Hasil untuk "Crystallography"

G. Winter

G. Langer, Serge X. Cohen, V. Lamzin et al.

A. Brunger

Sydney Hall, B. McMahon

Y. Hinuma, G. Pizzi, Y. Kumagai et al.

Systematic and automatic calculations of the electronic band structure are a crucial component of computationally-driven high-throughput materials screening. An algorithm, for any crystal, to derive a unique description of the crystal structure together with a recommended band path is indispensable for this task. The electronic band structure is typically sampled along a path within the first Brillouin zone including the surface in reciprocal space. Some points in reciprocal space have higher site symmetries and/or have higher constraints than other points regarding the electronic band structure and therefore are likely to be more important than other points. This work categorizes points in reciprocal space according to their symmetry and provides recommended band paths that cover all special wavevector (k-vector) points and lines necessarily and sufficiently. Points in reciprocal space are labeled such that there is no conflict with the crystallographic convention. The k-vector coefficients of labeled points, which are located at Brillouin zone face and edge centers as well as vertices, are derived based on a primitive cell compatible with the crystallographic convention, including those with axial ratio-dependent coordinates. Furthermore, we provide an open-source implementation of the algorithms within our SeeK-path python code, to allow researchers to obtain k-vector coefficients and recommended band paths in an automated fashion. Finally, we created a free online service to compute and visualise Brillouin Zone, labeled k-points and suggested band paths for any crystal structure, that we made available at this http URL .

R. Kidmose, Jonathan Juhl, P. Nissen et al.

Model building into experimental maps is a key element of structural biology, but can be both time consuming and error-prone. Here we present Namdinator, an easy-to-use tool that enables the user to run a Molecular Dynamics Flexible Fitting (MDFF) simulation in an automated manner through a pipeline system. Namdinator will modify an atomic model to fit within cryo-EM or crystallography density maps, and can be used advantageously for both the initial fitting of models, and for a geometrical optimization step to correct outliers, clashes and other model problems. We have benchmarked Namdinator against 39 deposited models and maps from cryo-EM and observe model improvements in 34 of these cases (87%). Clashes between atoms were reduced, and model-to-map fit and overall model geometry were improved, in several cases substantially. We show that Namdinator is able to model large scale conformational changes compared to the starting model. Namdinator is a fast and easy way to create suitable initial models for both cryo-EM and crystallography. It can fix model errors in the final steps of model building, and is usable for structural model builders at all skill levels. Namdinator is available as a web service (https://namdinator.au.dk), or can be run locally as a command-line tool. Synopsis A pipeline tool called Namdinator is presented that enables the user to run a Molecular Dynamics Flexible Fitting (MDFF) simulation in a fully automated manner, both online and locally. This provides a fast and easy way to create suitable initial models for both cryo-EM and crystallography and help fix errors in the final steps of model building.

D. Aragão, J. Aishima, Hima Cherukuvada et al.

A microfocus macromolecular crystallography beamline at the Australian Synchrotron is presented.

Satoru Hayami

We theoretically investigate the influence of uniaxial distortion on the stability of square skyrmion crystals, which are described as double-<i>Q</i> spin textures composed of two orthogonal spiral modulations, in noncentrosymmetric magnets. An effective spin model incorporating momentum-resolved frustrated exchange interactions and Dzyaloshinskii–Moriya (DM) interactions is analyzed using simulated-annealing calculations at low temperatures. The results reveal that uniaxial distortion drives a transformation from the double-<i>Q</i> square skyrmion crystal to a single-<i>Q</i> tilted conical spiral or vertical spiral state. The low-temperature phase diagrams further show that the stability region of the skyrmion crystal expands with increasing the magnitude of the DM interaction, making the phase more robust against the uniaxial anisotropy between exchange interactions parallel and perpendicular to the distortion axis. This study provides insight into how uniaxial strain and DM interactions cooperatively influence the formation and stability of skyrmion crystal phases in noncentrosymmetric magnetic systems.

Matthias Kellner, Ruben Rodriguez-Madrid, Jacob B. Holmes et al.

Structure determination by chemical-shift-driven NMR crystallography relies on comparing chemical shieldings measured in solid-state NMR experiments with simulations. However, computational cost limits the accuracy of shielding predictions, that usually rely on low-level electronic-structure approximations and neglect thermal and quantum mechanical nuclear motion, leading to large errors, especially for highly informative hydrogen-bonded protons. To address these limitations, we introduce a quantum-nuclei-corrected (QNC-NMR) approach. We generate inexpensively quantum ensembles using PET-MOLS, a novel machine-learning learning model of the interatomic potential transferable across molecular crystals. Using them as inputs to a chemical-shift model results in a two-fold improvement of the agreement with experiments for hydrogen-bonded protons, without the need for empirical corrections. The ability to sample structures consistent with the experimental conditions enables further refinement of the shielding model by finetuning it against measured shieldings. The favorable scaling with system size allows similar improvements for amorphous materials that are otherwise inaccessible to explicit DFT simulations.

Ilya Popov, Elena Besley

Moiré materials, typically confined to stacking atomically thin, two - dimensional (2D) layers such as graphene or transition metal dichalcogenides, have transformed our understanding of strongly correlated and topological quantum phenomena. The lattice mismatch and relative twist angle between 2D layers have shown to result in Moiré patterns associated with widely tunable electronic properties, ranging from Mott and Chern insulators to semi- and super-conductors. Extended to three-dimensional (3D) structures, Moiré materials unlock an entirely new crystallographic space defined by the elements of the 3D rotation group and translational symmetry of the constituent lattices. 3D Moiré crystals exhibit fascinating novel properties, often not found in the individual components, yet the general construction principles of 3D Moiré crystals remain largely unknown. Here we establish fundamental mathematical principles of 3D Moiré crystallography and propose a general method of 3D Moiré crystal construction using Clifford algebras over the field of rational numbers. We illustrate several examples of 3D Moiré structures representing realistic chemical frameworks and highlight their potential applications in condensed matter physics and solid-state chemistry.

X. X. Wei, B. Zhang, B. Wu et al.

Nanometer-thick passive films, which impart superior corrosion resistance to metals, are degraded in long-term service; they are also susceptible to chloride-induced localized attack. Here we show, by engineering crystallographic configurations upon metal matrices adjacent to their passive films, we obtain great enhancement of corrosion resistance of FeCr15Ni15 single crystal in sulphuric acid, with activation time up to two orders of magnitude longer than that of the non-engineered counterparts. Meanwhile, engineering crystallography decreases the passive current density and shifts the pitting potential to noble values. Applying anodic polarizations under a transpassivation potential, we make the metal matrices underneath the transpassive films highly uneven with {111}-terminated configurations, which is responsible for the enhancement of corrosion resistance. The transpassivation strategy also works in the commercial stainless steels where both grain interior and grain boundaries are rebuilt into the low-energy configurations. Our results demonstrate a technological implication in the pretreatment process of anti-corrosion engineering. Passive films on metal surfaces provide better corrosion resistance, but they can degrade in long-term service. Here the authors demonstrate a strategy to engineer crystallographic configuration at the metal/film interface to further improve corrosion resistance.

Qisheng Wang, Kun Zhang, Yin Cui et al.

Nan Yan, Nan Xia, Lingwen Liao et al.

A mysterious, long-pursued structure of a nanocluster-nanocrystal transition-sized nanoparticle is unraveled. The transition from nanocluster to nanocrystal is a central issue in nanoscience. The atomic structure determination of metal nanoparticles in the transition size range is challenging and particularly important in understanding the quantum size effect at the atomic level. On the basis of the rationale that the intra- and interparticle weak interactions play critical roles in growing high-quality single crystals of metal nanoparticles, we have reproducibly obtained ideal crystals of Au144(SR)60 and successfully solved its structure by x-ray crystallography (XRC); this structure was theoretically predicted a decade ago and has long been pursued experimentally but without success until now. Here, XRC reveals an interesting Au12 hollow icosahedron in thiolated gold nanoclusters for the first time. The Au–Au bond length, close to that of bulk gold, shows better thermal extensibility than the other Au–Au bond lengths in Au144(SR)60, providing an atomic-level perspective because metal generally shows better thermal extensibility than nonmetal materials. Thus, our work not only reveals the mysterious, long experimentally pursued structure of a transition-sized nanoparticle but also has important implications for the growth of high-quality, single-crystal nanoparticles, as well as for the understanding of the thermal extensibility of metals from the perspective of chemical bonding.

L. Maveyraud, L. Mourey

With the advent of structural biology in the drug discovery process, medicinal chemists gained the opportunity to use detailed structural information in order to progress screening hits into leads or drug candidates. X-ray crystallography has proven to be an invaluable tool in this respect, as it is able to provide exquisitely comprehensive structural information about the interaction of a ligand with a pharmacological target. As fragment-based drug discovery emerged in the recent years, X-ray crystallography has also become a powerful screening technology, able to provide structural information on complexes involving low-molecular weight compounds, despite weak binding affinities. Given the low numbers of compounds needed in a fragment library, compared to the hundreds of thousand usually present in drug-like compound libraries, it now becomes feasible to screen a whole fragment library using X-ray crystallography, providing a wealth of structural details that will fuel the fragment to drug process. Here, we review theoretical and practical aspects as well as the pros and cons of using X-ray crystallography in the drug discovery process.

A. Rubio, J. M. Montanero, M. Vakili et al.

We have produced superstable compound liquid microjets with a three-dimensional printed coaxial flow-focusing injector. The aqueous jet core is surrounded by a shell, a few hundred nanometers in thickness, of a low-concentration aqueous solution of a low-molecular-weight polymer. Due to the stabilizing effect of the polymeric shell, the minimum liquid flow rate leading to stable flow-focusing is decreased by one order of magnitude, resulting in much thinner and longer jets. Possible applications of this technique for Serial Femtosecond X-ray Crystallography are discussed.

Elyse A. Schriber, Daniel W. Paley, R. Bolotovsky et al.

Inorganic–organic hybrid materials represent a large share of newly reported structures, owing to their simple synthetic routes and customizable properties 1 . This proliferation has led to a characterization bottleneck: many hybrid materials are obligate microcrystals with low symmetry and severe radiation sensitivity, interfering with the standard techniques of single-crystal X-ray diffraction 2 , 3 and electron microdiffraction 4 – 11 . Here we demonstrate small-molecule serial femtosecond X-ray crystallography (smSFX) for the determination of material crystal structures from microcrystals. We subjected microcrystalline suspensions to X-ray free-electron laser radiation 12 , 13 and obtained thousands of randomly oriented diffraction patterns. We determined unit cells by aggregating spot-finding results into high-resolution powder diffractograms. After indexing the sparse serial patterns by a graph theory approach 14 , the resulting datasets can be solved and refined using standard tools for single-crystal diffraction data 15 – 17 . We describe the ab initio structure solutions of mithrene (AgSePh) 18 – 20 , thiorene (AgSPh) and tethrene (AgTePh), of which the latter two were previously unknown structures. In thiorene, we identify a geometric change in the silver–silver bonding network that is linked to its divergent optoelectronic properties 20 . We demonstrate that smSFX can be applied as a general technique for structure determination of beam-sensitive microcrystalline materials at near-ambient temperature and pressure. Small-molecule serial femtosecond X-ray crystallography (smSFX) characterizes microcrystals by indexing sparse serial XFEL diffraction frames, with little sample preparation, without beam damage, and at room temperature and pressure.

G. Brändén, R. Neutze

Bright future ahead for crystallography Macromolecular x-ray crystallography typically provides static snapshots of systems at equilibrium. Advances in time-resolved crystallography have made it possible to capture dynamics in biomolecules: large and small, fast and slow. Brändén and Neutze review techniques and concepts that have emerged from recent work at x-ray free electron laser sources and are now being applied in other settings and to a growing number of biological systems. Despite challenges in analyzing and relating these data to a biological context, experiments in this field have opened new frontiers in temporal and spatial resolution and yielded many new insights into nonequilibrium chemistry and conformational changes in biology. Science, aba0954, this issue p. eaba0954 A Review explains that time-resolved crystallography is growing rapidly based on serial approaches developed at x-ray free-electron lasers. BACKGROUND Conformational changes are essential for the correct functioning of biological macromolecules. Time-resolved x-ray crystallography extends an extremely successful method for the structural determination of biomolecules by incorporating time as a fourth dimension. Time-resolved x-ray diffraction studies are performed at room temperature so as to allow the biological reaction to evolve within crystals. This reaction must also be initiated throughout crystals—and x-ray diffraction data must be collected—at least as rapidly as the fastest time point of interest. Mature structural analysis tools of macromolecular crystallography can then be adapted to allow x-ray diffraction data to be analyzed in terms of time-dependent conformational changes. ADVANCES Decades of work using polychromatic x-ray pulses (Laue diffraction) at synchrotron radiation sources laid the experimental foundations underpinning the field of time-resolved macromolecular crystallography. Light-driven biological reactions can be rapidly initiated throughout crystals using short laser pulses and have therefore been a major focus for the field. Serial crystallography was first demonstrated 10 years ago at an x-ray free-electron laser (XFEL). In this approach, x-ray diffraction data are collected from a sequence of microcrystals, typically 10 μm or less in their largest dimension, that are being continuously replaced. X-ray diffraction data from thousands of microcrystals are then merged into a complete dataset. Sample delivery for serial crystallography experiments at an XFEL initially relied on liquid microjets, but many other sample-delivery technologies have since been developed, each with its own strengths and weaknesses. Serial crystallography has overcome many of the technical limitations that constrained time-resolved Laue diffraction and has thereby transformed the field, creating a renaissance of interest in time-resolved macromolecular crystallography. In this Review, we describe how time-resolved x-ray diffraction studies using XFEL pulses a few femtoseconds (10−15 s) in duration have allowed atomic motions in biological samples to be visualized on the time scales at which chemical bonds break or isomerize or at which electrons move. We illustrate the power of time-resolved serial crystallography to yield structural and functional insights on slower time scales by showcasing structural results from two energy-transducing membrane proteins, bacteriorhodopsin and photosystem II, neither of which were amenable to synchrotron-based time-resolved Laue diffraction. We also discuss structural results obtained when using mixing jets to diffuse reactants into microcrystals or when releasing photocaged compounds using a laser flash, which have allowed biological reactions that are not naturally light sensitive to be followed in time. OUTLOOK Time-resolved crystallography is transitioning from a highly technical domain of specialists into a flexible approach for elucidating structural and functional insights from macromolecules in their crystalline state. Although serial crystallography was first developed for XFEL-based studies, the recent transfer of time-resolved serial crystallography to synchrotron radiation facilities is critical for the growth of the user community. Nonspecialist user communities will also drive standardized experimental setups that further lower entry barriers for new users. Structural conclusions drawn from XFEL-based studies of ultrafast structural changes should be consolidated by repeating these experiments using lower power density photoexcitation conditions, and data analysis steps—from processing experimental data through to structural interpretation—need to be streamlined. As further structural insights emerge from an increasingly diverse set of macromolecules, it becomes possible to imagine a time when structural results from time-resolved diffraction experiments become as central to understanding a biological reaction as the resting-state structure of a macromolecule is today. Schematic illustration of a time-resolved serial crystallography study of a light-sensitive protein. A continuous stream of microcrystals (purple) is injected across a focused x-ray beam (orange) at a synchrotron or XFEL facility. Diffraction data collected from microcrystals photoactivated by a laser pulse (green) are compared against reference diffraction data without photoactivation. Electron density changes (inset: positive difference electron density, blue; negative, yellow) are modeled as changes in protein structure for each time delay between laser and x-ray pulse, providing structural insight into the biological reaction. Conformational changes within biological macromolecules control a vast array of chemical reactions in living cells. Time-resolved crystallography can reveal time-dependent structural changes that occur within protein crystals, yielding chemical insights in unparalleled detail. Serial crystallography approaches developed at x-ray free-electron lasers are now routinely used for time-resolved diffraction studies of macromolecules. These techniques are increasingly being applied at synchrotron radiation sources and to a growing diversity of macromolecules. Here, we review recent progress in the field, including visualizing ultrafast structural changes that guide the initial trajectories of light-driven reactions as well as capturing biologically important conformational changes on slower time scales, for which bacteriorhodopsin and photosystem II are presented as illustrative case studies.

Qing Zhao, Yue Deng, Nyalaliska W. Utomo et al.

Lithium metal is a promising anode for energy-dense batteries but is hindered by poor reversibility caused by continuous chemical and electrochemical degradation. Here we find that by increasing the Li plating capacity to high values (e.g., 10–50 mAh cm−2), Li deposits undergo a morphological transition to produce dense structures, composed of large grains with dominantly (110)Li crystallographic facets. The resultant Li metal electrodes manifest fast kinetics for lithium stripping/plating processes with higher exchange current density, but simultaneously exhibit elevated electrochemical stability towards the electrolyte. Detailed analysis of these findings reveal that parasitic electrochemical reactions are the major reason for poor Li reversibility, and that the degradation rate from parasitic electroreduction of electrolyte components is about an order of magnitude faster than from chemical reactions. The high-capacity Li electrodes provide a straightforward strategy for interrogating the solid electrolyte interphase (SEI) on Li —with unprecedented, high signal to noise. We find that an inorganic rich SEI is formed and is primarily concentrated around the edges of lithium particles. Our findings provide straightforward, but powerful approaches for enhancing the reversibility of Li and for fundamental studies of the interphases formed in liquid and solid-state electrolytes using readily accessible analytical tools. Lithium metal batteries offer high-capacity electrical energy storage but suffer from poor reversibility of the metal anode. Here, the authors report that at very high capacities, lithium deposits as dense structures with a preferred crystallite orientation, yielding highly reversible lithium anodes.

Michelangelo Marasco, John Kirkpatrick, Teresa Carlomagno et al.

SHP2 is a tyrosine phosphatase that plays a regulatory role in multiple intracellular signaling cascades and is known to be oncogenic in certain contexts. In the absence of effectors, SHP2 adopts an autoinhibited conformation with its N-SH2 domain blocking the active site. Given the key role of N-SH2 in regulating SHP2, this domain has been extensively studied, often by X-ray crystallography. Using a combination of structural analyses and molecular dynamics (MD) simulations we show that the crystallographic environment can significantly influence the structure of the isolated N-SH2 domain, resulting in misleading interpretations. As an orthogonal method to X-ray crystallography, we use a combination of NMR spectroscopy and MD simulations to accurately determine the conformation of apo N-SH2 in solution. In contrast to earlier reports based on crystallographic data, our results indicate that apo N-SH2 in solution primarily adopts a conformation with a fully zipped central β-sheet, and that partial unzipping of this β-sheet is promoted by binding of either phosphopeptides or even phosphate/sulfate ions.