Rapid phase elucidation of polycrystalline materials is essential for developing new materials of... more Rapid phase elucidation of polycrystalline materials is essential for developing new materials of chemical, pharmaceutical and industrial interest. Yet, the size and quantity of many crystalline phases are too small for routine X-ray diffraction analysis. This has become a workflow bottleneck in materials development, especially in high-throughput synthesis screening. Here we demonstrate the application of serial rotation electron diffraction (SerialRED) for high-throughput phase identification of complex polycrystalline zeolite products. The products were prepared from a combination of multiple framework T atoms ([Si,Ge,Al] or [Si,Ge,B]) and a simple organic structure-directing agent. We show that using SerialRED, five zeolite phases can be identified from a highly complex mixture. This includes phases with ultra-low contents undetectable using X-ray diffraction and phases with identical crystal morphology and similar unit cell parameters. By automatically and rapidly examining hun...
Three-dimensional electron diffraction (3D ED)/microcrystal electron diffraction (MicroED) techni... more Three-dimensional electron diffraction (3D ED)/microcrystal electron diffraction (MicroED) techniques are gaining in popularity. However, the data processing often does not fit existing graphical user interface software, instead requiring the use of the terminal or scripting. Scipion-ED, described in this article, provides a graphical user interface and extendable framework for processing of 3D ED/MicroED data. An illustrative project is described, in which multiple 3D ED/MicroED data sets collected on tetragonal lysozyme were processed with DIALS through the Scipion-ED interface. The ability to resolve unmodelled features in the electrostatic potential map was compared between three strategies for merging data sets.
Noncovalent interactions are essential in the formation and function of a diverse range of hybrid... more Noncovalent interactions are essential in the formation and function of a diverse range of hybrid materials. However, reliably identifying the noncovalent interactions in nanocrystalline materials remains challenging using conventional methods such as X-ray diffraction and spectroscopy. Here, we demonstrate that the entire range of noncovalent interactions in a nanocrystalline aluminophosphate hybrid material SCM-34 can be directly visualized by accurately determining all atomic positions using 3D electron diffraction (3D ED). The resolved hydrogen atoms reveal the protonation states of the inorganic and organic components. All the noncovalent hydrogen bonding, electrostatic, π–π stacking, and Van der Waals interactions were unambiguously resolved, providing a detailed insight into the material formation mechanism. The data are sufficiently accurate to distinguish the different types of covalent bonds based on their bond lengths, and we observed an elongated terminal P=O π-bond caus...
Three-dimensional rotation electron diffraction: software RED for automated data collection and d... more Three-dimensional rotation electron diffraction: software RED for automated data collection and data processing
EMC 2008 14th European Microscopy Congress 1–5 September 2008, Aachen, Germany
ABSTRACT In the Zn-rich Zn-Mg-RE alloys three groups of ternary hexagonal phases (Zn,Mg)58RE13, (... more ABSTRACT In the Zn-rich Zn-Mg-RE alloys three groups of ternary hexagonal phases (Zn,Mg)58RE13, (Zn,Mg)5RE, Zn6Mg3RE (also named Z-phase) are found to coexist with the icosahedral quasicrystal. In a study of the ternary Zn-Mg-Sm system, Drits et al. [1] first found the hexagonal Zn6Mg3Sm phase with a = 14.62 Å and c = 8.71 Å. Later, this hexagonal phase has also been found in the Zn-Mg-Y [2] and Zn-Mg-Gd [3] alloys and their crystal structures were determined by the single crystal X-ray diffraction analysis [2,3]. Recently, we found two new hexagonal phases, Zn3MgY phase with a = 9.082 Å and c = 9.415 Å and (Zn,Mg)4Ho phase with a ≅ 14.3 Å and c ≅ 14.1 Å [4–7] by substituting Mg for Zn in Zn5Y and Zn58Ho13, respectively. Their crystal structures were studied by single crystal X-ray and electron diffraction. Now these three phases have been extended to RE =Y, Sm, Gd, Dy, Ho, Er, Yb (see Table 1). Since these three phases have a high percentage of icosahedral coordination and therefore are crystalline approximants of the icosahedral i-phase. The connections of ICO (icosahedra) in these hexagonal phases are given in Table 1. The strong spots in the [100] electron diffraction patterns (EDPs) show pseudo ten-fold symmetry (see Fig. 1), due to the presence of two or four penetrated icosahedra (I2(P) or I4(P), respectively) in the structures, along the directions.
A DigitalMicrograph script InsteaDMatic has been developed to facilitate rapid automated continuo... more A DigitalMicrograph script InsteaDMatic has been developed to facilitate rapid automated continuous rotation electron diffraction (cRED) data acquisition. The script coordinates microscope functions, relevant for data collection, such as stage rotation, and camera functions, and stores the experiment metadata. The script is compatible with both JEOL and Thermo Fisher Scientific microscopes. A proof-of-concept has been performed through employing InsteaDMatic for data collection and structure determination of a ZSM-5 zeolite. The influence of illumination settings and electron dose rate on the quality of diffraction data, unit cell determination and structure solution has been investigated in order to optimize the data acquisition procedure.
3D electron diffraction (3D ED), also known as micro-crystal electron diffraction (MicroED), is a... more 3D electron diffraction (3D ED), also known as micro-crystal electron diffraction (MicroED), is a rapid, accurate, and robust method for structure determination of submicron-sized crystals. 3D ED has mainly been applied in material science until 2013, when MicroED was developed for studying macromolecular crystals. MicroED was considered as a cryo-electron microscopy method, as MicroED data collection is usually carried out in cryogenic conditions. As a result, some researchers may consider that 3D ED/MicroED data collection on crystals of small organic molecules can only be performed in cryogenic conditions. In this work, we determined the structure for sucrose and azobenzene tetracarboxylic acid (H4ABTC). The structure of H4ABTC is the first crystal structure ever reported for this molecule. We compared data quality and structure accuracy among datasets collected under cryogenic conditions and room temperature. With the improvement in data quality by data merging, it is possible t...
Abstract Three new micro-porous silicogermanates, ‖(NH 4 )F‖[(Ge 3.14 Si 6.86 )O 20 ] (SU-9), ‖(N... more Abstract Three new micro-porous silicogermanates, ‖(NH 4 )F‖[(Ge 3.14 Si 6.86 )O 20 ] (SU-9), ‖(NH 4 F‖[(Ge 6.78 Si 3.22 )O 20 ] (SU-10) and [(Ge 2.40 Si 9.60 )O 24 ] (SU-11) were synthesized under hydrothermal conditions with the presence of structure directing agents and the structures were solved by single crystal X-ray diffraction. SU-9 and SU-10 are built up by the double T4-rings (D4Rs) and they have the zeolite structure types of AST and ASV, respectively. SU-11 is built up by the T12-units and has the zeolite structure type of MFI. In three compounds, both silicon and germanium atoms are tetrahedrally coordinated with oxygen atoms and share the same tetrahedral sites.
3D electron diffraction (3DED) has been used to follow polymorph evolution in the crystallization... more 3D electron diffraction (3DED) has been used to follow polymorph evolution in the crystallization of glycine from aqueous solution. The three polymorphs of glycine which exist under ambient conditions follow the stability order β < α < γ. The least stable β polymorph forms within the first 3 min, but this begins to yield the α-form after only 1 min more. Both structures could be determined from continuous rotation electron diffraction data collected in less than 20 s on crystals of thickness ∼100 nm. Even though the γ-form is thermodynamically the most stable polymorph, kinetics favour the α-form, which dominates after prolonged standing. In the same sample, some β and one crystallite of the γ polymorph were also observed.
A one-pot method for encapsulation of dye, which can be applied for dye-sensitized solar cells (D... more A one-pot method for encapsulation of dye, which can be applied for dye-sensitized solar cells (DSSCs), and synthesis of hierarchical porous zeolitic imidazolate frameworks (ZIF-8), is reported. The size of the encapsulated dye tunes the mesoporosity and surface area of ZIF-8. The mesopore size, Langmuir surface area and pore volume are 15 nm, 960–1500 m 2 · g −1 and 0.36–0.61 cm 3 · g −1 , respectively. After encapsulation into ZIF-8, the dyes show longer emission lifetimes (greater than 4–8-fold) as compared to the corresponding non-encapsulated dyes, due to suppression of aggregation, and torsional motions.
Efficient use of energy for cooling applications is a very important and challenging field in sci... more Efficient use of energy for cooling applications is a very important and challenging field in science. Ultra-low temperature actuated (Tdriving < 80 °C) adsorption-driven chillers (ADCs) with water as the cooling agent are one environmentally benign option. The nanoscale metal-organic framework [Al(OH)(C6H2O4S)] denoted CAU-23 was discovered that possess favorable properties, including water adsorption capacity of 0.37 gH2O/gsorbent around p/p0 = 0.3 and cycling stability of at least 5000 cycles. Most importantly the material has a driving temperature down to 60 °C, which allows for the exploitation of yet mostly unused temperature sources and a more efficient use of energy. These exceptional properties are due to its unique crystal structure, which was unequivocally elucidated by single crystal electron diffraction. Monte Carlo simulations were performed to reveal the water adsorption mechanism at the atomic level. With its green synthesis, CAU-23 is an ideal material to realize...
Micro-crystal electron diffraction (MicroED) has shown great potential for structure determinatio... more Micro-crystal electron diffraction (MicroED) has shown great potential for structure determination of macromolecular crystals too small for X-ray diffraction. However, specimen preparation remains a major bottleneck. Here, we report a simple method for preparing MicroED specimens, named Preassis, in which excess liquid is removed through an EM grid with the assistance of pressure. We show the ice thicknesses can be controlled by tuning the pressure in combination with EM grids with appropriate hole sizes. Importantly, Preassis can handle a wide range of protein crystals grown in various buffer conditions including those with high viscosity, as well as samples with low crystal contents. Preassis is a simple and universal method for MicroED specimen preparation, and will significantly broaden the applications of MicroED.
Micro-crystal electron diffraction (MicroED) has recently shown potential for structural biology.... more Micro-crystal electron diffraction (MicroED) has recently shown potential for structural biology. It enables studying biomolecules from micron-sized 3D crystals that are too small to be studied by conventional X-ray crystallography. However, to the best of our knowledge, MicroED has only been applied to re-determine protein structures that had already been solved previously by X-ray diffraction. Here we present the first unknown protein structure — an R2lox enzyme — solved using MicroED. The structure was phased by molecular replacement using a search model of 35% sequence identity. The resulting electrostatic scattering potential map at 3.0 Å resolution was of sufficient quality to allow accurate model building and refinement. Our results demonstrate that MicroED has the potential to become a widely applicable tool for revealing novel insights into protein structure and function, opening up new opportunities for structural biologists.
Rapid phase elucidation of polycrystalline materials is essential for developing new materials of... more Rapid phase elucidation of polycrystalline materials is essential for developing new materials of chemical, pharmaceutical and industrial interest. Yet, the size and quantity of many crystalline phases are too small for routine X-ray diffraction analysis. This has become a workflow bottleneck in materials development, especially in high-throughput synthesis screening. Here we demonstrate the application of serial rotation electron diffraction (SerialRED) for high-throughput phase identification of complex polycrystalline zeolite products. The products were prepared from a combination of multiple framework T atoms ([Si,Ge,Al] or [Si,Ge,B]) and a simple organic structure-directing agent. We show that using SerialRED, five zeolite phases can be identified from a highly complex mixture. This includes phases with ultra-low contents undetectable using X-ray diffraction and phases with identical crystal morphology and similar unit cell parameters. By automatically and rapidly examining hun...
Three-dimensional electron diffraction (3D ED)/microcrystal electron diffraction (MicroED) techni... more Three-dimensional electron diffraction (3D ED)/microcrystal electron diffraction (MicroED) techniques are gaining in popularity. However, the data processing often does not fit existing graphical user interface software, instead requiring the use of the terminal or scripting. Scipion-ED, described in this article, provides a graphical user interface and extendable framework for processing of 3D ED/MicroED data. An illustrative project is described, in which multiple 3D ED/MicroED data sets collected on tetragonal lysozyme were processed with DIALS through the Scipion-ED interface. The ability to resolve unmodelled features in the electrostatic potential map was compared between three strategies for merging data sets.
Noncovalent interactions are essential in the formation and function of a diverse range of hybrid... more Noncovalent interactions are essential in the formation and function of a diverse range of hybrid materials. However, reliably identifying the noncovalent interactions in nanocrystalline materials remains challenging using conventional methods such as X-ray diffraction and spectroscopy. Here, we demonstrate that the entire range of noncovalent interactions in a nanocrystalline aluminophosphate hybrid material SCM-34 can be directly visualized by accurately determining all atomic positions using 3D electron diffraction (3D ED). The resolved hydrogen atoms reveal the protonation states of the inorganic and organic components. All the noncovalent hydrogen bonding, electrostatic, π–π stacking, and Van der Waals interactions were unambiguously resolved, providing a detailed insight into the material formation mechanism. The data are sufficiently accurate to distinguish the different types of covalent bonds based on their bond lengths, and we observed an elongated terminal P=O π-bond caus...
Three-dimensional rotation electron diffraction: software RED for automated data collection and d... more Three-dimensional rotation electron diffraction: software RED for automated data collection and data processing
EMC 2008 14th European Microscopy Congress 1–5 September 2008, Aachen, Germany
ABSTRACT In the Zn-rich Zn-Mg-RE alloys three groups of ternary hexagonal phases (Zn,Mg)58RE13, (... more ABSTRACT In the Zn-rich Zn-Mg-RE alloys three groups of ternary hexagonal phases (Zn,Mg)58RE13, (Zn,Mg)5RE, Zn6Mg3RE (also named Z-phase) are found to coexist with the icosahedral quasicrystal. In a study of the ternary Zn-Mg-Sm system, Drits et al. [1] first found the hexagonal Zn6Mg3Sm phase with a = 14.62 Å and c = 8.71 Å. Later, this hexagonal phase has also been found in the Zn-Mg-Y [2] and Zn-Mg-Gd [3] alloys and their crystal structures were determined by the single crystal X-ray diffraction analysis [2,3]. Recently, we found two new hexagonal phases, Zn3MgY phase with a = 9.082 Å and c = 9.415 Å and (Zn,Mg)4Ho phase with a ≅ 14.3 Å and c ≅ 14.1 Å [4–7] by substituting Mg for Zn in Zn5Y and Zn58Ho13, respectively. Their crystal structures were studied by single crystal X-ray and electron diffraction. Now these three phases have been extended to RE =Y, Sm, Gd, Dy, Ho, Er, Yb (see Table 1). Since these three phases have a high percentage of icosahedral coordination and therefore are crystalline approximants of the icosahedral i-phase. The connections of ICO (icosahedra) in these hexagonal phases are given in Table 1. The strong spots in the [100] electron diffraction patterns (EDPs) show pseudo ten-fold symmetry (see Fig. 1), due to the presence of two or four penetrated icosahedra (I2(P) or I4(P), respectively) in the structures, along the directions.
A DigitalMicrograph script InsteaDMatic has been developed to facilitate rapid automated continuo... more A DigitalMicrograph script InsteaDMatic has been developed to facilitate rapid automated continuous rotation electron diffraction (cRED) data acquisition. The script coordinates microscope functions, relevant for data collection, such as stage rotation, and camera functions, and stores the experiment metadata. The script is compatible with both JEOL and Thermo Fisher Scientific microscopes. A proof-of-concept has been performed through employing InsteaDMatic for data collection and structure determination of a ZSM-5 zeolite. The influence of illumination settings and electron dose rate on the quality of diffraction data, unit cell determination and structure solution has been investigated in order to optimize the data acquisition procedure.
3D electron diffraction (3D ED), also known as micro-crystal electron diffraction (MicroED), is a... more 3D electron diffraction (3D ED), also known as micro-crystal electron diffraction (MicroED), is a rapid, accurate, and robust method for structure determination of submicron-sized crystals. 3D ED has mainly been applied in material science until 2013, when MicroED was developed for studying macromolecular crystals. MicroED was considered as a cryo-electron microscopy method, as MicroED data collection is usually carried out in cryogenic conditions. As a result, some researchers may consider that 3D ED/MicroED data collection on crystals of small organic molecules can only be performed in cryogenic conditions. In this work, we determined the structure for sucrose and azobenzene tetracarboxylic acid (H4ABTC). The structure of H4ABTC is the first crystal structure ever reported for this molecule. We compared data quality and structure accuracy among datasets collected under cryogenic conditions and room temperature. With the improvement in data quality by data merging, it is possible t...
Abstract Three new micro-porous silicogermanates, ‖(NH 4 )F‖[(Ge 3.14 Si 6.86 )O 20 ] (SU-9), ‖(N... more Abstract Three new micro-porous silicogermanates, ‖(NH 4 )F‖[(Ge 3.14 Si 6.86 )O 20 ] (SU-9), ‖(NH 4 F‖[(Ge 6.78 Si 3.22 )O 20 ] (SU-10) and [(Ge 2.40 Si 9.60 )O 24 ] (SU-11) were synthesized under hydrothermal conditions with the presence of structure directing agents and the structures were solved by single crystal X-ray diffraction. SU-9 and SU-10 are built up by the double T4-rings (D4Rs) and they have the zeolite structure types of AST and ASV, respectively. SU-11 is built up by the T12-units and has the zeolite structure type of MFI. In three compounds, both silicon and germanium atoms are tetrahedrally coordinated with oxygen atoms and share the same tetrahedral sites.
3D electron diffraction (3DED) has been used to follow polymorph evolution in the crystallization... more 3D electron diffraction (3DED) has been used to follow polymorph evolution in the crystallization of glycine from aqueous solution. The three polymorphs of glycine which exist under ambient conditions follow the stability order β < α < γ. The least stable β polymorph forms within the first 3 min, but this begins to yield the α-form after only 1 min more. Both structures could be determined from continuous rotation electron diffraction data collected in less than 20 s on crystals of thickness ∼100 nm. Even though the γ-form is thermodynamically the most stable polymorph, kinetics favour the α-form, which dominates after prolonged standing. In the same sample, some β and one crystallite of the γ polymorph were also observed.
A one-pot method for encapsulation of dye, which can be applied for dye-sensitized solar cells (D... more A one-pot method for encapsulation of dye, which can be applied for dye-sensitized solar cells (DSSCs), and synthesis of hierarchical porous zeolitic imidazolate frameworks (ZIF-8), is reported. The size of the encapsulated dye tunes the mesoporosity and surface area of ZIF-8. The mesopore size, Langmuir surface area and pore volume are 15 nm, 960–1500 m 2 · g −1 and 0.36–0.61 cm 3 · g −1 , respectively. After encapsulation into ZIF-8, the dyes show longer emission lifetimes (greater than 4–8-fold) as compared to the corresponding non-encapsulated dyes, due to suppression of aggregation, and torsional motions.
Efficient use of energy for cooling applications is a very important and challenging field in sci... more Efficient use of energy for cooling applications is a very important and challenging field in science. Ultra-low temperature actuated (Tdriving < 80 °C) adsorption-driven chillers (ADCs) with water as the cooling agent are one environmentally benign option. The nanoscale metal-organic framework [Al(OH)(C6H2O4S)] denoted CAU-23 was discovered that possess favorable properties, including water adsorption capacity of 0.37 gH2O/gsorbent around p/p0 = 0.3 and cycling stability of at least 5000 cycles. Most importantly the material has a driving temperature down to 60 °C, which allows for the exploitation of yet mostly unused temperature sources and a more efficient use of energy. These exceptional properties are due to its unique crystal structure, which was unequivocally elucidated by single crystal electron diffraction. Monte Carlo simulations were performed to reveal the water adsorption mechanism at the atomic level. With its green synthesis, CAU-23 is an ideal material to realize...
Micro-crystal electron diffraction (MicroED) has shown great potential for structure determinatio... more Micro-crystal electron diffraction (MicroED) has shown great potential for structure determination of macromolecular crystals too small for X-ray diffraction. However, specimen preparation remains a major bottleneck. Here, we report a simple method for preparing MicroED specimens, named Preassis, in which excess liquid is removed through an EM grid with the assistance of pressure. We show the ice thicknesses can be controlled by tuning the pressure in combination with EM grids with appropriate hole sizes. Importantly, Preassis can handle a wide range of protein crystals grown in various buffer conditions including those with high viscosity, as well as samples with low crystal contents. Preassis is a simple and universal method for MicroED specimen preparation, and will significantly broaden the applications of MicroED.
Micro-crystal electron diffraction (MicroED) has recently shown potential for structural biology.... more Micro-crystal electron diffraction (MicroED) has recently shown potential for structural biology. It enables studying biomolecules from micron-sized 3D crystals that are too small to be studied by conventional X-ray crystallography. However, to the best of our knowledge, MicroED has only been applied to re-determine protein structures that had already been solved previously by X-ray diffraction. Here we present the first unknown protein structure — an R2lox enzyme — solved using MicroED. The structure was phased by molecular replacement using a search model of 35% sequence identity. The resulting electrostatic scattering potential map at 3.0 Å resolution was of sufficient quality to allow accurate model building and refinement. Our results demonstrate that MicroED has the potential to become a widely applicable tool for revealing novel insights into protein structure and function, opening up new opportunities for structural biologists.
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Papers by Xiaodong Zou