Comparing serial X-ray crystallography and microcrystal electron diffraction (MicroED) as methods for routine structure determination from small macromolecular crystals
RT XFEL structure of CypA solved using LCP injection system
Cyclophilin A↗
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Comparing serial X-ray crystallography and microcrystal electron diffraction (MicroED) as methods for routine structure determination from small macromolecular crystals
RT XFEL structure of CypA solved using MESH injection system
Cyclophilin A↗
MyD88 TIR domain higher-order assembly interactions revealed by microcrystal electron diffraction and serial femtosecond crystallography
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CXI↗
Upconversion on the Micrometer Scale: Impact of Local Heterogeneity
The properties of perovskite/naphtho[2,3-a]pyrene (NaPy) upconversion devices are investigated by a combination of atomic force microscopy and photoluminescence mapping to understand the role of microscopic heterogeneity in the ensemble device properties. The results emphasize strong microscopic inhomogeneity across the perovskite/NaPy upconversion device due to local formation of NaPy microcrystals. NaPy shows emission from three distinct states in the solid state: S 1 ′ emission at 520 nm, excimer emission at 560 nm, and S 1 ″ emission at 620 nm. Clear spatial differences in the emission spectrum under 405 nm excitation are found, highlighting that there is a strong microcrystal-to-microcrystal variation in the optical properties─emphasizing a need for multimodal measurements. Furthermore, our results indicate that microcrystals with strong emission from the strongly coupled low-energy state S 1 ″ (J-dimer) show much higher upconversion intensity than those with dominant emission from the high-energy S 1 ′ state (I-aggregate). Hence, our results suggest that microcrystals with strong emission from the low-energy state S 1 ″ act as isolated hotspots for upconversion.
Crystals↗
Refinements for Bragg coherent X-ray diffraction imaging: electron backscatter diffraction alignment and strain field computation
Bragg coherent X-ray diffraction imaging (BCDI) allows the 3D measurement of lattice strain along the scattering vector for specific microcrystals. If at least three linearly independent reflections are measured, the 3D variation of the full lattice strain tensor within the microcrystal can be recovered. However, this requires knowledge of the crystal orientation, which is typically attained via estimates based on crystal geometry or synchrotron microbeam Laue diffraction measurements. Presented here is an alternative method to determine the crystal orientation for BCDI measurements using electron backscatter diffraction (EBSD) to align Fe–Ni and Co–Fe alloy microcrystals on three different substrates. The orientation matrix is calculated from EBSD Euler angles and compared with the orientation determined using microbeam Laue diffraction. The average angular mismatch between the orientation matrices is less than ∼6°, which is reasonable for the search for Bragg reflections. The use of an orientation matrix derived from EBSD is demonstrated to align and measure five reflections for a single Fe–Ni microcrystal via multi-reflection BCDI. Using this data set, a refined strain field computation based on the gradient of the complex exponential of the phase is developed. This approach is shown to increase accuracy, especially in the presence of dislocations. The results demonstrate the feasibility of using EBSD to pre-align BCDI samples and the application of more efficient approaches to determine the full lattice strain tensor with greater accuracy.
42 ENGINEERING↗
De Nive Quinquangula: Pentagonal Snowflake Metal Nanocrystals as an Example of Emergence Phenomenon in Nanotechnology Complex Systems
The formation of snowflakes (SFL) is one of the most captivating phenomena in nature. The fabrication of multimetallic gold (Au) nanoparticles containing copper (Cu) and iron (Fe) is reported, which adopt snowflake-like morphology after nanoparticle aggregation. The synthesis of these snowflake-like Au microcrystals occurs mainly by kinetic control. In this process, a surfactant-assisted salt reduction method is employed on a heated substrate. Here, the metal salts react within seconds to form nanoparticles. This process results in a hierarchical structure with pseudo-pentagonal symmetry and chiroptical activity. We discuss how large superstructures emerge from nanoparticle aggregation, resembling natural snowflakes. However, unlike ice snowflakes, which exhibit hexagonal symmetry, the Au snowflakes display pentagonal symmetry. It is proposed that the formation of these snowflake-like microcrystals is the result of the complexity involved in the crystal growth process and represents an example of the phenomenon of emergence, which has become very significant in several fields of modern science, including physics, biology, chemistry, economics, philosophy, and poetry. The term emergent is used to evoke the collective behavior of a large number of microscopic constituents that is qualitatively different than the behaviors of the individual constituents.
36 MATERIALS SCIENCE↗
Chemical crystallography by serial femtosecond X-ray diffraction
Abstract 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.
36 MATERIALS SCIENCE↗
Small-wedge synchrotron and serial XFEL datasets for Cysteinyl leukotriene GPCRs
Structural studies of challenging targets such as G protein-coupled receptors (GPCRs) have accelerated during the last several years due to the development of new approaches, including small-wedge and serial crystallography. Here, we describe the deposition of seven datasets consisting of X-ray diffraction images acquired from lipidic cubic phase (LCP) grown microcrystals of two human GPCRs, Cysteinyl leukotriene receptors 1 and 2 (CysLT 1 R and CysLT 2 R), in complex with various antagonists. Five datasets were collected using small-wedge synchrotron crystallography (SWSX) at the European Synchrotron Radiation Facility with multiple crystals under cryo-conditions. Two datasets were collected using X-ray free electron laser (XFEL) serial femtosecond crystallography (SFX) at the Linac Coherent Light Source, with microcrystals delivered at room temperature into the beam within LCP matrix by a viscous media microextrusion injector. All seven datasets have been deposited in the open-access databases Zenodo and CXIDB. Here, we describe sample preparation and annotate crystallization conditions for each partial and full datasets. We also document full processing pipelines and provide wrapper scripts for SWSX and SFX data processing. A Correction to this paper has been published: https://doi.org/10.1038/s41597-020-00759-w
97 MATHEMATICS AND COMPUTING↗
Combining MicroED and native mass spectrometry for structural discovery of enzyme–small molecule complexes
With the goal of accelerating the discovery of small molecule–protein complexes, we leverage fast, low-dose, event-based electron counting microcrystal electron diffraction (MicroED) data collection and native mass spectrometry. This approach, which we term electron diffraction with native mass spectrometry (ED-MS), allows assignment of protein target structures bound to ligands with data obtained from crystal slurries soaked with mixtures of known inhibitors and crude biosynthetic reactions. This extends to libraries of printed ligands dispensed directly onto TEM grids for later soaking with microcrystal slurries, and complexes with noncovalent ligands. ED-MS resolves structures of the natural product, epoxide-based cysteine protease inhibitor E-64, and its biosynthetic analogs bound to the model cysteine protease, papain. It further identifies papain binding to its preferred natural products, by showing that two analogs of E-64 outcompete others in binding to papain crystals, and by detecting papain bound to E-64 and an analog from crude biosynthetic reactions, without purification. ED-MS also resolves binding of the CTX-M-14 β-lactamase, a target of active drug development, to the non-β-lactam inhibitor, avibactam, alone or in a cocktail of unrelated compounds. These results illustrate the utility of ED-MS for natural product ligand discovery and for structure-based screening of small molecule binders to macromolecular targets, promising utility for drug discovery.
MicroED↗
Multi-crystal native-SAD phasing at 5 keV with a helium environment
De novo structure determination from single-wavelength anomalous diffraction using native sulfur or phosphorus in biomolecules (native-SAD) is an appealing method to mitigate the labor-intensive production of heavy-atom derivatives and selenomethionyl substitutions. The native-SAD method is particularly attractive for membrane proteins, which are difficult to produce and often recalcitrant to grow into decent-sized crystals. Native-SAD uses lower-energy X-rays to enhance anomalous signals from sulfur or phosphorus. However, at lower energies, the scattering and absorption of air contribute to the background noise, reduce the signals and are thus adverse to native-SAD phasing. We have previously demonstrated native-SAD phasing at an energy of 5 keV in air at the NSLS-II FMX beamline. Here, the use of a helium path developed to reduce both the noise from background scattering and the air absorption of the diffracted X-ray beam are described. The helium path was used for collection of anomalous diffraction data at 5 keV for two proteins: thaumatin and the membrane protein TehA. Although anomalous signals from each individual crystal are very weak, robust anomalous signals are obtained from data assembled from micrometre-sized crystals. The thaumatin structure was determined from 15 microcrystals and the TehA structure from 18 microcrystals. These results demonstrate the usefulness of a helium environment in support of native-SAD phasing at 5 keV.
59 BASIC BIOLOGICAL SCIENCES↗
Retaining Geochemical Signatures during Aragonite-Calcite Transformation at Hydrothermal Conditions
Transformation of aragonite, a mineral phase metastable at Earth’s surface, to calcite widely occurs in both sedimentary and metamorphic systems with the presence of an aqueous phase. The transformation process can affect geochemical signatures of aragonite (a protolith). This study focused on quantification of the retention of Mg/Ca and Sr/Ca ratios, and δ18O during the transformation process as well as evaluation of the transformation rate. To investigate the effect of transformation from aragonite to calcite on elemental and stable isotope ratios, we conducted a series of experiments in NaCl solutions at temperatures between 120 and 184 °C. Two additional experiments at 250 °C were conducted to estimate the transformation rate of aragonite to calcite. Protolith materials consist of (1) synthetic (Mg; Sr-bearing or non-Mg; Sr bearing) needle-shaped microcrystals of aragonite (<5 µm in size) and (2) larger chips (>100 µm in size) of natural aragonite. X-ray diffraction (XRD) showed that microcrystals successfully transformed to calcite within 30 h and scanning electron microscopy (SEM) yielded a change in the crystal size to >10 µm in rhombohedral shape. Electron backscatter diffraction (EBSD) of the larger aragonite chips showed that transformation to randomly oriented calcite occurred at the rims and along the cracks while the core retained an aragonite crystal structure. Isotope-ratio mass spectrometry (IRMS) analyses showed that calcite δ18O was controlled by temperature and δ18O of the solution. The obtained calibration curve of isotope fractionation factor versus temperature is consistent with other studies. Inductively coupled plasma optical emission spectroscopy (ICP-OES) analyses showed that calcite partially or completely retained Mg/Ca and Sr/Ca ratios through the transformation.
58 GEOSCIENCES↗
Size-Dependent Photon Avalanching in Tm 3+ Doped LiYF 4 Nano, Micro, and Bulk Crystals
Photon avalanche (PA) is a highly nonlinear mode of upconversion that is characterized by 100–1000-fold increase in luminescence intensity upon minute increments of pumping power. The practical realization of numerous possible nano-bio-technology applications utilizing the PA phenomenon will require information on its susceptibility to the material volume and surface. In this report these parameters are investigated via experimental and theoretical PA. The two-color, highly nonlinear PA emission at 475 and 800 nm is clearly observed in bulk single crystal, individual microcrystals, and ensembles of colloidal core and core–shell nanoparticles of LiYF 4 host doped with either 3 or 8% of thulium ions. The properties of PA emission, such as PA nonlinearity, PA gain, PA intensity, and luminescence kinetics in these materials show dependence on crystal volume and surface quenching. Theoretical simulations provide understanding of key physical processes that influence PA performance. Moreover, photon avalanche single beam super-resolution imaging is realized for the first time in 3% Tm 3+ doped LiYF 4 core–shell nanoparticles. The obtained insights and predictions form a solid background for further development and applications of new optimized PA materials.
36 MATERIALS SCIENCE↗
Tailoring a 3D Covalent Organic Framework Toward Facile Functionalization
Three-dimensional covalent organic frameworks (3D COFs) are notably crystalline and stable, but their architectures and monomer structures make them difficult to functionalize. Here, a new strategy is presented to render COF-300 and other imine-linked frameworks amenable to facile functionalization in the last step of synthesis. By reducing the imine linkages to secondary amines and appending them with acetyl halide groups, the linkages are converted to electrophiles that can be readily reacted with nucleophilic guests. This route yields eight new COF-300 derivatives, bearing chloroacetyl, bromoacetyl, azide, cyano, amino, hydroxyl, methoxy, or thiomethyl groups appended to the inter-monomer linkages. The new materials are characterized through solid-state NMR, infrared spectroscopy, and powder X-ray diffraction, among other techniques, finding that the reported linkage transformations proceed to complete conversion while retaining the crystallinity of the materials. Microcrystal electron diffraction (microED) data are used to solve the evacuated structure of the amine-linked framework COF-300-AR for the first time, providing conclusive evidence of this framework's guest-induced phase change, along with the structure of the new framework COF-300-NH 2 . Finally, COF-300-NH 2 is shown to have significantly improved adsorption capacity for CO 2 and perfluoroalkyl substances (PFAS), highlighting the benefits of this synthetic strategy for the generation of customized adsorbents.
COF-300↗
Reaching the potential of electron diffraction
Microcrystal electron diffraction (MicroED) is an emerging structural technique in which submicron crystals are used to generate diffraction data for structural studies. Structures allow for the study of molecular-level architecture and drive hypotheses about modes of action, mechanisms, dynamics, and interactions with other molecules. Combining cryoelectron microscopy (cryo-EM) instrumentation with crystallographic techniques, MicroED has led to three-dimensional structural models of small molecules, peptides, and proteins and has generated tremendous interest due to its ability to use vanishingly small crystals. In this perspective, we describe the current state of the field for MicroED methodologies, including making and detecting crystals of the appropriate size for the technique, as well as ways to best handle and characterize these crystals. Our perspective provides insight into ways to unlock the full range of potential for MicroED to access previously intractable samples and describes areas of future development.
3D ED↗
Imaging Light‐Induced Migration of Dislocations in Halide Perovskites with 3D Nanoscale Strain Mapping
Abstract In recent years, halide perovskite materials have been used to make high‐performance solar cells and light‐emitting devices. However, material defects still limit device performance and stability. Here, synchrotron‐based Bragg coherent diffraction imaging is used to visualize nanoscale strain fields, such as those local to defects, in halide perovskite microcrystals. Significant strain heterogeneity within MAPbBr 3 (MA = CH 3 NH 3 + ) crystals is found in spite of their high optoelectronic quality, and both 〈100〉 and 〈110〉 edge dislocations are identified through analysis of their local strain fields. By imaging these defects and strain fields in situ under continuous illumination, dramatic light‐induced dislocation migration across hundreds of nanometers is uncovered. Further, by selectively studying crystals that are damaged by the X‐ray beam, large dislocation densities and increased nanoscale strains are correlated with material degradation and substantially altered optoelectronic properties assessed using photoluminescence microscopy measurements. These results demonstrate the dynamic nature of extended defects and strain in halide perovskites, which will have important consequences for device performance and operational stability.
36 MATERIALS SCIENCE↗
Polymer Passivated All Inorganic Micro‐Structured CsPbI x Br y Perovskite Toward Highly Efficient Photodetectors
Abstract Solution‐processed inorganic perovskites cause chemical and structural defects unfavorable for photodetector application. Using a binary solvent, defects in CsPbI x Br y (CPIB) perovskite are passivated with poly 4‐vinylpyridine (PVP) and Poly methyl methacrylate (PMMA) polymers. X‐ray photoelectron spectroscopy and FTIR spectra reveal a Lewis base‐acid interaction between Pb 2+ and polymer, confirming the passivation of CPIB perovskite. Scanning electron microscopy analysis shows a dual‐surface morphology with microribbons and microcrystals in perovskites. After PMMA treatment, CPIB perovskite exhibits a blue shift in the bandgap (1.8 to 1.95 eV), while the PVP induced a redshift, reducing the bandgap to 1.7 eV. Blue shift in PL analysis indicates modification of grain boundaries. A higher lifetime obtained for CPIB/PVP confirms the restraint of non‐radiative recombinations. Photodetectors are fabricated with pristine CPIB, CPIB/PVP, and CPIB/PMMA perovskites. The passivated CPIB/PVP‐based photodetector exhibits a quick rise time of ≈23 ms and a decay time of ≈17 ms. It also demonstrates a remarkable photoresponsivity of 23 mA W −1 , an internal quantum efficiency of 4.9%, and a detectivity of 15.0 × 10 10 Jones at 10 mW cm −2 light intensity. This approach shows the potential for environmentally stable polymers to passivate inorganic perovskites for high photodetection performance.
Shah, Shruti↗
Comparative Study of Solvatomorphs of Stryker's Reagent Using MicroED and Quantum Mechanics
Abstract The atomic position of hydrogen atoms in metal hydrides has been a long‐standing structural question in inorganic chemistry given that hydride delivery is integral to diverse chemical reactions. Microcrystal electron diffraction (microED), with it's increased sensitivity toward hydrogen atoms relative to X‐ray diffraction, offers a potential path to addressing this challenge. Herein, the first microED study of Stryker's reagent is reported, resulting in the structure of a new benzene solvate. Improved accuracy for hydrogen atom positions was obtained via a quantum crystallography (QCr) approach, Hirshfeld atom refinement (HAR). Structural and topological analysis supports edge bridging hydrides in the microED structure of a THF solvate form, consistent with previous diffraction studies. Interestingly, analysis of a new benzene solvate, discovered in this study, is consistent with mixed edge‐ and face‐bridging hydrides.
Jha, Kunal K. [Division of Chemistry &, Chemica↗