Structure determination of biogenic crystals directly from 3D electron diffraction data

Highly reflective assemblies of purine, pteridine, and flavin crystals are used in the coloration and visual systems of many different animals. However, structure determination of biogenic crystals by single-crystal XRD is challenging due to the submicrometer size and beam sensitivity of the crystals, and powder XRD is inhibited due to the small volumes of powders, crystalline impurity phases, and significant preferred orientation. Consequently, the crystal structures of many biogenic materials remain unknown. Herein, we demonstrate that the 3D electron diffraction (3D ED) technique provides a powerful alternative approach, reporting the successful structure determination of biogenic guanine crystals (from spider integument, fish scales, and scallop eyes) from 3D ED data confirmed by analysis of powder XRD data. The results show that all biogenic guanine crystals studied are the previously known β-polymorph. This study highlights the considerable potential of 3D ED for elucidating the structures of biogenic molecular crystals in the nanometer-to-micrometer size range. This opens up an important opportunity in the development of organic biomineralization, for which structural knowledge is critical for understanding the optical functions of biogenic materials and their possible applications as sustainable, biocompatible optical materials

Study of the effectiveness of crystal growth modifiers in the prevention of damage due to crystallization of sodium carbonates in stone artworks

The disintegration of stone materials used in sculpture and architecture due to the crystallization of salts is capable of irreparably damaging artistic objects and historic buildings. A number of phosphonates and carboxylates were tested here as potential crystallization modifiers for sodium carbonate crystallization. Precipitated phases during crystallization induced either by cooling or by evaporation tests were nahcolite (NaHCO3), natron (Na2CO3∙10H2O) and thermonatrite (Na2CO3∙H2O), identified using X-ray diffraction. By using the thermodynamic code PHREEQC and the calculation of the nucleation rate it was demonstrated that nahcolite had to be first phase formed during both tests. The formation of the other phases depended on the experimental conditions under which the two tests were conducted. Nahcolite nucleation is strongly inhibited in the presence of sodium citrate tribasic dihydrate (CA), polyacrylic acid 2100MW (PA) and etidronic acid (HEDP), when the additives are dosed at appropriate concentrations and the pH range of the resulting solution is about 8. Electrostatic attraction generated between the deprotonated organic additives and the cations present in solution appears to be the principal mechanism of additive-nahcolite interaction. Salt weathering tests, in addition to mercury intrusion porosimetry tests allowed to quantify the damage induced by such salts. FESEM observation of both salts grown on calcite single crystals and in limestone blocks subjected to salt crystallization tests allowed to identify the effect of these additives on crystal growth and development. The results show that PA seems to be the best inhibitor, while CA and HEDP, which show similar behaviors, are slightly less effective. The use of such effective crystallization inhibitors may lead to more efficient preventive conservation of ornamental stone affected by crystallization damage due to formation of sodium carbonate crystals

Three-dimensional electron diffraction for studying order, disorder and flexibility in metal-organic frameworks

Metal-organic frameworks (MOFs) represent a class of 3D crystalline porous materials composed of organic linkers and metal nodes. Over the years, tens of thousands of MOF architectures have been developed, addressing various applications such as gas storage and separation, catalysis, chemical sensing, ion exchange and drug delivery. One of the most fascinating properties of MOFs lies in their flexible character responsible, for example, for the rotational dynamics of linkers. Three-dimensional electron diffraction (3D ED) has shown to be a powerful tool to solve the structure of nano- or submicrometer-sized crystals coexisting in mixtures, overcoming the limitations of x-ray diffraction.  In this thesis the great potential of one continuous 3D ED protocol, namely continuous rotation electron diffraction (cRED), for the investigation of MOFs is described. cRED has routinely been used in the past decade for obtaining accurate atomic coordinates and perform structure determination of MOFs. In this thesis it is introduced how the limits of the classical approaches for structure determination by cRED can be tackled by individually adjusting the strategies to the requirements of the structures. Thanks to these approaches, full determination of complex structures and fine structural features previously considered impossible to retrieve by 3D ED data, can now be achieved. The complete structure determination of MOFs with highly complex structures, low crystallinity, sensitivity to electron beam and high-vacuum, displacive disorder and long-range structural dynamics is presented. Specifically, in this thesis it is shown how it was possible to achieve the ab initio full determination of MIL-100, an architecture with a unit cell of several hundred thousand cubic Ångstroms, and the discovery of a new class of materials (M-HAF-2), with a connectivity between those of MOFs and hydrogen-bonded organic frameworks. Additionally, the displacive disorder and dynamics in UiO-67 and MIL-140C were investigated showing for the first time that 3D ED can be applied for probing displacive disorder and molecular motion by analyzing the anisotropic displacement parameters. Methods to obtain maximum structure information from anisotropic atomic displacement parameters are also provided through careful investigations of the refinement of ZIF-EC1, MIL-140C and Ga(OH)(1,4-ndc)

Three-dimensional electron diffraction for studying order, disorder and flexibility in metal-organic frameworks

Metal-organic frameworks (MOFs) represent a class of 3D crystalline porous materials composed of organic linkers and metal nodes. Over the years, tens of thousands of MOF architectures have been developed, addressing various applications such as gas storage and separation, catalysis, chemical sensing, ion exchange and drug delivery. One of the most fascinating properties of MOFs lies in their flexible character responsible, for example, for the rotational dynamics of linkers. Three-dimensional electron diffraction (3D ED) has shown to be a powerful tool to solve the structure of nano- or submicrometer-sized crystals coexisting in mixtures, overcoming the limitations of x-ray diffraction.  In this thesis the great potential of one continuous 3D ED protocol, namely continuous rotation electron diffraction (cRED), for the investigation of MOFs is described. cRED has routinely been used in the past decade for obtaining accurate atomic coordinates and perform structure determination of MOFs. In this thesis it is introduced how the limits of the classical approaches for structure determination by cRED can be tackled by individually adjusting the strategies to the requirements of the structures. Thanks to these approaches, full determination of complex structures and fine structural features previously considered impossible to retrieve by 3D ED data, can now be achieved. The complete structure determination of MOFs with highly complex structures, low crystallinity, sensitivity to electron beam and high-vacuum, displacive disorder and long-range structural dynamics is presented. Specifically, in this thesis it is shown how it was possible to achieve the ab initio full determination of MIL-100, an architecture with a unit cell of several hundred thousand cubic Ångstroms, and the discovery of a new class of materials (M-HAF-2), with a connectivity between those of MOFs and hydrogen-bonded organic frameworks. Additionally, the displacive disorder and dynamics in UiO-67 and MIL-140C were investigated showing for the first time that 3D ED can be applied for probing displacive disorder and molecular motion by analyzing the anisotropic displacement parameters. Methods to obtain maximum structure information from anisotropic atomic displacement parameters are also provided through careful investigations of the refinement of ZIF-EC1, MIL-140C and Ga(OH)(1,4-ndc)

Probing Molecular Motions in Metal-Organic Frameworks by Three-Dimensional Electron Diffraction

Flexible metal–organic frameworks (MOFs) are known for their vast functional diversities and variable pore architectures. Dynamic motions or perturbations are among the highly desired flexibilities, which are key to guest diffusion processes. Therefore, probing such motions, especially at an atomic level, is crucial for revealing the unique properties and identifying the applications of MOFs. Nuclear magnetic resonance (NMR) and single-crystal X-ray diffraction (SCXRD) are the most important techniques to characterize molecular motions but require pure samples or large single crystals (>5 × 5 × 5 μm3), which are often inaccessible for MOF synthesis. Recent developments of three-dimensional electron diffraction (3D ED) have pushed the limits of single-crystal structural analysis. Accurate atomic information can be obtained by 3D ED from nanometer- and submicrometer-sized crystals and samples containing multiple phases. Here, we report the study of molecular motions by using the 3D ED method in MIL-140C and UiO-67, which are obtained as nanosized crystals coexisting in a mixture. In addition to an ab initio determination of their framework structures, we discovered that motions of the linker molecules could be revealed by observing the thermal ellipsoid models and analyzing the atomic anisotropic displacement parameters (ADPs) at room temperature (298 K) and cryogenic temperature (98 K). Interestingly, despite the same type of linker molecule occupying two symmetry-independent positions in MIL-140C, we observed significantly larger motions for the isolated linkers in comparison to those reinforced by π–π stacking. With an accuracy comparable to that of SCXRD, we show for the first time that 3D ED can be a powerful tool to investigate dynamics at an atomic level, which is particularly beneficial for nanocrystalline materials and/or phase mixtures

Metal-Hydrogen-Pi-Bonded Organic Frameworks

We report the synthesis and characterization of a new series of permanently porous, three-dimensional metal-organic frameworks (MOFs), M-HAF-2 (M= Fe, Ga or In), constructed from tetratopic, hydroxamate-based, chelating linkers. The structure of M-HAF-2 was determined by three-dimensional electron diffraction (3DED), revealing a unique interpenetrated hcb-a net topology. This unusual topology is enabled by the presence of free hydroxamate groups, which lead to the formation of a diverse network of cooperative interactions comprising single metal-hydroxamate nodes, staggered π–π interactions between linkers and H-bonding interactions between metal-coordinated and free hydroxamate groups. Such extensive, multimodal interconnectivity is reminiscent of the complex noncovalent interaction networks of proteins and endows M-HAF-2 frameworks with good thermal and exceptionally high chemical stability and allows them to readily undergo post-synthetic metal exchange (PSE). We demonstrate that M-HAF-2 can serve as versatile porous materials for ionic separations, likely aided by one-dimensional channels lined by continuously π-stacked aromatic groups and H-bonding hydroxamate functionalities. As a new addition to the small group of hydroxamate-based MOFs, M-HAF-2 represents a structural merger between MOFs and hydrogen-bonded organic frameworks (HOFs)