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Application of high-resolution Multiwavelength Anomalous Diffraction (MAD) allows the assignment of localized, partly delocalized, and fully delocalized oxidation in a series of trichromium imide isomers.
Abstract Understanding the electronic structures of high‐valent metal complexes aids the advancement of metal‐catalyzed cross coupling methodologies. A prototypical complex with formally high valency is [Cu(CF 3 ) 4 ] − (1), which has a formal Cu(III) oxidation state but whose physical analysis has led some to a Cu(I) assignment in an inverted ligand field model. Recent examinations of1by X‐ray spectroscopies have led previous authors to contradictory conclusions, motivating the re‐examination of its X‐ray absorption profile here by a complementary method, resonant diffraction anomalous fine structure (DAFS). From analysis of DAFS measurements for a series of seven mononuclear Cu complexes including1, here it is shown that there is a systematic trifluoromethyl effect on X‐ray absorption that blue shifts the resonant Cu K‐edge energy by 2–3 eV per CF 3 , completely accounting for observed changes in DAFS profiles between formally Cu(III) complexes like1and formally Cu(I) complexes like (Ph 3 P) 3 CuCF 3 (3). Thus, in agreement with the inverted ligand field model, the data presented herein imply that1is best described as containing a Cu(I) ion with d n count approaching 10.
Abstract A known trinuclear structure was used to design the heterobimetallic mixed‐valent, mixed‐ligand molecule [Co II (hfac) 3 −Na−Co III (acac) 3 ] ( 1 ). This was used as a template structure to develop heterotrimetallic molecules [Co II (hfac) 3 −Na−Fe III (acac) 3 ] ( 2 ) and [Ni II (hfac) 3 −Na−Co III (acac) 3 ] ( 3 ) via isovalent site‐specific substitution at either of the cobalt positions. Diffraction methods, synchrotron resonant diffraction, and multiple‐wavelength anomalous diffraction were applied beyond simple structural investigation to provide an unambiguous assignment of the positions and oxidation states for the periodic table neighbors in the heterometallic assemblies. Molecules of 2 and 3 are true heterotrimetallic rather than a statistical mixture of two heterobimetallic counterparts. Trinuclear platform 1 exhibits flexibility in accommodating a variety of di‐ and trivalent metals, which can be further utilized in the design of molecular precursors for the NaMM′O 4 functional oxide materials.
The performance of optoelectronic devices based on conjugated polymers is critically dependent upon molecular packing; however, the paracrystalline nature of these materials limits the amount of information that can be extracted from conventional X-ray diffraction. Resonant diffraction (also known as anomalous diffraction) occurs when the X-ray energy used coincides with an X-ray absorption edge in one of the constituent elements in the sample. The rapid changes in diffraction intensity that occur as the X-ray energy is varied across an absorption edge provide additional information that is lost in a conventional nonresonant experiment. Taking advantage of the fact that many conjugated polymers contain sulfur as heteroatoms, here we reveal pronounced resonant diffraction effects at the sulfur K-edge with a particular focus on the well-studied electron transporting polymer poly([N,N'-bis(2-octyldodecyl)-naphthalene-1,4,5,8-bis(dicarboximide)-2,6-diyl]-alt-5,5'-(2,2'-bithiophene)), P(NDI2OD-T2). The observed behavior is found to be consistent with the theory of resonant diffraction, and by simulating the energy-dependent peak intensity based on proposed crystal structures for P(NDI2OD-T2), we find that resonant diffraction can discriminate between different crystalline packing structures. The utilization of resonant diffraction opens up a new way to unlock important microstructural information about conjugated polymers for which only a handful of diffraction peaks are typically available.
Organic mixed ionic–electronic conductors (OMIECs) have the potential to enable diverse new technologies, ranging from novel in situ biosensors to flexible energy storage devices and neuromorphic computing platforms. However, their complex behavior in functional films involving electrolyte-induced swelling, ion ingress, and electrochemical doping inhibits rational material design. Of critical importance is an understanding of the specific location of the ions in the volumetrically doped material, yet this information is not readily available. Here, in this report, we present the use of grazing- incidence resonant X-ray diffraction (RXRD, also known as anomalous diffraction) at S and Cl K-edges to determine the structure of a doped, prototypical, semicrystalline polymer OMIEC based on oligo(ethylene glycol) substitution of regioregular polythiophene. The RXRD measurement provides two key insights. Quantitative analysis of the RXRD allows the determination of the position of the ion relative to the polymer backbone in the crystalline regions. We find that the anion is relatively distant from the backbone, nearer to the lamella mid-plane naively in conflict with expected Coulombic attraction between the ion and the doped polymer polaron. Comparison of RXRD to Cl – fluorescence (total Cl – ) allows determination of the relative order of doping between the crystalline and amorphous regions. We find preferential doping of the crystalline regions. Both insights, the preferential doping of crystals at low potential and the specific location of the counterion with respect to the polymer backbone, are critical to developing a microscopic understanding of transport in OMIECs.
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.
MeV ultrafast electron diffraction (MUED) is a pump-probe technique used to study the dynamic structural evolution of materials. An ultrashort laser pulse triggers structural changes, which are then probed by an ultrashort relativistic electron beam. To overcome low signal-to-noise ratios, diffraction patterns are averaged over thousands of shots. However, shot-to-shot instabilities in the electron beam can distort individual patterns, introducing uncertainty. Improving MUED accuracy requires detecting and removing these anomalous patterns from large datasets. In this work, we developed a fully unsupervised methodology for the detection of anomalous diffraction patterns. Using a convolutional autoencoder, we calculate the reconstruction mean squared error of the diffraction patterns. Based on the statistical analysis of this error, we provide the user an estimation of the probability that the pattern is normal, which also allows a posterior visual inspection of the images that are difficult to classify. This method has been trained with only 100 diffraction patterns and tested on 1521 patterns, resulting in a false positive rate between 0.2% and 0.4%, with a training time of 10 s per image and a test time of about 1 s per image. Here, the proposed methodology can also be applied to other diffraction techniques in which large datasets are collected that include faulty images due to instrumental instabilities.
In many organs, small openings across capillary endothelial cells (ECs) allow the diffusion of low–molecular weight compounds and small proteins between the blood and tissue spaces. These openings contain a diaphragm composed of radially arranged fibers, and current evidence suggests that a single-span type II transmembrane protein, plasmalemma vesicle-associated protein-1 (PLVAP), constitutes these fibers. Here, we present the three-dimensional crystal structure of an 89-amino acid segment of the PLVAP extracellular domain (ECD) and show that it adopts a parallel dimeric alpha-helical coiled-coil configuration with five interchain disulfide bonds. The structure was solved using single-wavelength anomalous diffraction from sulfur-containing residues (sulfur SAD) to generate phase information. Biochemical and circular dichroism (CD) experiments show that a second PLVAP ECD segment also has a parallel dimeric alpha-helical configuration—presumably a coiled coil—held together with interchain disulfide bonds. Overall, ~2/3 of the ~390 amino acids within the PLVAP ECD adopt a helical configuration, as determined by CD. We also determined the sequence and epitope of MECA-32, an anti-PLVAP antibody. Taken together, these data lend strong support to the model of capillary diaphragms formulated by Tse and Stan in which approximately ten PLVAP dimers are arranged within each 60- to 80-nm-diameter opening like the spokes of a bicycle wheel. Passage of molecules through the wedge-shaped pores is presumably determined both by the length of PLVAP—i.e., the long dimension of the pore—and by the chemical properties of amino acid side chains and N-linked glycans on the solvent-accessible faces of PLVAP.
Copper clusters feature prominently in both metalloenzymes and synthetic nanoclusters that mediate catalytic redox transformations of gaseous small molecules. Such reactions are critical to biological energy conversion and are expected to be crucial parts of renewable energy economies. However, the precise roles of individual metal atoms within clusters are difficult to elucidate, particularly for cluster systems that are dynamic under operating conditions. Here, we present a metal site-specific analysis of synthetic Cu 4 (μ 4 -S) clusters that mimic the Cu Z active site of the nitrous oxide reductase enzyme. Leveraging the ability to obtain structural snapshots of both inactive and active forms of the synthetic model system, we analyzed both states using resonant X-ray diffraction anomalous fine structure (DAFS), a technique that enables X-ray absorption profiles of individual metal sites within a cluster to be extracted independently. Using DAFS, we found that a change in cluster geometry between the inactive and active states is correlated to Cu site differentiation that is presumably required for efficient activation of N 2 O gas. More precisely, we hypothesize that the Cu δ+ ∙∙∙Cu δ- pairs produced upon site differentiation are poised for N 2 O activation, as supported by computational modeling. These results provide an unprecedented level of detail on the roles of individual metal sites within the synthetic cluster system and how those roles interplay with cluster geometry to impact the reactivity function. We expect this fundamental knowledge to inform understanding of metal clusters in settings ranging from (bio)molecular to nanocluster to extended solid systems involved in energy conversion.
The Structural Molecular Biology (SMB) macromolecular crystallography (MC) group at the Stanford Synchrotron Radiation Lightsource (SSRL) have developed state-of-the-art capabilities tailored for metalloenzyme structural analysis. Metalloproteins sit at the center of biology’s most audacious chemistry. From multi-electron redox catalysis to radical rearrangements and light-driven transformations, metal sites give proteins access to reaction landscapes that would otherwise be inaccessible under ambient conditions. Yet their study presents a fundamental paradox for MC studies: the very X-rays we use to reveal atomic structure can alter the electronic states we seek to understand. As the field moves beyond static snapshots toward mechanistic insight, success increasingly depends on our ability to maintain metal centers in their native state throughout the experiment. The SSRL SMB-MC beamlines integrate a suite of capabilities specifically designed to address these challenges. By combining in situ spectroscopic verification, intelligent dose management, controlled reaction initiation, optimized anomalous diffraction, and real-time crystallographic diffraction analysis, these tools enable researchers to interrogate metalloproteins with unprecedented rigor. This article explores how these complementary approaches are reshaping our ability to capture metalloprotein chemistry, and what this means for mechanistic studies at synchrotron beamlines.
The X-ray Bragg coherent diffractive imaging (CDI) technique assumes that the structure factor holds constant over the measured crystal. This approximation breaks down for materials exhibiting variations in the unit-cell configuration, such as piezo- and ferroelectrics. In that case, the strain field cannot be reliably determined from the reconstruction because the lattice deformation and the structure factor contribute concomitantly. Proposed here is a solution to this problem achieved by combining Bragg CDI and the multiwavelength anomalous diffraction approach that measures a Friedel pair of reflections at two different photon energies near an absorption edge. Comparing the obtained reconstructions with a parametric model that includes calculating the scattering amplitude as a function of wavelength and the unit-cell configuration, the contributions of the lattice deformation and the structure factor are separated. Simulations of the ferroelectric material BaTiO 3 demonstrate the possibility of simultaneous probing of the strain and displacement of the Ti atoms. The proposed method opens up an opportunity to apply coherent X-ray diffraction for nanoscale-resolved 3D mapping of polarization domains in micro- and nanocrystals.
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Metacaspases are highly conserved in plants and play essential roles in mediating programmed cell death, biotic and abiotic stress responses, and damage-induced innate immunity. Ca 2+ signaling induced by plant damage leads to activation of metacaspase from Arabidopsis thaliana (AtMC4), which subsequently processes a plant elicitor peptide to trigger downstream immuno-response. To understand the structural basis of AtMC4 activation by Ca 2+ , we previously determined its crystal structure and performed in-crystal Ca 2+ treatment to probe activation-associated conformational changes. To enable structure determination and in-crystal Ca 2+ activation analysis, we used microcrystals and related methods which were essential for our successful approach. Here, in this paper, we describe in detail the methods that we used for determination of AtMC4 structure using single-wavelength isomorphous replacement with anomalous signals assembled from 22 microcrystals. We also describe the method for in-crystal Ca 2+ soaking, microcrystal data collection, data assembly and analysis to obtain the activated structure of AtMC4 from 91 micro-sized crystals. The described methods may be useful to study other plant metacaspases and more broadly other plant enzymes for their structure determination and in-crystal functional characterization.
Na + is the most abundant ion in living organisms and plays essential roles in regulating nutrient uptake, muscle contraction, and neurotransmission. The identification of Na + in protein structures is crucial for gaining a deeper understanding of protein function in a physiological context. LeuT, a bacterial homolog of the neurotransmitter:sodium symporter family, uses the Na + gradient to power the uptake of amino acids into cells and has been used as a paradigm for the study of Na + -dependent transport systems. We have devised a low-energy multi-crystal approach for characterizing low-Z (Z ≤ 20) anomalous scattering ions such as Na + , Mg 2+ , K + , and Ca 2+ by combining Bijvoet-difference Fourier syntheses for ion detection and f” refinements for ion speciation. Using the approach, we experimentally identify two Na + bound near the central leucine binding site in LeuT. Using LeuT microcrystals, we also demonstrate that Na + may be depleted to study conformational changes in the LeuT transport cycle.
Eu(II)-containing chalcogenides are an emerging class of materials that are of great interest due to their high optical activity and intriguing magnetism. Here, we synthesized Eu 2 SiSe 4 as red-colored single crystals and characterized its structure with single-crystal X-ray diffraction, confirming the reported chiral monoclinic P2 1 symmetry at room temperature. The crystal structure of Eu 2 SiSe 4 comprises distorted SiSe 4 tetrahedral units and charge-balancing Eu(II) cations. Here, we develop a two-step solid-state synthesis method for Eu 2 SiSe 4 and compare it to the known boron chalcogenide method. We find the second-harmonic generation (SHG) activity of polycrystalline Eu 2 SiSe 4 to be ∼7 × AgGaS 2 , placing it among the highest-known SHG-active chalcogenides. No symmetry lowering is observed down to 100 K in single-crystal X-ray diffraction, although an anomalous expansion in the b-axis lattice parameter occurs and may be correlated to lattice modes of the SiSe 4 tetrahedra. We investigate the physical properties of Eu 2 SiSe 4 using magnetometry and heat capacity measurements and find a transition to an antiferromagnetic ground state at T N ≈ 5.5 K. The low-temperature transition releases less entropy than expected, which may be due to the complex crystal electric field effects of Eu(II).
Understanding the relationship between structure and function for biological assemblies can guide identification of new therapeutics, design of biomaterials, and development of biotechnological processes. Resonant X-ray scattering provides a chemically-specific approach to characterize complex biological structures based on anomalous or resonant scattering from a specific element or chemical moiety. Anomalous or resonant diffraction can provide structural details with high atomic resolution, while resonant X-ray scattering can provide structural details with lower resolution through tender or soft X-rays. Furthermore, we review applications, challenges, and opportunities for resonant X-ray scattering in the field of structural biology.