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Protonation changes the molecular architecture of the crystal structures, and thus modifies the intermolecular interactions in the studied structures.
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Structure elucidation via single-crystal methods has historically lacked experimental access to real-space information, instead relying exclusively on diffraction-space measurements of Bragg reflections. Here we exploit the dual-space imaging power of 4D scanning transmission electron microscopy to meaningfully integrate real-space information into the crystallographic workflow. We show that virtual apertures assembled by segmentation of high-angle annular dark-field images enable i) pixel-by-pixel separation of coherent Bragg signal from clusters of closely spaced nanocrystals and ii) selective extraction of integrated intensities from thinner subregions of individual specimens, facilitating retroactive tuning of multiple scattering artifacts. This strategy empowers us to simply pick and choose whichever nanoscale regions of interest generate the highest-quality diffraction patterns, allowing us to solve several independent structures of the metal-organic framework UiO-66 from specimens whose agglomerated morphology proved intractable for conventional microcrystal electron diffraction. Our method is compatible with both rotational and serial approaches to data processing, ultimately divulging the first scanning nanobeam electron diffraction structures determined by direct methods at subangstrom resolution.
Metal–ligand (M–L) multiply bonded complexes hold a central place in inorganic chemistry and catalysis: From fundamental and historical perspectives, these species have played a critical role in the articulation of important bonding principles (i.e. the vanadyl ion in the development of molecular orbital theory); from a practical perspective, these species are critical intermediates in a variety of chemical reactions (i.e. N 2 and O 2 reduction, H 2 O oxidation, and C–H functionalization). For many high-valent, early metal complexes, overlap of ligand-based electrons with vacant π-symmetry orbitals leads to strong M–L multiple bonds. The stability of these species enables straightforward characterization with a suite of standard spectroscopic and diffraction-based experiments. Mid- and late-transition metal complexes, with attendant higher d-electron counts, often support more reactive M–L multiply bonded fragments. The reactivity of these species simultaneously renders them attractive intermediates for catalysis but challenging synthetic targets to observe and characterize. A number of important strategies have been advanced to enable experimental characterization of mid- to late-metal–ligand multiply bonded species. Synthetic manipulation of the coordination geometry and ligand donicity, as well as introduction of sterically encumbering ligands, have each emerged as powerful methods to tame the inherent reactivity of kinetically labile M–L multiple bonds. While these efforts have resulted in families of well-characterized complexes and provided critical insights regarding structure and bonding, the synthetic derivatization required to stabilize M–L fragments of interest often obviates the substrate functionalization activity relevant to catalysis. Photochemical synthesis of reactive species provides a conceptually attractive strategy to generate reactive M–L fragments under conditions compatible with time-resolved or cryogenic steady-state characterization, and photogeneration has enabled observation of a number of reactive M–L fragments. The suite of tools available to characterize photogenerated reactive species is often more limited than typical for kinetically stabilized complexes and structural characterization is typically not possible. Recently, photocrystallographic experiments, in which reactive M–L multiply bonded intermediates are generated within single-crystal matrices, have been advanced as a strategy to interrogate the structures of reactive intermediates in C–H functionalization. Lastly, this Comment describes the historical antecedents to these experiments, highlights examples of photocrystallographic characterization of reactive intermediates, and discusses future opportunities.
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Compared with batch and vapor diffusion methods, counter diffusion can generate larger and higher-quality protein crystals yielding improved diffraction data and higher-resolution structures. Typically, counter-diffusion experiments are conducted in elongated chambers, such as glass capillaries, and the crystals are either directly measured in the capillary or extracted and mounted at the X-ray beamline. Despite the advantages of counter-diffusion protein crystallization, there are few fixed-target devices that utilize counter diffusion for crystallization. In this article, different designs of user-friendly counter-diffusion chambers are presented which can be used to grow large protein crystals in a 2D polymer microfluidic fixed-target chip. Methods for rapid chip fabrication using commercially available thin-film materials such as Mylar, propylene and Kapton are also detailed. Rules of thumb are provided to tune the nucleation and crystal growth to meet users' needs while minimizing sample consumption. These designs provide a reliable approach to forming large crystals and maintaining their hydration for weeks and even months. This allows ample time to grow, select and preserve the best crystal batches before X-ray beam time. Importantly, the fixed-target microfluidic chip has a low background scatter and can be directly used at beamlines without any crystal handling, enabling crystal quality to be preserved. The approach is demonstrated with serial diffraction of photoactive yellow protein, yielding 1.32 Å resolution at room temperature. Fabrication of this standard microfluidic chip with commercially available thin films greatly simplifies fabrication and provides enhanced stability under vacuum. These advances will further broaden microfluidic fixed-target utilization by crystallographers.
Here, temperature-dependent powder X-ray diffraction and magnetization measurements of Pr 2 In conclusively prove that the unusual anhysteretic first-order paramagnetic-ferromagnetic phase transition in the compound is related to concurrent changes in both the magnetic and crystallographic lattices. At the same time, the hexagonal Ni 2 In-type structure is stable at least between 6 and 298 K, including at T C = ~57 K. From the density functional theory calculations, the electronic structure of the compound is extraordinarily sensitive to minor changes in lattice parameters that occur across the phase transition, revealing the origin of strong magnetoelastic coupling. In the vicinity of T C , the maximum entropy change, ΔS Max = -16 J Kg -1 K -1 induced by a moderate magnetic field change of 20 kOe (ΔS Max = -20 J Kg -1 K -1 for 50 kOe magnetic field change) is comparable to other known potentially functional materials demonstrating large cryogenic magnetocaloric effect.
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XFEL diffraction frames from batch-crystallized Soybean Lipoxygenase-1 (SLO-1), revealing two crystal polymorphs arising from differential hydration during sample delivery
Insoluble polymer substrates functionalized with the amidoxime (R-C(NH 2 )=NOH) functional group have been demonstrated as a technically feasible platform for extracting uranium from seawater, a potential source of extremely abundant uranium for use as nuclear fuel. While it is possible to isolate macroscopic amounts of uranium from the ocean with a positive energy return on investment using these materials, both the economic and energetic costs are many times greater than those of terrestrial uranium mining. Currently, the major contribution to this cost is the production of the sorbent itself, so being able to recycle the sorbent even a small number of times will have a huge impact on lowering the cost of their use. However, amidoxime resins show capacity fading when stripped by strong acids, presently limiting their recyclability. Both alternative extractants and alternative elution chemistries are under development with promising results but are yet at too early a stage to make predictions about their ultimate success. Given the potentially huge impact of a successful recycling process on the viability of seawater extraction of uranium, there is a strong need to pursue additional routes to elution chemistry. During the course of this project, we studied the interactions of amidoxime-containing small molecules with the abundant metal ions in seawater, including Li, Na, K, Mg, Ca, Fe, Cu, and V, to understand the interactions of [UO 2 ] 2+ with amidoxime. By using small molecules with multiple adjacent functional groups, we crystallized the resulting metal complexes and used single crystal X-ray diffraction (SCXRD) as our primary tool for structural characterization. We also investigated the use of solutions of hydroxylammonium salts in weak acids as eluents for stripping and recycling amidoxime-based sorbents. The replacement of strong acids, which react with and destroy the amidoxime functional groups, with weak acids based on hydroxylammonium, a reagent that is actually used to make the amidoxime groups, is expected to avoid capacity loss on recycling and possibly even regenerate functionality that was lost due to exposure to the marine environment.
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Gaining a thorough understanding of biological systems requires building our knowledge about biological processes from the level of atoms and electrons, and up to whole organisms. Such comprehensive knowledge will allow for a predictive understanding of complex biological systems behavior. It will guide us in the design and development of novel therapeutics and vaccines to tackle existing health threats and to prepare for future pandemics, and it will provide information necessary to create new biomaterials and bio-inspired technologies through manipulation of biological macromolecules, their assemblies, single cells and even microorganisms. Reaching these goals will require a synergistic combination of multiple experimental techniques with molecular calculations and predictive simulations, and the design and development of new techniques and capabilities that bridge current knowledge and technology gaps. Neutron scattering provides unique information about the biomacromolecular structure and function and can play a major role in achieving these goals. A workshop was held to engage the scientific community in identifying pressing challenges in biochemistry, structural biology, enzymology and structure-guided drug design not solved with the current neutron scattering technologies or utilizing other structural biology techniques such as X-ray crystallography, NMR, and cryo-EM. The workshop brought together structural biology, biochemistry and computational experts, as well as early career researchers and students, creating a forum for discussing scientific advancement and collaboration. The workshop included a one-day satellite training workshop where graduate students and postdoctoral researchers were educated in the application of neutron crystallography and small-angle scattering in structural biology. Furthermore, the Instrument Scientific Advisory Board (ISAB) for the development of a macromolecular neutron diffractometer at ORNL’s Second Target Station was introduced at the workshop. The major outcome was that neutrons can provide atomic-level understanding of biomacromolecular structure, function and dynamics which is of paramount importance for addressing the identified challenges. Neutron crystallography, in particular, can resolve long-standing biochemical issues regarding enzyme function by delineating the underlying chemistry and can have a major impact on the design of small-molecule therapeutics, especially in combination with molecular computation (quantum chemistry and molecular dynamics simulations) and the emerging artificial intelligence (AI)-assisted drug design technologies. The unique properties of neutrons, including their high sensitivity to hydrogen and their non-destructive nature, make them ideal probes of biological matter. There is a palpable need in the scientific community to expand and enhance the impact of neutron sciences on biology. Neutron crystallography is the only structural biology method capable of determining positions of all hydrogen atoms in proteins, nucleic acids and their complexes at near-physiological temperatures and of unstable species at cryogenic temperatures. Moreover, neutron analysis is non-ionizing, non-destructive and does not perturb the structure or redox chemistry of active site metal centers and clusters in proteins, which can be invaluable for studying radiation-sensitive metalloprotein complexes. Further, neutron energies used in scattering applications are similar to atomic motions, permitting neutron spectroscopies to characterize the dynamics of biomacromolecules on the picosecond to microsecond timescales. The different sensitivities of neutrons to protium (H) and deuterium (D) isotopes of hydrogen allow enhanced visibility of specific parts of biological complexes through isotopic labeling. The impact of neutrons will be most powerful when neutron scattering is combined with complementary experimental techniques that use photons and electrons, and with high-performance computing. The interconnection and mutuality of the experimental and theoretical capabilities will drive discoveries in biological and health sciences to generate more complete picture of complex biological systems. The major limitation in the field of biological neutron crystallography has been signal-to-noise, demanding large samples that are difficult to produce for the majority of biomacromolecules and limiting the applicability of this technique in biological sciences. A neutron crystallography instrument at the Second Target Station will revolutionize biological science with neutrons by engaging a large scientific community of structural biologists, enabling successful neutron diffraction experiments from radically smaller biomacromolecular crystals, resolving unanswered biochemical questions, and meaningfully contributing to rational drug design. The meeting highlighted 10 grand challenges that will be addressed with this advanced capability over the next decade and beyond, and the recommendations required to help address them are given below.
The metalation chemistry of the phlorin, which is a non-aromatic tetrapyrrole macrocycle containing a single sp 3 -hybridized meso-carbon has remained underdeveloped, as compared to that of more traditional tetrapyrroles such as porphyrins, corroles and phthalocyanines. There have been few prior efforts to prepare metallophlorins, and those that have been reported have relied on either reduction or nucleophilic attack of parent metalloporphyrins, rather than direct metalation of freebase phlorin constructs. In this work, an alternate synthetic approach for preparation of gold(III) phlorin complexes that involves the first direct metalation of two different freebase phlorin derivatives (3H(Phl tBu ) and 3H(Phl F )) with AuBr 3 to produce the stable and fully isolable gold(III) phlorin complexes Au(Phl tBu ) and Au(Phl F ) is reported. The first structural characterization of a metallophlorin bearing geminal dimethyl substituents at the sp 3 -hybridized meso-carbon via X-ray crystallography is also reported. In addition to the preparation of Au(Phl tBu ) and Au(Phl F ), the UV-vis absorption and redox properties of these two gold(III) phlorins in comparison to those of their freebase homologues is also detailed. Notably, the metallophlorins are characterized by panchromatic absorbance profiles and intense and broad bands that span the long-visible and into the near-IR regions, as well as two fully reversible oxidation and reduction waves as probed by cyclic voltammetry. Lastly, the chlorination of Au(Phl tBu ) using PhI(Cl 2 ) was probed and it was found that this regioslective reaction generates monochlorinated (Au(Phl tBu Cl)) and dichlorinated (Au(Phl tBu Cl 2 )) products, which were both structurally characterized by X-ray crystallography.
Multipolar scattering models, such as the transferable aspherical atom model, account for atomic chemical interactions and provide a more accurate representation of experimental data. However, the simpler independent atom model (IAM), which assumes non-interacting atoms, is the only model available in the most widely used macromolecular refinement programs. This is primarily because IAM offers a hard-to-beat combination of computational efficiency and modelling power at typical macromolecular resolutions. By contrast, more accurate multipolar modelling has historically been limited due to its computational cost and the absence of an interface between software capable of calculating structure factors and gradients based on multipolar models and software designed for macromolecular refinement. This work introduces pyDiSCaMB , a Python software package designed to integrate between the computational crystallography toolbox ( cctbx ) and the quantum crystallography library DiSCaMB ( Densities in Structural Chemistry and Molecular Biology ), thus enabling multipolar scattering models in Phenix 's toolkit. The implementation, features and capabilities of pyDiSCaMB are presented, the runtimes for the calculation of structure factor and target gradients with respect to atomic parameters are explored, and Fourier images of electrostatic potential, electron density and deformation maps are computed as illustrative examples. The pyDiSCaMB library will make multipolar modelling widely available to the structural biology community, potentially transforming refinement and model-building for both crystallography and cryogenic electron microscopy (cryoEM).
X-ray free electron laser (XFEL) microcrystallography and synchrotron single-crystal crystallography are used to evaluate the role of organic substituent position on the optoelectronic properties of metal–organic chalcogenolates (MOChas). MOChas are crystalline 1D and 2D semiconducting hybrid materials that have varying optoelectronic properties depending on composition, topology, and structure. While MOChas have attracted much interest, small crystal sizes impede routine crystal structure determination. A series of constitutional isomers where the aryl thiol is functionalized by either methoxy or methyl ester are solved by small molecule serial femtosecond X-ray crystallography (smSFX) and single crystal rotational crystallography. While all the methoxy examples have a low quantum yield (0-1%), the methyl ester in the ortho position yields a high quantum yield of 22%. Here, the proximity of the oxygen atoms to the silver inorganic core correlates to a considerable enhancement of quantum yield. Four crystal structures are solved at a resolution range of 0.8–1.0 Å revealing a collapse of the 2D topology for functional groups in the 2- and 3- positions, resulting in needle-like crystals. Further analysis using density functional theory (DFT) and many-body perturbation theory (MBPT) enables the exploration of complex excitonic phenomena within easily prepared material systems.
The recent development of microcrystal electron diffraction (MicroED) in electron cryo-microscopy (cryo-EM) has addressed many of the challenges of X-ray crystallography [1], filling a long-standing need in organic chemistry for rapid and accurate high-resolution structural characterization [2]. Like X-ray crystallography, this is also a diffraction technique requiring crystalline specimens, but because high energy electrons have a more favorable ration of elastic to inelastic scattering [3], MicroED can acquire data using crystals that are orders of magnitude smaller than those needed for X-ray crystallography—even as small as 50 nm in length [4]. Additionally, the instrumentation required for MicroED is readily available, as many chemistry and biology labs already have access to cryo-capable transmission electron microscopes (TEM).