Pub Date : 2025-11-01DOI: 10.1107/S2052252525008218
Samuel Gallego-Parra , Hussien Helmy Hassan Osman , Virginia Monteseguro , Catalin Popescu , Javier Ruiz-Fuertes , Paula Kayser , Vanesa Paula Cuenca-Gotor , Tania María García-Sánchez , Francisco Javier Manjón , Julio Pellicer-Porres , Gastón Garbarino , Juan Ángel Sans
The room-temperature structure of Sr2FeIrO6, a double perovskite with notable magnetic and structural properties, has been debated extensively. Our high-resolution and high-pressure synchrotron-based powder X-ray diffraction findings provide compelling evidence to reconcile these divergent positions, laying groundwork for future research.
Double perovskites with the formula A2BB′O6, such as Sr2FeIrO6, are being explored as unique platforms for unveiling diverse structural, electronic and magnetic properties. Inclusion of 3d and 5d transition metals in the B and B′ sites, as in Sr2FeIrO6, enables the study of electron correlation and spin–orbit coupling effects to tailor promising properties. The structure of Sr2FeIrO6 under ambient conditions has been widely debated, with theoretical and experimental studies suggesting several potential structures. This uncertainty complicates the understanding of its magnetic and electronic behaviours. High-pressure X-ray diffraction measurements, complemented by high-resolution powder X-ray diffraction studies under ambient conditions, have provided a definitive structural characterization of Sr2FeIrO6, crucial for interpreting its properties and guiding future research.
{"title":"Unveiling the ambient-condition structure of Sr2FeIrO6: a triclinic phase through synchrotron-based X-ray techniques and high pressure","authors":"Samuel Gallego-Parra , Hussien Helmy Hassan Osman , Virginia Monteseguro , Catalin Popescu , Javier Ruiz-Fuertes , Paula Kayser , Vanesa Paula Cuenca-Gotor , Tania María García-Sánchez , Francisco Javier Manjón , Julio Pellicer-Porres , Gastón Garbarino , Juan Ángel Sans","doi":"10.1107/S2052252525008218","DOIUrl":"10.1107/S2052252525008218","url":null,"abstract":"<div><div>The room-temperature structure of Sr<sub>2</sub>FeIrO<sub>6</sub>, a double perovskite with notable magnetic and structural properties, has been debated extensively. Our high-resolution and high-pressure synchrotron-based powder X-ray diffraction findings provide compelling evidence to reconcile these divergent positions, laying groundwork for future research.</div></div><div><div>Double perovskites with the formula <em>A</em><sub>2</sub><em>BB</em>′O<sub>6</sub>, such as Sr<sub>2</sub>FeIrO<sub>6</sub>, are being explored as unique platforms for unveiling diverse structural, electronic and magnetic properties. Inclusion of 3<em>d</em> and 5<em>d</em> transition metals in the <em>B</em> and <em>B</em>′ sites, as in Sr<sub>2</sub>FeIrO<sub>6</sub>, enables the study of electron correlation and spin–orbit coupling effects to tailor promising properties. The structure of Sr<sub>2</sub>FeIrO<sub>6</sub> under ambient conditions has been widely debated, with theoretical and experimental studies suggesting several potential structures. This uncertainty complicates the understanding of its magnetic and electronic behaviours. High-pressure X-ray diffraction measurements, complemented by high-resolution powder X-ray diffraction studies under ambient conditions, have provided a definitive structural characterization of Sr<sub>2</sub>FeIrO<sub>6</sub>, crucial for interpreting its properties and guiding future research.</div></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"12 6","pages":"Pages 683-691"},"PeriodicalIF":3.6,"publicationDate":"2025-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145280380","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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 : 2025-11-01DOI: 10.1107/S2052252525009030
Sven Lidin
Polyphasic Fe2P2O7 is a prime example of how the temperature-dependent changes in structure shed light on the magnitudes of local interactions. State-of-the-art methods and equipment are prerequisites for the analysis of these, often subtle, effects.
{"title":"Sometimes Mother Nature only whispers","authors":"Sven Lidin","doi":"10.1107/S2052252525009030","DOIUrl":"10.1107/S2052252525009030","url":null,"abstract":"<div><div>Polyphasic Fe<sub>2</sub>P<sub>2</sub>O<sub>7</sub> is a prime example of how the temperature-dependent changes in structure shed light on the magnitudes of local interactions. State-of-the-art methods and equipment are prerequisites for the analysis of these, often subtle, effects.</div></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"12 6","pages":"Pages 635-636"},"PeriodicalIF":3.6,"publicationDate":"2025-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145377818","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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 : 2025-11-01DOI: 10.1107/S2052252525008383
Marta Kulik , Paulina Maria Dominiak
Electrostatic potential maps of proteins are calculated at various resolutions using the transferable aspherical atom model (TAAM) to determine the relations between the electrostatic potential and resolution for different atom types.
Common sense tells us that experimental maps of lower (worse) resolution obtained from cryogenic electron microscopy or three-dimensional electron diffraction convey less information than maps of higher (better) resolution. However, information regarding the presence of charged moieties is more visible at lower resolutions. To investigate this phenomenon from a theoretical perspective, we analyzed the effects of truncation of data from the high-resolution end (from 1 Å to 8 Å) on theoretical Fourier images of the electrostatic potential of protein crystals, using both the popular independent atom model (IAM) of scattering factors and the more accurate transferable aspherical atom model (TAAM) combined with the UBDB/MATTS data bank. We compared our findings with those obtained for theoretical Fourier images of electron density maps associated with X-ray diffraction. Strikingly, when IAM is applied, there is almost no qualitative difference between the Fourier maps of electrostatic potential and electron density, regardless of their resolution. In contrast, the Fourier electrostatic potential maps calculated with TAAM, when of lower resolution, strongly differ from the electron density maps at the positions of charged moieties. Comparing TAAM and IAM, in the case of Fourier electrostatic potential maps, the relative difference between them is usually greatest at lower resolution maps, with a noticeable dependence on atom type and charge. In the case of Fourier electron density maps, this relative difference is much smaller and becomes more apparent in higher resolution maps. Thus, the use of accurate scattering factors is much more important for lower resolution data than for higher resolution data if one wants to investigate charged systems.
{"title":"Protein electrostatic potential Fourier maps calculated using the transferable aspherical atom model and the independent atom model across resolutions","authors":"Marta Kulik , Paulina Maria Dominiak","doi":"10.1107/S2052252525008383","DOIUrl":"10.1107/S2052252525008383","url":null,"abstract":"<div><div>Electrostatic potential maps of proteins are calculated at various resolutions using the transferable aspherical atom model (TAAM) to determine the relations between the electrostatic potential and resolution for different atom types.</div></div><div><div>Common sense tells us that experimental maps of lower (worse) resolution obtained from cryogenic electron microscopy or three-dimensional electron diffraction convey less information than maps of higher (better) resolution. However, information regarding the presence of charged moieties is more visible at lower resolutions. To investigate this phenomenon from a theoretical perspective, we analyzed the effects of truncation of data from the high-resolution end (from 1 Å to 8 Å) on theoretical Fourier images of the electrostatic potential of protein crystals, using both the popular independent atom model (IAM) of scattering factors and the more accurate transferable aspherical atom model (TAAM) combined with the UBDB/MATTS data bank. We compared our findings with those obtained for theoretical Fourier images of electron density maps associated with X-ray diffraction. Strikingly, when IAM is applied, there is almost no qualitative difference between the Fourier maps of electrostatic potential and electron density, regardless of their resolution. In contrast, the Fourier electrostatic potential maps calculated with TAAM, when of lower resolution, strongly differ from the electron density maps at the positions of charged moieties. Comparing TAAM and IAM, in the case of Fourier electrostatic potential maps, the relative difference between them is usually greatest at lower resolution maps, with a noticeable dependence on atom type and charge. In the case of Fourier electron density maps, this relative difference is much smaller and becomes more apparent in higher resolution maps. Thus, the use of accurate scattering factors is much more important for lower resolution data than for higher resolution data if one wants to investigate charged systems.</div></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"12 6","pages":"Pages 616-632"},"PeriodicalIF":3.6,"publicationDate":"2025-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145308136","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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 : 2025-11-01DOI: 10.1107/S2052252525007547
Berthold Stöger , Matthias Weil , Robert Glaum , Karla Fejfarová , Vaclav Petříček , Michal Dušek , Eugen Libowitzky , Ekkehard Füglein
Thortveitite-related Fe2P2O7 shows three reversible phase transitions and has an incommensurately modulated crystal structure at room temperature.
The debate in the literature whether the triclinic room-temperature crystal structure of iron(II) pyrophosphate (Fe2P2O7) is centrosymmetric or not has been clearly resolved on the basis of new single-crystal X-ray intensity measurements. This study additionally revealed that Fe2P2O7 undergoes three reversible phase transitions between −140 and 190°C, with the modifications denoted with decreasing temperature as β, α3, α2 and α1. The room-temperature form, α2-Fe2P2O7, indeed crystallizes in a centrosymmetric but incommensurately modulated structure, a fact that has not been recognized for more than 40 years. For better comparison with the C-centred monoclinic thortveitite-type aristotype (space group type C2/m), the structure of the hettotype α2-Fe2P2O7 is described in the superspace group C1(αβγ)0 with a = 6.6393 (6), b = 8.4748 (6), c = 4.4839 (3) Å, α = 90.036 (5), β = 103.962 (7), γ = 92.929 (6)° and a modulation wavevector q = 0.4489 (3)a* + 0.2517 (3)b* + 0.3646 (3)c*. The α2 modification undergoes two phase transitions towards periodic structures. On heating, a triclinic structure described in C1 with very similar lattice parameters is realized above 85°C for the corresponding α3 modification. It can be considered as the non-modulated basic structure of the α2 modification. At about 185°C, α3-Fe2P2O7 transforms to the thortveitite-type β modification, which remains stable up to at least 1000°C. On cooling the α2 modification, a triclinic structure of the low-temperature α1 modification forms below −140°C, which can be considered as a twofold superstructure of the α3 modification with q = ½a* + ½b* + ½c*. The result of these phase transitions from the thortveitite-type β-modification via the triclinic α3 phase and the incommensurately modulated triclinic α2 modification to α1-Fe2P2O7 is the complete ordering of the pyrophosphate anion in the low-temperature phase with a P—O—P bridging angle of 151.91 (8)°. This ordering is accompanied by the lowering of the coordination number of one half of the Fe2+ ions from 6 to 5.
{"title":"New structural insights into Fe2P2O7 – unravelling an unresolved dispute and three reversible phase transitions","authors":"Berthold Stöger , Matthias Weil , Robert Glaum , Karla Fejfarová , Vaclav Petříček , Michal Dušek , Eugen Libowitzky , Ekkehard Füglein","doi":"10.1107/S2052252525007547","DOIUrl":"10.1107/S2052252525007547","url":null,"abstract":"<div><div>Thortveitite-related Fe<sub>2</sub>P<sub>2</sub>O<sub>7</sub> shows three reversible phase transitions and has an incommensurately modulated crystal structure at room temperature.</div></div><div><div>The debate in the literature whether the triclinic room-temperature crystal structure of iron(II) pyrophosphate (Fe<sub>2</sub>P<sub>2</sub>O<sub>7</sub>) is centrosymmetric or not has been clearly resolved on the basis of new single-crystal X-ray intensity measurements. This study additionally revealed that Fe<sub>2</sub>P<sub>2</sub>O<sub>7</sub> undergoes three reversible phase transitions between −140 and 190°C, with the modifications denoted with decreasing temperature as β, α<sub>3</sub>, α<sub>2</sub> and α<sub>1</sub>. The room-temperature form, α<sub>2</sub>-Fe<sub>2</sub>P<sub>2</sub>O<sub>7</sub>, indeed crystallizes in a centrosymmetric but incommensurately modulated structure, a fact that has not been recognized for more than 40 years. For better comparison with the <em>C</em>-centred monoclinic thortveitite-type aristotype (space group type <em>C</em>2/<em>m</em>), the structure of the hettotype α<sub>2</sub>-Fe<sub>2</sub>P<sub>2</sub>O<sub>7</sub> is described in the superspace group <em>C</em>1(αβγ)0 with <em>a</em> = 6.6393 (6), <em>b</em> = 8.4748 (6), <em>c</em> = 4.4839 (3) Å, α = 90.036 (5), β = 103.962 (7), γ = 92.929 (6)° and a modulation wavevector <strong>q</strong> = 0.4489 (3)<strong>a</strong>* + 0.2517 (3)<strong>b</strong>* + 0.3646 (3)<strong>c</strong>*. The α<sub>2</sub> modification undergoes two phase transitions towards periodic structures. On heating, a triclinic structure described in <em>C</em>1 with very similar lattice parameters is realized above 85°C for the corresponding α<sub>3</sub> modification. It can be considered as the non-modulated basic structure of the α<sub>2</sub> modification. At about 185°C, α<sub>3</sub>-Fe<sub>2</sub>P<sub>2</sub>O<sub>7</sub> transforms to the thortveitite-type β modification, which remains stable up to at least 1000°C. On cooling the α<sub>2</sub> modification, a triclinic structure of the low-temperature α<sub>1</sub> modification forms below −140°C, which can be considered as a twofold superstructure of the α<sub>3</sub> modification with <strong>q</strong> = ½<strong>a</strong>* + ½<strong>b</strong>* + ½<strong>c</strong>*. The result of these phase transitions from the thortveitite-type β-modification via the triclinic α<sub>3</sub> phase and the incommensurately modulated triclinic α<sub>2</sub> modification to α<sub>1</sub>-Fe<sub>2</sub>P<sub>2</sub>O<sub>7</sub> is the complete ordering of the pyrophosphate anion in the low-temperature phase with a P—O—P bridging angle of 151.91 (8)°. This ordering is accompanied by the lowering of the coordination number of one half of the Fe<sup>2+</sup> ions from 6 to 5.</div></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"12 6","pages":"Pages 670-682"},"PeriodicalIF":3.6,"publicationDate":"2025-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145251084","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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 : 2025-11-01DOI: 10.1107/S2052252525008917
Yu-Sheng Chen
High-energy synchrotron X-ray diffraction reveals the bonding topology and charge distribution in Nd2Fe14B, clarifying the atomic-scale origins of its exceptional magnetic performance. The study by Vosegaard et al. [(2025). IUCrJ12, 658–669] provides the first detailed charge density analysis of a heavy-rare-earth magnet, guiding future magnet design.
{"title":"Decoding the bonding in Nd2Fe14B: a synchrotron charge density perspective on a rare-earth magnet","authors":"Yu-Sheng Chen","doi":"10.1107/S2052252525008917","DOIUrl":"10.1107/S2052252525008917","url":null,"abstract":"<div><div>High-energy synchrotron X-ray diffraction reveals the bonding topology and charge distribution in Nd<sub>2</sub>Fe<sub>14</sub>B, clarifying the atomic-scale origins of its exceptional magnetic performance. The study by Vosegaard <em>et al.</em> [<span>(2025). IUCrJ12, 658–669</span>] provides the first detailed charge density analysis of a heavy-rare-earth magnet, guiding future magnet design.</div></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"12 6","pages":"Pages 633-634"},"PeriodicalIF":3.6,"publicationDate":"2025-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145372870","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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 : 2025-11-01DOI: 10.1107/S2052252525007602
Emilie Skytte Vosegaard , Jacob Svane , Bo Brummerstedt Iversen
Short-wavelength high-resolution synchrotron single-crystal X-ray diffraction data measured at 25 K are used to model the electron density of the super-strong magnet Nd2Fe14B and quantify its complex chemical interactions.
Chemical bonding determines the intrinsic properties of materials, but despite the super-strong metallic magnet Nd2Fe14B being a vital compound in modern life, the local chemical environment is not well understood. Nd2Fe14B has a very complex crystal structure with six independent Fe sites, two independent Nd sites and one B site, which in concert are responsible for the extremely high magnetic moment. Dense inorganic materials with excellent crystal quality and heavy atoms represent a strong challenge to X-ray charge density analysis, and indeed Nd2Fe14B has a mere suitability factor of 0.02 compared with 3–5 for typical organic molecular crystals. Here, we report high-energy (λ = 0.2482 Å) 25 K single-crystal synchrotron X-ray diffraction data suitable for multipole modelling of the X-ray charge density. The X-ray electron density shows local anisotropy in the bonding environment of the Fe atoms, and topological analysis quantifies that the Nd atoms are positive (∼+1), one Fe atom and B are negative (−1.7 and −0.44, respectively), and the remaining Fe atoms are close to neutral (±0.1). The d orbitals of all Fe atoms are close to being evenly populated, and bonding analysis establishes a multidirectional ‘metal-like’ framework. It is found that a single Fe atom is crucial for the 3D framework of the magnetic structure. Through structural refinement of synchrotron single-crystal X-ray diffraction data at 25 K, 100 K, 200 K and 300 K, anisotropic displacement parameters are obtained, and the Debye temperature is estimated to be 345–383 K.
{"title":"X-ray electron density analysis of chemical bonding in permanent magnet Nd2Fe14B","authors":"Emilie Skytte Vosegaard , Jacob Svane , Bo Brummerstedt Iversen","doi":"10.1107/S2052252525007602","DOIUrl":"10.1107/S2052252525007602","url":null,"abstract":"<div><div>Short-wavelength high-resolution synchrotron single-crystal X-ray diffraction data measured at 25 K are used to model the electron density of the super-strong magnet Nd<sub>2</sub>Fe<sub>14</sub>B and quantify its complex chemical interactions.</div></div><div><div>Chemical bonding determines the intrinsic properties of materials, but despite the super-strong metallic magnet Nd<sub>2</sub>Fe<sub>14</sub>B being a vital compound in modern life, the local chemical environment is not well understood. Nd<sub>2</sub>Fe<sub>14</sub>B has a very complex crystal structure with six independent Fe sites, two independent Nd sites and one B site, which in concert are responsible for the extremely high magnetic moment. Dense inorganic materials with excellent crystal quality and heavy atoms represent a strong challenge to X-ray charge density analysis, and indeed Nd<sub>2</sub>Fe<sub>14</sub>B has a mere suitability factor of 0.02 compared with 3–5 for typical organic molecular crystals. Here, we report high-energy (λ = 0.2482 Å) 25 K single-crystal synchrotron X-ray diffraction data suitable for multipole modelling of the X-ray charge density. The X-ray electron density shows local anisotropy in the bonding environment of the Fe atoms, and topological analysis quantifies that the Nd atoms are positive (∼+1), one Fe atom and B are negative (−1.7 and −0.44, respectively), and the remaining Fe atoms are close to neutral (±0.1). The <em>d</em> orbitals of all Fe atoms are close to being evenly populated, and bonding analysis establishes a multidirectional ‘metal-like’ framework. It is found that a single Fe atom is crucial for the 3D framework of the magnetic structure. Through structural refinement of synchrotron single-crystal X-ray diffraction data at 25 K, 100 K, 200 K and 300 K, anisotropic displacement parameters are obtained, and the Debye temperature is estimated to be 345–383 K.</div></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"12 6","pages":"Pages 658-669"},"PeriodicalIF":3.6,"publicationDate":"2025-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145185966","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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 : 2025-09-01DOI: 10.1107/S2052252525006141
Y. Ishii
Quasicrystals are long-range-ordered materials with rotational symmetry incompatible with periodicity. Takakura et al. [(2025). IUCrJ12, 435–443] present a study of a single grain of icosahedrite, the first natural icosahedral quasicrystal, which was found in a meteorite in 2009. Through detailed analysis of the diffraction peaks, they conclude that natural AlCuFe is an icosahedral quasicrystal superimposed by a phasonic modulation along the fivefold directions, which is similar to that observed in the synthetic quasicrystal. Based on knowledge of the synthesis and phase stability of icosahedral AlCuFe, they discuss the formation of icosahedrite in the meteorite.
{"title":"First high-resolution synchrotron X-ray study of icosahedrite, a natural quasicrystal from the Khatyrka meteorite","authors":"Y. Ishii","doi":"10.1107/S2052252525006141","DOIUrl":"10.1107/S2052252525006141","url":null,"abstract":"<div><div>Quasicrystals are long-range-ordered materials with rotational symmetry incompatible with periodicity. Takakura <em>et al.</em> [(2025). <em>IUCrJ</em><strong>12</strong>, 435–443] present a study of a single grain of icosahedrite, the first natural icosahedral quasicrystal, which was found in a meteorite in 2009. Through detailed analysis of the diffraction peaks, they conclude that natural AlCuFe is an icosahedral quasicrystal superimposed by a phasonic modulation along the fivefold directions, which is similar to that observed in the synthetic quasicrystal. Based on knowledge of the synthesis and phase stability of icosahedral AlCuFe, they discuss the formation of icosahedrite in the meteorite.</div></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"12 5","pages":"Pages 511-512"},"PeriodicalIF":3.6,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144690289","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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 : 2025-09-01DOI: 10.1107/S2052252525005810
Yalan Wei , Shifang Li , Xizhi Shi , Chaoyu He
This study identifies carbon crystal structures as 4-degree quotient graphs and proposes a novel approach for generating 3D 4-coordinate networks using 2D (2+1)-regular bipartite-like graphs. Through a random group and graph theory (RG2) method, we discover 509 new structures, including two low-energy phases (Pbam48 and Pbam40) that exhibit exceptional stability and potential applications as superhard carbon and quasi-direct band gap silicon materials in mechanical processing and solar photovoltaic technologies.
Post-graphite in cold-compression [Mao et al. (2003). Science302, 425–427] has attracted widespread research interest in condensed matter physics. Subsequently, many low-energy carbon phases, such as M-carbon, W-carbon and Z-carbon, have been proposed as structural candidates. Based on graph theory, we found that these 4-coordinated post-graphite candidates can not only be decomposed into 3-regular graphitic graphs but also yield (2+1)-regular graphs in a non-graphitic manner from different decomposition directions. This inspires a general idea of generating 3D 4-coordinate networks based on 2D (2+1)-regular bipartite-like graphs, which can be efficiently generated by a random method combined with group and graph theory (RG2). Associated with such a general graph-based method, a large number of 4-coordinate networks have been discovered and investigated by first-principles calculations as potential carbon/silicon phases. Most are confirmed as low-energy carbon/silicon phases and identified as direct or quasi-direct band gap semiconductors. Two complex configurations, Pbam48 and Pbam40, show energetic stabilities exceeding or comparable to the previously proposed Pbam24. They are further confirmed to be dynamically and mechanically stable phases as carbon/silicon. As carbon phases, Pbam48 and Pbam40 are superhard insulators with quasi-direct band gaps of 5.622 and 5.890 eV, and hardness values of 85.352 and 85.558 GPa, respectively. Their X-ray diffraction (XRD) results can largely explain the experimental XRD patterns of cold-compressed graphite. As silicon allotropes, Pbam48 and Pbam40 have quasi-direct band gaps of 1.386 and 1.451 eV, respectively, making them potential solar cell absorber materials.
后石墨冷压缩[Mao et al.(2003)]。[科学]302,425-427]在凝聚态物理领域引起了广泛的研究兴趣。随后，许多低能碳相，如m -碳、w-碳和z -碳，被提出作为候选结构。基于图论，我们发现这4个配位后石墨候选物不仅可以分解为3个正则图，而且可以从不同的分解方向以非石墨的方式生成（2+1）个正则图。这激发了基于2D（2+1）正则双分图生成三维四坐标网络的一般思想，该网络可以通过结合群图理论（RG2）的随机方法有效地生成。与这种通用的基于图的方法相关联，通过第一性原理计算已经发现并研究了大量的4坐标网络作为潜在的碳/硅相。大多数被确认为低能量碳/硅相，并被确定为直接或准直接带隙半导体。两个复杂的结构，Pbam48和Pbam40，显示出能量稳定性超过或与先前提出的Pbam24相当。进一步证实了它们是与碳/硅一样动态和机械稳定的相。作为碳相，Pbam48和Pbam40为超硬绝缘子，准直接带隙分别为5.622和5.890 eV，硬度分别为85.352和85.558 GPa。它们的x射线衍射（XRD）结果在很大程度上解释了冷压缩石墨的实验XRD图谱。作为硅同素异素体，Pbam48和Pbam40的准直接带隙分别为1.386和1.451 eV，是潜在的太阳能电池吸收材料。
{"title":"Low-energy tetrahedral networks for carbon and silicon from (2+1)-regular bipartite-like graphs","authors":"Yalan Wei , Shifang Li , Xizhi Shi , Chaoyu He","doi":"10.1107/S2052252525005810","DOIUrl":"10.1107/S2052252525005810","url":null,"abstract":"<div><div>This study identifies carbon crystal structures as 4-degree quotient graphs and proposes a novel approach for generating 3D 4-coordinate networks using 2D (2+1)-regular bipartite-like graphs. Through a random group and graph theory (RG2) method, we discover 509 new structures, including two low-energy phases (<em>Pbam</em>48 and <em>Pbam</em>40) that exhibit exceptional stability and potential applications as superhard carbon and quasi-direct band gap silicon materials in mechanical processing and solar photovoltaic technologies.</div></div><div><div>Post-graphite in cold-compression [Mao <em>et al.</em> (2003). <em>Science</em><strong>302</strong>, 425–427] has attracted widespread research interest in condensed matter physics. Subsequently, many low-energy carbon phases, such as M-carbon, W-carbon and Z-carbon, have been proposed as structural candidates. Based on graph theory, we found that these 4-coordinated post-graphite candidates can not only be decomposed into 3-regular graphitic graphs but also yield (2+1)-regular graphs in a non-graphitic manner from different decomposition directions. This inspires a general idea of generating 3D 4-coordinate networks based on 2D (2+1)-regular bipartite-like graphs, which can be efficiently generated by a random method combined with group and graph theory (RG2). Associated with such a general graph-based method, a large number of 4-coordinate networks have been discovered and investigated by first-principles calculations as potential carbon/silicon phases. Most are confirmed as low-energy carbon/silicon phases and identified as direct or quasi-direct band gap semiconductors. Two complex configurations, <em>Pbam</em>48 and <em>Pbam</em>40, show energetic stabilities exceeding or comparable to the previously proposed <em>Pbam</em>24. They are further confirmed to be dynamically and mechanically stable phases as carbon/silicon. As carbon phases, <em>Pbam</em>48 and <em>Pbam</em>40 are superhard insulators with quasi-direct band gaps of 5.622 and 5.890 eV, and hardness values of 85.352 and 85.558 GPa, respectively. Their X-ray diffraction (XRD) results can largely explain the experimental XRD patterns of cold-compressed graphite. As silicon allotropes, <em>Pbam</em>48 and <em>Pbam</em>40 have quasi-direct band gaps of 1.386 and 1.451 eV, respectively, making them potential solar cell absorber materials.</div></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"12 5","pages":"Pages 523-530"},"PeriodicalIF":3.6,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144731049","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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 : 2025-09-01DOI: 10.1107/S2052252525006062
Tomoki Imura , Yuhei Hosokawa , Kai-Chun Yang , Yuki Ban , Hsuan-Yu Shih , Junpei Yamamoto , Manuel Maestre-Reyna
Engineered in crystallo photosensitivity in a DNA-repair enzyme is carefully assessed for its suitability as a target for time-resolved crystallographic studies.
Co-crystal structures of a base-excision DNA-repair enzyme (human 8-oxoguanine DNA glycosylase; hOgg1) in complex with a photocaged 8-oxoguanine DNA lesion were determined before and after uncaging via illumination at 2.81 and 2.48 Å resolution, respectively. The structures were carefully reassessed to rapidly expand the target repertoire of light-triggered time-resolved macromolecular crystallography. Late-intermediate cryo-trapping after uncaging revealed the partial accommodation of 8-oxoguanine in the active site with 68% occupancy, which did not induce full active-site adaptation to the catalytic state. Crystal illumination led to a light-dependent loss of diffraction power, likely due to crystal-packing collapse during the very late reaction stages. This work therefore not only demonstrates that hOgg1 is well suited for time-resolved crystallography, but also that such analysis is necessary to determine further steps in its reaction.
{"title":"Revisiting the co-crystal structure of a DNA glycosylase with photocaged substrate: a suitable time-resolved crystallography target?","authors":"Tomoki Imura , Yuhei Hosokawa , Kai-Chun Yang , Yuki Ban , Hsuan-Yu Shih , Junpei Yamamoto , Manuel Maestre-Reyna","doi":"10.1107/S2052252525006062","DOIUrl":"10.1107/S2052252525006062","url":null,"abstract":"<div><div>Engineered <em>in crystallo</em> photosensitivity in a DNA-repair enzyme is carefully assessed for its suitability as a target for time-resolved crystallographic studies.</div></div><div><div>Co-crystal structures of a base-excision DNA-repair enzyme (human 8-oxoguanine DNA glycosylase; hOgg1) in complex with a photocaged 8-oxoguanine DNA lesion were determined before and after uncaging via illumination at 2.81 and 2.48 Å resolution, respectively. The structures were carefully reassessed to rapidly expand the target repertoire of light-triggered time-resolved macromolecular crystallography. Late-intermediate cryo-trapping after uncaging revealed the partial accommodation of 8-oxoguanine in the active site with 68% occupancy, which did not induce full active-site adaptation to the catalytic state. Crystal illumination led to a light-dependent loss of diffraction power, likely due to crystal-packing collapse during the very late reaction stages. This work therefore not only demonstrates that hOgg1 is well suited for time-resolved crystallography, but also that such analysis is necessary to determine further steps in its reaction.</div></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"12 5","pages":"Pages 515-522"},"PeriodicalIF":3.6,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144626391","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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 : 2025-09-01DOI: 10.1107/S2052252525005573
Jack Stephens , Ramesh Rijal , Daniel Sier , Nicholas T. T. Tran , Jonathan W. Dean , Paul Di Pasquale , Tony Kirk , Minh Dao , Chanh Q. Tran , Shusaku Hayama , Sofia Diaz-Moreno , Christopher T. Chantler
A new satellite is discovered in the manganese Kβ spectrum using extended-range high-energy-resolution fluorescence detection. Advanced insights on its structure and evolution are extracted with principal component analysis.
The discovery of the novel n = 2 satellite transition in the Kβ emission spectrum of manganese and its evolution with incident photon energy are presented. Using the XR-HERFD (extended-range high-energy-resolution fluorescence detection) technique, we conclusively demonstrate the existence of this phenomenon with a statistical significance corresponding to 652 σse across the measured spectrum, far above the discovery threshold of 3–6 σse. We apply principal component analysis (PCA) to the XR-HERFD data to extract advanced structural insights. The evolution of this novel spectral feature and physical process are quantified by incorporating regression, revealing the increase in intensity over a wide range of incident photon energies. We validate these findings through independent test data. These results directly challenge the conventional treatment of the many-body reduction factor S02 as a constant independent of incident photon energy in the standard XAFS (X-ray absorption fine structure) equation. Thereby, these results present compelling evidence that S02 should be modelled as a varying function of incident photon energy, marking the first observation of this behaviour in Kβ spectra. This facilitates a greater quantitative understanding of HERFD spectra and a comprehensive representation of many-body effects in condensed matter systems.
{"title":"Discovery of an energy-dependent many-body process in the Kβ spectrum of manganese metal using extended-range high-energy-resolution fluorescence detection with advanced structural insights from principal component analysis","authors":"Jack Stephens , Ramesh Rijal , Daniel Sier , Nicholas T. T. Tran , Jonathan W. Dean , Paul Di Pasquale , Tony Kirk , Minh Dao , Chanh Q. Tran , Shusaku Hayama , Sofia Diaz-Moreno , Christopher T. Chantler","doi":"10.1107/S2052252525005573","DOIUrl":"10.1107/S2052252525005573","url":null,"abstract":"<div><div>A new satellite is discovered in the manganese <em>K</em>β spectrum using extended-range high-energy-resolution fluorescence detection. Advanced insights on its structure and evolution are extracted with principal component analysis.</div></div><div><div>The discovery of the novel <em>n</em> = 2 satellite transition in the <em>K</em>β emission spectrum of manganese and its evolution with incident photon energy are presented. Using the XR-HERFD (extended-range high-energy-resolution fluorescence detection) technique, we conclusively demonstrate the existence of this phenomenon with a statistical significance corresponding to 652 σ<sub>se</sub> across the measured spectrum, far above the discovery threshold of 3–6 σ<sub>se</sub>. We apply principal component analysis (PCA) to the XR-HERFD data to extract advanced structural insights. The evolution of this novel spectral feature and physical process are quantified by incorporating regression, revealing the increase in intensity over a wide range of incident photon energies. We validate these findings through independent test data. These results directly challenge the conventional treatment of the many-body reduction factor <em>S</em><sub>0</sub><sup>2</sup> as a constant independent of incident photon energy in the standard XAFS (X-ray absorption fine structure) equation. Thereby, these results present compelling evidence that <em>S</em><sub>0</sub><sup>2</sup> should be modelled as a varying function of incident photon energy, marking the first observation of this behaviour in <em>K</em>β spectra. This facilitates a greater quantitative understanding of HERFD spectra and a comprehensive representation of many-body effects in condensed matter systems.</div></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"12 5","pages":"Pages 548-562"},"PeriodicalIF":3.6,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144954895","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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