Application of X-ray and Electron to Crystal Structure Characterization

A special issue of Crystals (ISSN 2073-4352). This special issue belongs to the section "Crystal Engineering".

Deadline for manuscript submissions: closed (11 January 2024) | Viewed by 7056

Special Issue Editors


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Guest Editor
A.V. Shubnikov Institute of Crystallography, Federal Scientific Research Centre “Crystallography and Pho-5 tonics”, Russian Academy of Sciences, 59, Leninsky prospect, 119333 Moscow, Russia
Interests: crystallography; X-ray; crystal structure

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Guest Editor
Shubnikov’s Institute of Crystallography, Federal Scientific Research Centre "Crystallography and Photonics", Russian Academy of Sciences, 119333 Moscow, Russia
Interests: crystallography; X-ray

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Guest Editor
Shubnikov Institute of Crystallography, Russian Academy of Sciences, 119333 Moscow, Russia
Interests: crystallography; small-angle scattering

Special Issue Information

Dear Colleagues,

I would like to welcome you to contribute to the latest Crystals Special Issue, which aims to share the crucial developments and advances in X-ray and electron diffraction methods being applied to the characterization of high-tech nanoscale crystalline structures. The main aim is to provide novel publications that would be of interest to readers and scholars worldwide. Prospective authors are invited to focus on theoretical and experimental studies that would provide substantial progress in understanding the X-ray and electron diffraction fundamentals that eventually enable the decoding of crystal structure data by means of X-ray structure analysis, coherent X-ray 4D optics, X-ray and electron microtomography, ptychography, and so forth.

Prof. Dr. Felix N Chukhovskii
Dr. Konarev V. Petr
Prof. Dr. Vladimir Vladimirovich Volkov
Guest Editors

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Keywords

  • fundamentals of high-resolution X-ray and fast electron diffraction microtomography
  • X-ray reciprocal-space mapping
  • X-ray crystal structure analysis
  • coherent X-ray 4D optics applications for nanoscale crystal structure determination
  • X-ray and electron ptychography analysis

Published Papers (7 papers)

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Research

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10 pages, 9191 KiB  
Article
Scattering of Ultrashort X-ray Pulses from Oriented NV Centers in the Diamond Structure
by Dmitry Makarov, Marat Eseev, Eugeny Gusarevich, Viktor Matveev, Ksenia Makarova and Mark Borisov
Crystals 2024, 14(2), 193; https://doi.org/10.3390/cryst14020193 - 14 Feb 2024
Viewed by 827
Abstract
It is well known that the basis of diffraction analysis of matter is scattering, including the scattering of ultrashort laser pulses. In the theory of scattering of ultrashort pulses, the pulse duration parameter is usually not taken into account, which leads to some [...] Read more.
It is well known that the basis of diffraction analysis of matter is scattering, including the scattering of ultrashort laser pulses. In the theory of scattering of ultrashort pulses, the pulse duration parameter is usually not taken into account, which leads to some error. This error may be more significant than the considered effects in the scattering of the pulse on the studied structure. In this paper, it is shown that the pulse duration parameter should be taken into account when scattering X-ray pulses on oriented diamonds with NV centers. It is shown that the scattering spectra can be used to judge the orientation of NV centers in the diamond structure. The obtained results may be very different from the widely used theory of diffraction analysis, which confirms the necessity of taking into account the pulse duration parameter in the diagnosis of complex structures. Full article
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10 pages, 2904 KiB  
Article
Comprehensive Recovery of Point Defect Displacement Field Function in Crystals by Computer X-ray Diffraction Microtomography
by Felix N. Chukhovskii, Petr V. Konarev and Vladimir V. Volkov
Crystals 2024, 14(1), 29; https://doi.org/10.3390/cryst14010029 - 26 Dec 2023
Viewed by 923
Abstract
In the case of the point defect in a crystal, the inverse Radon’s problem in X-ray diffraction microtomography has been solved. As is known, the crystal-lattice defect displacement field function f(r) = h·u(r) determines phases [...] Read more.
In the case of the point defect in a crystal, the inverse Radon’s problem in X-ray diffraction microtomography has been solved. As is known, the crystal-lattice defect displacement field function f(r) = h·u(r) determines phases − (±h)-structure factors incorporated into the Takagi–Taupin equations and provides the 2D image patterns by diffracted and transmitted waves propagating through a crystal (h is the diffraction vector and u(r) is the displacement field crystal-lattice-defects vector). Beyond the semi-kinematical approach for obtaining the analytical problem solution, the difference-equations-scheme of the Takagi–Taupin equations that, in turn, yield numerically controlled-accuracy problem solutions has been first applied and tested. Addressing the inverse Radon’s problem solution, the χ2-target function optimization method using the Nelder–Mead algorithm has been employed and tested in an example of recovering the Coulomb-type point defect structure in a crystal Si(111). As has been shown in the cases of the 2D noise-free fractional and integrated image patterns, based on the Takagi–Taupin solutions in the semi-kinematical and difference-scheme approaches, both procedures provide the χ2-target function global minimum, even if the starting-values of the point-defect vector P1 is chosen rather far away from the reference up to 40% in relative units. In the cases of the 2D Poisson-noise image patterns with noise levels up to 5%, the figures-of-merit values of the optimization procedures by the Nelder–Mead algorithm turn out to be high enough; the lucky trials number is 85%; and in contrast, for the statistically denoised 2D image patterns, they reach 0.1%. Full article
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19 pages, 6040 KiB  
Article
X-ray Crystal Structure, Hirshfeld Surface Analysis, DFT, and Anticancer Effect of 3-Hydroxy-6-phenyl-1,5-benzodiazepin-2-one Derivatives
by Sanae Lahmidi, Ahmad H. Bakheit, El Mokhtar Essassi, Joel T. Mague and Mohammed M. Alanazi
Crystals 2023, 13(12), 1693; https://doi.org/10.3390/cryst13121693 - 15 Dec 2023
Cited by 1 | Viewed by 1002
Abstract
This study investigated the crystallographic and electronic properties of 1,5-benzodiazepine compounds, namely: cis-(3S,4S)-3-hydroxy-7,8-dimethyl-4-phenyl-1,3,4,5-tetrahydro-1,5-benzodiazepin-2-one 3b, trans-(3R,4R)-1-ethyl-3-hydroxy-7,8-dimethyl-4-phenyl-1,3,4,5-tetrahydro-2H-1,5-benzodiazepin-2-one 4, and trans-(3S,4S) 1-ethyl-3-ethoxy-7,8-dimethyl-4-phenyl-1,3,4,5-tetrahydro-1,5-benzodiazepin-2-one 5. Hirshfeld surface analysis was also applied to discern the intermolecular interactions, highlighting the significance of hydrogen bonding, van der Waals [...] Read more.
This study investigated the crystallographic and electronic properties of 1,5-benzodiazepine compounds, namely: cis-(3S,4S)-3-hydroxy-7,8-dimethyl-4-phenyl-1,3,4,5-tetrahydro-1,5-benzodiazepin-2-one 3b, trans-(3R,4R)-1-ethyl-3-hydroxy-7,8-dimethyl-4-phenyl-1,3,4,5-tetrahydro-2H-1,5-benzodiazepin-2-one 4, and trans-(3S,4S) 1-ethyl-3-ethoxy-7,8-dimethyl-4-phenyl-1,3,4,5-tetrahydro-1,5-benzodiazepin-2-one 5. Hirshfeld surface analysis was also applied to discern the intermolecular interactions, highlighting the significance of hydrogen bonding, van der Waals forces, and the influence of specific substituents. Furthermore, the MESP maps created using the density functional theory revealed the electrostatic nature of these molecules. The absence of dark blue regions on the MESP maps and variations due to different functional groups and substitutions were noteworthy findings. Collectively, this research offers crucial insights into the behaviour, interactions, and potential applications of new compounds. Finally, the anticancer effects of compounds 3b, 4, and 5 were evaluated against three cancer cell lines and one normal cell line, and the results showed that 3b and 4 had potent antiproliferative effects against all three cancer cell lines. Full article
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20 pages, 5203 KiB  
Article
X-ray Diffraction, Spectroscopy, Optical Properties, NPA, NBO, FMO, and Hirshfeld Surface Analyses of Two Newly Synthesized Piperidinium Ionic Liquids
by Youness El Bakri, Shaaban K. Mohamed, Atazaz Ahsin, Etify A. Bakhite, Islam S. Marae, Safiyyah A. H. Al-waleedy, Joel T. Mague and Rashad Al-Salahi
Crystals 2023, 13(11), 1583; https://doi.org/10.3390/cryst13111583 - 14 Nov 2023
Viewed by 878
Abstract
The present study elaborates on the synthesis, crystal structure, and computational studies of two new ionic liquids. In the crystal structure, [C5H12N][C21H14ClN2O2S] (4a), the anions form chains along the [...] Read more.
The present study elaborates on the synthesis, crystal structure, and computational studies of two new ionic liquids. In the crystal structure, [C5H12N][C21H14ClN2O2S] (4a), the anions form chains along the a-axis direction through C—H···π(ring) interactions. These are connected into layers that run approximately parallel to the ac plane by a variety of hydrogen bonds. In the compound structure, [C5H12N][C18H15N2O2S] (4b), the two ions are primarily associated by an N—H···N hydrogen bond. In the crystal structure, layers parallel to the bc plane are formed by pairs of C—H···O and N—H···S hydrogen bonds and by C—H···π(ring) interactions. A theoretical study reveals that 4a has lower energy than 4b and is more stable. The NBO and DOS studies further confine the liquids’ structural reactivity and electronic properties. The quantum theory of atoms in a molecule (QTAIM) analysis reveals the important non-covalent interactions among the fragments and charge transfer. The global reactivity descriptors indicate their molecular reactivity relationship with the presence of functional groups. The remarkable polarizability (αo) and hyperpolarizability (βo) values indicate their optical and nonlinear optical (NLO) properties. Furthermore, the analysis performed by CrystalExplorer shows the intermolecular interactions and reactive sites between cations and anions in ionic liquids. The 2D fingerprint plots and Hirshfeld surfaces indicate the major interactions of crystals with neighboring elements in crystal packing. For both compounds, the H···H interactions are significantly higher than the other element interactions. Full article
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11 pages, 4133 KiB  
Article
Flux Growth and Characterization of Bulk InVO4 Crystals
by Olesia Voloshyna, Mikhail V. Gorbunov, Daria Mikhailova, Andrey Maljuk, Silvia Seiro and Bernd Büchner
Crystals 2023, 13(10), 1439; https://doi.org/10.3390/cryst13101439 - 28 Sep 2023
Viewed by 772
Abstract
The flux growth of InVO4 bulk single crystals has been explored for the first time. The reported eutectic composition at a ratio of V2O5:InVO4 = 1:1 could not be used as a self-flux since no sign of [...] Read more.
The flux growth of InVO4 bulk single crystals has been explored for the first time. The reported eutectic composition at a ratio of V2O5:InVO4 = 1:1 could not be used as a self-flux since no sign of melting was observed up to 1100 °C. Crystals of InVO4 of typical size 0.5 × 1 × 7 mm3 were obtained using copper pyrovanadate (Cu2V2O7) as a flux, using Pt crucibles. X-ray powder diffraction confirmed the orthorhombic Cmcm structure. Rests of the flux material were observed on the sample surface, with occasional traces of Pt indicating some level of reaction with the crucible. X-ray absorption spectroscopy showed that oxidation states of indium and vanadium ions are +3 and +5, respectively. The size and high quality of the obtained InVO4 crystals makes them excellent candidates for further study of their physical properties. Full article
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16 pages, 4458 KiB  
Article
A Probe to Surface Reactivity, Crystal Structure, and DFT Investigations for Newly Synthesized 4,5-bis(4-Nitrophenyl)-8a-phenyl-decahydro-[1,3]diazino[4,5-d]pyrimidine-2,7-dione: A Combined Theoretical and Experimental Study
by Youness El Bakri, Malahat Kurbanova, Atazaz Ahsin, Nacaf Ramazanzade and Rashad Al-Salahi
Crystals 2023, 13(6), 942; https://doi.org/10.3390/cryst13060942 - 11 Jun 2023
Cited by 4 | Viewed by 1027
Abstract
The multicomponent reaction of 4-nitrobenzaldehyde with acetophenone and urea in the presence of HCl was investigated, and, as a result, 4,5-bis(4-nitrophenyl)-8a-phenyl-decahydro-[1,3]diazino[4,5-d]pyrimidine-2,7-dione was synthesized. The structure of the synthesized compound was confirmed by the X-ray method. We performed Hirshfeld surfaces (HS) analysis and two-dimensional [...] Read more.
The multicomponent reaction of 4-nitrobenzaldehyde with acetophenone and urea in the presence of HCl was investigated, and, as a result, 4,5-bis(4-nitrophenyl)-8a-phenyl-decahydro-[1,3]diazino[4,5-d]pyrimidine-2,7-dione was synthesized. The structure of the synthesized compound was confirmed by the X-ray method. We performed Hirshfeld surfaces (HS) analysis and two-dimensional (2D) fingerprint plots for the studied compound to obtain surface reactivity and intermolecular interactions. The H∙∙∙H interactions were found to be higher, up to 32.2%, while the percentage C∙∙∙O contact was found to be the lowest among the reported interactions for single crystal packing. The energy framework analysis shows the strength of interaction energy within fragments of a single crystal at 3.08 A distances. The DFT study shows structural reactivity and a reduced HOMO-LUMO gap up to 4.0 eV. The NPA study reveals the reactivity and excellent charge transfer within the structure. The TD-DFT study reveals the absorbance in the UV region and excited state parameters during crucial transitions (transitions with maximum oscillator strength). The investigated compound shows excellent optical and nonlinear optical (NLO) properties, as indicated by its polarizability (αo) and hyperpolarizability (βo) values. Full article
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Review

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13 pages, 3398 KiB  
Review
Decoding Material Structures with Scanning Electron Diffraction Techniques
by Sangmoon Yoon
Crystals 2024, 14(3), 275; https://doi.org/10.3390/cryst14030275 - 14 Mar 2024
Viewed by 932
Abstract
Recent advancements in electron detectors and computing power have revolutionized the rapid recording of millions of 2D diffraction patterns across a grid of probe positions, known as four-dimensional scanning transmission electron microscopy (4D-STEM). These datasets serve as the foundation for innovative STEM imaging [...] Read more.
Recent advancements in electron detectors and computing power have revolutionized the rapid recording of millions of 2D diffraction patterns across a grid of probe positions, known as four-dimensional scanning transmission electron microscopy (4D-STEM). These datasets serve as the foundation for innovative STEM imaging techniques like integrated center of mass (iCOM) and symmetry STEM (S-STEM). This paper delves into the application of 4D-STEM datasets for diffraction analysis. We therefore use the term scanning electron diffraction (SED) instead of 4D-STEM in this review. We comprehensively explore groundbreaking diffraction methods based on SED, structured into two main segments: (i) utilizing an atomic-scale electron probe and (ii) employing a nanoscale electron probe. Achieving an atomic-scale electron probe necessitates a significant convergence angle (α > 30 mrad), leading to interference between direct and diffracted beams, distinguishing it from its nanoscale counterpart. Additionally, integrating machine learning approaches with SED experiments holds promise in various directions, as discussed in this review. Our aim is to equip materials scientists with valuable insights for characterizing atomic structures using cutting-edge SED techniques. Full article
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