In: IUCrJ
Publication Date: 2018-07-31
Keywords: chiralitystructure analysisconfigurational changephase transitionsintermolecular interactionsamino acids
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• 37
Unknown
International Union of Crystallography (IUCr)
In: IUCrJ
Publication Date: 2018-07-31
Description: The recent paper by Belo, Pereira, Freire, Argyriou, Eckert & Bordallo [(2018), IUCrJ, 5, 6–12] reports observations that may lead one to think of very strong and visible consequences of the parity-violation energy difference between enantiomers of a molecule, namely alanine. If proved, this claim would have an enormous impact for research in structural chemistry. However, alternative, more realistic, explanations of their experiments have not been ruled out by the authors. Moreover, the theoretical calculations carried out to support the hypothesis are unable to differentiate between enantiomers (molecules or crystals). Therefore, the conclusions drawn by Belo et al. (2018) are deemed inappropriate as the data presented do not contain sufficient information to reach such a conclusion.
Keywords: parity-violation energyenantiomersphase transitionsamino acids
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• 38
Unknown
International Union of Crystallography (IUCr)
In: IUCrJ
Publication Date: 2018-08-09
Description: During the past few years, serial crystallography methods have undergone continuous development and serial data collection has become well established at high-intensity synchrotron-radiation beamlines and XFEL radiation sources. However, the application of experimental phasing to serial crystallography data has remained a challenging task owing to the inherent inaccuracy of the diffraction data. Here, a particularly gentle method for incorporating heavy atoms into micrometre-sized crystals utilizing lipidic cubic phase (LCP) as a carrier medium is reported. Soaking in LCP prior to data collection offers a new, efficient and gentle approach for preparing heavy-atom-derivative crystals directly before diffraction data collection using serial crystallography methods. This approach supports effective phasing by utilizing a reasonably low number of diffraction patterns. Using synchrotron radiation and exploiting the anomalous scattering signal of mercury for single isomorphous replacement with anomalous scattering (SIRAS) phasing resulted in high-quality electron-density maps that were sufficient for building a complete structural model of proteinase K at 1.9 Å resolution using automatic model-building tools.
Keywords: serial crystallographySIRAS phasinglipidic cubic phaseheavy-atom soakingde novo protein structure determination
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• 39
Unknown
International Union of Crystallography (IUCr)
In: IUCrJ
Publication Date: 2018-08-09
Description: Inherent protein flexibility, poor or low-resolution diffraction data or poorly defined electron-density maps often inhibit the building of complete structural models during X-ray structure determination. However, recent advances in crystallographic refinement and model building often allow completion of previously missing parts. This paper presents algorithms that identify regions missing in a certain model but present in homologous structures in the Protein Data Bank (PDB), and graft' these regions of interest. These new regions are refined and validated in a fully automated procedure. Including these developments in the PDB-REDO pipeline has enabled the building of 24 962 missing loops in the PDB. The models and the automated procedures are publicly available through the PDB-REDO databank and webserver. More complete protein structure models enable a higher quality public archive but also a better understanding of protein function, better comparison between homologous structures and more complete data mining in structural bioinformatics projects.
Keywords: loop buildingstructural re-buildingPDB-REDOmodel completioncrystallography
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• 40
Unknown
International Union of Crystallography (IUCr)
In: IUCrJ
Publication Date: 2018-08-09
Description: Cyclobutane pyrimidine dimer (CPD) photolyases harness the energy of blue light to repair UV-induced DNA CPDs. Upon binding, CPD photolyases cause the photodamage to flip out of the duplex DNA and into the catalytic site of the enzyme. This process, called base-flipping, induces a kink in the DNA, as well as an unpaired bubble, which are stabilized by a network of protein–nucleic acid interactions. Previously, several co-crystal structures have been reported in which the binding mode of CPD photolyases has been studied in detail. However, in all cases the internucleoside linkage of the photodamage site was a chemically synthesized formacetal analogue and not the natural phosphodiester. Here, the first crystal structure and conformational analysis via molecular-dynamics simulations of a class II CPD photolyase in complex with photodamaged DNA that contains a natural cyclobutane pyrimidine dimer with an intra-lesion phosphodiester linkage are presented. It is concluded that a highly conserved bubble-intruding region (BIR) mediates stabilization of the open form of CPD DNA when complexed with class II CPD photolyases.
Keywords: class II CPD photolyasesDNA repairDNA distortioncyclobutane pyrimidine dimercrystal structure
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• 41
Unknown
International Union of Crystallography (IUCr)
In: IUCrJ
Publication Date: 2018-11-09
Description: Cryo-EM now commonly generates close-to-atomic resolution as well as intermediate resolution maps from macromolecules observed in isolation and in situ. Interpreting these maps remains a challenging task owing to poor signal in the highest resolution shells and the necessity to select a threshold for density analysis. In order to facilitate this process, a statistical framework for the generation of confidence maps by multiple hypothesis testing and false discovery rate (FDR) control has been developed. In this way, three-dimensional confidence maps contain signal separated from background noise in the form of local detection rates of EM density values. It is demonstrated that confidence maps and FDR-based thresholding can be used for the interpretation of near-atomic resolution single-particle structures as well as lower resolution maps determined by subtomogram averaging. Confidence maps represent a conservative way of interpreting molecular structures owing to minimized noise. At the same time they provide a detection error with respect to background noise, which is associated with the density and is particularly beneficial for the interpretation of weaker cryo-EM densities in cases of conformational flexibility and lower occupancy of bound molecules and ions in the structure.
Keywords: electron cryo-microscopysignal detectionfalse discovery ratecryo-EM densitysubtomogram averaginglocal resolutionligand binding
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• 42
Unknown
International Union of Crystallography (IUCr)
In: IUCrJ
Publication Date: 2018-11-09
Description: A new method to estimate the trajectories of particle motion and the amount of cumulative beam damage in electron cryo-microscopy (cryo-EM) single-particle analysis is presented. The motion within the sample is modelled through the use of Gaussian process regression. This allows a prior likelihood that favours spatially and temporally smooth motion to be associated with each hypothetical set of particle trajectories without imposing hard constraints. This formulation enables the a posteriori likelihood of a set of particle trajectories to be expressed as a product of that prior likelihood and an observation likelihood given by the data, and this a posteriori likelihood to then be maximized. Since the smoothness prior requires three parameters that describe the statistics of the observed motion, an efficient stochastic method to estimate these parameters is also proposed. Finally, a practical algorithm is proposed that estimates the average amount of cumulative radiation damage as a function of radiation dose and spatial frequency, and then fits relative B factors to that damage in a robust way. The method is evaluated on three publicly available data sets, and its usefulness is illustrated by comparison with state-of-the-art methods and previously published results. The new method has been implemented as Bayesian polishing in RELION-3, where it replaces the existing particle-polishing method, as it outperforms the latter in all tests conducted.
Keywords: Bayesian particle polishingbeam-induced motion correctioncryo-EMsingle-particle analysiselectron cryo-microscopy
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• 43
Unknown
International Union of Crystallography (IUCr)
In: IUCrJ
Publication Date: 2018-11-19
Description: β-Propeller proteins form one of the largest families of protein structures, with a pseudo-symmetrical fold made up of subdomains called blades. They are not only abundant but are also involved in a wide variety of cellular processes, often by acting as a platform for the assembly of protein complexes. WD40 proteins are a subfamily of propeller proteins with no intrinsic enzymatic activity, but their stable, modular architecture and versatile surface have allowed evolution to adapt them to many vital roles. By computationally reverse-engineering the duplication, fusion and diversification events in the evolutionary history of a WD40 protein, a perfectly symmetrical homologue called Tako8 was made. If two or four blades of Tako8 are expressed as single polypeptides, they do not self-assemble to complete the eight-bladed architecture, which may be owing to the closely spaced negative charges inside the ring. A different computational approach was employed to redesign Tako8 to create Ika8, a fourfold-symmetrical protein in which neighbouring blades carry compensating charges. Ika2 and Ika4, carrying two or four blades per subunit, respectively, were found to assemble spontaneously into a complete eight-bladed ring in solution. These artificial eight-bladed rings may find applications in bionanotechnology and as models to study the folding and evolution of WD40 proteins.
Keywords: bioinformaticsprotein structurecomputational modellingmolecular simulationstructural biologyWD40 proteinsβ-propeller proteins
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• 44
Unknown
International Union of Crystallography (IUCr)
In: IUCrJ
Publication Date: 2018-11-01
Keywords: X-ray scatteringGISAXSimage healingreconstructiondistorted-wave Born approximation
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• 45
Unknown
International Union of Crystallography (IUCr)
In: IUCrJ
Publication Date: 2018-11-01
Description: Poly(ADP-ribose) polymerase 1 (PARP-1), an enzyme that modifies nuclear proteins by poly(ADP-ribosyl)ation, regulates various cellular activities and restricts the lytic replication of oncogenic gammaherpesviruses by inhibiting the function of replication and transcription activator (RTA), a key switch molecule of the viral life cycle. A viral PARP-1-interacting protein (vPIP) encoded by murine gammaherpesvirus 68 (MHV-68) orf49 facilitates lytic replication by disrupting interactions between PARP-1 and RTA. Here, the structure of MHV-68 vPIP was determined at 2.2 Å resolution. The structure consists of 12 α-helices with characteristic N-terminal β-strands (Nβ) and forms a V-shaped-twist dimer in the asymmetric unit. Structure-based mutagenesis revealed that Nβ and the α1 helix (residues 2–26) are essential for the nuclear localization and function of vPIP; three residues were then identified (Phe5, Ser12 and Thr16) that were critical for the function of vPIP and its interaction with PARP-1. A recombinant MHV-68 harboring mutations of these three residues showed severely attenuated viral replication both in vitro and in vivo. Moreover, ORF49 of Kaposi's sarcoma-associated herpesvirus also directly interacted with PARP-1, indicating a conserved mechanism of action of vPIPs. The results elucidate the novel molecular mechanisms by which oncogenic gammaherpesviruses overcome repression by PARP-1 using vPIPs.
Keywords: viral PARP-1-interacting proteinopen reading frame 49poly(ADP-ribose) polymerase 1murine gammaherpesvirus 68Kaposi's sarcoma-associated herpesvirusstructure determinationX-ray crystallography
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• 46
Unknown
International Union of Crystallography (IUCr)
In: IUCrJ
Publication Date: 2018-09-06
Keywords: single-particle three-dimensional imagingX-ray free electron lasersimaging virus particlesimage analysisthree-dimensional reconstructionatomic scale structure
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• 47
Unknown
International Union of Crystallography (IUCr)
In: IUCrJ
Publication Date: 2018-09-06
Description: In this study, the nature and characteristics of a short Br...π interaction observed in an ebselen derivative, 2-(2-bromophenyl)benzo[d][1,2]selenazol-3(2H)-one, has been explored. The electronic nature of this Br...π interaction was investigated via high-resolution X-ray diffraction and periodic density functional theory calculations using atoms-in-molecules (AIM) analysis. This study unravels the simultaneous presence of σ-hole and π-hole bonding characteristics in the same interaction. The dual characteristics of this unique Br...π interaction are further established via molecular electrostatic potentials (MESPs) and natural bond orbitals (NBOs).
Keywords: σ-hole bondingπ-hole bondingebselenelectron densitymolecular electrostatic potentialscrystal engineeringcharge, spin and momentum densitiescomputational modellingmolecular crystals
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• 48
Unknown
International Union of Crystallography (IUCr)
In: IUCrJ
Publication Date: 2018-09-06
Description: Diffraction before destruction using X-ray free-electron lasers (XFELs) has the potential to determine radiation-damage-free structures without the need for crystallization. This article presents the three-dimensional reconstruction of the Melbournevirus from single-particle X-ray diffraction patterns collected at the LINAC Coherent Light Source (LCLS) as well as reconstructions from simulated data exploring the consequences of different kinds of experimental sources of noise. The reconstruction from experimental data suffers from a strong artifact in the center of the particle. This could be reproduced with simulated data by adding experimental background to the diffraction patterns. In those simulations, the relative density of the artifact increases linearly with background strength. This suggests that the artifact originates from the Fourier transform of the relatively flat background, concentrating all power in a central feature of limited extent. We support these findings by significantly reducing the artifact through background removal before the phase-retrieval step. Large amounts of blurring in the diffraction patterns were also found to introduce diffuse artifacts, which could easily be mistaken as biologically relevant features. Other sources of noise such as sample heterogeneity and variation of pulse energy did not significantly degrade the quality of the reconstructions. Larger data volumes, made possible by the recent inauguration of high repetition-rate XFELs, allow for increased signal-to-background ratio and provide a way to minimize these artifacts. The anticipated development of three-dimensional Fourier-volume-assembly algorithms which are background aware is an alternative and complementary solution, which maximizes the use of data.
Keywords: XFELsMelbourneviruscoherent diffractive imagingLCLSimage reconstruction
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• 49
Unknown
International Union of Crystallography (IUCr)
In: IUCrJ
Publication Date: 2018-10-09
Description: Under almost all circumstances, electron diffraction patterns contain information about the phases of structure factors, a consequence of the short wavelength of an electron and its strong Coulombic interaction with matter. However, extracting this information remains a challenge and no generic method exists. In this work, a set of simple analytical expressions is derived for the intensity distribution in convergent-beam electron diffraction (CBED) patterns recorded under three-beam conditions. It is shown that these expressions can be used to identify features in three-beam CBED patterns from which three-phase invariants can be extracted directly, without any iterative refinement processes. The octant, in which the three-phase invariant lies, can be determined simply by inspection of the indexed CBED patterns (i.e. the uncertainty of the phase measurement is ±22.5°). This approach is demonstrated with the experimental measurement of three-phase invariants in two simple test cases: centrosymmetric Si and non-centrosymmetric GaAs. This method may complement existing structure determination methods by providing direct measurements of three-phase invariants to replace guessed' invariants in ab initio phasing methods and hence provide more stringent constraints to the structure solution.
Keywords: crystallographic phase problemthree-phase invariantsconvergent-beam electron diffractionstructure determinationenantiomorph ambiguitynanocrystalsdynamical studiesmultiple scattering
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• 50
Unknown
International Union of Crystallography (IUCr)
In: IUCrJ
Publication Date: 2018-10-11
Description: Basement membranes are extracellular structures of epithelia and endothelia that have collagen IV scaffolds of triple α-chain helical protomers that associate end-to-end, forming networks. The molecular mechanisms by which the noncollagenous C-terminal domains of α-chains direct the selection and assembly of the α1α2α1 and α3α4α5 hetero-oligomers found in vivo remain obscure. Autoantibodies against the noncollagenous domains of the α3α4α5 hexamer or mutations therein cause Goodpasture's or Alport's syndromes, respectively. To gain further insight into oligomer-assembly mechanisms as well as into Goodpasture's and Alport's syndromes, crystal structures of noncollagenous domains produced by recombinant methods were determined. The spontaneous formation of canonical homohexamers (dimers of trimers) of these domains of the α1, α3 and α5 chains was shown and the components of the Goodpasture's disease epitopes were viewed. Crystal structures of the α2 and α4 noncollagenous domains generated by recombinant methods were also determined. These domains spontaneously form homo-oligomers that deviate from the canonical architectures since they have a higher number of subunits (dimers of tetramers and of hexamers, respectively). Six flexible structural motifs largely explain the architectural variations. These findings provide insight into noncollagenous domain folding, while supporting the in vivo operation of extrinsic mechanisms for restricting the self-assembly of noncollagenous domains. Intriguingly, Alport's syndrome missense mutations concentrate within the core that nucleates the folding of the noncollagenous domain, suggesting that this syndrome, when owing to missense changes, is a folding disorder that is potentially amenable to pharmacochaperone therapy.
Keywords: collagen type IVnetwork assembly(IV)NC1 hexamersGoodpasture's diseaseAlport's syndrome
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• 51
Unknown
International Union of Crystallography (IUCr)
In: IUCrJ
Publication Date: 2018-10-18
Description: This study investigated the structural and magnetic properties of Mn3−xFexGa alloys (x = 0, 0.2, 0.4, 0.6, 0.8, 1) under different heat-treatment conditions. A tetragonal structure was observed in samples that were heat treated at 623 K for three days followed by quenching in ice water. These tetragonal alloys present large coercive fields in the range 0.8–5 kOe and low saturation magnetization, and have great potential for application in spin-transfer torque-based devices. A hexagonal structure was observed in samples subjected to heat treatment at 883 K for three days following quenching in ice water. A moderate decrease in the coercive field has been observed for the hexagonal alloys compared with those with a tetragonal structure. However, the Mn3−xFexGa alloys with a hexagonal structure exhibit other attractive magnetic properties, including collinear and non-collinear magnetic properties, holding high promise for technological applications. A face-centred-cubic (f.c.c.) structure was observed when subjected to annealing at 1073 K for three days followed by quenching in ice water. In contrast to the tetragonal and hexagonal structures, all f.c.c. alloys exhibit antiferromagnetic behaviour. This versatile material can display a wide range of multi-functionalities attributed to its tuneable crystal structure. This investigation will guide the design of multiple structures of these materials in order to utilise the wide functionalities for practical applications.
Keywords: Mn–Fe–Ga alloystetragonal Heusler alloysmultiple structural materials
Electronic ISSN: 2052-2525
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• 52
Unknown
International Union of Crystallography (IUCr)
In: IUCrJ
Publication Date: 2018-07-21
Description: The main descriptors of chemical bonding such as bond order (BO) and electron density at the bond critical point, ρc, are customarily used to understand the crystal and electronic structure of materials, as well as to predict their reactivity and stability. They can be obtained in the framework of crystal chemistry and quantum chemistry approaches, which are mostly applied as alternatives to each other. This paper verifies the convergence of the two approaches by analyzing a plethora of quantum chemistry data available in the literature. The exponential correlation between the electron descriptors [BOij and ρc(ij)] and the length of chemical bonds, Rij, which is basic in crystal chemistry, was confirmed for 72 atom pairs, regardless of the nature of their interactions (ionic/covalent, metal–metal, etc.). The difference between the BOij (Rij) correlations obtained in this work and those accepted in crystal chemistry for the same atomic pairs does not exceed the dispersion of quantum chemistry data, confirming the qualitative validity of the BO conservation principle. Various examples are presented to show that knowledge of the exponential parameters ensures a surprisingly simple determination of two basic electron descriptors in any complex compound with known interatomic distances. In particular, the BO analysis for 20 Re6-cluster complexes illustrates the BO conservation for systems with delocalized electrons. Despite the significant transfer of electron density from the Re–Re to the Re–ligand bonds, the total number of Re valence electrons used in bonding remains close to the formal value of seven electrons.
Keywords: chemical bondingbond orderbond lengthsbond critical pointelectron densityconservation principles
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• 53
Unknown
International Union of Crystallography (IUCr)
In: IUCrJ
Publication Date: 2018-07-21
Description: In recent years, the success of serial femtosecond crystallography and the paucity of beamtime at X-ray free-electron lasers have motivated the development of serial microcrystallography experiments at storage-ring synchrotron sources. However, especially at storage-ring sources, if a crystal is too small it will have suffered significant radiation damage before diffracting a sufficient number of X-rays into Bragg peaks for peak-indexing software to determine the crystal orientation. As a consequence, the data frames of small crystals often cannot be indexed and are discarded. Introduced here is a method based on the expand–maximize–compress (EMC) algorithm to solve protein structures, specifically from data frames for which indexing methods fail because too few X-rays are diffracted into Bragg peaks. The method is demonstrated on a real serial microcrystallography data set whose signals are too weak to be indexed by conventional methods. In spite of the daunting background scatter from the sample-delivery medium, it was still possible to solve the protein structure at 2.1 Å resolution. The ability of the EMC algorithm to analyze weak data frames will help to reduce sample consumption. It will also allow serial microcrystallography to be performed with crystals that are otherwise too small to be feasibly analyzed at storage-ring sources.
Keywords: X-ray serial microcrystallographysparse dataEMC algorithmprotein microcrystallographystorage-ring synchrotron sources
Electronic ISSN: 2052-2525
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• 54
Unknown
International Union of Crystallography (IUCr)
In: IUCrJ
Publication Date: 2018-07-21
Description: Heterogeneous catalysts are of great interest in many industrial processes for environmental reasons and, during recent years, a great effort has been devoted to obtain metal–organic frameworks (MOFs) with improved catalytic behaviour. Few supramolecular metal–organic frameworks (SMOFs) are stable under ambient conditions and those with anchored catalysts exhibit favourable properties. However, this paper presents an innovative approach that consists of using metal nodes as both structural synthons and catalysts. Regarding the latter, metalloporphyrins are suitable candidates to play both roles simultaneously. In fact, there are a number of papers that report coordination compounds based on metalloporphyrins exhibiting these features. Thus, the aim of this bioinspired work was to obtain stable SMOFs (at room temperature) based on metalloporphyrins and explore their catalytic activity. This work reports the environmentally friendly microwave-assisted synthesis and characterization of the compound [H(bipy)]2[(MnTPPS)(H2O)2]·2bipy·14H2O (TPPS = meso-tetraphenylporphine-4,4′,4′′,4′′′-tetrasulfonic acid and bipy = 4,4′-bipyridine). This compound is the first example of an MnTPPS-based SMOF, as far as we are aware, and has been structurally and thermally characterized through single-crystal X-ray diffraction, IR spectroscopy, thermogravimetry and transmission electron microscopy. Additionally, this work explores not only the catalytic activity of this compound but also of the compounds μ-O-[FeTCPP]2·16DMF and [CoTPPS0.5(bipy)(H2O)2]·6H2O. The structural features of these supramolecular materials, with accessible networks and high thermal stability, are responsible for their excellent behaviour as heterogeneous catalysts for different oxidation, condensation (aldol and Knoevenagel) and one-pot cascade reactions.
Keywords: metalloporphyrinssupramolecular MOFsheterogeneous catalystsKnoevenagel condensationsaldol condensationsone-pot cascade reactions
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• 55
Unknown
International Union of Crystallography (IUCr)
In: IUCrJ
Publication Date: 2018-07-28
Description: Liquid microjets are a common means of delivering protein crystals to the focus of X-ray free-electron lasers (FELs) for serial femtosecond crystallography measurements. The high X-ray intensity in the focus initiates an explosion of the microjet and sample. With the advent of X-ray FELs with megahertz rates, the typical velocities of these jets must be increased significantly in order to replenish the damaged material in time for the subsequent measurement with the next X-ray pulse. This work reports the results of a megahertz serial diffraction experiment at the FLASH FEL facility using 4.3 nm radiation. The operation of gas-dynamic nozzles that produce liquid microjets with velocities greater than 80 m s−1 was demonstrated. Furthermore, this article provides optical images of X-ray-induced explosions together with Bragg diffraction from protein microcrystals exposed to trains of X-ray pulses repeating at rates of up to 4.5 MHz. The results indicate the feasibility for megahertz serial crystallography measurements with hard X-rays and give guidance for the design of such experiments.
Keywords: X-ray free-electron lasersFELsX-ray FEL pulse trainsmegahertz repetition rates
Electronic ISSN: 2052-2525
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• 56
Unknown
International Union of Crystallography (IUCr)
In: IUCrJ
Publication Date: 2018-08-09
Description: The natural sII-type clathrasil chibaite [chemical formula SiO2·(M12,M16), where Mx denotes a guest molecule] was investigated using single-crystal X-ray diffraction and Raman spectroscopy in the temperature range from 273 to 83 K. The O atoms of the structure at room temperature, which globally conforms to space group Fd{\overline 3}m [V = 7348.9 (17) Å3, a = 19.4420 (15) Å], have anomalous anisotropic displacement parameters indicating a static or dynamic disorder. With decreasing temperature, the crystal structure shows a continuous symmetry-lowering transformation accompanied by twinning. The intensities of weak superstructure reflections increase as temperature decreases. A monoclinic twinned superstructure was derived at 100 K [A2/n, V = 7251.0 (17) Å3, a′ = 23.7054 (2), b′ = 13.6861 (11), c′ = 23.7051 (2) Å, β′ = 109.47°]. The transformation matrix from the cubic to the monoclinic system is ai′ = (½ 1 ½ / ½ 0 −½ / ½ −1 ½). The A2/n host framework has Si—O bond lengths and Si—O—Si angles that are much closer to known values for stable silicate-framework structures compared with the averaged Fd{\overline 3}m model. As suggested from band splitting observed in the Raman spectra, the [512]-type cages (one crystallographically unique in Fd{\overline 3}m, four different in A2/n) entrap the hydrocarbon species (CH4, C2H6, C3H8, i-C4H10). The [51264]-type cage was found to be unique in both structure types. It contains the larger hydrocarbon molecules C2H6, C3H8 and i-C4H10.
Keywords: chibaiteclathrasilshydrocarbonsRaman spectroscopyX-ray diffractionlow temperature
Electronic ISSN: 2052-2525
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• 57
Unknown
International Union of Crystallography (IUCr)
In: IUCrJ
Publication Date: 2018-08-30
Description: Phytochromes are red-light photoreceptors that were first characterized in plants, with homologs in photosynthetic and non-photosynthetic bacteria known as bacteriophytochromes (BphPs). Upon absorption of light, BphPs interconvert between two states denoted Pr and Pfr with distinct absorption spectra in the red and far-red. They have recently been engineered as enzymatic photoswitches for fluorescent-marker applications in non-invasive tissue imaging of mammals. This article presents cryo- and room-temperature crystal structures of the unusual phytochrome from the non-photosynthetic myxobacterium Stigmatella aurantiaca (SaBphP1) and reveals its role in the fruiting-body formation of this photomorphogenic bacterium. SaBphP1 lacks a conserved histidine (His) in the chromophore-binding domain that stabilizes the Pr state in the classical BphPs. Instead it contains a threonine (Thr), a feature that is restricted to several myxobacterial phytochromes and is not evolutionarily understood. SaBphP1 structures of the chromophore binding domain (CBD) and the complete photosensory core module (PCM) in wild-type and Thr-to-His mutant forms reveal details of the molecular mechanism of the Pr/Pfr transition associated with the physiological response of this myxobacterium to red light. Specifically, key structural differences in the CBD and PCM between the wild-type and the Thr-to-His mutant involve essential chromophore contacts with proximal amino acids, and point to how the photosignal is transduced through the rest of the protein, impacting the essential enzymatic activity in the photomorphogenic response of this myxobacterium.
Keywords: phytochromesphotoreceptorsphotosynthetic bacteriamyxobacteriaabsorption spectra
Electronic ISSN: 2052-2525
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• 58
Unknown
International Union of Crystallography (IUCr)
In: IUCrJ
Publication Date: 2018-08-30
Description: The question of whether intermolecular interactions in crystals originate from localized atom...atom interactions or as a result of holistic molecule...molecule close packing is a matter of continuing debate. In this context, the newly introduced Roby–Gould bond indices are reported for intermolecular σ-hole' interactions, such as halogen bonding and chalcogen bonding, and compared with those for hydrogen bonds. A series of 97 crystal systems exhibiting these interaction motifs obtained from the Cambridge Structural Database (CSD) has been analysed. In contrast with conventional bond-order estimations, the new method separately estimates the ionic and covalent bond indices for atom...atom and molecule...molecule bond orders, which shed light on the nature of these interactions. A consistent trend in charge transfer from halogen/chalcogen bond-acceptor to bond-donor groups has been found in these intermolecular interaction regions via Hirshfeld atomic partitioning of the electron populations. These results, along with the conservation of bond orders' tested in the interaction regions, establish the significant role of localized atom...atom interactions in the formation of these intermolecular binding motifs.
Keywords: intermolecular interactionsbond orderionicityhydrogen bondinghalogen bondingcrystal engineeringcomputational modellingmolecular crystals
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• 59
Unknown
International Union of Crystallography (IUCr)
In: IUCrJ
Publication Date: 2018-01-26
Description: With the intention of producing the most comprehensive treatment of the prevalence of crystal polymorphism among structurally characterized materials, all polymorphic compounds flagged as such within the Cambridge Structural Database (CSD) are analysed and a list of crystallographically characterized organic polymorphic compounds is assembled. Classifying these structures into subclasses of anhydrates, salts, hydrates, non-hydrated solvates and cocrystals reveals that there are significant variations in polymorphism prevalence as a function of crystal type, a fact which has not previously been recognized in the literature. It is also shown that, as a percentage, polymorphic entries are decreasing temporally within the CSD, with the notable exception of cocrystals, which continue to rise at a rate that is a constant fraction of the overall entries. Some phenomena identified that require additional scrutiny include the relative prevalence of temperature-induced phase transitions among organic salts and the paucity of polymorphism in crystals with three or more chemical components.
Keywords: phase transitionspolymorphshydratescocrystalsCambridge Structural Database
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• 60
Unknown
International Union of Crystallography (IUCr)
In: IUCrJ
Publication Date: 2018-01-26
Description: The crystal structure of the excitonic insulator Ta2NiSe5 has been investigated under a range of pressures, as determined by the complementary analysis of both single-crystal and powder synchrotron X-ray diffraction measurements. The monoclinic ambient-pressure excitonic insulator phase II transforms upon warming or under a modest pressure to give the semiconducting C-centred orthorhombic phase I. At higher pressures (i.e. 〉3 GPa), transformation to the primitive orthorhombic semimetal phase III occurs. This transformation from phase I to phase III is a pressure-induced first-order phase transition, which takes place through coherent sliding between weakly coupled layers. This structural phase transition is significantly influenced by Coulombic interactions in the geometric arrangement between interlayer Se ions. Furthermore, upon cooling, phase III transforms into the monoclinic phase IV, which is analogous to the excitonic insulator phase II. Finally, the excitonic interactions appear to be retained despite the observed layer sliding transition.
Keywords: inorganic materialshigh-pressure single-crystal X-ray diffractionexcitonic insulators
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• 61
Unknown
International Union of Crystallography (IUCr)
In: IUCrJ
Publication Date: 2018-01-26
Description: Determining macromolecular structures from X-ray data with resolution worse than 3 Å remains a challenge. Even if a related starting model is available, its incompleteness or its bias together with a low observation-to-parameter ratio can render the process unsuccessful or very time-consuming. Yet, many biologically important macromolecules, especially large macromolecular assemblies, membrane proteins and receptors, tend to provide crystals that diffract to low resolution. A new algorithm to tackle this problem is presented that uses a multivariate function to simultaneously exploit information from both an initial partial model and low-resolution single-wavelength anomalous diffraction data. The new approach has been used for six challenging structure determinations, including the crystal structures of membrane proteins and macromolecular complexes that have evaded experts using other methods, and large structures from a 3.0 Å resolution F1-ATPase data set and a 4.5 Å resolution SecYEG–SecA complex data set. All of the models were automatically built by the method to Rfree values of between 28.9 and 39.9% and were free from the initial model bias.
Keywords: low resolutionX-ray crystallographysingle-wavelength anomalous diffractionmultivariate statisticsmodel biasstructure determinationmembrane proteinsrefinementmulti-protein complexes
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• 62
Unknown
International Union of Crystallography (IUCr)
In: IUCrJ
Publication Date: 2018-01-26
Description: Molecular-dynamics (MD) simulations of Bragg and diffuse X-ray scattering provide a means of obtaining experimentally validated models of protein conformational ensembles. This paper shows that compared with a single periodic unit-cell model, the accuracy of simulating diffuse scattering is increased when the crystal is modeled as a periodic supercell consisting of a 2 × 2 × 2 layout of eight unit cells. The MD simulations capture the general dependence of correlations on the separation of atoms. There is substantial agreement between the simulated Bragg reflections and the crystal structure; there are local deviations, however, indicating both the limitation of using a single structure to model disordered regions of the protein and local deviations of the average structure away from the crystal structure. Although it was anticipated that a simulation of longer duration might be required to achieve maximal agreement of the diffuse scattering calculation with the data using the supercell model, only a microsecond is required, the same as for the unit cell. Rigid protein motions only account for a minority fraction of the variation in atom positions from the simulation. The results indicate that protein crystal dynamics may be dominated by internal motions rather than packing interactions, and that MD simulations can be combined with Bragg and diffuse X-ray scattering to model the protein conformational ensemble.
Keywords: diffuse scatteringprotein crystallographyX-ray diffractionmolecular-dynamics simulationprotein conformational ensemblestaphylococcal nucleaseX-ray crystallographymolecular crystalsmolecular simulation
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• 63
Unknown
International Union of Crystallography (IUCr)
In: IUCrJ
Publication Date: 2018-02-22
Description: Conformational changes drive protein function, including catalysis, allostery and signaling. X-ray diffuse scattering from protein crystals has frequently been cited as a probe of these correlated motions, with significant potential to advance our understanding of biological dynamics. However, recent work has challenged this prevailing view, suggesting instead that diffuse scattering primarily originates from rigid-body motions and could therefore be applied to improve structure determination. To investigate the nature of the disorder giving rise to diffuse scattering, and thus the potential applications of this signal, a diverse repertoire of disorder models was assessed for its ability to reproduce the diffuse signal reconstructed from three protein crystals. This comparison revealed that multiple models of intramolecular conformational dynamics, including ensemble models inferred from the Bragg data, could not explain the signal. Models of rigid-body or short-range liquid-like motions, in which dynamics are confined to the biological unit, showed modest agreement with the diffuse maps, but were unable to reproduce experimental features indicative of long-range correlations. Extending a model of liquid-like motions to include disorder across neighboring proteins in the crystal significantly improved agreement with all three systems and highlighted the contribution of intermolecular correlations to the observed signal. These findings anticipate a need to account for intermolecular disorder in order to advance the interpretation of diffuse scattering to either extract biological motions or aid structural inference.
Keywords: diffuse scatteringintermolecular correlations
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• 64
Unknown
International Union of Crystallography (IUCr)
In: IUCrJ
Publication Date: 2018-03-28
Description: For many years, quasicrystals were observed only as solid-state metallic alloys, yet current research is now actively exploring their formation in a variety of soft materials, including systems of macromolecules, nanoparticles and colloids. Much effort is being invested in understanding the thermodynamic properties of these soft-matter quasicrystals in order to predict and possibly control the structures that form, and hopefully to shed light on the broader yet unresolved general questions of quasicrystal formation and stability. Moreover, the ability to control the self-assembly of soft quasicrystals may contribute to the development of novel photonics or other applications based on self-assembled metamaterials. Here a path is followed, leading to quantitative stability predictions, that starts with a model developed two decades ago to treat the formation of multiple-scale quasiperiodic Faraday waves (standing wave patterns in vibrating fluid surfaces) and which was later mapped onto systems of soft particles, interacting via multiple-scale pair potentials. The article reviews, and substantially expands, the quantitative predictions of these models, while correcting a few discrepancies in earlier calculations, and presents new analytical methods for treating the models. In so doing, a number of new stable quasicrystalline structures are found with octagonal, octadecagonal and higher-order symmetries, some of which may, it is hoped, be observed in future experiments.
Keywords: quasicrystalssoft matterpattern formation
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• 65
Unknown
International Union of Crystallography (IUCr)
In: IUCrJ
Publication Date: 2018-03-28
Description: Photoinitiated solid-state reactions are known to affect the physical properties of coordination polymers, such as fluorescence and sorption behaviour, and also afford extraordinary architectures (e.g. three-periodic structures with polyorganic ligands). However, the construction of novel photo-sensitive coordination polymers requires an understanding of the factors which govern the mutual disposition of reactive fragments. A series of zinc(II) malonate complexes with 1,2-bis(pyridin-4-yl)ethylene and its photo-insensitive analogues has been synthesized for the purpose of systematic analysis of their underlying nets and mutual disposition of N-donor ligands. The application of a big data-set analysis for the prediction of a variety of possible complex compositions, coordination environments and networks for a four-component system has been demonstrated for the first time. Seven of the nine compounds possess one of the highly probable topologies for their underlying nets; in addition, two novel closely related four-coordinated networks were obtained. Complexes containing 1,2-bis(pyridin-4-yl)ethylene and 1,2-bis(pyridin-4-yl)ethane form isoreticular compounds more readily than those with 4,4′-bipyridine and 1,2-bis(pyridin-4-yl)ethylene. The effects of the precursor, either zinc(II) nitrate or zinc(II) acetate, on the composition and dimensionality of the resulting architecture are discussed. For three of the four novel complexes containing 1,2-bis(pyridin-4-yl)ethylene, the single-crystal-to-single-crystal [2 + 2] cycloaddition reactions were carried out. UV irradiation of these crystals afforded either the 0D→1D or the 3D→3D transformations, with and without network changes. One of the two 3D→3D transformations was accompanied by solvent (H2O) cleavage.
Keywords: crystal engineeringcrystal structure predictionscoordination polymersorganic solid-state reactionscycloaddition reactionssingle-crystal-to-single-crystal transformationsphoto-sensitive ligands
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• 66
Unknown
International Union of Crystallography (IUCr)
In: IUCrJ
Publication Date: 2018-04-07
Description: Pharmaceutical salt solvates (dimethyl sulfoxide, DMSO) of the drug triamterene with the coformers acetic, succinic, adipic, pimelic, azelaic and nicotinic acid and ibuprofen are prepared by liquid-assisted grinding and solvent-evaporative crystallization. The modified ΔpKa rule as proposed by Cruz-Cabeza [(2012). CrystEngComm, 14, 6362–6365] is in close agreement with the results of this study. All adducts were characterized by X-ray diffraction and thermal analytical techniques, including single-crystal X-ray diffraction, powder X-ray diffraction, differential scanning calorimetry and thermal gravimetric analysis. Hydrogen-bonded motifs combined to form a variety of extended tapes and sheets. Analysis of the crystal structures showed that all adducts existed as salt solvates and contained the aminopyridinium–carboxylate heterodimer, except for the solvate containing triamterene, ibuprofen and DMSO, as a result of the presence of a strong and stable hemitriamterenium duplex. A search of the Cambridge Structural Database (CSD 5.36, Version 1.18) to determine the frequency of occurrence of the putative supramolecular synthons found in this study showed good agreement with previous work.
Keywords: triamterenepKa analysiscrystal engineeringliquid-assisted grindingpharmaceutical salt solvateshydrogen bondingmotif analysisstable duplex structures
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• 67
Unknown
International Union of Crystallography (IUCr)
In: IUCrJ
Publication Date: 2018-04-20
Keywords: X-ray lasersXFELsprotein dynamicsstructural biology
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• 68
Unknown
International Union of Crystallography (IUCr)
In: IUCrJ
Publication Date: 2018-04-20
Description: Structural changes in tridymite have been investigated by molecular dynamics simulation. Two thermal processes were carried out, one cooling from the high-temperature hexagonal structure of tridymite (HP-tridymite) and the other heating from the low-temperature monoclinic structure of tridymite (MX1-tridymite). The former process showed that HP, LHP (low-temperature hexagonal structure), OC (orthorhombic structure with C2221 symmetry) and OP (orthorhombic structure with P212121 symmetry)-like structures appeared in sequence. In contrast, the latter process showed that MX1, OP, OC, LHP and HP-like structures appeared in sequence. Detailed analysis of the calculated structures showed that the configuration underwent stepwise changes associated with several characteristic modes. First, the structure of HP-tridymite determined from diffraction experiments was identified as a time-averaged structure in a similar manner to β-cristobalite, thus indicating the important role of floppy modes of oxygen atoms at high temperature – one of the common features observed in silica crystals and glass. Secondly, the main structural changes were ascribed to a combination of distortion of the six-membered rings in the layers and misalignment between layers. We suggest that the slowing down of floppy oxygen movement invokes the multistage emergence of structures with lower symmetry on cooling. This study therefore not only reproduces the sequence of the main polymorphic transitions in tridymite, except for the appearance of the monoclinic phase, but also explains the microscopic dynamic structural changes in detail.
Keywords: silicatridymitemolecular dynamicsstructurephase transitionspolymorphs
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• 69
Unknown
International Union of Crystallography (IUCr)
In: IUCrJ
Publication Date: 2018-04-20
Description: The structural origin of absorption and fluorescence anisotropy of the single crystal of the π-conjugated heterocyclic system 5,6,10b-triazaacephenanthrylene, TAAP, is presented in this study. X-ray analysis shows that the crystal framework in the space group P\overline{1} is formed by centrosymmetric dimers of face-to-face mutually oriented TAAP molecules joined by π–π non-covalent interactions. The conformation of the TAAP molecule is stabilized by intramolecular C—H...N(sp2), N(sp2)H...π(CN), and C—H...O(sp2) hydrogen bonds. The presence of weak π–π interactions is confirmed by quantum theory of atoms in molecules (QTAIM) and non-covalent interaction (NCI) analysis. The analysis of the optical spectra of TAAP in solution and in the solid state does not allow the specification of the aggregation type. DFT calculations for the dimer in the gas phase indicate that the lowest singlet excitation is forbidden by symmetry, suggesting H-type aggregation, even though the overall absorption spectrum is bathochromically shifted as for the J-type. The experimental determination of the permanent dipole moment of a TAAP molecule in 1,4-dioxane solution indicates the presence of the monomer form. The calculated absorption and emission spectra of the crystal in a simple approximation are consistent with the experimentally determined orientation of the absorption and emission transition dipole moments in TAAP single crystals. The electrostatic interaction between monomers with a permanent dipole moment (ca 4 D each) could result in the unusual spectroscopic JH-aggregate behaviour of the TAAP dimer.
Keywords: optical materialsfluorescenceanisotropyJH aggregatestriazaacephenanthrylene (TAAP)hydrogen bondingπ–π interactionstransition dipole moments
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• 70
Unknown
International Union of Crystallography (IUCr)
In: IUCrJ
Publication Date: 2018-02-15
Description: Electron crystallography is a discipline that currently attracts much attention as method for inorganic, organic and macromolecular structure solution. EIGER, a direct-detection hybrid pixel detector developed at the Paul Scherrer Institut, Switzerland, has been tested for electron diffraction in a transmission electron microscope. EIGER features a pixel pitch of 75 × 75 µm2, frame rates up to 23 kHz and a dead time between frames as low as 3 µs. Cluster size and modulation transfer functions of the detector at 100, 200 and 300 keV electron energies are reported and the data quality is demonstrated by structure determination of a SAPO-34 zeotype from electron diffraction data.
Keywords: EIGERhybrid pixel detectorselectron crystallographySAPO-34
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• 71
Unknown
International Union of Crystallography (IUCr)
In: IUCrJ
Publication Date: 2018-02-15
Description: The existence of isomerism in coordination polymeric structures offers opportunities to understand structure–function relationships. Herein the serendipitous isolation is reported of two isomeric double-pillared-layer coordination polymeric structures arising from two different types of carboxylate bonding of benzene-1,4-dicarboxylate ligands to zinc(II), which constitutes a new type of structural isomerism. The different bonding modes not only alter the shape and size of the pores, but also the nature of interpenetration and photoreactivity. Although two trans,cis,trans-bpeb ligands with conjugated olefin bonds are aligned in close proximity in both of the structures, one isomer undergoes a double [2 + 2] cycloaddition reaction and the second isomer only offers an incomplete single cycloaddition product. This work demonstrates how small changes in the structural connectivity can have an impact on the overall structural, physical and chemical properties of such materials.
Keywords: cycloaddition reactionssupramolecular isomerismmetal–organic frameworksMOFscoordination polymerssingle-crystal-to-single-crystal transformationscrystal engineeringcrystallization and crystal growthsolid-state transformationsstructural isomerism
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• 72
Unknown
International Union of Crystallography (IUCr)
In: IUCrJ
Publication Date: 2018-02-21
Description: Cytochrome bc1, a dimeric multi-subunit electron-transport protein embedded in the inner mitochondrial membrane, is a major drug target for the treatment and prevention of malaria and toxoplasmosis. Structural studies of cytochrome bc1 from mammalian homologues co-crystallized with lead compounds have underpinned structure-based drug design to develop compounds with higher potency and selectivity. However, owing to the limited amount of cytochrome bc1 that may be available from parasites, all efforts have been focused on homologous cytochrome bc1 complexes from mammalian species, which has resulted in the failure of some drug candidates owing to toxicity in the host. Crystallographic studies of the native parasite proteins are not feasible owing to limited availability of the proteins. Here, it is demonstrated that cytochrome bc1 is highly amenable to single-particle cryo-EM (which uses significantly less protein) by solving the apo and two inhibitor-bound structures to ∼4.1 Å resolution, revealing clear inhibitor density at the binding site. Therefore, cryo-EM is proposed as a viable alternative method for structure-based drug discovery using both host and parasite enzymes.
Keywords: cryo-electron microscopycryo-EMmembrane proteinselectron-transport chainmalariacytochrome bc1
Electronic ISSN: 2052-2525
Topics: Geosciences , Physics
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• 73
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International Union of Crystallography (IUCr)
In: IUCrJ
Publication Date: 2018-03-06
Keywords: crystallographytherapeutic medicinesstructure-guided drug developmenteditorial
Electronic ISSN: 2052-2525
Topics: Geosciences , Physics
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• 74
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International Union of Crystallography (IUCr)
In: IUCrJ
Publication Date: 2018-03-06
Keywords: diffuse scatteringintermolecular correlationsLLM models
Electronic ISSN: 2052-2525
Topics: Geosciences , Physics
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• 75
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International Union of Crystallography (IUCr)
In: IUCrJ
Publication Date: 2018-03-06
Keywords: nanomaterialscellular imagingcoherent diffractive imagingCDIequal slope tomographyESTscanning transmission X-ray microscopygeneralized Fourier iterative reconstructionGENFIREmulti-model imaging
Electronic ISSN: 2052-2525
Topics: Geosciences , Physics
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• 76
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International Union of Crystallography (IUCr)
In: IUCrJ
Publication Date: 2018-01-04
Keywords: functional materialsstructural scienceeditorial
Electronic ISSN: 2052-2525
Topics: Geosciences , Physics
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• 77
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International Union of Crystallography (IUCr)
In: IUCrJ
Publication Date: 2018-01-04
Keywords: carbonic anhydrase IIproton transferwater dynamicshigh pressure
Electronic ISSN: 2052-2525
Topics: Geosciences , Physics
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• 78
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International Union of Crystallography (IUCr)
In: IUCrJ
Publication Date: 2018-01-11
Description: Until recently, the occurrence of conformational entropy in protein crystal contacts was considered to be a very unlikely event. A study based on the most accurately refined protein structures demonstrated that side-chain conformational entropy and static disorder might be common in protein crystal lattices. The present investigation uses structures refined using ensemble refinement to show that although paradoxical, conformational entropy is likely to be the major factor in the emergence and integrity of the protein condensed phase. This study reveals that the role of shape entropy and local entropic forces expands beyond the onset of crystallization. For the first time, the complete pattern of intermolecular interactions by protein atoms in crystal lattices is presented, which shows that van der Waals interactions dominate in crystal formation.
Keywords: protein crystalsstatic disorderdynamic disorderconformational entropyelastic molecular shapeoscillating crystal latticelocal entropic forceX-ray crystallographycrystallizationcrystal growth
Electronic ISSN: 2052-2525
Topics: Geosciences , Physics
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• 79
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International Union of Crystallography (IUCr)
In: IUCrJ
Publication Date: 2018-01-11
Description: Knowledge of the interactions between nanomaterials and large-size mammalian cells, including cellular uptake, intracellular localization and translocation, has greatly advanced nanomedicine and nanotoxicology. Imaging techniques that can locate nanomaterials within the structures of intact large-size cells at nanoscale resolution play crucial roles in acquiring this knowledge. Here, the quantitative imaging of intracellular nanomaterials in three dimensions was performed by combining dual-energy contrast X-ray microscopy and an iterative tomographic algorithm termed equally sloped tomography (EST). Macrophages with a size of ∼20 µm that had been exposed to the potential antitumour agent [Gd@C82(OH)22]n were investigated. Large numbers of nanoparticles (NPs) aggregated within the cell and were mainly located in phagosomes. No NPs were observed in the nucleus. Imaging of the nanomedicine within whole cells advanced the understanding of the high-efficiency antitumour activity and the low toxicity of this agent. This imaging technique can be used to probe nanomaterials within intact large-size cells at nanometre resolution uniformly in three dimensions and may greatly benefit the fields of nanomedicine and nanotoxicology.
Keywords: cellular imagingX-ray tomographyequally sloped tomographydual-energy contrastcomputed tomographynanoscienceX-ray microscopyimagingstructure determination
Electronic ISSN: 2052-2525
Topics: Geosciences , Physics
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• 80
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