Journal articles: '3D crystal structure'

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Yang, Quanxin, Xin Zhang, Hongliang Liu, Xuping Wang, Yingying Ren, Shan He, Xiaojin Li, and Pengfei Wu. "Dynamic relaxation process of a 3D super crystal structure in a Cu:KTN crystal." Chinese Optics Letters 18, no. 2 (2020): 021901. http://dx.doi.org/10.3788/col202018.021901.

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Jang, Kiyoung, Hyun Gi Kim, Sandi Hnit San Hlaing, MinSoung Kang, Hui-Woog Choe, and Yong Ju Kim. "A Short Review on Cryoprotectants for 3D Protein Structure Analysis." Crystals 12, no. 2 (January 19, 2022): 138. http://dx.doi.org/10.3390/cryst12020138.

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The three-dimensional structure of protein is determined by analyzing diffraction data collected using X-ray beams. However, X-ray beam can damage protein crystals during data collection, lowering the quality of the crystal data. A way to prevent such damage is by treating protein crystals with cryoprotectants. The cryoprotectant stabilizes the protein crystal and prevents lowering the quality of the diffraction data. Many kinds of cryoprotectants are commercially available, and various treatment methods have also been reported. However, incorrect selection or treatment of such cryoprotectants may lead to deterioration of crystal diffraction data when using X-ray beams.

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Lanza, Arianna, Eleonora Margheritis, Enrico Mugnaioli, Valentina Cappello, Gianpiero Garau, and Mauro Gemmi. "Nanobeam precession-assisted 3D electron diffraction reveals a new polymorph of hen egg-white lysozyme." IUCrJ 6, no. 2 (January 15, 2019): 178–88. http://dx.doi.org/10.1107/s2052252518017657.

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Recent advances in 3D electron diffraction have allowed the structure determination of several model proteins from submicrometric crystals, the unit-cell parameters and structures of which could be immediately validated by known models previously obtained by X-ray crystallography. Here, the first new protein structure determined by 3D electron diffraction data is presented: a previously unobserved polymorph of hen egg-white lysozyme. This form, with unit-cell parameters a = 31.9, b = 54.4, c = 71.8 Å, β = 98.8°, grows as needle-shaped submicrometric crystals simply by vapor diffusion starting from previously reported crystallization conditions. Remarkably, the data were collected using a low-dose stepwise experimental setup consisting of a precession-assisted nanobeam of ∼150 nm, which has never previously been applied for solving protein structures. The crystal structure was additionally validated using X-ray synchrotron-radiation sources by both powder diffraction and single-crystal micro-diffraction. 3D electron diffraction can be used for the structural characterization of submicrometric macromolecular crystals and is able to identify novel protein polymorphs that are hardly visible in conventional X-ray diffraction experiments. Additionally, the analysis, which was performed on both nanocrystals and microcrystals from the same crystallization drop, suggests that an integrated view from 3D electron diffraction and X-ray microfocus diffraction can be applied to obtain insights into the molecular dynamics during protein crystal growth.

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Ren, Lin, Yan Li Shi, Xue Hao, and Run Lan Tian. "Experimental System for the Micro-Nanofabrication of Three-Dimensional Structures by Femtosecond Laser Two-Photon Absorption." Advanced Materials Research 760-762 (September 2013): 746–49. http://dx.doi.org/10.4028/www.scientific.net/amr.760-762.746.

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Fundamentals of two-photon photopolymerization have been introduced and a 3D femtosecond laser micro-nanofabrication system has been built. In this paper, 3D CAD data model based on femtosecond laser micro-nanofabrication system have been also discussed. The 3D various sphere-rod photonic crystal structure mimicking real atom structures in electronic crystals have been fabricated.

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Kaminsky, Werner, Trevor Snyder, and Peter Moeck. "3D printing of crystallographic models and open access databases." Acta Crystallographica Section A Foundations and Advances 70, a1 (August 5, 2014): C1278. http://dx.doi.org/10.1107/s205327331408721x.

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Although introduced 30 years ago, cost and performance improvements have only recently made 3D printing affordable. The industry wide input file format for 3D printers incorporates explicit mesh - `STL' data. Molecules and crystal structures, when including symmetry, crystal morphologies, or crystal defects are encoded in the parametrical `CIF' syntax. Free software for converting directly CIF data to STL files has just been developed, available online [1]. First examples of printed 3D models from STL-files created with these programs include molecules of sucrose, herapathite [2a], caffeine, humulone [2b], an alpha-quartz crystal and its Japanese {112} twin or a brilliant cut diamond. Far more CIF encoded models are available, even open access. The Crystallography Open Database (COD) features over 245,000 entries and has recently developed into the world's premier open-access source for structures of small to medium unit cell-sized inorganic and molecular crystals [3a], complementing the well-established open-access Worldwide Protein Data Bank [3b]. The Cambridge Crystallographic Data Centre in the United Kingdom provides crystal structure data of small (organic) molecules free for bona fide research [3c]. Structural data on inorganic crystals, metals and alloys can be obtained free of charge from the Inorganic Material Database (AtomWork) [3d]. Related to the COD, the crystallographic open-access databases [3e] ("COD offspring") provide CIF data for interdisciplinary college education. With this basic infrastructure in place, any interested college educator may print out her or his favorite crystallographic structure model in 3D and use it in hands on class room demonstrations [3f].

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Yang, Taimin, Steve Waitschat, Andrew Kentaro Inge, Norbert Stock, Xiaodong Zou, and Hongyi Xu. "A Comparison of Structure Determination of Small Organic Molecules by 3D Electron Diffraction at Cryogenic and Room Temperature." Symmetry 13, no. 11 (November 9, 2021): 2131. http://dx.doi.org/10.3390/sym13112131.

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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 to reveal hydrogen atom positions in small organic molecule structures under both temperature conditions. The experimental results showed that, if the sample is stable in the vacuum environment of a transmission electron microscope (TEM), the data quality of datasets collected under room temperature is at least as good as data collected under cryogenic conditions according to various indicators (resolution, I/σ(I), CC1/2 (%), R1, Rint, ADRA).

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Su, Jie, Yue-Biao Zhang, Yifeng Yun, Hiroyasu Furukawa, Felipe Gándara, Adam Duong, Xiaodong Zou, and Omar Yaghi. "The First Covalent Organic Framework solved by Rotation Electron Diffraction." Acta Crystallographica Section A Foundations and Advances 70, a1 (August 5, 2014): C191. http://dx.doi.org/10.1107/s2053273314098088.

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Covalent organic frameworks (COFs) represent an exciting new type of porous organic materials, which are constructed with organic building units via strong covalent bonds.[1] The structure determination of COFs is challenging, due to the difficulty in growing sufficiently large crystals suitable for single crystal X-ray diffraction, and low resolution and peak broadening for powder X-ray diffraction. Crystal structures of COFs are typically determined by modelling building with the aid of geometry principles in reticular chemistry and powder X-ray diffraction data. Here, we report the single-crystal structure of a new COF (COF-320) determined by 3D rotation electron diffraction (RED),[2] a technique applied in this context for the first time. The RED method can collect an almost complete three-dimensional electron diffraction dataset, and is a useful technique for structure determination of micron- and nanosized single crystals. To minimize electron beam damage, the RED dataset was collected at 89 K. 3D reciprocal lattice of COF-320 was reconstructed from the ED frames using the RED – data processing software[2]. As the resolution of the RED data only reached 1.6 Å, the simulated annealing parallel tempering algorithm in the FOX software package [3] was used to find a starting molecular arrangement from the 3D RED data. Finally, the crystal structure of COF-320 was solved in the space group of I-42d and refined using the SHELXL software package. The single-crystal structure of COF-320 exhibits a 3D extended framework by linking the tetrahedral organic building blocks and biphenyl linkers through imine-bonds forming a highly porous 9-fold interwoven diamond net.

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Zhang, Chenxi, Xuemin Chen, Bo Liu, Jiachen Zang, Tuo Zhang, and Guanghua Zhao. "Preparation and Unique Three-Dimensional Self-Assembly Property of Starfish Ferritin." Foods 12, no. 21 (October 25, 2023): 3903. http://dx.doi.org/10.3390/foods12213903.

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The structure and assembly properties of ferritin derived from aquatic products remain to be explored. Constructing diverse three-dimensional (3D) protein architectures with the same building blocks has important implications for nutrient delivery, medicine and materials science. Herein, ferritin from Asterias forbesii (AfFer) was prepared, and its crystal structure was resolved at 1.91 Å for the first time. Notably, different from the crystal structure of other reported ferritin, AfFer exhibited a BCT lattice arrangement in its crystals. Bioinspired by the crystal structure of AfFer, we described an effective approach for manufacturing 3D porous, crystalline nanoarchitectures by redesigning the shared protein interface involved in different 3D protein arrays. Based on this strategy, two 3D superlattices of body-centered tetragonal and simple cubicwere constructed with ferritin molecules as the building blocks. This study provided a potentially generalizable strategy for constructing different 3D protein-based crystalline biomaterials with the same building blocks.

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Chen, S., D. Li, M. Wang, and D. Wei. "Fabrication of a point defect photonic crystal based on diamond structure with a cavity and its microwave properties." Proceedings of the Institution of Mechanical Engineers, Part B: Journal of Engineering Manufacture 225, no. 11 (September 12, 2011): 2071–77. http://dx.doi.org/10.1177/0954405411398760.

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This paper presents a novel fabrication method for three-dimensional (3D) ceramic point defect photonic crystals. The 3D defect photonic crystal, which possesses an air cavity, has been designed by cutting a rectangular shape (3.5 mm × 3.5 mm × 7 mm) in the centre of a photonic crystal with a diamond lattice structure model (50 mm × 30 mm × 20 mm) with a lattice constant of 7 mm. Stereolithography (SL) technology was applied to fabricate resin moulds with an inverse-diamond structure incorporating the defect, and high solid content aqueous ceramic slurry was prepared and injected into the moulds. After gel-casting, drying, and high-temperature sintering, ceramic 3D photonic crystals with intact structure and minimal shrinkage were obtained. The penetration of an electric field with resonant modes of about 3 mm into the host lattice was observed by measuring the <110> direction of the samples, which resulted from the rectangular air cavity resonator. The results show that this method can be used to fabricate ceramic 3D point defect photonic crystals with a complex 3D structure.

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Nicolopoulos, Stavros, Mauro Gemmi, Alexander Eggeman, Paul Midgley, and Athanassios Galanis. "TEM Random & Ultra-fast Precession ED Tomography for analysis of nm crystals." Acta Crystallographica Section A Foundations and Advances 70, a1 (August 5, 2014): C371. http://dx.doi.org/10.1107/s2053273314096284.

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Since the invention of Precession Electron Diffraction (PED) in Transmission Electron Microscopy (TEM) by Vincent & Midgley [1] in 1994 and mainly after the introduction of dedicated PED devices to different TEM, the structure of various nano-sized crystals have been solved by Electron Crystalography. The most popular technique that was recently developed based on beam precession is the 3D Precession Diffraction Tomography (PEDT) [2]. A series of ED patterns are collected every 10while the sample is tilted around the goniometer axis. By the automatic measurement of ED intensities (ADT 3D software), the unit cell, crystal symmetry and the detailed crystal structure can be determined. A large number of crystal structures, such as complex metals, alloys, organic pigments, MOF, catalysts etc., have been solved by the 3D PEDT technique. A drawback of 3D PEDT (especially for beam sensitive materials) is the long acquisition times (45–120 min), due to the time consuming step of tracking the crystal under the beam during tilting. To deal with this problem, we have developed two novel approaches: the Random Electron Diffraction Tomography (rPEDT) technique and the Ultra-Fast 3D diffraction tomography (UF PEDT) [3]. By rPEDT technique, a sample area (few microns), where several crystals in different (random) orientations are present, is scanned rapidly using an ASTAR precession device (NanoMEGAS SPRL). PED patterns of all scanned crystals are collected by a fast speed CCD camera (up to 120 frames/sec; 8/12 bit). Concerning UF PEDT, the data acquisition time can be 10-20 times faster compared to hitherto 3D PEDT procedure. UF PEDT can be applied when the crystal shift is stable and reproducible during tilting the sample for a specific tilt range. Thus, such crystals can be tracked by shifting the beam following the crystal displacement during tilting (using ASTAR beam scanning). Obtained PED patterns can be recorded with a fast CCD camera, while crystal is tilted. As a conclusion, rPEDT and UF-PEDT can be considered as breakthrough techniques in electron crystallography as they can be performed in any commercial TEM. Both techniques reduce considerable 3D intensity data acquisition time, and allow the analysis of unknown compounds, including beam sensitive organic crystals, as fast techniques prevents crystal beam damage. The authors acknowledge financial support from EU ESTEEM-2 project (European Network for Electron Microscopy www.esteem2.eu).

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Gorelik, Tatiana E., Stefan Habermehl, Aleksandr A. Shubin, Tim Gruene, Kaname Yoshida, Peter Oleynikov, Ute Kaiser, and Martin U. Schmidt. "Crystal structure of copper perchlorophthalocyanine analysed by 3D electron diffraction." Acta Crystallographica Section B Structural Science, Crystal Engineering and Materials 77, no. 4 (July 29, 2021): 662–75. http://dx.doi.org/10.1107/s2052520621006806.

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Copper perchlorophthalocyanine (CuPcCl16, CuC32N8Cl16, Pigment Green 7) is one of the commercially most important green pigments. The compound is a nanocrystalline fully insoluble powder. Its crystal structure was first addressed by electron diffraction in 1972 [Uyeda et al. (1972). J. Appl. Phys. 43, 5181–5189]. Despite the commercial importance of the compound, the crystal structure remained undetermined until now. Using a special vacuum sublimation technique, micron-sized crystals could be obtained. Three-dimensional electron diffraction (3D ED) data were collected in two ways: (i) in static geometry using a combined stage-tilt/beam-tilt collection scheme and (ii) in continuous rotation mode. Both types of data allowed the crystal structure to be solved by direct methods. The structure was refined kinematically with anisotropic displacement parameters for all atoms. Due to the pronounced crystal mosaicity, a dynamic refinement was not feasible. The unit-cell parameters were verified by Rietveld refinement from powder X-ray diffraction data. The crystal structure was validated by many-body dispersion density functional theory (DFT) calculations. CuPcCl16 crystallizes in the space group C2/m (Z = 2), with the molecules arranged in layers. The structure agrees with that proposed in 1972.

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Zou, Xiaodong. "Single Crystal 3D Rotation Electron Diffraction from Nano-sized Crystals." Acta Crystallographica Section A Foundations and Advances 70, a1 (August 5, 2014): C366. http://dx.doi.org/10.1107/s2053273314096338.

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Electron crystallography is an important technique for structure analysis of nano-sized materials. Crystals too small or too complicated to be studied by X-ray diffraction can be investigated by electron crystallography. However, conventional TEM methods requires high TEM skills and strong crystallographic knowledge, which many synthetic materials scientists and chemists do not have. We recently developed the software-based Rotation Electron Diffraction (RED) method for automated collection and processing of 3D electron diffraction data. Complete single crystal 3D electron diffraction data can be collected from nano- and micron-sized crystals in less than one hour by combining electron beam tilt and goniometer tilt, which are controlled by the RED – data collection software.3 The unit cell, possible space groups and electron diffraction intensities can be obtained from the RED data using the RED data processing software. The figure below illustrates the data collection and data processing of a zeolite silicalite-1 by RED. 1427 ED frames were collected in less than 1 hour from a crystal of 800 x 400 x 200 nm in size. A 3D reciprocal lattice of silicalite-1 was reconstructed from the ED frames, from which the unit cell parameters and space group were determined (P21/n, a=20.02Å, b=20.25Å, c=13.35Å, alfa=90.130, beta=90.740, gamma=90.030. It was possible to cut the 3D reciprocal lattice perpendicular to any directions and study the reflection conditions. The reflection intensities could be extracted. The structure of the calcined silicalite-1 could be solved from the RED data by routine direct methods using SHELX-97. All 78 unique Si and O atoms could be located and refined to an accuracy better than 0.08 Å. The RED method has been applied for structure solution of a wide range of crystals and shown to be very powerful and efficient. Now a structure determination can be achieved within a few hours, from the data collection to structure solution. We will present several examples including unknown inorganic compounds, metal-organic frameworks and organic structures solved from the RED data. Different parameters that affect the RED data quality and thus the structure determination will be discussed. The methods are general and can be applied to any crystalline materials.

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Kobler, Aaron, and Christian Kübel. "Towards 3D crystal orientation reconstruction using automated crystal orientation mapping transmission electron microscopy (ACOM-TEM)." Beilstein Journal of Nanotechnology 9 (February 15, 2018): 602–7. http://dx.doi.org/10.3762/bjnano.9.56.

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To relate the internal structure of a volume (crystallite and phase boundaries) to properties (electrical, magnetic, mechanical, thermal), a full 3D reconstruction in combination with in situ testing is desirable. In situ testing allows the crystallographic changes in a material to be followed by tracking and comparing the individual crystals and phases. Standard transmission electron microscopy (TEM) delivers a projection image through the 3D volume of an electron-transparent TEM sample lamella. Only with the help of a dedicated TEM tomography sample holder is an accurate 3D reconstruction of the TEM lamella currently possible. 2D crystal orientation mapping has become a standard method for crystal orientation and phase determination while 3D crystal orientation mapping have been reported only a few times. The combination of in situ testing with 3D crystal orientation mapping remains a challenge in terms of stability and accuracy. Here, we outline a method to 3D reconstruct the crystal orientation from a superimposed diffraction pattern of overlapping crystals without sample tilt. Avoiding the typically required tilt series for 3D reconstruction enables not only faster in situ tests but also opens the possibility for more stable and more accurate in situ mechanical testing. The approach laid out here should serve as an inspiration for further research and does not make a claim to be complete.

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Li, Hanying, Huolin L. Xin, David A. Muller, and Lara A. Estroff. "Visualizing the 3D Internal Structure of Calcite Single Crystals Grown in Agarose Hydrogels." Science 326, no. 5957 (November 26, 2009): 1244–47. http://dx.doi.org/10.1126/science.1178583.

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Single crystals are usually faceted solids with homogeneous chemical compositions. Biogenic and synthetic calcite single crystals, however, have been found to incorporate macromolecules, spurring investigations of how large molecules are distributed within the crystals without substantially disrupting the crystalline lattice. Here, electron tomography reveals how random, three-dimensional networks of agarose nanofibers are incorporated into single crystals of synthetic calcite by allowing both high- and low-energy fiber/crystal interface facets to satisfy network curvatures. These results suggest that physical entrapment of polymer aggregates is a viable mechanism by which macromolecules can become incorporated inside inorganic single crystals. As such, this work has implications for understanding the structure and formation of biominerals as well as toward the development of new high–surface area, single-crystal composite materials.

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Borkowska, Monika, and Radosław Mrówczyński. "Triptycene Based 3D Covalent Organic Frameworks (COFs)—An Emerging Class of 3D Structures." Symmetry 15, no. 9 (September 21, 2023): 1803. http://dx.doi.org/10.3390/sym15091803.

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Covalent Organic Frameworks (COFs) are a newly emerged class of porous materials consisting of organic building blocks linked by strong covalent bonds. The physical and chemical properties of COFs, i.e., modularity, porosity, well-developed specific surface area, crystallinity, and chemical-thermal stability, make them a good application material, especially in the aspects of adsorption and gas separation. The organic compositions of their building blocks also render them with biocompatible properties; therefore, they also have potential in biomedical applications. Depending on the symmetry of the building blocks, COF materials form two-dimensional (2D COF) or three-dimensional (3D COF) crystal structures. 3D COF structures have a higher specific surface area, they are much lighter due to their low density, and they have a larger volume than 2D COF crystals, but, unlike the latter, 3D COF crystals are less frequently obtained and studied. Selecting and obtaining suitable building blocks to form a stable 3D COF crystal structure is challenging and therefore of interest to the chemical community. Triptycene, due to its 3D structure, is a versatile building block for the synthesis of 3D COFs. Polymeric materials containing triptycene fragments show good thermal stability parameters and have a very well-developed surface area. They often tend to be characterized by more than one type of porosity and exhibit impressive gas adsorption properties. The introduction of a triptycene backbone into the structure of 3D COFs is a relatively new procedure, the results of which only began to be published in 2020. Triptycene-based 3D COFs show interesting physicochemical properties, i.e., high physical stability and high specific surface area. In addition, they have variable porosities with different pore diameters, capable of adsorbing both gases and large biological molecules. These promising parameters, guaranteed by the addition of a triptycene backbone to the 3D structure of COFs, may create new opportunities for the application of such materials in many industrial and biomedical areas. This review aims to draw attention to the symmetry of the building blocks used for COF synthesis. In particular, we discussed triptycene as a building block for the synthesis of 3D COFs and we present the latest results in this area.

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Das, Partha Pratim, Sergi Plana-Ruiz, Athanassios S. Galanis, Andrew Stewart, Fotini Karavasili, Stavros Nicolopoulos, Holger Putz, Irene Margiolaki, Maria Calamiotou, and Gianluca Iezzi. "Structure Determination Feasibility of Three-Dimensional Electron Diffraction in Case of Limited Data." Symmetry 14, no. 11 (November 8, 2022): 2355. http://dx.doi.org/10.3390/sym14112355.

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During the last two decades, three-dimensional electron diffraction (3D ED) has undergone a renaissance, starting with the introduction of precession (Precession Electron Diffraction Tomography, PEDT) that led to variations on the idea of collecting as much of the diffraction space as possible in order to solve crystal structures from sub-micron sized crystals. The most popular of these acquisition methods is based on the continuous tilting/rotation of the crystal (so-called Microcrystal Electron Diffraction, MicroED) akin to the oscillating crystal method in X-ray crystallography, which was enabled by the increase of sensitivity and acquisition speed in electron detectors. While 3D ED data is more complex than the equivalent X-ray data due to the higher proportion of dynamical scattering, the same basic principles of what is required in terms of data quality and quantity in order to solve a crystal structure apply; high completeness, high data resolution and good signal-to-noise statistics on measured reflection intensities. However, it may not always be possible to collect data in these optimum conditions, the most common limitations being the tilt range of the goniometer stage, often due to a small pole piece gap or the use of a non-tomography holder, or the position of the sample on the TEM grid, which may be too close to a grid bar and then the specimen of interest becomes occluded during tilting. Other factors that can limit the quality of the acquired data include the limited dynamic range of the detector, which can result on truncated intensities, or the sensitivity of the crystal to the electron beam, whereby the crystallinity of the particle is changing under the illumination of the beam. This limits the quality and quantity of the measured intensities and makes structure analysis of such data challenging. Under these circumstances, traditional approaches may fail to elucidate crystal structures, and global optimization methods may be used here as an alternative powerful tool. In this context, this work presents a systematic study on the application of a global optimization method to crystal structure determination from 3D ED data. The results are compared with known structure models and crystal phases obtained from traditional ab initio structure solution methods demonstrating how this strategy can be reliably applied to the analysis of partially complete 3D ED data.

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Gurung, Kshitij, Petr Šimek, Alexandr Jegorov, and Lukáš Palatinus. "Structure and absolute configuration of natural fungal product beauveriolide I, isolated from Cordyceps javanica, determined by 3D electron diffraction." Acta Crystallographica Section C Structural Chemistry 80, no. 3 (February 27, 2024): 56–61. http://dx.doi.org/10.1107/s2053229624001359.

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Beauveriolides, including the main beauveriolide I {systematic name: (3R,6S,9S,13S)-9-benzyl-13-[(2S)-hexan-2-yl]-6-methyl-3-(2-methylpropyl)-1-oxa-4,7,10-triazacyclotridecane-2,5,8,11-tetrone, C27H41N3O5}, are a series of cyclodepsipeptides that have shown promising results in the treatment of Alzheimer's disease and in the prevention of foam cell formation in atherosclerosis. Their crystal structure studies have been difficult due to their tiny crystal size and fibre-like morphology, until now. Recent developments in 3D electron diffraction methodology have made it possible to accurately study the crystal structures of submicron crystals by overcoming the problems of beam sensitivity and dynamical scattering. In this study, the absolute structure of beauveriolide I was determined by 3D electron diffraction. The cyclodepsipeptide crystallizes in the space group I2 with lattice parameters a = 40.2744 (4), b = 5.0976 (5), c = 27.698 (4) Å and β = 105.729 (6)°. After dynamical refinement, its absolute structure was determined by comparing the R factors and calculating the z-scores of the two possible enantiomorphs of beauveriolide I.

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Wang, B., J. A. Rodríguez, and M. A. Cappelli. "3D woodpile structure tunable plasma photonic crystal." Plasma Sources Science and Technology 28, no. 2 (February 20, 2019): 02LT01. http://dx.doi.org/10.1088/1361-6595/ab0011.

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Zubko, Maciej, Joanna Wspaniała, Danuta Stróż, and Enrico Mugnaioli. "Electron Diffraction Reinvestigation of CdCr₂Se₄ and ZnCr_2-xV_xSe₄ Spinel Structures." Solid State Phenomena 203-204 (June 2013): 262–65. http://dx.doi.org/10.4028/www.scientific.net/ssp.203-204.262.

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Crystal structure of two spinel single crystals CdCr2Se4 and ZnCr2-xVxSe4 have been reinvestigated using automated electron diffraction tomography method with beam precession. 3D reciprocal space have been reconstructed base on recorded tilt series. For both samples crystal structure was refined and the cubic symmetry with space group Fd-3m was confirmed. No additional electron potential has been located beside occupied atom sites.

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Suzuki, Yoshihisa, Masayuki Tsukamoto, Takahisa Fujiwara, and Yuuta Uehara. "High pressure crystallization and crystallography of glucose isomerase." Acta Crystallographica Section A Foundations and Advances 70, a1 (August 5, 2014): C1190. http://dx.doi.org/10.1107/s2053273314088093.

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Crystallization of protein is still a "bottleneck" for the three-dimensional (3D) structure analysis of a protein molecule. Therefore, the study on the acceleration of the crystallization is important. Visuri et al. repoted, for the first time, that the crystallization of glucose isomerase (GI) crystals was significantly enhanced with increasing pressure [1], while they did not discuss further effects of pressure on the crystallization. We measured solubilities, growth rates of a crystal face, step velocities and two-dimensional (2D) nucleation rates, three-dimensional (3D) nucleation rates of the GI crystal under high pressure. From these results, we found the negative molar volume change of crystallization delta V, the decrease in a step ledge surface energy and the increase in a step kinetic coefficient with increasing pressure. Activation volume of crystallization delta V‡ was discussed and the absolute value of it was almost half of that of delta V [2]. X-ray crystallography is also very important to study how the three dimensional structure of protein is related to its function under high pressure at atomic level. Kundrot et al. analyzed the crystal structure of lysozyme at 100 MPa using a beryllium (Be) cell. The crystal was prepared under 0.1 MPa. Charron et al. reported that thaumatin crystals grown under 150 MPa were analyzed under 0.1 MPa. Although Kundrot et al. concluded that the protein structure under high pressure was compressed, they could not estimate the influence of the bond structure of the crystal at 0.1 MPa on the compressed structure. In Charron's case, the thaumatin structures in crystals prepared under 0.1 MPa and 150 MPa were almost identical, when they did X-ray analyses of both crystals at 0.1 MPa. From these two results, we considered that compression of the crystals was reversible. We conducted both Kundrot's and Charron's methods for GI using a stand-alone type Be vessel [3]. We found that (1) GI molecule was reversibly compressed under high pressure, (2) the distributions of water sites around GI molecules were almost identical in the range of pressures from 0.1 to 100 MPa.

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Amari, Shinji, Ryoichi Kataoka, Takashi Ikegami, and Noriaki Hirayama. "HLA-Modeler: Automated Homology Modeling of Human Leukocyte Antigens." International Journal of Medicinal Chemistry 2013 (November 27, 2013): 1–6. http://dx.doi.org/10.1155/2013/690513.

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The three-dimensional (3D) structures of human leukocyte antigen (HLA) molecules are indispensable for the studies on the functions at molecular level. We have developed a homology modeling system named HLA-modeler specialized in the HLA molecules. Segment matching algorithm is employed for modeling and the optimization of the model is carried out by use of the PFROSST force field considering the implicit solvent model. In order to efficiently construct the homology models, HLA-modeler uses a local database of the 3D structures of HLA molecules. The structure of the antigenic peptide-binding site is important for the function and the 3D structure is highly conserved between various alleles. HLA-modeler optimizes the use of this structural motif. The leave-one-out cross-validation using the crystal structures of class I and class II HLA molecules has demonstrated that the rmsds of nonhydrogen atoms of the sites between homology models and crystal structures are less than 1.0 Å in most cases. The results have indicated that the 3D structures of the antigenic peptide-binding sites can be reproduced by HLA-modeler at the level almost corresponding to the crystal structures.

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Borgstahl, Gloria. "Dealing with Aperiodic Protein Crystal Structures." Acta Crystallographica Section A Foundations and Advances 70, a1 (August 5, 2014): C778. http://dx.doi.org/10.1107/s2053273314092213.

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Protein crystals can be aperiodic. They will diffract X-rays, and are therefore a crystal, but their diffraction is not periodic. This means that their diffraction pattern cannot be simply be indexed by a typical three-dimensional unit cell and space group. Aperiodic crystals include "quasi-crystals" as well as "modulated" crystals. In the latter case, the modulation can be positional or occupational and these modulations can be incommensurate with the normal periodic lattice [1]. An overview of aperiodic protein crystal diffraction will be presented with examples. The discussion will then focus on the characteristics of incommensurately modulated crystals followed by a more detailed discussion of how to solve these crystals. The following details of structure solution will be presented: (1) data collection perils; (2) specialized diffraction data processing in (3+1)D space using a q-vector [2]; (3) how to get an approximation of the structure in 3D space; (4) the assignment of the (3+1)D space group; and the ultimate (5) crystallographic refinement in superspace[3]. Future directions and needs will be discussed.

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Safriani, Lusi, Ian Sopian, Tuti Susilawati, and Sahrul Hidayat. "Fabrication of Photonic Crystal Based on Polystyrene Particles." Materials Science Forum 827 (August 2015): 271–75. http://dx.doi.org/10.4028/www.scientific.net/msf.827.271.

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Photonic crystals are dielectric materials with different refractive index or permittivity periodically. Photonic crystals have widely application for future technology such as waveguide, optical transistor, cavity of laser and biosensor. Photonic crystals can be fabricated in three types i.e 1D, 2D and 3D structure. In this paper, we report the successful fabrication of 3D photonic crystal from polystyrene particles. The fabrication process began with the synthesis of polystyrene particles followed by deposition on glass and flexible substrate using self-assembly method. We obtained polystyrene monodispered particles which have a uniform shaped with diameter 320 nm. Self-assembly method resulted to the arrangement of polystyrene particles on glass and flexible substrate. Stop band which is related to its optical property are at wavelength of 721 nm and 631 nm for photonic crystal on glass and flexible substrate, respectively. We found that filling fraction of photonic crystal on flexible substrate is lower than that of glass substrate due to some defects.

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Sharma, Varun, Bubun Banerjee, Aditi Sharma, and Vivek Kumar Gupta. "Synthesis, X-ray crystal structure, Hirshfeld surface analysis, and molecular docking studies of DMSO/H2O solvate of 5-chlorospiro[indoline-3,7'-pyrano[3,2-c:5,6-c']dichromene]-2,6',8'-trione." European Journal of Chemistry 12, no. 4 (December 31, 2021): 382–88. http://dx.doi.org/10.5155/eurjchem.12.4.382-388.2141.

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The title compound, 5-chlorospiro[indoline-3,7'-pyrano[3,2-c:5,6-c']dichromene]-2,6',8'-trione was synthesized via one-pot pseudo three-component reaction between one equivalent of 5-chloroisatin and two equivalents of 4-hydroxycoumarin using mandelic acid as catalyst in aqueous ethanol at 110 °C. The synthesized compound was characterized by FT-IR, 1H NMR, and HRMS techniques. Single crystals were grown for crystal structure determination by using single X-ray crystallography technique. It was found that the crystals are triclinic with space group P-1 and Z = 1. The crystal structure was solved by direct method and refined by full-matrix least-squares procedures to a final R-value of 0.0688 for 6738 observed reflections. The crystal structure was stabilized by elaborate system of O-H···O, N-H···O, and C-H···O interactions with the formation of supramolecular structures. 3D Hirshfeld surfaces and allied 2D fingerprint plots were analyzed for molecular interactions. Molecular docking studies have been performed to get insights into the inhibition property of this molecule for Human topoisomerase IIα.

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Kirsh, D. V., O. P. Soldatova, A. V. Kupriyanov, I. A. Lyozin, and I. V. Lyozina. "3D crystal structure identification using fuzzy neural networks." Optical Memory and Neural Networks 26, no. 4 (October 2017): 249–56. http://dx.doi.org/10.3103/s1060992x17040026.

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Palatinus, Lukáš, Cinthia Corrêa, Gwladys Mouillard, Philippe Boullay, and Damien Jacob. "Accurate structure refinement from 3D electron diffraction data." Acta Crystallographica Section A Foundations and Advances 70, a1 (August 5, 2014): C374. http://dx.doi.org/10.1107/s2053273314096259.

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Structure determination from electron diffraction data has seen an enormous progress over the past few years. At present, complex structures with hundreds of atoms in the unit cell can be solved from electron diffraction using the concept of electron diffraction tomography (EDT), possibly combined with precession electron diffraction (PED) [1]. Unfortunately, the initial model is typically optimized using the kinematical approximation to calculate model diffracted intensities. This approximation is quite inaccurate for electron diffraction and leads to high figures of merit and inaccurate results with unrealistically low standard uncertainties. The obvious remedy to the problem is the use of dynamical diffraction theory to calculate the model intensities in structure refinement. This technique has been known and used before, but it has not become very popular, because good fits could be obtained only for sufficiently perfect and sufficiently thin crystals. It has been shown recently on several zone-axis patterns [2] that the quality of the refinement can be improved by using precession electron diffraction. In the present contribution we demonstrate that the same approach can be successfully used to refine crystal structures against non-oriented patterns acquired by EDT combined with PED (PEDT in short). Because the PEDT technique provides three-dimensional diffraction information, it can be used for a complete structure refinement. Several test examples demonstrate that the dynamical structure refinement yields better figures of merit and more accurate results than the refinement using kinematical approximation.

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Chu, Kuo-Hsiung, Jo-Hsiang Chen, Kuo-Bin Hong, Yu-Ming Huang, Shih-Wen Chiu, Fu-Yao Ke, Chia-Wei Sun, Tsung-Sheng Kao, Chin-Wei Sher, and Hao-Chung Kuo. "Study of High Polarized Nanostructure Light-Emitting Diode." Crystals 12, no. 4 (April 11, 2022): 532. http://dx.doi.org/10.3390/cryst12040532.

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In this study, we investigated the characteristic difference between the two different configurations of the three-dimensional shell–core nanorod LED. We achieve a degree of polarization of 0.545 for tip-free core–shell nanorod LED and 0.188 for tip core–shell nanorod LED by combining the three-dimensional (3D) structure LED with photonic crystal. The ability of low symmetric modes generated by photonic crystals to enhance degree of polarization has been demonstrated through simulations of photonic crystals. In addition, light confinement in GaN-based nanorod structures is induced by total internal reflection at the GaN/air interface. The combination of 3D core–shell nanorod LED and photonic crystals cannot only produce a light source with a high degree of polarization, but also a narrow divergence angle up to 56°. These 3D LEDs may pave the way for future novel optoelectronic components.

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Helliwell, John R. "Relating protein crystal structure to ligand-binding thermodynamics." Acta Crystallographica Section F Structural Biology Communications 78, no. 12 (November 28, 2022): 403–7. http://dx.doi.org/10.1107/s2053230x22011244.

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An important interface between biophysical chemistry and biological crystal structures involves whether it is possible to relate experimental calorimetry measurements of protein ligand binding to 3D structures. This has proved to be challenging. The probes of the structure of matter, namely X-rays, neutrons and electrons, have challenges of one type or another in their use. This article focuses on saccharide binding to lectins as a theme, yet after 25 years or so it is still a work in progress to connect 3D structure to binding energies. Whilst this study involved one type of protein (lectins) and one class of ligand (monosaccharides), i.e. it was specific, it was of general importance, as measured for instance by its wide impact. The impetus for writing this update now, as a Scientific Comment, is that a breakthrough in neutron crystal structure determinations of saccharide-bound lectins has been achieved. It is suggested here that this new research from neutron protein crystallography could improve, i.e. reduce, the errors in the estimated binding energies.

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Peresypkina, E. V., and V. A. Blatov. "Structure-forming components in crystals of ternary and quaternary 3d-metal complex fluorides." Acta Crystallographica Section B Structural Science 59, no. 3 (May 23, 2003): 361–77. http://dx.doi.org/10.1107/s0108768103007572.

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Crystallochemical analysis and classification were performed for 139 ternary and quaternary complex fluorides with the general formula M1 n M2 m M3F6, belonging to 33 structure types. Using coordination sequences and the uniformity criterion the structure-forming ionic sublattices or their combinations were found, which are responsible for the formation of stable periodic frameworks. Analysis of structure-forming motifs allows the interpretation of the crystal structures of complex fluorides as close packings of F ions with M1, M2 and M3 cations, partially occupying tetrahedral and octahedral voids, or as the packings of [M3F6] complex ions with M1 and M2 countercations in the voids. Cationic sublattices are noted to play an essential role, while forming crystal structures of complex fluorides. Relationships between the composition of structure-forming sublattices, the composition of compounds, and the size and charge of ions belonging to the sublattices were analysed under normal conditions, with thermal and high-pressure polymorphic transitions. Rules were formulated to predict the crystal structures of complex fluorides with a given chemical composition.

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Karasev, M. O., V. A. Fomina, I. N. Karaseva, and D. V. Pushkin. "Crystallochemical Role of Benzoate and Phenylacetate Ions in Structures of Coordination 3d-Metal Compounds." Координационная химия 49, no. 4 (April 1, 2023): 246–56. http://dx.doi.org/10.31857/s0132344x23700226.

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A crystal chemical analysis of the 3d-metal benzoate- and phenylacetate-containing compounds is carried out in terms of the stereoatomic crystal structure model using characteristics of the Voronoi–Dirichlet polyhedra. Coordination types of benzoate and phenylacetate anions toward the transition metals from Ti to Zn are considered. The influence of the coordination type on the characteristics of M–O bonds in the crystal structures is revealed. The electron-donating ability of benzoate and phenylacetate anions toward 3d metals is quantitatively estimated using the 18-electron rule.

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Liu, Guang-Xiang, Yan Wang, Liang-Fang Huang, Xue-Jun Kong, and Hong Chen. "A 3D 3d-4f Heterometallic Coordination Polymer: Synthesis, Crystal Structure and Properties." Journal of Inorganic and Organometallic Polymers and Materials 18, no. 3 (June 13, 2008): 358–63. http://dx.doi.org/10.1007/s10904-008-9212-1.

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Truong, Khai-Nghi, Sho Ito, Jakub M. Wojciechowski, Christian R. Göb, Christian J. Schürmann, Akihito Yamano, Mark Del Campo, et al. "Making the Most of 3D Electron Diffraction: Best Practices to Handle a New Tool." Symmetry 15, no. 8 (August 8, 2023): 1555. http://dx.doi.org/10.3390/sym15081555.

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Along with the adoption of three-dimensional electron diffraction (3D ED/MicroED) as a mainstream tool for structure determination from sub-micron single crystals, questions about best practices regarding each step along the workflow, from data collection to structure solutions, arise. In this paper, we discuss three particular aspects of a 3D ED/MicroED experiment which, after hundreds of structures solved in Rigaku’s laboratories, we have found to be important to consider carefully. First, for a representative model system of a hydrated compound (trehalose dihydrate), we show that cryo-transfer of the sample into the diffractometer is an effective means to prevent dehydration, while cooling of the sample without cryo-transfer yields a marginal improvement only. Next, we demonstrate for a small (tyrosine) and a large (clarithromycin) organic compound, how a simplified and fast workflow for dynamical diffraction calculations can determine absolute crystal structures with high confidence. Finally, we discuss considerations and trade-offs for choosing an optimal effective crystal-to-detector distance; while a long distance is mandatory for a protein (thaumatin) example, even a small molecule with difficult diffraction behavior (cystine) yields superior results at longer distances than the one used by default.

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Ruseikina, Anna V., Maxim V. Grigoriev, Leonid A. Solovyov, Vladimir A. Chernyshev, Aleksandr S. Aleksandrovsky, Alexander S. Krylov, Svetlana N. Krylova, et al. "A Challenge toward Novel Quaternary Sulfides SrLnCuS3 (Ln = La, Nd, Tm): Unraveling Synthetic Pathways, Structures and Properties." International Journal of Molecular Sciences 23, no. 20 (October 18, 2022): 12438. http://dx.doi.org/10.3390/ijms232012438.

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We report on the novel heterometallic quaternary sulfides SrLnCuS3 (Ln = La, Nd, Tm), obtained as both single crystals and powdered samples. The structures of both the single crystal and powdered samples of SrLaCuS3 and SrNdCuS3 belong to the orthorhombic space group Pnma but are of different structural types, while both samples of SrTmCuS3 crystallize in the orthorhombic space group Cmcm with the structural type KZrCuS3. Three-dimensional crystal structures of SrLaCuS3 and SrNdCuS3 are formed from the (Sr/Ln)S7 capped trigonal prisms and CuS4 tetrahedra. In SrLaCuS3, alternating 2D layers are stacked, while the main backbone of the structure of SrNdCuS3 is a polymeric 3D framework [(Sr/Ln)S7]n, strengthened by 1D polymeric chains (CuS4)n with 1D channels, filled by the other Sr2+/Ln3+ cations, which, in turn, form 1D dimeric ribbons. A 3D crystal structure of SrTmCuS3 is constructed from the SrS6 trigonal prisms, TmS6 octahedra and CuS4 tetrahedra. The latter two polyhedra are packed together into 2D layers, which are separated by 1D chains (SrS6)n and 1D free channels. In both crystal structures of SrLaCuS3 obtained in this work, the crystallographic positions of strontium and lanthanum were partially mixed, while only in the structure of SrNdCuS3, solved from the powder X-ray diffraction data, were the crystallographic positions of strontium and neodymium partially mixed. Band gaps of SrLnCuS3 (Ln = La, Nd, Tm) were found to be 1.86, 1.94 and 2.57 eV, respectively. Both SrNdCuS3 and SrTmCuS3 were found to be paramagnetic at 20–300 K, with the experimental magnetic characteristics being in good agreement with the corresponding calculated parameters.

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Ai, Xingtian, Chenguang Sun, Hui Zhang, Jian Sun, Luxiao Xie, Guodong Liu, and Guifeng Chen. "Simulation of the Inductor Structure to Improve FZ Thermal Fields." Coatings 13, no. 9 (September 7, 2023): 1565. http://dx.doi.org/10.3390/coatings13091565.

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The floating zone (FZ) is one of the important methods for pulling silicon single crystals, but there are still problems of an unstable thermal field and crystallization difficulties. They will directly affect the growth of single crystals, resulting in defects and even fractures, seriously reducing production efficiency. Based on this, the effect of the modified inductor structure on the FZ thermal field is investigated in this paper. Using COMSOL 6.0 simulation software, 2D and 3D FZ models are established. The inductor steps under the 2D model and the inductor slits under the 3D model are compared to analyze the effects of steps and slits on the 8-inch FZ thermal field and melt flow. The distributions of temperature fields and melt flow in the melting zone under the action of the axial magnetic field are calculated by finite element analysis. The results show that the melt under the introduction of steps in the 2D model and the cross-slit structure in the 3D model is the most stable and favorable for crystal growth, which matches the actual production.

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Weippert, Valentin, and Dirk Johrendt. "High-pressure synthesis and crystal structure of SrGa4As4." Acta Crystallographica Section E Crystallographic Communications 75, no. 11 (October 22, 2019): 1643–45. http://dx.doi.org/10.1107/s2056989019013562.

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Strontium tetragallate(II,III) tetraarsenide, SrGa4As4, was synthesized in a Walker-type multianvil apparatus under high-pressure/high-temperature conditions of 8 GPa and 1573 K. The compound crystallizes in a new structure type (P3221, Z = 3) as a three-dimensional (3D) framework of corner-sharing SrAs8 quadratic antiprisms with strontium situated on a twofold rotation axis (Wyckoff position 3b). This arrangement is surrounded by a 3D framework which can be described as alternately stacked layers of either condensed GaIIIAs4 tetrahedra or honeycomb-like layers built up from distorted ethane-like GaII 2As6 units comprising Ga—Ga bonds.

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Jha, Kunal Kumar, Barbara Gruza, Michał Leszek Chodkiewicz, Christian Jelsch, and Paulina Maria Dominiak. "Refinements on electron diffraction data of β-glycine in MoPro: a quest for an improved structure model." Journal of Applied Crystallography 54, no. 4 (July 7, 2021): 1234–43. http://dx.doi.org/10.1107/s160057672100580x.

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The advancement in 3D electron diffraction (3D ED) techniques that lead to a revolution in molecular structure determination using nano-sized crystals is now achieving atomic resolution. The structures can be obtained from 3D ED data with tools similar to those used for X-ray structure determination. In this context, the MoPro software, originally designed for structure and charge density refinements using X-ray diffraction data, has been adapted. Structure refinement on 3D ED data was achieved via implementation of electron scattering factors available in the literature and by application of the Mott–Bethe equation to X-ray scattering factors computed from the multipolar atom model. The multipolar model was parametrized using the transferable pseudoatom databanks ELMAM2 and UBDB. Applying the independent atom model (IAM), i.e. spherical neutral atom refinement, to 3D ED data on β-glycine in MoPro resulted in structure and refinement statistics comparable to those obtained from other well known software. Use of the transferred aspherical atom model (TAAM) led to improvement of the refinement statistics and a better fit of the model to the 3D ED data as compared with the spherical atom refinement. The anisotropic displacement parameters of non-H atoms appear underestimated by typically 0.003 Å2 for the non-H atoms in IAM refinement compared with TAAM. Thus, MoPro is shown to be an effective tool for crystal structure refinement on 3D ED data and allows use of a spherical or a multipolar atom model. Electron density databases can be readily transferred with no further modification needed when the Mott–Bethe equation is applied.

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Bogdanov, S. P., M. M. Sychev, and L. A. Lebedev. "The Al₂O₃-3D-ceramics' structure changing when sintering." NOVYE OGNEUPORY (NEW REFRACTORIES), no. 9 (December 29, 2018): 35–39. http://dx.doi.org/10.17073/1683-4518-2018-9-35-39.

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It was proposed to regard the ceramic products with periodic topology as the systems having the multilevel organized structures. The development of the structure was studied at diﬀerent scales levels after the sintering at 1700 °С for the corundum ceramics prepared by 3D-printing. The peculiarities of the geometry change were shown for the 3d-printed layered structure, for the material's grain structure and for the crystal lattice parameters of the α-Al2O3grains.Ill. 5. Ref.8.

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Radzieowski, Mathis, Steffen Klenner, Rolf-Dieter Hoffmann, and Oliver Janka. "Structure solution of incommensurately modulated La6MnSb15." Zeitschrift für Kristallographie - Crystalline Materials 235, no. 8-9 (September 25, 2020): 291–301. http://dx.doi.org/10.1515/zkri-2020-0034.

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AbstractLa6MnSb15 is synthesized from the constituent elements in quartz ampoules at 973 K. Crucial for the quality of the obtained single-crystals was a slow cooling rate of 2 K h−1. The crystal structure of La6MnSb15 was investigated via single-crystal X-ray diffraction experiments, leading to the observation of superstructure reflections as described in the literature. Two crystals, with refined compositions of La6MnSb15 (1) and La6MnSb14.66(1) (2) were obtained from different batches, yet both showed an orthorhombic body centered unit cell as well as additional reflections at q1 = (0,0,0.258(1)) for crystal (1) and q1 = (0,0,0.244(1)) for crystal (2). The structure could be solved and refined in superspace group Immm(00γ)000 (71.1.12.1), leading to a concise structural model. Due to γ not being exactly 1/4, an incommensurate modulation is present in the presented compounds. In order to describe the structural influence of the modulation in 3D, different approximants were chosen and the differences compared. Additionally, the temperature dependence of the electrical resistivity was investigated, indicating a metallic behavior of the title compound. This result is in line with the retro-theoretical investigation in the literature that counts excess electrons when using the Zintl–Klemm–Busmann concept. 121Sb Mößbauer-spectroscopic investigations at 78 K show a broad signal with an average isomeric shift of δ ∼ −10 mm s−1, in line with a negatively charged Sb species. The massive line broadening can be explained by the large number of crystallographic antimony sites in the basic structure and the approximant.

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Hovmöller, Sven, Daliang Zhang, Daniel Grüner, Xiaodong Zou, and Peter Oleynikov. "Collecting 3D electron diffraction data for crystal structure determination." Acta Crystallographica Section A Foundations of Crystallography 65, a1 (August 16, 2009): s228. http://dx.doi.org/10.1107/s0108767309095312.

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Yamauchi, Sho, and Keiji Suzuki. "Robot Design Method Using 3D Printed Inner Crystal Structure." IEEJ Transactions on Electronics, Information and Systems 139, no. 9 (September 1, 2019): 1051–58. http://dx.doi.org/10.1541/ieejeiss.139.1051.

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Gipson, B., X. Zeng, and H. Stahlberg. "2dx - Automated 3D structure reconstruction from 2D crystal data." Microscopy and Microanalysis 14, S2 (August 2008): 1290–91. http://dx.doi.org/10.1017/s1431927608081919.

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Chen, Teng-Hao, Semin Lee, Amar H. Flood, and Ognjen Š. Miljanić. "How to print a crystal structure model in 3D." CrystEngComm 16, no. 25 (2014): 5488–93. http://dx.doi.org/10.1039/c4ce00371c.

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We present a simple procedure for the conversion of Crystallographic Information Files (CIFs) into Virtual Reality Modelling Language (VRML2, .wrl) files, which can be used as input files for three-dimensional (3D) printing.

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Jiang, Linhua, Dilyana Georgieva, Igor Nederlof, Zunfeng Liu, and Jan Pieter Abrahams. "Image Processing and Lattice Determination for Three-Dimensional Nanocrystals." Microscopy and Microanalysis 17, no. 6 (November 18, 2011): 879–85. http://dx.doi.org/10.1017/s1431927611012244.

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AbstractThree-dimensional nanocrystals can be studied by electron diffraction using transmission cryo-electron microscopy. For molecular structure determination of proteins, such nanosized crystalline samples are out of reach for traditional single-crystal X-ray crystallography. For the study of materials that are not sensitive to the electron beam, software has been developed for determining the crystal lattice and orientation parameters. These methods require radiation-hard materials that survive careful orienting of the crystals and measuring diffraction of one and the same crystal from different, but known directions. However, as such methods can only deal with well-oriented crystalline samples, a problem exists for three-dimensional (3D) crystals of proteins and other radiation sensitive materials that do not survive careful rotational alignment in the electron microscope. Here, we discuss our newly released software AMP that can deal with nonoriented diffraction patterns, and we discuss the progress of our new preprocessing program that uses autocorrelation patterns of diffraction images for lattice determination and indexing of 3D nanocrystals.

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Madura, Izabela. "Hierarchical model of molecular crystals." Acta Crystallographica Section A Foundations and Advances 70, a1 (August 5, 2014): C549. http://dx.doi.org/10.1107/s2053273314094509.

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Spatial arrangement of molecules in molecular crystals depends on properties of molecules building up the crystal, and in particular on the nature of interactions occurring between them. The knowledge about primary and subsequent interactions building up the 3D structure seems to be important in many aspects, just to mention crystal engineering and crystallization processes. If the only interactions between molecules are isotropic van der Waals interactions, the observed structure will resemble a close-packing arrangement. The presence of any directional interactions leads, in accordance to Kitaigorodsky's principles,[1] to the symmetry breaking of the close-packing structure, and resulting crystal exhibits hierarchical organization. The presentation will discuss consequences of directional intermolecular interactions and their impact on generation and organization of successive levels of the hierarchical architecture in crystals. The strategy for identification, analysis and hierarchization of weak intermolecular interactions will also be presented. Selected examples will serve to illustrate usefulness of the proposed model for the discussion on molecular symmetry, supramolecular synthons' equivalency, polymorphism, isomorphism or packing.

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He, Zhenhua, Shifei Zhu, and Canhui Liu. "Preparation and characterization of porous Al2O3 based on nano-Al2O3 powders and PLA template by microwave sintering." Processing and Application of Ceramics 14, no. 2 (2020): 128–33. http://dx.doi.org/10.2298/pac2002128h.

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Macroporous and mesoporous Al2O3 body was prepared using mesh screening shaped polylactic acid (PLA) template. The mesh screening shaped PLA template was made from 3D cylindrical model by adjusting the PLA filling rate at 30 vol.%. After 3D printing, the PLA template was filled with Al2O3 nano-powders and microwave sintered at 1673K for 20min. During the sintering, the PLA template was decomposed and left large pores which could promote sintering of Al2O3. The Al2O3 sintered body showed macroporous structure with the pore size of 100 to 300 nm and also mesoporosity with local single crystal structure. The average pore diameter of mesoporous structures in the Al2O3 sintered body was about 7.6 nm. The Vickers hardness of the porous Al2O3 is 1.254 ? 0.039GPa. The obtained results confirmed that 3D-printed PLA template assisted microwave sintering is a promising technical processing for the fabrication of macroporous and mesoporous Al2O3 with local single crystal structure.

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Shevchenko, V. Ya, and G. D. Ilyushin. "Cluster Self-Organization of Intermetallic Systems: Clusters-Precursors K15, K6, K5, and K4 for the Self-Assembly of Crystal Structures Pu31Rh20-tI204, Pu20Os12-tI32, (Pu4Co)2(Pu4)-tI28, (Ti4Ni)2(Bi4)-tI28, and Bi4-tI8." Физика и химия стекла 49, no. 6 (November 1, 2023): 580–96. http://dx.doi.org/10.31857/s0132665123600413.

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Using the ToposPro software package, a combinatorial-topological analysis and modeling of the self-assembly of the following crystal structures with space group I4/mcm are realized: Pu31Rh20-tI204: a = 11.076 Å, c = 36.933 Å, V = 4530.86 Å3, Pu20Os12-tI32: a = 10.882 Å, c = 5.665 Å, V = 670.8 Å3. (Pu4Co)2 (Pu4)-tI28: a = 10.475 Å, c = 5.340 Å, V = 585.9Å3. (Ti4Ni)2(Bi4)-tI28: a = 10.554 Å, c = 4.814 Å, V = 536.2Å3, Bi4-tI8: a = 8.518 Å, c = 4.164 Å, V = 302.15 Å3. For the crystal structure of Pu31Rh20-tI204, 113 variants of the cluster representation of the 3D atomic network with the following number of structural units are established: 4 (14 variants), 5 (61 variants), and 6 (38 variants). A variant of the self-assembly of the crystal structure with the participation of three types of framework-forming polyhedra is considered: K15 = Pu@14(Rh2Pu5)2 with symmetry –42m, double pyramids K10 = (Rh@Pu4)2 with symmetry 4, and octahedra K6 = 0@8(Rh2Pu6) with symmetry mmm and spacers Rh. For the crystal structure of Pu20Os12-tI32, framework-forming pyramid-shaped polyhedra K5 = 0@OsPu4 with symmetry 4, as well as spacers Pu and Os, are defined. For the crystal structure (Ti4Ni)2(Bi4), frame-forming pyramids K5 = 0@Ti4Ni and tetrahedra K4 = 0@Bi4) are defined. For the crystal structure (Pu4Co)2(Pu4)-tI28, frame-forming pyramids K5 = 0@ Pu4Co and tetrahedra K4 = 0@Pu4 are defined. For the crystal structure of Bi4-tI8, frame-forming tetrahedra K4 = 0@Bi4 are defined. The symmetric and topological code of self-assembly processes of 3D structures is reconstructed from clusters-precursors in the following form: primary chain → layer → framework.

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Xiang, Hang, Zhemin Chai, Wenjun Kou, Huanchao Zhong, and Jiawei Xiang. "An Investigation of the Energy Harvesting Capabilities of a Novel Three-Dimensional Super-Cell Phononic Crystal with a Local Resonance Structure." Sensors 24, no. 2 (January 7, 2024): 361. http://dx.doi.org/10.3390/s24020361.

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Using the piezoelectric (PZT) effect, energy-harvesting has become possible for phononic crystal (PnC). Low-frequency vibration energy harvesting is more of a challenge, which can be solved by local resonance phononic crystals (LRPnCs). A novel three-dimensional (3D) energy harvesting LRPnC is proposed and further analyzed using the finite element method (FEM) software COMSOL. The 3D LRPnC with spiral unit-cell structures is constructed with a low initial frequency and wide band gaps (BGs). According to the large vibration deformation of the elastic beam near the scatterer, a PZT sheet is mounted in the surface of that beam, to harvest the energy of elastic waves using the PZT effect. To further improve the energy-harvesting performance, a 5 × 5 super-cell is numerically constructed. Numerical simulations show that the present 3D super-cell PnC structure can make full use of the advantages of the large vibration deformation and the PZT effect, i.e., the BGs with a frequency range from 28.47 Hz to 194.21 Hz with a bandwidth of 142.7 Hz, and the maximum voltage output is about 29.3 V under effective sound pressure with a peak power of 11.5 µW. The present super-cell phononic crystal structure provides better support for low-frequency vibration energy harvesting, when designing PnCs, than that of the traditional Prague type.

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Tian, Kun, Min Peng, Ping Wu, Chu Hang Liao, and Fa Yin Huang. "Biomineralization of the Hydroxyapatite with 3D-Structure for Enamel Reconstruction." Advanced Materials Research 391-392 (December 2011): 633–37. http://dx.doi.org/10.4028/www.scientific.net/amr.391-392.633.

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Tooth morphogenesis results from reciprocal interactions between oral epithelium and ectomesenchyme culminating in the formation of mineralized tissues, enamel, and dentin. Based on these basic theory, we design a organic molecules model to induced the crystallization of hydroxyapatite to synthesized tooth-like calcium phosphate/hydroxyapatite with 3D-structure in a controllable way in vitro. We observed that hydroxyapatite nanorods can be controlled followed by in situ phosphorylation process and triggered by conditions of pH and ionic strength. The results showed that he dentinal tubule were blocked by neonatal hydroxyapatite layer and this composite a continuous structure of columns crystal with size of 30-80nm. At the same time, XRD showed that the precipitation was calcium fluoride phosphate and Ca:P was 1.6. Furthermore, there were column crystal with parallel direction inside, as same as the crystal array in the top of enamel rod. The results suggest that collagen monolayer may be useful in the modulation of mineral behavior during in situ dental tissue engineering.

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Porta, Jason, Jeff Lovelace, and Gloria E. O. Borgstahl. "How to assign a (3 + 1)-dimensional superspace group to an incommensurately modulated biological macromolecular crystal." Journal of Applied Crystallography 50, no. 4 (June 30, 2017): 1200–1207. http://dx.doi.org/10.1107/s1600576717007294.

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Periodic crystal diffraction is described using a three-dimensional (3D) unit cell and 3D space-group symmetry. Incommensurately modulated crystals are a subset of aperiodic crystals that need four to six dimensions to describe the observed diffraction pattern, and they have characteristic satellite reflections that are offset from the main reflections. These satellites have a non-integral relationship to the primary lattice and requireqvectors for processing. Incommensurately modulated biological macromolecular crystals have been frequently observed but so far have not been solved. The authors of this article have been spearheading an initiative to determine this type of crystal structure. The first step toward structure solution is to collect the diffraction data making sure that the satellite reflections are well separated from the main reflections. Once collected they can be integrated and then scaled with appropriate software. Then the assignment of the superspace group is needed. The most common form of modulation is in only one extra direction and can be described with a (3 + 1)D superspace group. The (3 + 1)D superspace groups for chemical crystallographers are fully described in Volume C ofInternational Tables for Crystallography. This text includes all types of crystallographic symmetry elements found in small-molecule crystals and can be difficult for structural biologists to understand and apply to their crystals. This article provides an explanation for structural biologists that includes only the subset of biological symmetry elements and demonstrates the application to a real-life example of an incommensurately modulated protein crystal.

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Bíró, Domokos, László Jakab-Farkas, András Kelemen, Sándor Papp, Mohamed Fathy Hasaneen, Miklós Menyhárd, Sándor Gurbán, and Péter B. Barna. "Effect of Oxygen Doping on the Structure of TiN Surface Coatings." MACRo 2015 1, no. 1 (March 1, 2015): 315–24. http://dx.doi.org/10.1515/macro-2015-0031.

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AbstractIn the present work the influence of the level of oxygen doping on the structure of TiN films was investigated by dedicated experiments. The films were deposited at 400°C in an all metal UHV device by unbalanced magnetron sputtering at the same Ar and nitrogen flow rates, but the oxygen flow rate was changed in the experiments, incorporating oxygen in the range of 4 and 20 at.%. The structure of the films was investigated by XRD, Auger electron (AES) and X-ray photon electron (XPS) spectroscopy and transmission electron microscopy (TEM). The results discovered the crystal face anisotropy in the incorporation-segregation of oxygen leading to the change of the <111> texture to <002>. The structure analysis revealed that the <002> texture is developing also by competitive growth of crystals, which is the result of the limitation of the growth of the <111> oriented crystals by the TiO2 layer developing on their growth surface by the segregated oxygen species. The oxygen incorporating in the crystal lattice on the 002 crystal faces of the <002> oriented crystals is segregated by surface spinodal decomposition, developing nm sized 3D TiO-2 inclusion both in the bulk of the columns and the column boundaries.

Journal articles on the topic '3D crystal structure'

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