Pub Date : 2024-09-01DOI: 10.1107/S2052252524007681
Róża Jastrzębska , Tomasz Poręba , Federico Cova , Daniel M. Tchoń , Anna Makal
A pressure-induced triclinic-to-monoclinic phase transition has been caught ‘in the act’ in the course of a wider series of high-pressure synchrotron diffraction experiments conducted on a moderately photoluminescent gold(I) compound. Our experiments illustrate how conducting a fast series of experiments, enabled by modern equipment at synchrotrons, can lead to an inaccurate estimation of the actual pressure of a phase transformation.
A pressure-induced triclinic-to-monoclinic phase transition has been caught ‘in the act’ over a wider series of high-pressure synchrotron diffraction experiments conducted on a large, photoluminescent organo-gold(I) compound. Here, we describe the mechanism of this single-crystal-to-single-crystal phase transition, the onset of which occurs at ∼0.6 GPa, and we report a high-quality structure of the new monoclinic phase, refined using aspherical atomic scattering factors. Our case illustrates how conducting a fast series of diffraction experiments, enabled by modern equipment at synchrotron facilities, can lead to overestimation of the actual pressure of a phase transition due to slow transformation kinetics.
{"title":"Structure–property relationship of a complex photoluminescent arylacetylide-gold(I) compound. I: a pressure-induced phase transformation caught in the act","authors":"Róża Jastrzębska , Tomasz Poręba , Federico Cova , Daniel M. Tchoń , Anna Makal","doi":"10.1107/S2052252524007681","DOIUrl":"10.1107/S2052252524007681","url":null,"abstract":"<div><p>A pressure-induced triclinic-to-monoclinic phase transition has been caught ‘in the act’ in the course of a wider series of high-pressure synchrotron diffraction experiments conducted on a moderately photoluminescent gold(I) compound. Our experiments illustrate how conducting a fast series of experiments, enabled by modern equipment at synchrotrons, can lead to an inaccurate estimation of the actual pressure of a phase transformation.</p></div><div><p>A pressure-induced triclinic-to-monoclinic phase transition has been caught ‘in the act’ over a wider series of high-pressure synchrotron diffraction experiments conducted on a large, photoluminescent organo-gold(I) compound. Here, we describe the mechanism of this single-crystal-to-single-crystal phase transition, the onset of which occurs at ∼0.6 GPa, and we report a high-quality structure of the new monoclinic phase, refined using aspherical atomic scattering factors. Our case illustrates how conducting a fast series of diffraction experiments, enabled by modern equipment at synchrotron facilities, can lead to overestimation of the actual pressure of a phase transition due to slow transformation kinetics.</p></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"11 5","pages":"Pages 737-743"},"PeriodicalIF":2.9,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11364033/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142043945","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-01DOI: 10.1107/S2052252524008157
Nikolaos I. Prasianakis
The use of convolutional neural networks can revolutionize XRD analysis by significantly reducing processing times. Demonstration against synthetic and real mineral mixture data provide a first assessment of the accuracy of such methods.
{"title":"AI-enhanced X-ray diffraction analysis: towards real-time mineral phase identification and quantification","authors":"Nikolaos I. Prasianakis","doi":"10.1107/S2052252524008157","DOIUrl":"10.1107/S2052252524008157","url":null,"abstract":"<div><p>The use of convolutional neural networks can revolutionize XRD analysis by significantly reducing processing times. Demonstration against synthetic and real mineral mixture data provide a first assessment of the accuracy of such methods.</p></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"11 5","pages":"Pages 647-648"},"PeriodicalIF":2.9,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11364041/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142107580","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-01DOI: 10.1107/S2052252524006298
Fan Zhang , Jan Ilavsky
This review examines the use of ultra-small angle X-ray scattering (USAXS), a nondestructive technique for analyzing the multi-scale microstructures of hard materials such as ceramics, metals and composites. It discusses the principles, benefits and challenges of USAXS, along with its potential to advance materials development and optimize manufacturing processes, while also considering future enhancements through multimodal characterization and machine learning.
Owing to their exceptional properties, hard materials such as advanced ceramics, metals and composites have enormous economic and societal value, with applications across numerous industries. Understanding their microstructural characteristics is crucial for enhancing their performance, materials development and unleashing their potential for future innovative applications. However, their microstructures are unambiguously hierarchical and typically span several length scales, from sub-ångstrom to micrometres, posing demanding challenges for their characterization, especially for in situ characterization which is critical to understanding the kinetic processes controlling microstructure formation. This review provides a comprehensive description of the rapidly developing technique of ultra-small angle X-ray scattering (USAXS), a nondestructive method for probing the nano-to-micrometre scale features of hard materials. USAXS and its complementary techniques, when developed for and applied to hard materials, offer valuable insights into their porosity, grain size, phase composition and inhomogeneities. We discuss the fundamental principles, instrumentation, advantages, challenges and global status of USAXS for hard materials. Using selected examples, we demonstrate the potential of this technique for unveiling the microstructural characteristics of hard materials and its relevance to advanced materials development and manufacturing process optimization. We also provide our perspective on the opportunities and challenges for the continued development of USAXS, including multimodal characterization, coherent scattering, time-resolved studies, machine learning and autonomous experiments. Our goal is to stimulate further implementation and exploration of USAXS techniques and inspire their broader adoption across various domains of hard materials science, thereby driving the field toward discoveries and further developments.
先进陶瓷、金属和复合材料等硬质材料因其卓越的性能而具有巨大的经济和社会价值,可应用于众多行业。了解它们的微观结构特征对于提高性能、材料开发和释放未来创新应用的潜力至关重要。然而,它们的微观结构具有明确的层次性,通常跨越多个长度尺度,从亚恩斯特到微米不等,这给它们的表征带来了严峻的挑战,尤其是原位表征,这对于了解控制微观结构形成的动力学过程至关重要。本综述全面介绍了快速发展的超小角度 X 射线散射(USAXS)技术,这是一种探测硬质材料纳米到微米尺度特征的无损方法。USAXS 及其补充技术专为硬质材料开发并应用于硬质材料,为深入了解其孔隙率、晶粒尺寸、相组成和不均匀性提供了宝贵的资料。我们将讨论用于硬质材料的 USAXS 的基本原理、仪器、优势、挑战和全球现状。我们通过选定的示例,展示了该技术在揭示硬质材料微观结构特征方面的潜力及其与先进材料开发和制造工艺优化的相关性。我们还从多模态表征、相干散射、时间分辨研究、机器学习和自主实验等角度阐述了继续发展 USAXS 所面临的机遇和挑战。我们的目标是激励进一步实施和探索 USAXS 技术,并鼓励在硬材料科学的各个领域更广泛地采用这些技术,从而推动该领域的发现和进一步发展。
{"title":"Bridging length scales in hard materials with ultra-small angle X-ray scattering – a critical review","authors":"Fan Zhang , Jan Ilavsky","doi":"10.1107/S2052252524006298","DOIUrl":"10.1107/S2052252524006298","url":null,"abstract":"<div><p>This review examines the use of ultra-small angle X-ray scattering (USAXS), a nondestructive technique for analyzing the multi-scale microstructures of hard materials such as ceramics, metals and composites. It discusses the principles, benefits and challenges of USAXS, along with its potential to advance materials development and optimize manufacturing processes, while also considering future enhancements through multimodal characterization and machine learning.</p></div><div><p>Owing to their exceptional properties, hard materials such as advanced ceramics, metals and composites have enormous economic and societal value, with applications across numerous industries. Understanding their microstructural characteristics is crucial for enhancing their performance, materials development and unleashing their potential for future innovative applications. However, their microstructures are unambiguously hierarchical and typically span several length scales, from sub-ångstrom to micrometres, posing demanding challenges for their characterization, especially for <em>in situ</em> characterization which is critical to understanding the kinetic processes controlling microstructure formation. This review provides a comprehensive description of the rapidly developing technique of ultra-small angle X-ray scattering (USAXS), a nondestructive method for probing the nano-to-micrometre scale features of hard materials. USAXS and its complementary techniques, when developed for and applied to hard materials, offer valuable insights into their porosity, grain size, phase composition and inhomogeneities. We discuss the fundamental principles, instrumentation, advantages, challenges and global status of USAXS for hard materials. Using selected examples, we demonstrate the potential of this technique for unveiling the microstructural characteristics of hard materials and its relevance to advanced materials development and manufacturing process optimization. We also provide our perspective on the opportunities and challenges for the continued development of USAXS, including multimodal characterization, coherent scattering, time-resolved studies, machine learning and autonomous experiments. Our goal is to stimulate further implementation and exploration of USAXS techniques and inspire their broader adoption across various domains of hard materials science, thereby driving the field toward discoveries and further developments.</p></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"11 5","pages":"Pages 675-694"},"PeriodicalIF":2.9,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11364042/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141859755","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-01DOI: 10.1107/S2052252524006766
Titouan Simonnet , Sylvain Grangeon , Francis Claret , Nicolas Maubec , Mame Diarra Fall , Rachid Harba , Bruno Galerne
A deep neural network approach to the identification and quantification of powder X-ray diffraction patterns was applied and proved successful for the quantitative description of complex mineralogical assemblages consisting of up to four minerals with different structures, including different space groups, for which data augmentation is not straightforward.
Mineral identification and quantification are key to the understanding and, hence, the capacity to predict material properties. The method of choice for mineral quantification is powder X-ray diffraction (XRD), generally using a Rietveld refinement approach. However, a successful Rietveld refinement requires preliminary identification of the phases that make up the sample. This is generally carried out manually, and this task becomes extremely long or virtually impossible in the case of very large datasets such as those from synchrotron X-ray diffraction computed tomography. To circumvent this issue, this article proposes a novel neural network (NN) method for automating phase identification and quantification. An XRD pattern calculation code was used to generate large datasets of synthetic data that are used to train the NN. This approach offers significant advantages, including the ability to construct databases with a substantial number of XRD patterns and the introduction of extensive variability into these patterns. To enhance the performance of the NN, a specifically designed loss function for proportion inference was employed during the training process, offering improved efficiency and stability compared with traditional functions. The NN, trained exclusively with synthetic data, proved its ability to identify and quantify mineral phases on synthetic and real XRD patterns. Trained NN errors were equal to 0.5% for phase quantification on the synthetic test set, and 6% on the experimental data, in a system containing four phases of contrasting crystal structures (calcite, gibbsite, dolomite and hematite). The proposed method is freely available on GitHub and allows for major advances since it can be applied to any dataset, regardless of the mineral phases present.
矿物鉴定和定量是了解材料特性的关键,因此也是预测材料特性的关键。矿物定量的首选方法是粉末 X 射线衍射 (XRD),一般采用里特维尔德细化方法。不过,要成功进行里特维尔德细化,需要对构成样品的各相进行初步鉴定。这通常需要人工完成,而在同步辐射 X 射线衍射计算机断层扫描等超大数据集的情况下,这项工作会变得非常漫长,甚至几乎不可能完成。为了规避这一问题,本文提出了一种新颖的神经网络 (NN) 方法,用于自动识别和量化相位。利用 XRD 图案计算代码生成大量合成数据集,用于训练神经网络。这种方法具有显著的优势,包括能够构建具有大量 XRD 图案的数据库,并能在这些图案中引入广泛的可变性。为了提高 NN 的性能,在训练过程中采用了专门设计的比例推理损失函数,与传统函数相比,该函数具有更高的效率和稳定性。完全使用合成数据训练的 NN 证明了其在合成和真实 XRD 图样上识别和量化矿物相的能力。在一个包含四种晶体结构截然不同的矿物相(方解石、吉比特石、白云石和赤铁矿)的系统中,经过训练的 NN 在合成测试集上的矿物相量化误差为 0.5%,在实验数据上的误差为 6%。所提出的方法可在 GitHub 上免费获取,并可应用于任何数据集,无论存在何种矿物相,因此具有重大的进步意义。
{"title":"Phase quantification using deep neural network processing of XRD patterns","authors":"Titouan Simonnet , Sylvain Grangeon , Francis Claret , Nicolas Maubec , Mame Diarra Fall , Rachid Harba , Bruno Galerne","doi":"10.1107/S2052252524006766","DOIUrl":"10.1107/S2052252524006766","url":null,"abstract":"<div><p>A deep neural network approach to the identification and quantification of powder X-ray diffraction patterns was applied and proved successful for the quantitative description of complex mineralogical assemblages consisting of up to four minerals with different structures, including different space groups, for which data augmentation is not straightforward.</p></div><div><p>Mineral identification and quantification are key to the understanding and, hence, the capacity to predict material properties. The method of choice for mineral quantification is powder X-ray diffraction (XRD), generally using a Rietveld refinement approach. However, a successful Rietveld refinement requires preliminary identification of the phases that make up the sample. This is generally carried out manually, and this task becomes extremely long or virtually impossible in the case of very large datasets such as those from synchrotron X-ray diffraction computed tomography. To circumvent this issue, this article proposes a novel neural network (NN) method for automating phase identification and quantification. An XRD pattern calculation code was used to generate large datasets of synthetic data that are used to train the NN. This approach offers significant advantages, including the ability to construct databases with a substantial number of XRD patterns and the introduction of extensive variability into these patterns. To enhance the performance of the NN, a specifically designed loss function for proportion inference was employed during the training process, offering improved efficiency and stability compared with traditional functions. The NN, trained exclusively with synthetic data, proved its ability to identify and quantify mineral phases on synthetic and real XRD patterns. Trained NN errors were equal to 0.5% for phase quantification on the synthetic test set, and 6% on the experimental data, in a system containing four phases of contrasting crystal structures (calcite, gibbsite, dolomite and hematite). The proposed method is freely available on GitHub and allows for major advances since it can be applied to any dataset, regardless of the mineral phases present.</p></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"11 5","pages":"Pages 859-870"},"PeriodicalIF":2.9,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11364039/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141916724","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-01DOI: 10.1107/S2052252524006730
Laura Pacoste , Vladislav Mikhailovich Ignat’ev , Paulina Maria Dominiak , Xiaodong Zou
<div><p>We apply for the first time the transferable aspherical atom model (TAAM) for the refinement of a metal complex structure against 3D ED data. Our results show that TAAM significantly outperforms the independent atom model (IAM) by more accurately depicting the electrostatic potential, particularly in low-resolution ranges. We found that using TAAM for organic ligands is more important than an accurate description of the metal centre in the refinement against 3D ED data.</p></div><div><p>This study examines various methods for modelling the electron density and, thus, the electrostatic potential of an organometallic complex for use in crystal structure refinement against 3D electron diffraction (ED) data. It focuses on modelling the scattering factors of iron(III), considering the electron density distribution specific for coordination with organic linkers. We refined the structural model of the metal–organic complex, iron(III) acetylacetonate (FeAcAc), using both the independent atom model (IAM) and the transferable aspherical atom model (TAAM). TAAM refinement initially employed multipolar parameters from the MATTS databank for acetylacetonate, while iron was modelled with a spherical and neutral approach (TAAM ligand). Later, custom-made TAAM scattering factors for Fe—O coordination were derived from DFT calculations [TAAM-ligand-Fe(III)]. Our findings show that, in this compound, the TAAM scattering factor corresponding to Fe<sup>3+</sup> has a lower scattering amplitude than the Fe<sup>3+</sup> charged scattering factor described by IAM. When using scattering factors corresponding to the oxidation state of iron, IAM inaccurately represents electrostatic potential maps and overestimates the scattering potential of the iron. In addition, TAAM significantly improved the fitting of the model to the data, shown by improved <em>R</em><sub>1</sub> values, goodness-of-fit (GooF) and reduced noise in the Fourier difference map (based on the residual distribution analysis). For 3D ED, <em>R</em><sub>1</sub> values improved from 19.36% (IAM) to 17.44% (TAAM-ligand) and 17.49% (TAAM-ligand-Fe<sup>3+</sup>), and for single-crystal X-ray diffraction (SCXRD) from 3.82 to 2.03% and 1.98%, respectively. For 3D ED, the most significant <em>R</em><sub>1</sub> reductions occurred in the low-resolution region (8.65–2.00 Å), dropping from 20.19% (IAM) to 14.67% and 14.89% for TAAM-ligand and TAAM-ligand-Fe(III), respectively, with less improvement in high-resolution ranges (2.00–0.85 Å). This indicates that the major enhancements are due to better scattering modelling in low-resolution zones. Furthermore, when using TAAM instead of IAM, there was a noticeable improvement in the shape of the thermal ellipsoids, which more closely resembled those of an SCXRD-refined model. This study demonstrates the applicability of more sophisticated scattering factors to improve the refinement of metal–organic complexes against 3D ED data, suggesting the need for more a
{"title":"On the structure refinement of metal complexes against 3D electron diffraction data using multipolar scattering factors","authors":"Laura Pacoste , Vladislav Mikhailovich Ignat’ev , Paulina Maria Dominiak , Xiaodong Zou","doi":"10.1107/S2052252524006730","DOIUrl":"10.1107/S2052252524006730","url":null,"abstract":"<div><p>We apply for the first time the transferable aspherical atom model (TAAM) for the refinement of a metal complex structure against 3D ED data. Our results show that TAAM significantly outperforms the independent atom model (IAM) by more accurately depicting the electrostatic potential, particularly in low-resolution ranges. We found that using TAAM for organic ligands is more important than an accurate description of the metal centre in the refinement against 3D ED data.</p></div><div><p>This study examines various methods for modelling the electron density and, thus, the electrostatic potential of an organometallic complex for use in crystal structure refinement against 3D electron diffraction (ED) data. It focuses on modelling the scattering factors of iron(III), considering the electron density distribution specific for coordination with organic linkers. We refined the structural model of the metal–organic complex, iron(III) acetylacetonate (FeAcAc), using both the independent atom model (IAM) and the transferable aspherical atom model (TAAM). TAAM refinement initially employed multipolar parameters from the MATTS databank for acetylacetonate, while iron was modelled with a spherical and neutral approach (TAAM ligand). Later, custom-made TAAM scattering factors for Fe—O coordination were derived from DFT calculations [TAAM-ligand-Fe(III)]. Our findings show that, in this compound, the TAAM scattering factor corresponding to Fe<sup>3+</sup> has a lower scattering amplitude than the Fe<sup>3+</sup> charged scattering factor described by IAM. When using scattering factors corresponding to the oxidation state of iron, IAM inaccurately represents electrostatic potential maps and overestimates the scattering potential of the iron. In addition, TAAM significantly improved the fitting of the model to the data, shown by improved <em>R</em><sub>1</sub> values, goodness-of-fit (GooF) and reduced noise in the Fourier difference map (based on the residual distribution analysis). For 3D ED, <em>R</em><sub>1</sub> values improved from 19.36% (IAM) to 17.44% (TAAM-ligand) and 17.49% (TAAM-ligand-Fe<sup>3+</sup>), and for single-crystal X-ray diffraction (SCXRD) from 3.82 to 2.03% and 1.98%, respectively. For 3D ED, the most significant <em>R</em><sub>1</sub> reductions occurred in the low-resolution region (8.65–2.00 Å), dropping from 20.19% (IAM) to 14.67% and 14.89% for TAAM-ligand and TAAM-ligand-Fe(III), respectively, with less improvement in high-resolution ranges (2.00–0.85 Å). This indicates that the major enhancements are due to better scattering modelling in low-resolution zones. Furthermore, when using TAAM instead of IAM, there was a noticeable improvement in the shape of the thermal ellipsoids, which more closely resembled those of an SCXRD-refined model. This study demonstrates the applicability of more sophisticated scattering factors to improve the refinement of metal–organic complexes against 3D ED data, suggesting the need for more a","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"11 5","pages":"Pages 878-890"},"PeriodicalIF":2.9,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11364031/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141987916","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-01DOI: 10.1107/S2052252524005591
Time-resolved serial femtosecond crystallography experiments can be performed with samples delivered on solid supports. Sample consumption is significantly reduced when compared with the popular crystal-delivery system via high-viscosity extrusion.
X-ray free-electron laser (XFEL) light sources have enabled the rapid growth of time-resolved structural experiments, which provide crucial information on the function of macromolecules and their mechanisms. Here, the aim was to commission the SwissMX fixed-target sample-delivery system at the SwissFEL Cristallina experimental station using the PSI-developed micro-structured polymer (MISP) chip for pump–probe time-resolved experiments. To characterize the system, crystals of the light-sensitive protein light–oxygen–voltage domain 1 (LOV1) from Chlamydomonas reinhardtii were used. Using different experimental settings, the accidental illumination, referred to as light contamination, of crystals mounted in wells adjacent to those illuminated by the pump laser was examined. It was crucial to control the light scattering from and through the solid supports otherwise significant contamination occurred. However, the results here show that the opaque MISP chips are suitable for defined pump–probe studies of a light-sensitive protein. The experiment also probed the sub-millisecond structural dynamics of LOV1 and indicated that at Δt = 10 µs a covalent thioether bond is established between reactive Cys57 and its flavin mononucleotide cofactor. This experiment validates the crystals to be suitable for in-depth follow-up studies of this still poorly understood signal-transduction mechanism. Importantly, the fixed-target delivery system also permitted a tenfold reduction in protein sample consumption compared with the more common high-viscosity extrusion-based delivery system. This development creates the prospect of an increase in XFEL project throughput for the field.
{"title":"Fixed-target pump–probe SFX: eliminating the scourge of light contamination","authors":"","doi":"10.1107/S2052252524005591","DOIUrl":"10.1107/S2052252524005591","url":null,"abstract":"<div><p>Time-resolved serial femtosecond crystallography experiments can be performed with samples delivered on solid supports. Sample consumption is significantly reduced when compared with the popular crystal-delivery system via high-viscosity extrusion.</p></div><div><p>X-ray free-electron laser (XFEL) light sources have enabled the rapid growth of time-resolved structural experiments, which provide crucial information on the function of macromolecules and their mechanisms. Here, the aim was to commission the SwissMX fixed-target sample-delivery system at the SwissFEL Cristallina experimental station using the PSI-developed micro-structured polymer (MISP) chip for pump–probe time-resolved experiments. To characterize the system, crystals of the light-sensitive protein light–oxygen–voltage domain 1 (LOV1) from <em>Chlamydomonas reinhardtii</em> were used. Using different experimental settings, the accidental illumination, referred to as light contamination, of crystals mounted in wells adjacent to those illuminated by the pump laser was examined. It was crucial to control the light scattering from and through the solid supports otherwise significant contamination occurred. However, the results here show that the opaque MISP chips are suitable for defined pump–probe studies of a light-sensitive protein. The experiment also probed the sub-millisecond structural dynamics of LOV1 and indicated that at Δ<em>t</em> = 10 µs a covalent thioether bond is established between reactive Cys57 and its flavin mononucleotide cofactor. This experiment validates the crystals to be suitable for in-depth follow-up studies of this still poorly understood signal-transduction mechanism. Importantly, the fixed-target delivery system also permitted a tenfold reduction in protein sample consumption compared with the more common high-viscosity extrusion-based delivery system. This development creates the prospect of an increase in XFEL project throughput for the field.</p></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"11 5","pages":"Pages 749-761"},"PeriodicalIF":2.9,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11364036/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141558790","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-01DOI: 10.1107/S2052252524006808
Michał Leszek Chodkiewicz , Barbara Olech , Kunal Kumar Jha , Paulina Maria Dominiak , Krzysztof Woźniak
Kinematical Hirshfeld atom refinement has been applied to electron diffraction data for the first time, but the effect of using an aspherical atom model is overshadowed by dynamical scattering effects. Dynamical independent atom model refinement leads to significantly improved structures, suggesting that dynamical refinement is also necessary to obtain the full advantage of using aspherical atom models.
Reaching beyond the commonly used spherical atomic electron density model allows one to greatly improve the accuracy of hydrogen atom structural parameters derived from X-ray data. However, the effects of atomic asphericity are less explored for electron diffraction data. In this work, Hirshfeld atom refinement (HAR), a method that uses an accurate description of electron density by quantum mechanical calculation for a system of interest, was applied for the first time to the kinematical refinement of electron diffraction data. This approach was applied here to derive the structure of ordinary hexagonal ice (Ih). The effect of introducing HAR is much less noticeable than in the case of X-ray refinement and it is largely overshadowed by dynamical scattering effects. It led to only a slight change in the O—H bond lengths (shortening by 0.01 Å) compared with the independent atom model (IAM). The average absolute differences in O—H bond lengths between the kinematical refinements and the reference neutron structure were much larger: 0.044 for IAM and 0.046 Å for HAR. The refinement results changed considerably when dynamical scattering effects were modelled – with extinction correction or with dynamical refinement. The latter led to an improvement of the O—H bond length accuracy to 0.021 Å on average (with IAM refinement). Though there is a potential for deriving more accurate structures using HAR for electron diffraction, modelling of dynamical scattering effects seems to be a necessary step to achieve this. However, at present there is no software to support both HAR and dynamical refinement.
超越常用的球形原子电子密度模型,可以大大提高从 X 射线数据中得出的氢原子结构参数的准确性。然而,人们对电子衍射数据中原子非球面性的影响探索较少。在这项工作中,Hirshfeld 原子细化法(HAR)首次被应用于电子衍射数据的运动学细化,该方法通过量子力学计算对相关系统的电子密度进行精确描述。这种方法被用于推导普通六方冰(Ih)的结构。与 X 射线细化相比,引入 HAR 的影响要小得多,它在很大程度上被动态散射效应所掩盖。与独立原子模型(IAM)相比,它只导致 O-H 键长度的轻微变化(缩短了 0.01 Å)。运动学细化结果与参考中子结构之间 O-H 键长度的平均绝对差异要大得多:IAM 为 0.044 Å,HAR 为 0.046 Å。在对动态散射效应进行建模时,细化结果发生了很大变化--采用消光校正或动态细化。后者使 O-H 键长度的平均精度提高到 0.021 Å(采用 IAM 精炼)。虽然使用 HAR 进行电子衍射有可能得出更精确的结构,但动态散射效应建模似乎是实现这一目标的必要步骤。然而,目前还没有同时支持 HAR 和动态细化的软件。
{"title":"Hirshfeld atom refinement and dynamical refinement of hexagonal ice structure from electron diffraction data","authors":"Michał Leszek Chodkiewicz , Barbara Olech , Kunal Kumar Jha , Paulina Maria Dominiak , Krzysztof Woźniak","doi":"10.1107/S2052252524006808","DOIUrl":"10.1107/S2052252524006808","url":null,"abstract":"<div><p>Kinematical Hirshfeld atom refinement has been applied to electron diffraction data for the first time, but the effect of using an aspherical atom model is overshadowed by dynamical scattering effects. Dynamical independent atom model refinement leads to significantly improved structures, suggesting that dynamical refinement is also necessary to obtain the full advantage of using aspherical atom models.</p></div><div><p>Reaching beyond the commonly used spherical atomic electron density model allows one to greatly improve the accuracy of hydrogen atom structural parameters derived from X-ray data. However, the effects of atomic asphericity are less explored for electron diffraction data. In this work, Hirshfeld atom refinement (HAR), a method that uses an accurate description of electron density by quantum mechanical calculation for a system of interest, was applied for the first time to the kinematical refinement of electron diffraction data. This approach was applied here to derive the structure of ordinary hexagonal ice (I<sub>h</sub>). The effect of introducing HAR is much less noticeable than in the case of X-ray refinement and it is largely overshadowed by dynamical scattering effects. It led to only a slight change in the O—H bond lengths (shortening by 0.01 Å) compared with the independent atom model (IAM). The average absolute differences in O—H bond lengths between the kinematical refinements and the reference neutron structure were much larger: 0.044 for IAM and 0.046 Å for HAR. The refinement results changed considerably when dynamical scattering effects were modelled – with extinction correction or with dynamical refinement. The latter led to an improvement of the O—H bond length accuracy to 0.021 Å on average (with IAM refinement). Though there is a potential for deriving more accurate structures using HAR for electron diffraction, modelling of dynamical scattering effects seems to be a necessary step to achieve this. However, at present there is no software to support both HAR and dynamical refinement.</p></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"11 5","pages":"Pages 730-736"},"PeriodicalIF":2.9,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11364029/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141792562","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-01DOI: 10.1107/S2052252524008121
Helen W. Leung , Royston C. B. Copley , Giulio I. Lampronti , Sarah J. Day , Lucy K. Saunders , Duncan N. Johnstone , Paul A. Midgley
3D electron diffraction (3DED) was used to elucidate the structure of a new ninth polymorph of indomethacin from an amorphous solid dispersion, which are product formulations used to improve the dissolution performance of active pharmaceutical ingredients with poor aqueous solubility. Insights from the structure solution allowed for a simpler crystallization route for this polymorph to be deduced, demonstrating the relevance of 3DED within drug development.
3D electron diffraction (3DED) is increasingly employed to determine molecular and crystal structures from micro-crystals. Indomethacin is a well known, marketed, small-molecule non-steroidal anti-inflammatory drug with eight known polymorphic forms, of which four structures have been elucidated to date. Using 3DED, we determined the structure of a new ninth polymorph, σ, found within an amorphous solid dispersion, a product formulation sometimes used for active pharmaceutical ingredients with poor aqueous solubility. Subsequently, we found that σ indomethacin can be produced from direct solvent evaporation using dichloromethane. These results demonstrate the relevance of 3DED within drug development to directly probe product formulations.
{"title":"From formulation to structure: 3D electron diffraction for the structure solution of a new indomethacin polymorph from an amorphous solid dispersion","authors":"Helen W. Leung , Royston C. B. Copley , Giulio I. Lampronti , Sarah J. Day , Lucy K. Saunders , Duncan N. Johnstone , Paul A. Midgley","doi":"10.1107/S2052252524008121","DOIUrl":"10.1107/S2052252524008121","url":null,"abstract":"<div><p>3D electron diffraction (3DED) was used to elucidate the structure of a new ninth polymorph of indomethacin from an amorphous solid dispersion, which are product formulations used to improve the dissolution performance of active pharmaceutical ingredients with poor aqueous solubility. Insights from the structure solution allowed for a simpler crystallization route for this polymorph to be deduced, demonstrating the relevance of 3DED within drug development.</p></div><div><p>3D electron diffraction (3DED) is increasingly employed to determine molecular and crystal structures from micro-crystals. Indomethacin is a well known, marketed, small-molecule non-steroidal anti-inflammatory drug with eight known polymorphic forms, of which four structures have been elucidated to date. Using 3DED, we determined the structure of a new ninth polymorph, σ, found within an amorphous solid dispersion, a product formulation sometimes used for active pharmaceutical ingredients with poor aqueous solubility. Subsequently, we found that σ indomethacin can be produced from direct solvent evaporation using dichloromethane. These results demonstrate the relevance of 3DED within drug development to directly probe product formulations.</p></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"11 5","pages":"Pages 744-748"},"PeriodicalIF":2.9,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11364028/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142080329","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-07-01DOI: 10.1107/S2052252524003658
Masako Kato , L. R. MacGillivray (Editor)
Platinum(II) complexes exhibit intense luminescence based on their molecular arrangement and chromic luminescence, which is a color change in response to gentle stimuli such as vapor exposure or weak mechanical forces. Both the molecular and the crystal designs for soft crystals are critical to effectively control the chromic phenomenon of platinum(II) complexes.
Platinum(II) complexes of square-planar geometry are interesting from a crystal engineering viewpoint because they exhibit strong luminescence based on the self-assembly of molecular units. The luminescence color changes in response to gentle stimuli, such as vapor exposure or weak mechanical forces. Both the molecular and the crystal designs for soft crystals are critical to effectively generate the chromic luminescence phenomenon of Pt(II) complexes. In this topical review, strategies for fabricating chromic luminescent Pt(II) complexes are described from a crystal design perspective, focusing on the structural regulation of Pt(II) complexes that exhibit assembly-induced luminescence via metal–metal interactions and structural control of anionic Pt(II) complexes using cations. The research progress on the evolution of various chromic luminescence properties of Pt(II) complexes, including the studies conducted by our group, are presented here along with the latest research outcomes, and an overview of the frontiers and future potential of this research field is provided.
{"title":"Chromic soft crystals based on luminescent platinum(II) complexes","authors":"Masako Kato , L. R. MacGillivray (Editor)","doi":"10.1107/S2052252524003658","DOIUrl":"10.1107/S2052252524003658","url":null,"abstract":"<div><p>Platinum(II) complexes exhibit intense luminescence based on their molecular arrangement and chromic luminescence, which is a color change in response to gentle stimuli such as vapor exposure or weak mechanical forces. Both the molecular and the crystal designs for soft crystals are critical to effectively control the chromic phenomenon of platinum(II) complexes.</p></div><div><p>Platinum(II) complexes of square-planar geometry are interesting from a crystal engineering viewpoint because they exhibit strong luminescence based on the self-assembly of molecular units. The luminescence color changes in response to gentle stimuli, such as vapor exposure or weak mechanical forces. Both the molecular and the crystal designs for soft crystals are critical to effectively generate the chromic luminescence phenomenon of Pt(II) complexes. In this topical review, strategies for fabricating chromic luminescent Pt(II) complexes are described from a crystal design perspective, focusing on the structural regulation of Pt(II) complexes that exhibit assembly-induced luminescence via metal–metal interactions and structural control of anionic Pt(II) complexes using cations. The research progress on the evolution of various chromic luminescence properties of Pt(II) complexes, including the studies conducted by our group, are presented here along with the latest research outcomes, and an overview of the frontiers and future potential of this research field is provided.</p></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"11 4","pages":"Pages 442-452"},"PeriodicalIF":2.9,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11220876/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141300715","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-07-01DOI: 10.1107/S2052252524003634
A. Zwolenik , D. Tchoń , A. Makal , C.-Y. Su (Editor)
A new polymorph of 1,3-diacetylpyrene that is luminescent in the solid state and a prominent negative thermal expansion material has been obtained from its melt. A thorough structural characterization of this new crystal form was performed in a wide temperature and pressure range using single-crystal X-ray diffraction. Structural studies have been combined with steady-state UV–Vis spectroscopy and periodic density functional theory calculations. A previously published methodology of crystal placement in a diamond anvil cell has been successfully applied in predicting optimal 2°AP-β sample orientation, ensuring >80% data coverage and enabling unrestrained Hirshfeld atom refinements for high-pressure structures as well as analysis of anharmonic oscillations.
A new polymorph of 1,3-diacetylpyrene has been obtained from its melt and thoroughly characterized using single-crystal X-ray diffraction, steady-state UV–Vis spectroscopy and periodic density functional theory calculations. Experimental studies covered the temperature range from 90 to 390 K and the pressure range from atmospheric to 4.08 GPa. Optimal sample placement in a diamond anvil cell according to our previously presented methodology ensured over 80% data coverage up to 0.8 Å for a monoclinic sample. Unrestrained Hirshfeld atom refinement of the high-pressure crystal structures was successful and anharmonic behavior of carbonyl oxygen atoms was observed. Unlike the previously characterized polymorph, the structure of 2°AP-β is based on infinite π-stacks of antiparallel 2°AP molecules. 2°AP-β displays piezochromism and piezofluorochromism which are directly related to the variation in interplanar distances within the π-stacking. The importance of weak intermolecular interactions is reflected in the substantial negative thermal expansion coefficient of −55.8 (57) MK−1 in the direction of C—H⋯O interactions.
{"title":"Evolution of structure and spectroscopic properties of a new 1,3-diacetylpyrene polymorph with temperature and pressure","authors":"A. Zwolenik , D. Tchoń , A. Makal , C.-Y. Su (Editor)","doi":"10.1107/S2052252524003634","DOIUrl":"10.1107/S2052252524003634","url":null,"abstract":"<div><p>A new polymorph of 1,3-diacetylpyrene that is luminescent in the solid state and a prominent negative thermal expansion material has been obtained from its melt. A thorough structural characterization of this new crystal form was performed in a wide temperature and pressure range using single-crystal X-ray diffraction. Structural studies have been combined with steady-state UV–Vis spectroscopy and periodic density functional theory calculations. A previously published methodology of crystal placement in a diamond anvil cell has been successfully applied in predicting optimal 2°AP-β sample orientation, ensuring >80% data coverage and enabling unrestrained Hirshfeld atom refinements for high-pressure structures as well as analysis of anharmonic oscillations.</p></div><div><p>A new polymorph of 1,3-diacetylpyrene has been obtained from its melt and thoroughly characterized using single-crystal X-ray diffraction, steady-state UV–Vis spectroscopy and periodic density functional theory calculations. Experimental studies covered the temperature range from 90 to 390 K and the pressure range from atmospheric to 4.08 GPa. Optimal sample placement in a diamond anvil cell according to our previously presented methodology ensured over 80% data coverage up to 0.8 Å for a monoclinic sample. Unrestrained Hirshfeld atom refinement of the high-pressure crystal structures was successful and anharmonic behavior of carbonyl oxygen atoms was observed. Unlike the previously characterized polymorph, the structure of 2°AP-β is based on infinite π-stacks of antiparallel 2°AP molecules. 2°AP-β displays piezochromism and piezofluorochromism which are directly related to the variation in interplanar distances within the π-stacking. The importance of weak intermolecular interactions is reflected in the substantial negative thermal expansion coefficient of −55.8 (57) MK<sup>−1</sup> in the direction of C—H⋯O interactions.</p></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"11 4","pages":"Pages 519-527"},"PeriodicalIF":2.9,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11220879/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140897554","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}