A mechanism of ferritin crystallization revealed by cryo-STEM tomography.

Protein crystallization is important in structural biology, disease research and pharmaceuticals. It has recently been recognized that nonclassical crystallization-involving initial formation of an amorphous precursor phase-occurs often in protein, organic and inorganic crystallization processes1-5. A two-step nucleation theory has thus been proposed, in which initial low-density, solvated amorphous aggregates subsequently densify, leading to nucleation4,6,7. This view differs from classical nucleation theory, which implies that crystalline nuclei forming in solution have the same density and structure as does the final crystalline state1. A protein crystallization mechanism involving this classical pathway has recently been observed directly8. However, a molecular mechanism of nonclassical protein crystallization9-15 has not been established9,11,14. To determine the nature of the amorphous precursors and whether crystallization takes place within them (and if so, how order develops at the molecular level), three-dimensional (3D) molecular-level imaging of a crystallization process is required. Here we report cryogenic scanning transmission microscopy tomography of ferritin aggregates at various stages of crystallization, followed by 3D reconstruction using simultaneous iterative reconstruction techniques to provide a 3D picture of crystallization with molecular resolution. As crystalline order gradually increased in the studied aggregates, they exhibited an increase in both order and density from their surface towards their interior. We observed no highly ordered small structures typical of a classical nucleation process, and occasionally we observed several ordered domains emerging within one amorphous aggregate, a phenomenon not predicted by either classical or two-step nucleation theories. Our molecular-level analysis hints at desolvation as the driver of the continuous order-evolution mechanism, a view that goes beyond current nucleation models, yet is consistent with a broad spectrum of protein crystallization mechanisms.

Halide perovskite dynamics at work: Large cations at 2D-on-3D interfaces are mobile.

SignificanceSurface engineering of halide perovskites (HaPs), semiconductors with amazing optoelectronic properties, is critical to improve the performance and ambient stability of HaP-based solar cells and light emitting diodes (LEDs). Ultrathin layers of two-dimensional (2D) analogs of the three-dimensional (3D) HaPs are particularly attractive for this because of their chemical similarities but higher ambient stability. But do such 2D/3D interfaces actually last, given that ions in HaPs move readily-i.e., what happens at those interfaces on the atomic scale? A special electron microscopy, which as a bonus also reveals the true conditions for nondestructive analysis, shows that the large ions that are a necessary part of the 2D films can move into the 3D HaP, a fascinating illustration of panta rei in HaPs.

Encapsulation of Uranium Oxide in Multiwall WS2 Nanotubes.

Uranium is a high-value energy element, yet also poses an appreciable environmental burden. The demand for a straightforward, low energy, and environmentally friendly method for encapsulating uranium species can be beneficial for long-term storage of spent uranium fuel and a host of other applications. Leveraging on the low melting point (60 °C) of uranyl nitrate hexahydrate and nanocapillary effect, a uranium compound is entrapped in the hollow core of WS2 nanotubes. Followingly, the product is reduced at elevated temperatures in a hydrogen atmosphere. Nanocrystalline UO2 nanoparticles anchor within the WS2 nanotube lumen are obtained through this procedure. Such methodology can find utilization in the processing of spent nuclear fuel or other highly active radionuclides as well as a fuel for deep space missions. Moreover, the low melting temperatures of different heavy metal-nitrate hydrates, pave the way for their encapsulation within the hollow core of the WS2 nanotubes, as demonstrated herein.

Silica Biomineralization with Lignin Involves Si-O-C Bonds That Stabilize Radicals.

Plants undergo substantial biomineralization of silicon, which is deposited primarily in cell walls as amorphous silica. The mineral formation could be moderated by the structure and chemistry of lignin, a polyphenol polymer that is a major constituent of the secondary cell wall. However, the reactions between lignin and silica have not yet been well elucidated. Here, we investigate silica deposition onto a lignin model compound. Polyphenyl propanoid was synthesized from coniferyl alcohol by oxidative coupling with peroxidase in the presence of acidic tetramethyl orthosilicate, a silicic acid precursor. Raman, Fourier transform infrared, and X-ray photoelectron spectroscopies detected changes in lignin formation in the presence of silicic acid. Bonds between the Si-O/Si-OH residues and phenoxyl radicals and lignin functional groups formed during the first 3 h of the reaction, while silica continued to form over 3 days. Thermal gravimetric analysis indicated that lignin yields increased in the presence of silicic acid, possibly via the stabilization of phenolic radicals. This, in turn, resulted in shorter stretches of the lignin polymer. Silica deposition initiated within a lignin matrix via the formation of covalent Si-O-C bonds. The silica nucleants grew into 2-5 nm particles, as observed via scanning transmission electron microscopy and energy-dispersive X-ray spectroscopy. Additional silica precipitated into an extended gel. Collectively, our results demonstrate a reciprocal relation by which lignin polymerization catalyzes the formation of silica, and at the same time silicic acid enhances lignin polymerization and yield.

Asymmetric misfit nanotubes: Chemical affinity outwits the entropy at high-temperature solid-state reactions.

Asymmetric two-dimensional (2D) structures (often named Janus), like SeMoS and their nanotubes, have tremendous scope in material chemistry, nanophotonics, and nanoelectronics due to a lack of inversion symmetry and time-reversal symmetry. The synthesis of these structures is fundamentally difficult owing to the entropy-driven randomized distribution of chalcogens. Indeed, no Janus nanotubes were experimentally prepared, so far. Serendipitously, a family of asymmetric misfit layer superstructures (tubes and flakes), including LaX-TaX2 (where X = S/Se), were synthesized by high-temperature chemical vapor transport reaction in which the Se binds exclusively to the Ta atoms and La binds to S atoms rather than the anticipated random distribution. With increasing Se concentration, the LaS-TaX2 misfit structure gradually transformed into a new LaS-TaSe2-TaSe2 superstructure. No misfit structures were found for xSe = 1. These counterintuitive results shed light on the chemical selectivity and stability of misfit compounds and 2D alloys, in general. The lack of inversion symmetry in these asymmetric compounds induces very large local electrical dipoles. The loss of inversion and time-reversal symmetries in the chiral nanotubes offers intriguing physical observations and applications.

Intrinsic Magnetic (EuIn)As Nanowire Shells with a Unique Crystal Structure.

In the pursuit of magneto-electronic systems nonstoichiometric magnetic elements commonly introduce disorder and enhance magnetic scattering. We demonstrate the growth of (EuIn)As shells, with a unique crystal structure comprised of a dense net of Eu inversion planes, over InAs and InAs1-xSbx core nanowires. This is imaged with atomic and elemental resolution which reveal a prismatic configuration of the Eu planes. The results are supported by molecular dynamics simulations. Local magnetic and susceptibility mappings show magnetic response in all nanowires, while a subset bearing a DC signal points to ferromagnetic order. These provide a mechanism for enhancing Zeeman responses, operational at zero applied magnetic field. Such properties suggest that the obtained structures can serve as a preferred platform for time-reversal symmetry broken one-dimensional states including intrinsic topological superconductivity.

Plate-like Guanine Biocrystals Form via Templated Nucleation of Crystal Leaflets on Preassembled Scaffolds.

Controlling the morphology of crystalline materials is challenging, as crystals have a strong tendency toward thermodynamically stable structures. Yet, organisms form crystals with distinct morphologies, such as the plate-like guanine crystals produced by many terrestrial and aquatic species for light manipulation. Regulation of crystal morphogenesis was hypothesized to entail physical growth restriction by the surrounding membrane, combined with fine-tuned interactions between organic molecules and the growing crystal. Using cryo-electron tomography of developing zebrafish larvae, we found that guanine crystals form via templated nucleation of thin leaflets on preassembled scaffolds made of 20-nm-thick amyloid fibers. These leaflets then merge and coalesce into a single plate-like crystal. Our findings shed light on the biological regulation of crystal morphogenesis, which determines their optical properties.

Nanotubes from Ternary WS2(1-x)Se2x Alloys: Stoichiometry Modulated Tunable Optical Properties.

Nanotubes of transition metal dichalcogenides such as WS2 and MoS2 offer unique quasi-1D properties and numerous potential applications. Replacing sulfur by selenium would yield ternary WS2(1-x)Se2x (0 ≤ x ≤ 1; WSSe) nanotubes, which are expected to reveal strong modulation in their absorption edge as a function of selenium content, xSe. Solid WO2.72 oxide nanowhiskers were employed as a sacrificial template to gain a high yield of the nanotubes with a rather uniform size distribution. Though sulfur and selenium belong to the same period, their chemical reactivity with oxide nanowhiskers differed appreciably. Here, the closed ampoule technique was utilized to achieve the completion of the solid-vapor reaction in short time scales instead of the conventional flow reactor method. The structure and chemical composition of the nanotubes were analyzed in detail. X-ray and electron diffractions indicated a systematic modulation of the WSSe lattice upon increasing the selenium content. Detailed chemical mapping showed that the sulfur and selenium atoms are distributed in random positions on the anion lattice site of the nanotubes. The optical excitonic features and absorption edges of the WSSe nanotubes do not vary linearly with the composition xSe, which was further confirmed by density functional theory calculations. The WSSe nanotubes were shown to exhibit strong light-matter interactions forming exciton-polariton quasiparticles, which was corroborated by finite-difference time-domain simulations. Transient absorption analysis permitted following the excited state dynamics and elucidating the mechanism of the strong coupling. Thus, nanotubes of the ternary WSSe alloys offer strong band gap tunability, which would be useful for multispectral vision devices and other optoelectronic applications.

Toward Compositional Contrast by Cryo-STEM.

Electron microscopy (EM) is the most versatile tool for the study of matter at scales ranging from subatomic to visible. The high vacuum environment and the charged irradiation require careful stabilization of many specimens of interest. Biological samples are particularly sensitive due to their composition of light elements suspended in an aqueous medium. Early investigators developed techniques of embedding and staining with heavy metal salts for contrast enhancement. Indeed, the Nobel Prize in 1974 recognized Claude, de Duve, and Palade for establishment of the field of cell biology, largely due to their developments in separation and preservation of cellular components for electron microscopy. A decade later, cryogenic fixation was introduced. Vitrification of the water avoids the need for dehydration and provides an ideal matrix in which the organic macromolecules are suspended; the specimen represents a native state, suddenly frozen in time at temperatures below -150 °C. The low temperature maintains a low vapor pressure for the electron microscope, and the amorphous nature of the medium avoids diffraction contrast from crystalline ice. Such samples are extremely delicate, however, and cryo-EM imaging is a race for information in the face of ongoing damage by electron irradiation. Through this journey, cryo-EM enhanced the resolution scale from membranes to molecules and most recently to atoms. Cryo-EM pioneers, Dubochet, Frank, and Henderson, were awarded the Nobel Prize in 2017 for high resolution structure determination of biological macromolecules.A relatively untapped feature of cryo-EM is its preservation of composition. Nothing is added and nothing removed. Analytical spectroscopies based on electron energy loss or X-ray emission can be applied, but the very small interaction cross sections conflict with the weak exposures required to preserve sample integrity. To what extent can we interpret quantitatively the pixel intensities in images themselves? Conventional cryo-transmission electron microscopy (TEM) is limited in this respect, due to the strong dependence of the contrast transfer on defocus and the absence of contrast at low spatial frequencies.Inspiration comes largely from a different modality for cryo-tomography, using soft X-rays. Contrast depends on the difference in atomic absorption between carbon and oxygen in a region of the spectrum between their core level ionization energies, the so-called water window. Three dimensional (3D) reconstruction provides a map of the local X-ray absorption coefficient. The quantitative contrast enables the visualization of organic materials without stain and measurement of their concentration quantitatively. We asked, what aspects of the quantitative contrast might be transferred to cryo-electron microscopy?Compositional contrast is accessible in scanning transmission EM (STEM) via incoherent elastic scattering, which is sensitive to the atomic number Z. STEM can be regarded as a high energy, low angle diffraction measurement performed pixel by pixel with a weakly convergent beam. When coherent diffraction effects are absent, that is, in amorphous materials, a dark field signal measures quantitatively the flux scattered from the specimen integrated over the detector area. Learning to interpret these signals will open a new dimension in cryo-EM. This Account describes our efforts so far to introduce STEM for cryo-EM and tomography of biological specimens. We conclude with some thoughts on further developments.

Cation-Ligand Complexation Mediates the Temporal Evolution of Colloidal Fluoride Nanocrystals through Transient Aggregation.

Colloidal inorganic nanofluorides have aroused great interest for various applications with their development greatly accelerated thanks to advanced synthetic approaches. Nevertheless, understanding their colloidal evolution and the factors that affect their dispersion could improve the ability to rationally design them. Here, using a multimodal in situ approach that combines DLS, NMR, and cryogenic-TEM, we elucidate the formation dynamics of nanofluorides in water through a transient aggregative phase. Specifically, we demonstrate that ligand-cation interactions mediate a transient aggregation of as-formed CaF2 nanocrystals (NCs) which governs the kinetics of the colloids' evolution. These observations shed light on key stages through which CaF2 NCs are dispersed in water, highlighting fundamental aspects of nanofluorides formation mechanisms. Our findings emphasize the roles of ligands in NCs' synthesis beyond their function as surfactants, including their ability to mediate colloidal evolution by complexing cationic precursors, and should be considered in the design of other types of NCs.

Pathway-Dependent Coordination Networks: Crystals versus Films.

We demonstrate the formation of both metallo-organic crystals and nanoscale films that have entirely different compositions and structures despite using the same set of starting materials. This difference is the result of an unexpected cation exchange process. The reaction of an iron polypyridyl complex with a copper salt by diffusion of one solution into another resulted in iron-to-copper exchange, concurrent ligand rearrangement, and the formation of metal-organic frameworks (MOFs). This observation shows that polypyridyl complexes can be used as expendable precursors for the growth of MOFs. In contrast, alternative depositions of the iron polypyridyl complex with a copper salt by automated spin coating on conductive metal oxides resulted in the formation of electrochromic coatings, and the structure and redox properties of the iron complex were retained. The possibility to form such different networks from the same set of molecular building blocks by "in solution" versus "on surface" coordination chemistry broadens the synthetic space to design functional materials.

Improving the quality factors of plasmonic silver cavities for strong coupling with quantum emitters.

Plasmonic cavities (PCs) made of metallic nanostructures can concentrate electromagnetic radiation into an ultrasmall volume, where it might strongly interact with quantum emitters. In recent years, there has been much interest in studying such a strong coupling in the limit of single emitters. However, the lossy nature of PCs, reflected in their broad spectra, limits their quality factors and hence their performance as cavities. Here, we study the effect of the adhesion layer used in the fabrication of metal nanostructures on the spectral linewidths of bowtie-structured PCs. Using dark-field microspectroscopy, as well as electron energy loss spectroscopy, it is found that a reduction in the thickness of the chromium adhesion layer we use from 3 nm to 0.1 nm decreases the linewidths of both bright and dark plasmonic modes. We further show that it is possible to fabricate bowtie PCs without any adhesion layer, in which case the linewidth may be narrowed by as much as a factor of 2. Linewidth reduction increases the quality factor of these PCs accordingly, and it is shown to facilitate reaching the strong-coupling regime with semiconductor quantum dots.

Flexible STEM with Simultaneous Phase and Depth Contrast.

Recent advances in scanning transmission electron microscopy (STEM) have rekindled interest in multi-channel detectors and prompted the exploration of unconventional scan patterns. These emerging needs are not yet addressed by standard commercial hardware. The system described here incorporates a flexible scan generator that enables exploration of low-acceleration scan patterns, while data are recorded by a scalable eight-channel array of nonmultiplexed analog-to-digital converters. System integration with SerialEM provides a flexible route for automated acquisition protocols including tomography. Using a solid-state quadrant detector with additional annular rings, we explore the generation and detection of various STEM contrast modes. Through-focus bright-field scans relate to phase contrast, similarly to wide-field TEM. More strikingly, comparing images acquired from different off-axis detector elements reveals lateral shifts dependent on defocus. Compensation of this parallax effect leads to decomposition of integrated differential phase contrast (iDPC) to separable contributions relating to projected electric potential and to defocus. Thus, a single scan provides both a computationally refocused phase contrast image and a second image in which the signed intensity, bright or dark, represents the degree of defocus.

Inducing Defects in 19F-Nanocrystals Provides Paramagnetic-free Relaxation Enhancement for Improved In Vivo Hotspot MRI.

Paramagnetic relaxation enhancement (PRE) is the current strategy of choice for enhancing magnetic resonance imaging (MRI) contrast and for accelerating MRI acquisition schemes. Yet, debates regarding lanthanides' biocompatibility and PRE-effect on MRI signal quantification have raised the need for alternative strategies for relaxation enhancement. Herein, we show an approach for shortening the spin-lattice relaxation time (T1) of fluoride-based nanocrystals (NCs) that are used for in vivo 19F-MRI, by inducing crystal defects in their solid-crystal core. By utilizing a phosphate-based rather than a carboxylate-based capping ligand for the synthesis of CaF2 NCs, we were able to induce grain boundary defects in the NC lattice. The obtained defects led to a 10-fold shorter T1 of the NCs' fluorides. Such paramagnetic-free relaxation enhancement of CaF2 NCs, gained without affecting either their size or their colloidal characteristics, improved 4-fold the obtained 19F-MRI signal-to-noise ratio, allowing their use, in vivo, with enhanced hotspot MRI sensitivity.

Unusual Surface Texture, Dimensions and Morphology Variations of Chiral and Single Crystals*.

We demonstrate here a unique metallo-organic material where the appearance and the internal crystal structure are in contradiction. The egg-shaped (ovoid) crystals have a brain-like texture. Although these micro-sized crystals are monodispersed; like fingerprints their grainy surfaces are never exactly alike. Remarkably, our X-ray and electron diffraction studies unexpectedly revealed that these structures are single-crystals comprising a continuous coordination network of two differently shaped homochiral channels. By using the same building blocks under different reaction conditions, a rare series of crystals have been obtained that are uniquely rounded in their shape. In stark contrast to the brain-like crystals, these isostructural and monodispersed crystals have a comparatively smooth appearance. The sizes of these crystals vary by several orders of magnitude.

Guest Transition Metals in Host Inorganic Nanocapsules: Single Sites, Discrete Electron Transfer, and Atomic Scale Structure.

Host-guest solution chemistry with a wide range of organic hosts is an important and established research area, while the use of inorganic hosts is a more nascent area of research. In the recent past in a few cases, Keplerate-type molybdenum oxide-based porous, spherical clusters, shorthand notation {Mo132}, have been used as hosts for organic guests. Here, we demonstrate the synthetically controlled encapsulation of first-row transition metals (M = Mn, Fe, and Co) within a Keplerate cluster that was lined on the inner core with phosphate anions, {Mo132PO4}. The resulting M2+x⊂{Mo132PO4} host-guest complexes were characterized by 31P NMR and ENDOR spectroscopy that substantiated the encapsulation of the first-row transition metal guest. Magnetic susceptibility measurements showed that the encapsulation of up to 10 equiv showed little magnetic interaction between the encapsulated metals, which indicated that each guest atom occupied a single site. Visualization of the capsules and differentiation of the Mo atoms of the capsule framework and the encapsulated transition metal were possible using spherical and chromatic double aberration-corrected electron microscopy combined with energy-filtered TEM (EFTEM) elemental maps. In addition, use of visible light-induced XPS for chemically resolved electrical measurements (CREM) confirmed the successful encapsulation of M within {Mo132PO4} and furthermore showed photoinduced electron transfer from M to Mo. In the future, such targeted electron transfer between host {Mo132} and a transition metal guest could be used as photoinitiated switches using inorganic compounds and for single site photocatalytic reactions in confined space.

Chiral and SHG-Active Metal-Organic Frameworks Formed in Solution and on Surfaces: Uniformity, Morphology Control, Oriented Growth, and Postassembly Functionalization.

We demonstrate the formation of uniform and oriented metal-organic frameworks using a combination of anion effects and surface chemistry. Subtle but significant morphological changes result from the nature of the coordinative counteranion of the following metal salts: NiX2 with X = Br-, Cl-, NO3-, and OAc-. Crystals could be obtained in solution or by template surface growth. The latter results in truncated crystals that resemble a half structure of the solution-grown ones. The oriented surface-bound metal-organic frameworks (sMOFs) are obtained via a one-step solvothermal approach rather than in a layer-by-layer approach. The MOFs are grown on Si/SiOx substrates modified with an organic monolayer or on glass substrates covered with a transparent conductive oxide (TCO). Regardless of the different morphologies, the crystallographic packing is nearly identical and is not affected by the type of anion or by solution versus the surface chemistry. A propeller-type arrangement of the nonchiral ligands around the metal center affords a chiral structure with two geometrically different helical channels in a 2:1 ratio with the same handedness. To demonstrate the accessibility and porosity of the macroscopically oriented channels, a chromophore (resorufin sodium salt) was successfully embedded into the channels of the crystals by diffusion from solution, resulting in fluorescent crystals. These "colored" crystals displayed polarized emission (red) with a high polarization ratio because of the alignment of these dyes imposed by the crystallographic structure. A second-harmonic generation (SHG) study revealed Kleinman symmetry-forbidden nonlinear optical properties. These surface-bound and oriented SHG-active MOFs have the potential for use as single nonlinear optical (NLO) devices.

Detection of isolated protein-bound metal ions by single-particle cryo-STEM.

Metal ions play essential roles in many aspects of biological chemistry. Detecting their presence and location in proteins and cells is important for understanding biological function. Conventional structural methods such as X-ray crystallography and cryo-transmission electron microscopy can identify metal atoms on protein only if the protein structure is solved to atomic resolution. We demonstrate here the detection of isolated atoms of Zn and Fe on ferritin, using cryogenic annular dark-field scanning transmission electron microscopy (cryo-STEM) coupled with single-particle 3D reconstructions. Zn atoms are found in a pattern that matches precisely their location at the ferroxidase sites determined earlier by X-ray crystallography. By contrast, the Fe distribution is smeared along an arc corresponding to the proposed path from the ferroxidase sites to the mineral nucleation sites along the twofold axes. In this case the single-particle reconstruction is interpreted as a probability distribution function based on the average of individual locations. These results establish conditions for detection of isolated metal atoms in the broader context of electron cryo-microscopy and tomography.

The effects of sample conductivity on the efficacy of dynamic nuclear polarization for sensitivity enhancement in solid state NMR spectroscopy.

In recent years dynamic nuclear polarization (DNP) has greatly expanded the range of materials systems that can be studied by solid state NMR spectroscopy. To date, the majority of systems studied by DNP were insulating materials including organic and inorganic solids. However, many technologically-relevant materials used in energy conversion and storage systems are electrically conductive to some extent or are employed as composites containing conductive additives. Such materials introduce challenges in their study by DNP-NMR which include microwave absorption and sample heating that were not thoroughly investigated so far. Here we examine several commercial carbon allotropes, commonly employed as electrodes or conductive additives, and consider their effect on the extent of solvent polarization achieved in DNP from nitroxide biradicals. We then address the effect of sample conductivity systematically by studying a series of carbons with increasing electrical conductivity prepared via glucose carbonization. THz spectroscopy measurements are used to determine the extent of µw absorption. Our results show that while the DNP performance significantly drops in samples containing the highly conductive carbons, sufficient signal enhancement can still be achieved with some compromise on conductivity. Furthermore, we show that the deleterious effect of conductive additives on DNP enhancements can be partially overcome through pulse-DNP experiments.

Surface-Guided CsPbBr3 Perovskite Nanowires on Flat and Faceted Sapphire with Size-Dependent Photoluminescence and Fast Photoconductive Response.

All-inorganic lead halide perovskite nanowires have been the focus of increasing interest since they exhibit improved stability compared to their hybrid organic-inorganic counterparts, while retaining their interesting optical and optoelectronic properties. Arrays of surface-guided nanowires with controlled orientations and morphology are promising as building blocks for various applications and for systematic research. We report the horizontal and aligned growth of CsPbBr3 nanowires with a uniform crystallographic orientation on flat and faceted sapphire surfaces to form arrays with 6-fold and 2-fold symmetries, respectively, along specific directions of the sapphire substrate. We observed waveguiding behavior and diameter-dependent photoluminescence emission well beyond the quantum confinement regime. The arrays were easily integrated into multiple devices, displaying p-type behavior and photoconductivity. Photodetectors based on those nanowires exhibit the fastest rise and decay times for any CsPbBr3-based photodetectors reported so far. One-dimensional arrays of halide perovskite nanowires are a promising platform for investigating the intriguing properties and potential applications of these unique materials.