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Structural and magnetic phase transitions in Eu1-xLaxFe3(BO3)4 (x = 0, 0.18). Eu1-xLaxFe3(BO3)4的结构相变和磁相变(x = 0,0.18)。
IF 1.3 3区 化学 Q3 CHEMISTRY, MULTIDISCIPLINARY Pub Date : 2025-02-01 Epub Date: 2024-12-23 DOI: 10.1107/S2052520624011569
Ekaterina S Smirnova, Kirill V Frolov, Ekaterina V Sidorova, Timofei A Sorokin, Olga A Alekseeva, Anton V Guskov, Pavel G Gagarin, Irina A Gudim

The crystal structures and hyperfine magnetic parameters of EuFe3(BO3)4 and mixed Eu0.82La0.18Fe3(BO3)4 were studied over a wide temperature range in order to analyze correlations of the structural and magnetic features and the phase transitions in multiferroic compounds of the rare-earth iron borate family. The chemical compositions of the crystals are reported from X-ray fluorescence analysis. The crystal structures of EuFe3(BO3)4 and Eu0.82La0.18Fe3(BO3)4 were determined using single-crystal X-ray diffraction in the temperature range 25-500 K. A structural phase transition is observed in EuFe3(BO3)4 below 89 K which is related to distortions in the interatomic distances and angles. The most significant of which are for R-O, R-B, R-Fe, Fe-O and Fe-Fe distances, and the angles between the BO3 triangles and the ab plane. There is no structural phase transition in lanthanum-doped EuFe3(BO3)4 based on specific heat measurements (2.2-101.3 K) and structure analysis (25-500 K), and the temperature dependences of the interatomic distances and angles are smooth. The lengths of the superexchange paths needed for the appearance of a structural phase transition in RFe3(BO3)4 have been proposed. Negative thermal expansion is observed for both compounds below 90 K, resulting from a growth of the interatomic Fe-Fe distances in the iron chains during cooling. The largest atomic displacement parameters are observed for O atoms (O2), indicating that they have the highest mobility. The magnetic properties of EuFe3(BO3)4 and Eu0.82La0.18Fe3(BO3)4 were analyzed using Mössbauer spectroscopy in the temperature range 4.5-298 K. Néel temperatures (TN) of 34.57 (1) and 32.22 (1) K are obtained based on Mössbauer spectroscopy for the pure and doped crystals, respectively. The maximum specific heat capacity temperature dependence related to the magnetic phase transition for the doped crystal is observed at 31.2 K. A violation of the strict arrangement of antiferromagnetic ordering in the ab plane in the La-doped crystals at low temperatures is suggested. The magnetic contributions of the two structural positions of the iron ions to the Mössbauer spectra could not be distinguished in either pure and doped compounds, regardless of whether they are in the paramagnetic and antiferromagnetic regions.

在较宽的温度范围内研究了EuFe3(BO3)4和混合Eu0.82La0.18Fe3(BO3)4的晶体结构和超细磁性参数,以分析稀土硼酸铁族多铁化合物的结构和磁性特征与相变的相关性。用x射线荧光分析报告了晶体的化学成分。在25 ~ 500 K的温度范围内,用单晶x射线衍射测定了EuFe3(BO3)4和Eu0.82La0.18Fe3(BO3)4的晶体结构。在89 K以下,EuFe3(BO3)4发生了结构相变,这与原子间距离和角度的畸变有关。其中最重要的是R-O、R-B、R-Fe、Fe-O和Fe-Fe之间的距离,以及BO3三角形与ab平面之间的夹角。基于比热测量(2.2 ~ 101.3 K)和结构分析(25 ~ 500 K),镧掺杂EuFe3(BO3)4没有发生结构相变,原子间距离和原子间角的温度依赖性较好。提出了RFe3(BO3)4中出现结构相变所需的超交换路径长度。两种化合物在低于90k时均观察到负热膨胀,这是由于冷却过程中铁链中Fe-Fe原子间距离的增加。O原子(O2)的原子位移参数最大,表明它们具有最高的迁移率。利用Mössbauer光谱分析了EuFe3(BO3)4和Eu0.82La0.18Fe3(BO3)4在4.5 ~ 298 K范围内的磁性能。通过Mössbauer光谱分析得到纯晶体和掺杂晶体的n温度(TN)分别为34.57(1)和32.22 (1)K。在31.2 K时观察到掺杂晶体与磁相变相关的最大比热容温度依赖性。在低温下,la掺杂晶体在ab平面上违反了严格的反铁磁有序排列。铁离子的两个结构位置对Mössbauer光谱的磁贡献在纯化合物和掺杂化合物中都无法区分,无论它们是在顺磁区还是反铁磁区。
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引用次数: 0
Photoelasticity of crystals with the scheelite structure: quantum mechanical calculations. 白钨矿结构晶体的光弹性:量子力学计算。
IF 1.3 3区 化学 Q3 CHEMISTRY, MULTIDISCIPLINARY Pub Date : 2025-02-01 Epub Date: 2025-01-06 DOI: 10.1107/S2052520624011673
Nataliya M Demyanyshyn, Bohdan G Mytsyk, Anatoliy S Andrushchak, Andriy V Kityk

We report a complete set of elastic, piezooptic and photoelastic tensor constants of scheelite crystals CaMoO4, BaMoO4, BaWO4 and PbWO4 determined by density functional theory (DFT) calculations using the quantum chemical software package CRYSTAL17. The modulation parameter, i.e. the change in the crystal optical path normalized by thickness and mechanical stress, was calculated based on piezooptic and elastic compliance tensor constants. For the geometries of the most effective piezo-optic interactions, this parameter reaches rather large values (16-17) × 10-12 m2 N-1. Anisotropy of the photoelastic and acoustooptic effects is explored by means of indicative surfaces, considering the directions of light propagation and polarization, the direction of uniaxial compression or lattice distortion caused by the propagation of the acoustic wave. DFT calculations indicate BaWO4 and PbWO4 crystals as the most effective acousto-optic materials, predicting the figure of merit constant M2 ∼ 20 × 10-15 s3 kg-1. The methodology proposed combines the DFT calculations and photoelasticity caused by uniaxial compression of the crystal lattice, with particular emphasis on its anisotropy. It can be considered as part of optical engineering aimed at preliminary assessment of the photoelastic properties of crystal materials, thus assisting in their selection for synthesis and relevant applications.

本文报道了白钨晶体CaMoO4、BaMoO4、BaWO4和PbWO4的一套完整的弹性、压电和光弹性张量常数,并利用量子化学软件包CRYSTAL17通过密度泛函理论(DFT)计算得到。基于压电柔度张量常数和弹性柔度张量常数计算调制参数,即厚度和机械应力归一化后晶体光路的变化。对于最有效的压电-光学相互作用的几何形状,该参数达到相当大的值(16-17)× 10-12 m2 N-1。考虑到光的传播方向和偏振方向,以及声波传播引起的单轴压缩或晶格畸变方向,利用指示面探讨了光弹性和声光效应的各向异性。DFT计算表明,BaWO4和PbWO4晶体是最有效的声光材料,并预测了性能常数M2 ~ 20 × 10-15 s3 kg-1。所提出的方法将DFT计算与晶格单轴压缩引起的光弹性相结合,特别强调其各向异性。它可以被认为是光学工程的一部分,旨在初步评估晶体材料的光弹性特性,从而帮助它们的合成和相关应用的选择。
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引用次数: 0
Crystal structure and doping in synthetic enstatite: an analysis of Li/Fe3+-doped single-crystal samples. 合成顽辉石的晶体结构与掺杂:Li/Fe3+掺杂单晶样品的分析。
IF 1.3 3区 化学 Q3 CHEMISTRY, MULTIDISCIPLINARY Pub Date : 2025-02-01 Epub Date: 2025-01-14 DOI: 10.1107/S2052520624011624
Paolo Ballirano, Beatrice Celata, Alessandro Pacella, Andrea Bloise, Ferdinando Bosi

A series of Li+/Fe3+-doped enstatite crystals of composition Mg(2-2x)LixFexSi2O6 were synthesized and structurally characterized. Under the selected experimental conditions, we grew three crystals of Pbca orthopyroxene (OPX: x = 0.270-0.313) and two crystals of Pbcn protopyroxene (PPX: x = 0.156-0.164) using the flux-growth technique. The observed variation in the polyhedral volume and distortion of the M2 octahedron as a function of Li/Fe3+ doping suggests the presence of an upper limit, at least for the OPX samples. The same linear relation was observed between the polyhedral volume and ⟨M1-O⟩ bond length across all analysed samples, including the endmembers protoenstatite (PEN), orthoenstatite (OEN) and LiFe3+Si2O6. It seems that the M2 octahedron plays a crucial role in stabilizing the pyroxene topology in either the PEN or the OEN form, because the PPX and OPX samples show two distinct linear relations between the M2O6 polyhedral volume and ⟨M2-O⟩, with the PPX trend converging toward the parameters of the LiFe3+Si2O6 endmember, whereas the OPX trend, including OEN, diverges largely from these parameters.

合成了一系列Li+/Fe3+掺杂的顽辉石晶体,组成为Mg(2-2x)LixFexSi2O6,并进行了结构表征。在选定的实验条件下,我们利用通量生长技术生长出了三颗Pbca正晶(OPX: x = 0.270-0.313)和两颗Pbcn原晶(PPX: x = 0.156-0.164)。观察到的M2八面体的多面体体积和畸变随Li/Fe3+掺杂的变化表明存在一个上限,至少对于OPX样品是如此。在所有分析样品中,包括端元原顽辉石(PEN)、正顽辉石(OEN)和LiFe3+Si2O6,多面体体积与< _1 - o >键长之间都观察到相同的线性关系。M2八面体似乎在稳定PEN或OEN形式的焦石拓扑结构中起着至关重要的作用,因为PPX和OPX样品在M2O6多面体体积和< M2- o >之间表现出两种明显的线性关系,PPX趋势向LiFe3+Si2O6端元的参数收敛,而OPX趋势,包括OEN,在很大程度上偏离这些参数。
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引用次数: 0
Polymorph sampling with coupling to extended variables: enhanced sampling of polymorph energy landscapes and free energy perturbation of polymorph ensembles. 与扩展变量耦合的多晶体采样:多晶体能谱的增强采样和多晶体集合的自由能扰动。
IF 1.3 3区 化学 Q3 CHEMISTRY, MULTIDISCIPLINARY Pub Date : 2024-12-01 DOI: 10.1107/S205252062400132X
Eric J Chan, Mark E Tuckerman

A novel approach to computationally enhance the sampling of molecular crystal structures is proposed and tested. This method is based on the use of extended variables coupled to a Monte Carlo based crystal polymorph generator. Inspired by the established technique of quasi-random sampling of polymorphs using the rigid molecule constraint, this approach represents molecular clusters as extended variables within a thermal reservoir. Polymorph unit-cell variables are generated using pseudo-random sampling. Within this framework, a harmonic coupling between the extended variables and polymorph configurations is established. The extended variables remain fixed during the inner loop dedicated to polymorph sampling, enforcing a stepwise propagation of the extended variables to maintain system exploration. The final processing step results in a polymorph energy landscape, where the raw structures sampled to create the extended variable trajectory are re-optimized without the thermal coupling term. The foundational principles of this approach are described and its effectiveness using both a Metropolis Monte Carlo type algorithm and modifications that incorporate replica exchange is demonstrated. A comparison is provided with pseudo-random sampling of polymorphs for the molecule coumarin. The choice to test a design of this algorithm as relevant for enhanced sampling of crystal structures was due to the obvious relation between molecular structure variables and corresponding crystal polymorphs as representative of the inherent vapor to crystal transitions that exist in nature. Additionally, it is shown that the trajectories of extended variables can be harnessed to extract fluctuation properties that can lead to valuable insights. A novel thermodynamic variable is introduced: the free energy difference between ensembles of Z' = 1 and Z' = 2 crystal polymorphs.

本文提出并测试了一种通过计算增强分子晶体结构采样的新方法。该方法基于扩展变量与基于蒙特卡罗的晶体多态生成器的结合使用。受利用刚性分子约束对多晶体进行准随机取样的成熟技术的启发,这种方法将分子簇表示为热库中的扩展变量。多晶体单胞变量是通过伪随机抽样生成的。在此框架内,扩展变量与多晶体构型之间建立了谐波耦合。在多态采样的内循环中,扩展变量保持固定,强制扩展变量逐步传播,以保持系统探索。最后的处理步骤会产生一个多形态能谱,在该能谱中,为创建扩展变量轨迹而采样的原始结构会在没有热耦合项的情况下重新优化。本文介绍了这种方法的基本原理,并展示了使用 Metropolis Monte Carlo 算法和包含复制交换的修改算法的有效性。并与香豆素分子的多态伪随机抽样进行了比较。之所以选择这种算法设计来测试晶体结构的增强采样,是因为分子结构变量与相应的晶体多晶体之间存在明显的关系,这代表了自然界中存在的固有气态到晶体的转变。此外,研究还表明,可以利用扩展变量的轨迹来提取波动特性,从而获得有价值的见解。本文引入了一个新的热力学变量:Z' = 1 和 Z' = 2 晶体多晶体集合之间的自由能差。
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引用次数: 0
The seventh blind test of crystal structure prediction: structure ranking methods. 晶体结构预测的第七次盲测:结构排序法。
IF 1.3 3区 化学 Q3 CHEMISTRY, MULTIDISCIPLINARY Pub Date : 2024-12-01 DOI: 10.1107/S2052520624008679
Lily M Hunnisett, Nicholas Francia, Jonas Nyman, Nathan S Abraham, Srinivasulu Aitipamula, Tamador Alkhidir, Mubarak Almehairbi, Andrea Anelli, Dylan M Anstine, John E Anthony, Joseph E Arnold, Faezeh Bahrami, Michael A Bellucci, Gregory J O Beran, Rajni M Bhardwaj, Raffaello Bianco, Joanna A Bis, A Daniel Boese, James Bramley, Doris E Braun, Patrick W V Butler, Joseph Cadden, Stephen Carino, Ctirad Červinka, Eric J Chan, Chao Chang, Sarah M Clarke, Simon J Coles, Cameron J Cook, Richard I Cooper, Tom Darden, Graeme M Day, Wenda Deng, Hanno Dietrich, Antonio DiPasquale, Bhausaheb Dhokale, Bouke P van Eijck, Mark R J Elsegood, Dzmitry Firaha, Wenbo Fu, Kaori Fukuzawa, Nikolaos Galanakis, Hitoshi Goto, Chandler Greenwell, Rui Guo, Jürgen Harter, Julian Helfferich, Johannes Hoja, John Hone, Richard Hong, Michal Hušák, Yasuhiro Ikabata, Olexandr Isayev, Ommair Ishaque, Varsha Jain, Yingdi Jin, Aling Jing, Erin R Johnson, Ian Jones, K V Jovan Jose, Elena A Kabova, Adam Keates, Paul F Kelly, Jiří Klimeš, Veronika Kostková, He Li, Xiaolu Lin, Alexander List, Congcong Liu, Yifei Michelle Liu, Zenghui Liu, Ivor Lončarić, Joseph W Lubach, Jan Ludík, Alexander A Maryewski, Noa Marom, Hiroyuki Matsui, Alessandra Mattei, R Alex Mayo, John W Melkumov, Bruno Mladineo, Sharmarke Mohamed, Zahrasadat Momenzadeh Abardeh, Hari S Muddana, Naofumi Nakayama, Kamal Singh Nayal, Marcus A Neumann, Rahul Nikhar, Shigeaki Obata, Dana O'Connor, Artem R Oganov, Koji Okuwaki, Alberto Otero-de-la-Roza, Sean Parkin, Antonio Parunov, Rafał Podeszwa, Alastair J A Price, Louise S Price, Sarah L Price, Michael R Probert, Angeles Pulido, Gunjan Rajendra Ramteke, Atta Ur Rehman, Susan M Reutzel-Edens, Jutta Rogal, Marta J Ross, Adrian F Rumson, Ghazala Sadiq, Zeinab M Saeed, Alireza Salimi, Kiran Sasikumar, Sivakumar Sekharan, Kenneth Shankland, Baimei Shi, Xuekun Shi, Kotaro Shinohara, A Geoffrey Skillman, Hongxing Song, Nina Strasser, Jacco van de Streek, Isaac J Sugden, Guangxu Sun, Krzysztof Szalewicz, Lu Tan, Kehan Tang, Frank Tarczynski, Christopher R Taylor, Alexandre Tkatchenko, Petr Touš, Mark E Tuckerman, Pablo A Unzueta, Yohei Utsumi, Leslie Vogt-Maranto, Jake Weatherston, Luke J Wilkinson, Robert D Willacy, Lukasz Wojtas, Grahame R Woollam, Yi Yang, Zhuocen Yang, Etsuo Yonemochi, Xin Yue, Qun Zeng, Tian Zhou, Yunfei Zhou, Roman Zubatyuk, Jason C Cole

A seventh blind test of crystal structure prediction has been organized by the Cambridge Crystallographic Data Centre. The results are presented in two parts, with this second part focusing on methods for ranking crystal structures in order of stability. The exercise involved standardized sets of structures seeded from a range of structure generation methods. Participants from 22 groups applied several periodic DFT-D methods, machine learned potentials, force fields derived from empirical data or quantum chemical calculations, and various combinations of the above. In addition, one non-energy-based scoring function was used. Results showed that periodic DFT-D methods overall agreed with experimental data within expected error margins, while one machine learned model, applying system-specific AIMnet potentials, agreed with experiment in many cases demonstrating promise as an efficient alternative to DFT-based methods. For target XXXII, a consensus was reached across periodic DFT methods, with consistently high predicted energies of experimental forms relative to the global minimum (above 4 kJ mol-1 at both low and ambient temperatures) suggesting a more stable polymorph is likely not yet observed. The calculation of free energies at ambient temperatures offered improvement of predictions only in some cases (for targets XXVII and XXXI). Several avenues for future research have been suggested, highlighting the need for greater efficiency considering the vast amounts of resources utilized in many cases.

剑桥晶体学数据中心组织了第七次晶体结构预测盲测。测试结果分为两部分,第二部分重点介绍了晶体结构稳定性排序方法。这项工作涉及由一系列结构生成方法产生的标准化结构种子集。来自 22 个研究小组的参与者应用了几种周期性 DFT-D 方法、机器学习势能、从经验数据或量子化学计算中得出的力场,以及上述方法的各种组合。此外,还使用了一种非基于能量的评分函数。结果表明,周期性 DFT-D 方法总体上与实验数据吻合,误差在预期范围内,而应用特定系统 AIMnet 电位的机器学习模型在许多情况下与实验吻合,表明有望成为基于 DFT 方法的有效替代方法。对于目标 XXXII,周期性 DFT 方法达成了共识,相对于全局最小值,实验形式的预测能量始终较高(在低温和常温下均高于 4 kJ mol-1),这表明可能尚未观察到更稳定的多晶体。环境温度下的自由能计算仅在某些情况下(目标 XXVII 和 XXXI)提高了预测结果。考虑到在许多情况下需要使用大量资源,我们提出了未来研究的几条途径,强调了提高效率的必要性。
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引用次数: 0
Symmetry, magnetic transitions and multiferroic properties of B-site-ordered A2MnB'O6 perovskites (B' = [Co, Ni]). B位有序A2MnB' o6钙钛矿(B' = [Co, Ni])的对称性、磁跃迁和多铁性
IF 1.3 3区 化学 Q3 CHEMISTRY, MULTIDISCIPLINARY Pub Date : 2024-12-01 DOI: 10.1107/S2052520624009454
Jose Luis Garcia-Muñoz, Xiaodong Zhang, Gloria Subías, Javier Blasco

The presence of magnetic atoms at the A and B sites and the coupling between these two spin subsystems in perovskites gives rise to a variety of exciting effects. In particular this coupling attracts interest from the field of novel multiferroic and magnetoelectric oxides. Moreover, magnetic double perovskites presenting cationic order at the B sites incorporate an additional modulation that can favor symmetry breaking, multiferroic, magnetoelectric and polar phases. Here, we describe the magnetic structures obtained from neutron diffraction and analyze the symmetry properties of well ordered A2MnB'O6 double perovskites with A = Lu, Yb, Tm, Er, Ho, Y, Tb, La0.5Tb0.5, La and B' = Co or Ni. A rich variety of magnetic orders is formed that have been identified and described, and their symmetry properties are discussed in relation to the multiferroic and magnetoelectric properties of the different compounds.

钙钛矿中A位和B位磁原子的存在以及这两个自旋子系统之间的耦合产生了各种激发效应。特别是这种耦合引起了新型多铁性和磁电氧化物领域的兴趣。此外,在B位呈现阳离子有序的磁性双钙钛矿包含了一个额外的调制,可以促进对称破缺、多铁性、磁电和极性相。本文描述了中子衍射获得的磁性结构,并分析了A = Lu, Yb, Tm, Er, Ho, Y, Tb, La0.5Tb0.5, La和B' = Co或Ni的有序A2MnB' o6双钙钛矿的对称性。形成了丰富多样的已被识别和描述的磁序,并讨论了它们的对称性与不同化合物的多铁性和磁电性的关系。
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引用次数: 0
The seventh blind test of crystal structure prediction: structure generation methods. 晶体结构预测的第七次盲测:结构生成方法。
IF 1.3 3区 化学 Q3 CHEMISTRY, MULTIDISCIPLINARY Pub Date : 2024-12-01 DOI: 10.1107/S2052520624007492
Lily M Hunnisett, Jonas Nyman, Nicholas Francia, Nathan S Abraham, Claire S Adjiman, Srinivasulu Aitipamula, Tamador Alkhidir, Mubarak Almehairbi, Andrea Anelli, Dylan M Anstine, John E Anthony, Joseph E Arnold, Faezeh Bahrami, Michael A Bellucci, Rajni M Bhardwaj, Imanuel Bier, Joanna A Bis, A Daniel Boese, David H Bowskill, James Bramley, Jan Gerit Brandenburg, Doris E Braun, Patrick W V Butler, Joseph Cadden, Stephen Carino, Eric J Chan, Chao Chang, Bingqing Cheng, Sarah M Clarke, Simon J Coles, Richard I Cooper, Ricky Couch, Ramon Cuadrado, Tom Darden, Graeme M Day, Hanno Dietrich, Yiming Ding, Antonio DiPasquale, Bhausaheb Dhokale, Bouke P van Eijck, Mark R J Elsegood, Dzmitry Firaha, Wenbo Fu, Kaori Fukuzawa, Joseph Glover, Hitoshi Goto, Chandler Greenwell, Rui Guo, Jürgen Harter, Julian Helfferich, Detlef W M Hofmann, Johannes Hoja, John Hone, Richard Hong, Geoffrey Hutchison, Yasuhiro Ikabata, Olexandr Isayev, Ommair Ishaque, Varsha Jain, Yingdi Jin, Aling Jing, Erin R Johnson, Ian Jones, K V Jovan Jose, Elena A Kabova, Adam Keates, Paul F Kelly, Dmitry Khakimov, Stefanos Konstantinopoulos, Liudmila N Kuleshova, He Li, Xiaolu Lin, Alexander List, Congcong Liu, Yifei Michelle Liu, Zenghui Liu, Zhi Pan Liu, Joseph W Lubach, Noa Marom, Alexander A Maryewski, Hiroyuki Matsui, Alessandra Mattei, R Alex Mayo, John W Melkumov, Sharmarke Mohamed, Zahrasadat Momenzadeh Abardeh, Hari S Muddana, Naofumi Nakayama, Kamal Singh Nayal, Marcus A Neumann, Rahul Nikhar, Shigeaki Obata, Dana O'Connor, Artem R Oganov, Koji Okuwaki, Alberto Otero-de-la-Roza, Constantinos C Pantelides, Sean Parkin, Chris J Pickard, Luca Pilia, Tatyana Pivina, Rafał Podeszwa, Alastair J A Price, Louise S Price, Sarah L Price, Michael R Probert, Angeles Pulido, Gunjan Rajendra Ramteke, Atta Ur Rehman, Susan M Reutzel-Edens, Jutta Rogal, Marta J Ross, Adrian F Rumson, Ghazala Sadiq, Zeinab M Saeed, Alireza Salimi, Matteo Salvalaglio, Leticia Sanders de Almada, Kiran Sasikumar, Sivakumar Sekharan, Cheng Shang, Kenneth Shankland, Kotaro Shinohara, Baimei Shi, Xuekun Shi, A Geoffrey Skillman, Hongxing Song, Nina Strasser, Jacco van de Streek, Isaac J Sugden, Guangxu Sun, Krzysztof Szalewicz, Benjamin I Tan, Lu Tan, Frank Tarczynski, Christopher R Taylor, Alexandre Tkatchenko, Rithwik Tom, Mark E Tuckerman, Yohei Utsumi, Leslie Vogt-Maranto, Jake Weatherston, Luke J Wilkinson, Robert D Willacy, Lukasz Wojtas, Grahame R Woollam, Zhuocen Yang, Etsuo Yonemochi, Xin Yue, Qun Zeng, Yizu Zhang, Tian Zhou, Yunfei Zhou, Roman Zubatyuk, Jason C Cole

A seventh blind test of crystal structure prediction was organized by the Cambridge Crystallographic Data Centre featuring seven target systems of varying complexity: a silicon and iodine-containing molecule, a copper coordination complex, a near-rigid molecule, a cocrystal, a polymorphic small agrochemical, a highly flexible polymorphic drug candidate, and a polymorphic morpholine salt. In this first of two parts focusing on structure generation methods, many crystal structure prediction (CSP) methods performed well for the small but flexible agrochemical compound, successfully reproducing the experimentally observed crystal structures, while few groups were successful for the systems of higher complexity. A powder X-ray diffraction (PXRD) assisted exercise demonstrated the use of CSP in successfully determining a crystal structure from a low-quality PXRD pattern. The use of CSP in the prediction of likely cocrystal stoichiometry was also explored, demonstrating multiple possible approaches. Crystallographic disorder emerged as an important theme throughout the test as both a challenge for analysis and a major achievement where two groups blindly predicted the existence of disorder for the first time. Additionally, large-scale comparisons of the sets of predicted crystal structures also showed that some methods yield sets that largely contain the same crystal structures.

剑桥晶体学数据中心(Crystallographic Data Centre)组织了第七次晶体结构预测盲测,对七个不同复杂程度的目标系统进行了预测:一个含硅和碘分子、一个铜配位复合物、一个近刚性分子、一个共晶体、一个多形态小型农用化学品、一个高柔性多形态候选药物和一个多形态吗啉盐。在这两部分中的第一部分中,重点介绍了结构生成方法,许多晶体结构预测(CSP)方法在小型但灵活的农用化学品化合物方面表现出色,成功地再现了实验观察到的晶体结构,而在复杂度较高的系统方面,成功的方法却寥寥无几。一项粉末 X 射线衍射(PXRD)辅助研究表明,使用 CSP 可以成功地从低质量的 PXRD 图样中确定晶体结构。此外,还探讨了如何利用 CSP 预测可能的共晶化学计量,展示了多种可能的方法。晶体学无序是整个测试的一个重要主题,它既是对分析的挑战,也是一项重大成就,两个小组首次盲目预测了无序的存在。此外,对预测晶体结构集的大规模比较也表明,一些方法得出的晶体结构集基本上包含相同的晶体结构。
{"title":"The seventh blind test of crystal structure prediction: structure generation methods.","authors":"Lily M Hunnisett, Jonas Nyman, Nicholas Francia, Nathan S Abraham, Claire S Adjiman, Srinivasulu Aitipamula, Tamador Alkhidir, Mubarak Almehairbi, Andrea Anelli, Dylan M Anstine, John E Anthony, Joseph E Arnold, Faezeh Bahrami, Michael A Bellucci, Rajni M Bhardwaj, Imanuel Bier, Joanna A Bis, A Daniel Boese, David H Bowskill, James Bramley, Jan Gerit Brandenburg, Doris E Braun, Patrick W V Butler, Joseph Cadden, Stephen Carino, Eric J Chan, Chao Chang, Bingqing Cheng, Sarah M Clarke, Simon J Coles, Richard I Cooper, Ricky Couch, Ramon Cuadrado, Tom Darden, Graeme M Day, Hanno Dietrich, Yiming Ding, Antonio DiPasquale, Bhausaheb Dhokale, Bouke P van Eijck, Mark R J Elsegood, Dzmitry Firaha, Wenbo Fu, Kaori Fukuzawa, Joseph Glover, Hitoshi Goto, Chandler Greenwell, Rui Guo, Jürgen Harter, Julian Helfferich, Detlef W M Hofmann, Johannes Hoja, John Hone, Richard Hong, Geoffrey Hutchison, Yasuhiro Ikabata, Olexandr Isayev, Ommair Ishaque, Varsha Jain, Yingdi Jin, Aling Jing, Erin R Johnson, Ian Jones, K V Jovan Jose, Elena A Kabova, Adam Keates, Paul F Kelly, Dmitry Khakimov, Stefanos Konstantinopoulos, Liudmila N Kuleshova, He Li, Xiaolu Lin, Alexander List, Congcong Liu, Yifei Michelle Liu, Zenghui Liu, Zhi Pan Liu, Joseph W Lubach, Noa Marom, Alexander A Maryewski, Hiroyuki Matsui, Alessandra Mattei, R Alex Mayo, John W Melkumov, Sharmarke Mohamed, Zahrasadat Momenzadeh Abardeh, Hari S Muddana, Naofumi Nakayama, Kamal Singh Nayal, Marcus A Neumann, Rahul Nikhar, Shigeaki Obata, Dana O'Connor, Artem R Oganov, Koji Okuwaki, Alberto Otero-de-la-Roza, Constantinos C Pantelides, Sean Parkin, Chris J Pickard, Luca Pilia, Tatyana Pivina, Rafał Podeszwa, Alastair J A Price, Louise S Price, Sarah L Price, Michael R Probert, Angeles Pulido, Gunjan Rajendra Ramteke, Atta Ur Rehman, Susan M Reutzel-Edens, Jutta Rogal, Marta J Ross, Adrian F Rumson, Ghazala Sadiq, Zeinab M Saeed, Alireza Salimi, Matteo Salvalaglio, Leticia Sanders de Almada, Kiran Sasikumar, Sivakumar Sekharan, Cheng Shang, Kenneth Shankland, Kotaro Shinohara, Baimei Shi, Xuekun Shi, A Geoffrey Skillman, Hongxing Song, Nina Strasser, Jacco van de Streek, Isaac J Sugden, Guangxu Sun, Krzysztof Szalewicz, Benjamin I Tan, Lu Tan, Frank Tarczynski, Christopher R Taylor, Alexandre Tkatchenko, Rithwik Tom, Mark E Tuckerman, Yohei Utsumi, Leslie Vogt-Maranto, Jake Weatherston, Luke J Wilkinson, Robert D Willacy, Lukasz Wojtas, Grahame R Woollam, Zhuocen Yang, Etsuo Yonemochi, Xin Yue, Qun Zeng, Yizu Zhang, Tian Zhou, Yunfei Zhou, Roman Zubatyuk, Jason C Cole","doi":"10.1107/S2052520624007492","DOIUrl":"10.1107/S2052520624007492","url":null,"abstract":"<p><p>A seventh blind test of crystal structure prediction was organized by the Cambridge Crystallographic Data Centre featuring seven target systems of varying complexity: a silicon and iodine-containing molecule, a copper coordination complex, a near-rigid molecule, a cocrystal, a polymorphic small agrochemical, a highly flexible polymorphic drug candidate, and a polymorphic morpholine salt. In this first of two parts focusing on structure generation methods, many crystal structure prediction (CSP) methods performed well for the small but flexible agrochemical compound, successfully reproducing the experimentally observed crystal structures, while few groups were successful for the systems of higher complexity. A powder X-ray diffraction (PXRD) assisted exercise demonstrated the use of CSP in successfully determining a crystal structure from a low-quality PXRD pattern. The use of CSP in the prediction of likely cocrystal stoichiometry was also explored, demonstrating multiple possible approaches. Crystallographic disorder emerged as an important theme throughout the test as both a challenge for analysis and a major achievement where two groups blindly predicted the existence of disorder for the first time. Additionally, large-scale comparisons of the sets of predicted crystal structures also showed that some methods yield sets that largely contain the same crystal structures.</p>","PeriodicalId":7320,"journal":{"name":"Acta crystallographica Section B, Structural science, crystal engineering and materials","volume":" ","pages":""},"PeriodicalIF":1.3,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11789161/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142455733","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Polymorphism of Pb5(PO4)3OHδ within the LK-99 mixture. LK-99混合物中Pb5(PO4)3OHδ的多态性。
IF 1.3 3区 化学 Q3 CHEMISTRY, MULTIDISCIPLINARY Pub Date : 2024-12-01 DOI: 10.1107/S2052520624010023
Mingyu Xu, Haozhe Wang, Cameron Vojvodin, Jayasubba Reddy Yarava, Tuo Wang, Weiwei Xie

During the synthetic exploration targeting the polycrystalline compound LK-99, an unexpected phase, Pb5(PO4)3OHδ, was identified as a byproduct. We elucidated the composition of this compound through single-crystal X-ray diffraction analysis. Subsequent synthesis of the target compounds was achieved via high-temperature solid-state pellet reactions. The newly identified Pb5(PO4)3OHδ has an orthorhombic crystal structure with space group Pnma, representing a unique structure differing from the hexagonal apatite phases of Pb10(PO4)6O and Pb5(PO4)3OH. Comprehensive temperature- and magnetic-field-dependent magnetization studies unveiled a temperature-independent magnetic characteristic of Pb5(PO4)3OHδ. Solid-state nuclear magnetic resonance spectroscopy was employed to decipher the origins of the phase stability and confirm the presence of hydrogen atoms in Pb5(PO4)3OHδ. These investigations revealed the presence of protonated oxygen sites, in addition to the interstitial water molecules within the structure, which may play critical roles in stabilizing the orthorhombic phase.

在针对多晶化合物LK-99的合成探索过程中,发现了一种意想不到的副产物Pb5(PO4)3OHδ。我们通过单晶x射线衍射分析确定了该化合物的组成。随后的目标化合物的合成是通过高温固体球团反应实现的。新鉴定的Pb5(PO4)3OHδ具有具有空间基Pnma的正交晶型结构,与Pb10(PO4) 60和Pb5(PO4)3OH的六方磷灰石相不同,具有独特的结构。综合温度和磁场依赖性磁化研究揭示了Pb5(PO4)3OHδ与温度无关的磁特性。采用固体核磁共振波谱法分析了Pb5(PO4)3OHδ相稳定性的来源,并证实了Pb5(PO4)3OHδ中存在氢原子。这些研究表明,除了结构内的间隙水分子外,质子化氧位点的存在可能在稳定正交相中起关键作用。
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引用次数: 0
The seventh blind test highlights exciting developments in crystal structure prediction. 第七次盲测突出了晶体结构预测方面令人兴奋的发展。
IF 1.3 3区 化学 Q3 CHEMISTRY, MULTIDISCIPLINARY Pub Date : 2024-12-01 DOI: 10.1107/S2052520624011570
Mihails Arhangelskis

Two reports on the seventh blind test on crystal structure prediction extensively discuss the cutting-edge avant-garde methods of structure generation and energy ranking.

关于第七次晶体结构预测盲测的两篇报道广泛讨论了结构生成和能量排序的前沿前沿方法。
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引用次数: 0
The incommensurate composite YxOs4B4 (x = 1.161). 不相容的复合材料 YxOs4B4 (x = 1.161)。
IF 1.3 3区 化学 Q3 CHEMISTRY, MULTIDISCIPLINARY Pub Date : 2024-12-01 DOI: 10.1107/S205252062400982X
Berthold Stöger, Oksana Sologub, Leonid Salamakha

YxOs4B4 (x = 1.161) crystallizes as a tetragonal incommensurate composite of columns of Y atoms extending along [001] in an Os4B4 framework. The structure was refined using the superspace approach. The basic structure of the Y subsystem can be idealized as having I4/mmm symmetry, with a crystallographically unique Y atom located on the 4/mmm position. The actual superspace symmetry is P42/nmc(00σ3)s0s0. The Y atoms feature only subtle positional modulation in the [001] direction. The Os4B4 subsystem [P42/ncm(00σ3)00ss superspace symmetry] is built of columns of edge-sharing Os4 tetrahedra extending along [001] and B2 dumbbells. The Os4 tetrahedra feature pronounced positional modulation with a distinct variation of the Os-Os bond lengths. Modulation of the B2 dumbbells is best described as a rotation about the [001] axis.

YxOs4B4(x = 1.161)在 Os4B4 框架中结晶为由沿 [001] 延伸的 Y 原子列组成的四方不对称复合体。该结构采用超空间方法进行了细化。Y 子系统的基本结构可理想化为具有 I4/mmm 对称性,晶体学上唯一的 Y 原子位于 4/mmm 位置。实际的超空间对称性为 P42/nmc(00σ3)s0s0。Y 原子在 [001] 方向上只有细微的位置调制。Os4B4 子系统[P42/ncm(00σ3)00ss 超空间对称性]由沿[001]和 B2 哑铃延伸的边缘共享 Os4 四面体列组成。Os4 四面体具有明显的位置调制特征,Os-Os 键长度变化明显。B2 哑铃的调制最好地描述为围绕 [001] 轴的旋转。
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引用次数: 0
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Acta crystallographica Section B, Structural science, crystal engineering and materials
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