Visualization of the effect of additives on the nanostructures of individual bio-inspired calcite crystals

Crossing length scales: X-ray approaches to studying the structure of biological materials

Biological materials have outstanding properties. With ease, challenging mechanical, optical or electrical properties are realised from comparatively `humble' building blocks. The key strategy to realise these properties is through extensive hierarchical structuring of the material from the millimetre to the nanometre scale in 3D. Though hierarchical structuring in biological materials has long been recognized, the 3D characterization of such structures remains a challenge. To understand the behaviour of materials, multimodal and multi-scale characterization approaches are needed. In this review, we outline current X-ray analysis approaches using the structures of bone and shells as examples. We show how recent advances have aided our understanding of hierarchical structures and their functions, and how these could be exploited for future research directions. We also discuss current roadblocks including radiation damage, data quantity and sample preparation, as well as strategies to address them.

Visualizing the Internal Nanocrystallinity of Calcite Due to Nonclassical Crystallization by 3D Coherent X-Ray Diffraction Imaging

The internal crystallinity of calcite is investigated for samples synthesized using two approaches: precipitation from solution and the ammonium carbonate diffusion method. Scanning electron microscopy (SEM) analyses reveal that the calcite products precipitated using both approaches have a well-defined rhombohedron shape, consistent with the euhedral crystal habit of the mineral. The internal structure of these calcite crystals is characterized using Bragg coherent diffraction imaging (BCDI) to determine the 3D electron density and the atomic displacement field. BCDI reconstructions for crystals synthesized using the ammonium carbonate diffusion approach have the expected euhedral shape, with internal strain fields and few internal defects. In contrast, the crystals synthesized by precipitation from solution have very complex external shapes and defective internal structures, presenting null electron density regions and pronounced displacement field distributions. These heterogeneities are interpreted as multiple crystalline domains, created by a nonclassical crystallization mechanism, where smaller nanoparticles coalescence into the final euhedral particles. The combined use of SEM, X-ray diffraction (XRD), and BCDI allows for structurally differentiating calcite crystals grown with different approaches, opening new opportunities to understand how grain boundaries and internal defects alter calcite reactivity.

Optimising a method for aragonite precipitation in simulated biogenic calcification media

Resolving how factors such as temperature, pH, biomolecules and mineral growth rate influence the geochemistry and structure of biogenic CaCO3, is essential to the effective development of palaeoproxies. Here we optimise a method to precipitate the CaCO3 polymorph aragonite from seawater, under tightly controlled conditions that simulate the saturation state (Ω) of coral calcification fluids. We then use the method to explore the influence of aspartic acid (one of the most abundant amino acids in coral skeletons) on aragonite structure and morphology. Using ≥200 mg of aragonite seed (surface area 0.84 m2), to provide a surface for mineral growth, in a 330 mL seawater volume, generates reproducible estimates of precipitation rate over Ωaragonite = 6.9-19.2. However, unseeded precipitations are highly variable in duration and do not provide consistent estimates of precipitation rate. Low concentrations of aspartic acid (1-10 μM) promote aragonite formation, but high concentrations (≥ 1 mM) inhibit precipitation. The Raman spectra of aragonite precipitated in vitro can be separated from the signature of the starting seed by ensuring that at least 60% of the analysed aragonite is precipitated in vitro (equivalent to using a seed of 200 mg and precipitating 300 mg aragonite in vitro). Aspartic acid concentrations ≥ 1mM caused a significant increase in the full width half maxima of the Raman aragonite v1 peak, reflective of increased rotational disorder in the aragonite structure. Changes in the organic content of coral skeletons can drive variations in the FWHM of the Raman aragonite ν1 peak, and if not accounted for, may confuse the interpretation of calcification fluid saturation state from this parameter.

Different skeletal protein toolkits achieve similar structure and performance in the tropical coral Stylophora pistillata and the temperate Oculina patagonica

Stony corals (order: Scleractinia) differ in growth form and structure. While stony corals have gained the ability to form their aragonite skeleton once in their evolution, the suite of proteins involved in skeletogenesis is different for different coral species. This led to the conclusion that the organic portion of their skeleton can undergo rapid evolutionary changes by independently evolving new biomineralization-related proteins. Here, we used liquid chromatography-tandem mass spectrometry to sequence skeletogenic proteins extracted from the encrusting temperate coral Oculina patagonica. We compare it to the previously published skeletal proteome of the branching subtropical corals Stylophora pistillata as both are regarded as highly resilient to environmental changes. We further characterized the skeletal organic matrix (OM) composition of both taxa and tested their effects on the mineral formation using a series of overgrowth experiments on calcite seeds. We found that each species utilizes a different set of proteins containing different amino acid compositions and achieve a different morphology modification capacity on calcite overgrowth. Our results further support the hypothesis that the different coral taxa utilize a species-specific protein set comprised of independent gene co-option to construct their own unique organic matrix framework. While the protein set differs between species, the specific predicted roles of the whole set appear to underline similar functional roles. They include assisting in forming the extracellular matrix, nucleation of the mineral and cell signaling. Nevertheless, the different composition might be the reason for the varying organization of the mineral growth in the presence of a particular skeletal OM, ultimately forming their distinct morphologies.

Positively Charged Additives Facilitate Incorporation in Inorganic Single Crystals

Incorporation of guest additives within inorganic single crystals offers a unique strategy for creating nanocomposites with tailored properties. While anionic additives have been widely used to control the properties of crystals, their effective incorporation remains a key challenge. Here, we show that cationic additives are an excellent alternative for the synthesis of nanocomposites, where they are shown to deliver exceptional levels of incorporation of up to 70 wt % of positively charged amino acids, polymer particles, gold nanoparticles, and silver nanoclusters within inorganic single crystals. This high additive loading endows the nanocomposites with new functional properties, including plasmon coupling, bright fluorescence, and surface-enhanced Raman scattering (SERS). Cationic additives are also shown to outperform their acidic counterparts, where they are highly active in a wider range of crystal systems, owing to their outstanding colloidal stability in the crystallization media and strong affinity for the crystal surfaces. This work demonstrates that although often overlooked, cationic additives can make valuable crystallization additives to create composite materials with tailored composition-structure-property relationships. This versatile and straightforward approach advances the field of single-crystal composites and provides exciting prospects for the design and fabrication of new hybrid materials with tunable functional properties.

Composite Porous Liquid for Recyclable Sequestration, Storage and In Situ Catalytic Conversion of Carbon Dioxide at Room Temperature

Permanent pores combined with fluidity renders flow processability to porous liquids otherwise not seen in porous solids. Although porous liquids have been utilized for sequestration of different gases and their separation, there is still a dearth of studies for deploying in situ chemical reactions to convert adsorbed gases into utility chemicals. Here, we show the design and development of a new type of solvent-less and hybrid (meso-)porous liquid composite, which, as demonstrated for the first time, can be used for in situ carbon mineralization of adsorbed CO₂ . The recyclable porous liquid composite comprising polymer-surfactant modified hollow silica nanorods and carbonic anhydrase enzyme not only sequesters (5.5 cm³  g^-1 at 273 K and 1 atm) and stores CO₂ but is also capable of driving an in situ enzymatic reaction for hydration of CO₂ to HCO₃ ^- ion, subsequently converting it to CaCO₃ due to reaction with pre-dissolved Ca²⁺ . Light and electron microscopy combined with X-ray diffraction reveals the nucleation and growth of calcite and aragonite crystals. Moreover, the liquid-like property of the porous composite material can be harnessed by executing the same reaction via diffusion of complimentary Ca²⁺ and HCO₃ ^- ions through different compartments separated by an interfacial channel. These studies provide a proof of concept of deploying chemical reactions within porous liquids for developing utility chemical from adsorbed molecules.

Local Light-Controlled Generation of Calcium Carbonate and Barium Carbonate Biomorphs via Photochemical Stimulation

Photochemical activation is proposed as a general method for controlling the crystallization of sparingly soluble carbonates in space and time. The photogeneration of carbonate in an alkaline environment is achieved upon photo‐decarboxylation of an organic precursor by using a conventional 365 nm UV LED. Local irradiation was conducted focusing the LED light on a 300 μm radius spot on a closed glass crystallization cell. The precursor solution was optimized to avoid the precipitation of the photoreaction organic byproducts and prevent photo‐induced pH changes to achieve the formation of calcium carbonate only in the corresponding irradiated area. The crystallization was monitored in real‐time by time‐lapse imaging. The method is also shown to work in gels. Similarly, it was also shown to photo‐activate locally the formation of barium carbonate biomorphs. In the last case, the morphology of these biomimetic structures was tuned by changing the irradiation intensity.

Bragg Coherent Diffraction Imaging for In Situ Studies in Electrocatalysis

Electrocatalysis is at the heart of a broad range of physicochemical applications that play an important role in the present and future of a sustainable economy. Among the myriad of different electrocatalysts used in this field, nanomaterials are of ubiquitous importance. An increased surface area/volume ratio compared to bulk makes nanoscale catalysts the preferred choice to perform electrocatalytic reactions. Bragg coherent diffraction imaging (BCDI) was introduced in 2006 and since has been applied to obtain 3D images of crystalline nanomaterials. BCDI provides information about the displacement field, which is directly related to strain. Lattice strain in the catalysts impacts their electronic configuration and, consequently, their binding energy with reaction intermediates. Even though there have been significant improvements since its birth, the fact that the experiments can only be performed at synchrotron facilities and its relatively low resolution to date (∼10 nm spatial resolution) have prevented the popularization of this technique. Herein, we will briefly describe the fundamentals of the technique, including the electrocatalysis relevant information that we can extract from it. Subsequently, we review some of the computational experiments that complement the BCDI data for enhanced information extraction and improved understanding of the underlying nanoscale electrocatalytic processes. We next highlight success stories of BCDI applied to different electrochemical systems and in heterogeneous catalysis to show how the technique can contribute to future studies in electrocatalysis. Finally, we outline current challenges in spatiotemporal resolution limits of BCDI and provide our perspectives on recent developments in synchrotron facilities as well as the role of machine learning and artificial intelligence in addressing them.

High-Throughput 3D Ensemble Characterization of Individual Core-Shell Nanoparticles with X-ray Free Electron Laser Single-Particle Imaging

The structures as building blocks for designing functional nanomaterials have fueled the development of versatile nanoprobes to understand local structures of noncrystalline specimens. Progress in analyzing structures of individual specimens with atomic scale accuracy has been notable recently. In most cases, however, only a limited number of specimens are inspected lacking statistics to represent the systems with structural inhomogeneity. Here, by employing single-particle imaging with X-ray free electron lasers and algorithms for multiple-model 3D imaging, we succeeded in investigating several thousand specimens in a couple of hours and identified intrinsic heterogeneities with 3D structures. Quantitative analysis has unveiled 3D morphology, facet indices, and elastic strain. The 3D elastic energy distribution is further corroborated by molecular dynamics simulations to gain mechanical insight at the atomic level. This work establishes a route to high-throughput characterization of individual specimens in large ensembles, hence overcoming statistical deficiency while providing quantitative information at the nanoscale.

Spatio-Chemical Heterogeneity of Defect-Engineered Metal-Organic Framework Crystals Revealed by Full-Field Tomographic X-ray Absorption Spectroscopy

The introduction of structural defects in metal-organic frameworks (MOFs), often achieved through the fractional use of defective linkers, is emerging as a means to refine the properties of existing MOFs. These linkers, missing coordination fragments, create unsaturated framework nodes that may alter the properties of the MOF. A property-targeted utilization of this approach demands an understanding of the structure of the defect-engineered MOF. We demonstrate that full-field X-ray absorption near-edge structure computed tomography can help to improve our understanding. This was demonstrated by visualizing the chemical heterogeneity found in defect-engineered HKUST-1 MOF crystals. A non-uniform incorporation and zonation of the defective linker was discovered, leading to the presence of clusters of a second coordination polymer within HKUST-1. The former is suggested to be responsible, in part, for altered MOF properties; thereby, advocating for a spatio-chemically resolved characterization of MOFs.

Generality of liquid precursor phases in gas diffusion-based calcium carbonate synthesis

We confirm the presence of liquid calcium carbonate precursor species in absence of additives in gas diffusion systems.

Three-dimensional strain dynamics govern the hysteresis in heterogeneous catalysis

Understanding catalysts strain dynamic behaviours is crucial for the development of cost-effective, efficient, stable and long-lasting catalysts. Here, we reveal in situ three-dimensional strain evolution of single gold nanocrystals during a catalytic CO oxidation reaction under operando conditions with coherent X-ray diffractive imaging. We report direct observation of anisotropic strain dynamics at the nanoscale, where identically crystallographically-oriented facets are qualitatively differently affected by strain leading to preferential active sites formation. Interestingly, the single nanoparticle elastic energy landscape, which we map with attojoule precision, depends on heating versus cooling cycles. The hysteresis observed at the single particle level is following the normal/inverse hysteresis loops of the catalytic performances. This approach opens a powerful avenue for studying, at the single particle level, catalytic nanomaterials and deactivation processes under operando conditions that will enable profound insights into nanoscale catalytic mechanisms.

Super-Resolution Microscopy Reveals Shape and Distribution of Dislocations in Single-Crystal Nanocomposites

With their potential to offer new properties, single crystals containing nanoparticles provide an attractive class of nanocomposite materials. However, to fully profit from these, it is essential that we can characterise their 3D structures, identifying the locations of individual nanoparticles, and the defects present within the host crystals. Using calcite crystals containing quantum dots as a model system, we here use 3D stochastic optical reconstruction microscopy (STORM) to locate the positions of the nanoparticles within the host crystal. The nanoparticles are shown to preferentially associate with dislocations in a manner previously recognised for atomic impurities, rendering these defects visible by STORM. Our images also demonstrate that the types of dislocations formed at the crystal/substrate interface vary according to the nucleation face, and dislocation loops are observed that have entirely different geometries to classic misfit dislocations. This approach offers a rapid, easily accessed, and non-destructive method for visualising the dislocations present within crystals, and gives insight into the mechanisms by which additives become occluded within crystals.

In situ three-dimensional imaging of strain in gold nanocrystals during catalytic oxidation

The chemical properties of materials are dependent on dynamic changes in their three-dimensional (3D) structure as well as on the reactive environment. We report an in situ 3D imaging study of defect dynamics of a single gold nanocrystal. Our findings offer an insight into its dynamic nanostructure and unravel the formation of a nanotwin network under CO oxidation conditions. In situ/operando defect dynamics imaging paves the way to elucidate chemical processes at the single nano-object level towards defect-engineered nanomaterials.