Density functional theory (DFT) calculations were used to investigate the efficacy of pure graphene (G), Mo-decorated graphene and Mo-decorated reduced graphene oxide (rGO) in removing nitrate anion (NO3−) pollutants. Initially, the adsorption mechanism was analyzed to identify the most probable position of nitrate adsorption through optimized geometries, adsorption energy, bond length and electronic structures. Subsequently, a comprehensive analysis was executed to examine the adsorption properties of the NO3− anion. Analyses of the adsorption energy, charge density difference and density of states indicated that defect sites, functional groups and Mo-atom decorations in graphene could significantly enhance the nitrate adsorption energy. The results indicated that the adsorption mechanisms of the NO3− anion on pure G, Mo-decorated G and Mo-decorated rGO were different. NO3–Mo-decorated rGO demonstrated the highest adsorption energy. Conversely, NO3–pure G exhibited the lowest adsorption energy, while the NO3–Mo-decorated G showed the highest Fermi energy. Bader and projected density of states analyses suggest that the orbitals in the NO3–Mo-decorated G structure occupy the largest share in the valence band compared with the NO3–Mo-decorated rGO structure, which led to high electron accumulation. Consequently, the NO3–Mo-decorated rGO structure allows the complete absorption of nitrate, resulting in the breaking of chemical bonds. These results indicate that the NO3–Mo-decorated rGO structure has the highest nitrate absorption energy among the studied structures.
{"title":"Theoretical investigation of adsorptive nitrate ion removal by pure graphene, Mo-decorated graphene and reduced graphene oxide based adsorbents: a DFT study","authors":"Nazanin Mohseninia, Nafiseh Memarian, Hamid Rezagholipour Dizaji","doi":"10.1107/S1600576725000032","DOIUrl":"https://doi.org/10.1107/S1600576725000032","url":null,"abstract":"<p>Density functional theory (DFT) calculations were used to investigate the efficacy of pure graphene (G), Mo-decorated graphene and Mo-decorated reduced graphene oxide (rGO) in removing nitrate anion (NO<sub>3</sub><sup>−</sup>) pollutants. Initially, the adsorption mechanism was analyzed to identify the most probable position of nitrate adsorption through optimized geometries, adsorption energy, bond length and electronic structures. Subsequently, a comprehensive analysis was executed to examine the adsorption properties of the NO<sub>3</sub><sup>−</sup> anion. Analyses of the adsorption energy, charge density difference and density of states indicated that defect sites, functional groups and Mo-atom decorations in graphene could significantly enhance the nitrate adsorption energy. The results indicated that the adsorption mechanisms of the NO<sub>3</sub><sup>−</sup> anion on pure G, Mo-decorated G and Mo-decorated rGO were different. NO<sub>3</sub>–Mo-decorated rGO demonstrated the highest adsorption energy. Conversely, NO<sub>3</sub>–pure G exhibited the lowest adsorption energy, while the NO<sub>3</sub>–Mo-decorated G showed the highest Fermi energy. Bader and projected density of states analyses suggest that the orbitals in the NO<sub>3</sub>–Mo-decorated G structure occupy the largest share in the valence band compared with the NO<sub>3</sub>–Mo-decorated rGO structure, which led to high electron accumulation. Consequently, the NO<sub>3</sub>–Mo-decorated rGO structure allows the complete absorption of nitrate, resulting in the breaking of chemical bonds. These results indicate that the NO<sub>3</sub>–Mo-decorated rGO structure has the highest nitrate absorption energy among the studied structures.</p>","PeriodicalId":48737,"journal":{"name":"Journal of Applied Crystallography","volume":"58 1","pages":"194-206"},"PeriodicalIF":5.2,"publicationDate":"2025-01-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143253785","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-01-30DOI: 10.1107/S1600576724012536
Marek Kotrlý, Josef Uher, Jan Jakubek, Roman Skála, Jana Boháčová, Ivana Turková, Kamila Starkbaumová
The forensic field has until now been missing more versatile equipment for non-destructive characterization, analysis and inspection of 2D and 3D objects. Also, the need for increasingly frequent analysis of art forgeries, where non-destructive analysis is required at least in the first step, is calling for a multimodal solution. A prototype device for robotic analysis, imaging and mapping of 3D objects is being developed and tested to be used in these areas. The system is based on the principle of integrating imaging and analytical technologies onto six-axis robotic arms, which allow substantial flexibility in the sample size or shape. The system enables non-destructive examination of a wide spectrum of samples with complicated curvatures. The new generation of X-ray imaging detectors provide a high picture quality with a spatial resolution level in the micrometre range in 2D or 3D imaging. The basic version of the robotic scanner allows transmission X-ray imaging and mapping of the individual photons with high-sensitivity and high-resolution detectors. The broad capabilities of XRD imaging are now being complemented by X-ray fluorescence point analysis and mapping, multispectral macro imaging, and multispectral X-ray diffraction analysis.
{"title":"New robotic tools for multimodal non-destructive analysis and characterization of 2D and 3D objects","authors":"Marek Kotrlý, Josef Uher, Jan Jakubek, Roman Skála, Jana Boháčová, Ivana Turková, Kamila Starkbaumová","doi":"10.1107/S1600576724012536","DOIUrl":"https://doi.org/10.1107/S1600576724012536","url":null,"abstract":"<p>The forensic field has until now been missing more versatile equipment for non-destructive characterization, analysis and inspection of 2D and 3D objects. Also, the need for increasingly frequent analysis of art forgeries, where non-destructive analysis is required at least in the first step, is calling for a multimodal solution. A prototype device for robotic analysis, imaging and mapping of 3D objects is being developed and tested to be used in these areas. The system is based on the principle of integrating imaging and analytical technologies onto six-axis robotic arms, which allow substantial flexibility in the sample size or shape. The system enables non-destructive examination of a wide spectrum of samples with complicated curvatures. The new generation of X-ray imaging detectors provide a high picture quality with a spatial resolution level in the micrometre range in 2D or 3D imaging. The basic version of the robotic scanner allows transmission X-ray imaging and mapping of the individual photons with high-sensitivity and high-resolution detectors. The broad capabilities of XRD imaging are now being complemented by X-ray fluorescence point analysis and mapping, multispectral macro imaging, and multispectral X-ray diffraction analysis.</p>","PeriodicalId":48737,"journal":{"name":"Journal of Applied Crystallography","volume":"58 1","pages":"168-179"},"PeriodicalIF":5.2,"publicationDate":"2025-01-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143253830","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-01-24DOI: 10.1107/S1600576724011841
Jiayi Wang, Lidan Gao, Ming Li, Yiming Yang, Yanchun Li, Hu Cheng, Longlong Fan, Youkang Wang, Huilong Guo, Quanjie Jia
The performance of a double-crystal Laue-case monochromator has been evaluated for the Engineering Material beamline at the High Energy Photon Source. Expanding on the xrt framework, the crystal simulation incorporates the Penning–Polder and multilamellar models to determine the crystal diffraction profiles and utilizes two approaches, analytical expression and discrete point, for crystal depiction. The simulation accounts for the heat load by treating it as both face distortion and bulk distortion. Three scenarios are discussed: an ideally bent crystal without heat load, a bent crystal with thermally induced face distortion and a bent crystal with thermally induced bulk distortion. The mutual consistency in tracing confirms the validity of the crystal simulation. Two thermal distortion assessment tools are available: one for the rapid evaluation of the impact of significant distortions, and the other for the refined reflection of interior lattice plane distortions, which constitutes a key innovation of the simulation. The tracing outcomes offer valuable guidance for decision making and risk mitigation in the optical design process.
{"title":"Simulation of bent Laue crystals for a high-energy X-ray monochromator with heat load consideration","authors":"Jiayi Wang, Lidan Gao, Ming Li, Yiming Yang, Yanchun Li, Hu Cheng, Longlong Fan, Youkang Wang, Huilong Guo, Quanjie Jia","doi":"10.1107/S1600576724011841","DOIUrl":"https://doi.org/10.1107/S1600576724011841","url":null,"abstract":"<p>The performance of a double-crystal Laue-case monochromator has been evaluated for the Engineering Material beamline at the High Energy Photon Source. Expanding on the <i>xrt</i> framework, the crystal simulation incorporates the Penning–Polder and multilamellar models to determine the crystal diffraction profiles and utilizes two approaches, analytical expression and discrete point, for crystal depiction. The simulation accounts for the heat load by treating it as both face distortion and bulk distortion. Three scenarios are discussed: an ideally bent crystal without heat load, a bent crystal with thermally induced face distortion and a bent crystal with thermally induced bulk distortion. The mutual consistency in tracing confirms the validity of the crystal simulation. Two thermal distortion assessment tools are available: one for the rapid evaluation of the impact of significant distortions, and the other for the refined reflection of interior lattice plane distortions, which constitutes a key innovation of the simulation. The tracing outcomes offer valuable guidance for decision making and risk mitigation in the optical design process.</p>","PeriodicalId":48737,"journal":{"name":"Journal of Applied Crystallography","volume":"58 1","pages":"154-167"},"PeriodicalIF":5.2,"publicationDate":"2025-01-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143253322","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-01-24DOI: 10.1107/S1600576724011956
Sergey V. Rashchenko
The problem of extracting basic (e.g. bond lengths and angles) and advanced (e.g. polyhedron volumes and effective coordination numbers) crystal chemical parameters from large datasets of CIFs in a quick and flexible way is addressed by a lightweight Python library with a graphical user interface (GUI). A description of library functionality in the GUI and scripting modes followed by examples based on open-access data demonstrate its advantages for crystallographers working with pressure-, temperature- and chemistry-induced structural variations, as well as with analysis of structural databases.
{"title":"crystchemlib: a Python library and GUI for analysis of crystal structure datasets","authors":"Sergey V. Rashchenko","doi":"10.1107/S1600576724011956","DOIUrl":"https://doi.org/10.1107/S1600576724011956","url":null,"abstract":"<p>The problem of extracting basic (<i>e.g.</i> bond lengths and angles) and advanced (<i>e.g.</i> polyhedron volumes and effective coordination numbers) crystal chemical parameters from large datasets of CIFs in a quick and flexible way is addressed by a lightweight Python library with a graphical user interface (GUI). A description of library functionality in the GUI and scripting modes followed by examples based on open-access data demonstrate its advantages for crystallographers working with pressure-, temperature- and chemistry-induced structural variations, as well as with analysis of structural databases.</p>","PeriodicalId":48737,"journal":{"name":"Journal of Applied Crystallography","volume":"58 1","pages":"290-295"},"PeriodicalIF":5.2,"publicationDate":"2025-01-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143253049","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-12-24DOI: 10.1107/S1600576724011695
John Badger
In a small-angle X-ray scattering analysis of protein molecules in solution the calculation of the pair distribution function, P(r), is invariably performed by an indirect Fourier transform. This approach models a P(r) to fit the available intensity data, I(q). The determination of P(r) via a direct transform from I(q) has been dismissed as unworkable since the range of q that is experimentally measured is necessarily incomplete. Here, it is shown that, provided suitable measures are taken to estimate unmeasured low-resolution data and avoid a sharp data truncation at the high-resolution data limit, the appearance of significant artifacts in the resulting P(r) may be circumvented. Using several examples taken from the Small Angle Scattering Biological Data Bank, it is demonstrated that the P(r) obtained by a direct transform are in close agreement with the P(r) obtained using the popular indirect transform program GNOM.
{"title":"Calculation of pair distribution functions from small-angle X-ray scattering protein data by direct transform","authors":"John Badger","doi":"10.1107/S1600576724011695","DOIUrl":"https://doi.org/10.1107/S1600576724011695","url":null,"abstract":"<p>In a small-angle X-ray scattering analysis of protein molecules in solution the calculation of the pair distribution function, <i>P</i>(<i>r</i>), is invariably performed by an indirect Fourier transform. This approach models a <i>P</i>(<i>r</i>) to fit the available intensity data, <i>I</i>(<i>q</i>). The determination of <i>P</i>(<i>r</i>) via a direct transform from <i>I</i>(<i>q</i>) has been dismissed as unworkable since the range of <i>q</i> that is experimentally measured is necessarily incomplete. Here, it is shown that, provided suitable measures are taken to estimate unmeasured low-resolution data and avoid a sharp data truncation at the high-resolution data limit, the appearance of significant artifacts in the resulting <i>P</i>(<i>r</i>) may be circumvented. Using several examples taken from the Small Angle Scattering Biological Data Bank, it is demonstrated that the <i>P</i>(<i>r</i>) obtained by a direct transform are in close agreement with the <i>P</i>(<i>r</i>) obtained using the popular indirect transform program <i>GNOM</i>.</p>","PeriodicalId":48737,"journal":{"name":"Journal of Applied Crystallography","volume":"58 1","pages":"119-127"},"PeriodicalIF":5.2,"publicationDate":"2024-12-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143253180","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}