| Data process and reduce: APEX4[1] GUI: Olex2[2] Structure solution: SHELXT[3] Structure refinement: SHELXL[4] Space group determination: XPREP[5] |
案例来源：Dalton Trans. 2023, 52, 13146–13153. DOI[6]: 10.1039/d3dt02460a.CCDC[7]: 2262744. | | Structure 230222d-iPr-NH (CCDC 2262744): C30 H46 Cl4 Co N2 - Looking at the HKLF instruction it seems that the cell has been changed after the initial integration, the data should really be reintegrated in the correct cell. This may also help to improve the Rint. Again the I/sigma drops below 3 at ~2theta = 45, if this remains the case after reintegration the data should be truncated here and a note added to the experimental. These CheckCif A and B alerts are raised by this structure. This is for your information only - you may wish to address these issues before re-submitting your cif file to the CCDC. 414_ALERT_2_A Short Intra D—H..H-X H2 ..H27 1.61 Ang. The Ueq values of the following atoms are extremely large (Ueq = > 0.15). Either the occupancy is set too high for these atom, or you might need to explore the possibility that these atoms are involved in some form of disorder: Cl3 Cl4 C30. Answer: Effective data standards (I/sigma above 2) were applied to the new data integration process, thus the data were truncated by 0.91 Å (2θ = 45°). The disordered dichloromethane (labeled as Cl3 Cl4 C30) has been treated properly. The alert "414_ALERT_2_A Short Intra D—H..H-X H2 ..H27 1.61 Ang." have been solved. A new alert "THETM01_ALERT_3_A The value of sine(theta_max)/wavelength is less than 0.550 Calculated sin(theta_max)/wavelength = 0.5477" was raised due to the data truncation and a proper author response was added into the new cif file, which have been updated in CCDC. | 结构230222d-iPr-NH (CCDC 2262744): C30 H46 Cl4 Co N2 查看HKLF指令，看起来在最初积分之后晶胞已改变，数据应当在正确晶胞下重新积分。这可能也有助于改善Rint。还有，信噪比I/sigma在2θ约为45°时降至低于3，如果重新积分仍然如此则应将数据截断于此，并在实验部分进行说明。 该结构出现以下CheckCif A和B警报。此信息仅供参考——您可能希望在将您的CIF重新提交给CCDC之前解决这些问题。 414_ALERT_2_A Short Intra D—H..H-X H2 ..H27 1.61 Ang. 以下这些原子的Ueq值太大（Ueq大于等于0.15）。要么这些原子的占有率设置太高，要么这些原子可能存在某种形式的无序：Cl3 Cl4 C30。 答复：在新的数据积分过程中应用了有效数据标准（信噪比大于2），因此数据截断在0.91 Å（2θ = 45°）。无序的二氯甲烷（Cl3 Cl4 C30）已进行适当处理。警报“414_ALERT_2_A Short Intra D—H..H-X H2 ..H27 1.61 Ang.”已解决。由于数据截断出现了一个新的警报“THETM01_ALERT_3_A The value of sine(theta_max)/wavelength is less than 0.550 Calculated sin(theta_max)/wavelength = 0.5477”，该问题在CCDC中已更新的新CIF中给出了适当的作者回应。 |
如图1所示，该结构中HKLF指令中有一个变换矩阵（transformationmatrix），审稿人认为当前晶胞在积分之后发生了变化，要求重新在正确的设置下进行数据还原，游离的溶剂二氯甲烷Ueq值过大，需要进行相应的处理（无序）。 ▲图1 CCDC 2262744结构投稿状态 如图2所示，分辨率高于0.93 Å（2θ = 45°）时信噪比已开始低于3，因此审稿人认为这些信噪比低于3的数据其实是噪音，要求将数据分辨率截断于此。 ▲图2 数据分辨率情况 结构解析已经知道正确空间群为单斜晶系的P21/c，因此在数据处理的Bravais Lattice这一步选择程序默认的Monoclinic P进行后续处理即可，如图3所示。 ▲图3 Bravais Lattice选择 根据审稿人意见以及数据统计，在图像积分这一步将分辨率截断设置为0.93 Å（或者按照信噪比大于2的标准截断至0.91 Å）即可，如图4所示。 ▲图4 分辨率截断 重新处理结果如图5所示，在正确对称性设置下还原的数据，HKLF指令后就没有变换矩阵了，对结构中的无序做了适当处理。 ▲图5 ▲图1 CCDC 2262744结构发表状态 视频演示操作请参阅： 审稿意见-为什么要在正确的晶胞下进行数据还原1：https://www.bilibili.com/video/BV1Pu411K753 如需论文文档以及晶体数据用于练习，可从以下链接下载： （1） 链接：https://pan.quark.cn/s/8f02e59de58e 提取码：q7Gi （2） 链接：https://pan.baidu.com/s/1I87QY8mg1Tx8ZwS7I07ThA 提取码：j1um | [1] Bruker (2021). APEX4 (Version 2021.4-1). Program for Data Collection on Area Detectors. Bruker AXS Inc., Madison, Wisconsin, USA. [2] Dolomanov, O. V.; Bourhis, L. J.; Gildea, R. J.; Howard, J. A. K.; Puschmann, H. OLEX2: A Complete Structure Solution, Refinement and Analysis Program. J. Appl. Cryst. 2009, 42, 339–341. DOI: 10.1107/S0021889808042726. [3] Sheldrick, G. M. SHELXT – Integrated Space-Group and Crystal Structure Determination. Acta Cryst. 2015, A71, 3–8. DOI: 10.1107/S2053273314026370. [4] (a) Sheldrick, G. M. SHELXL-2019/3, Program for Crystal Structure Refinement, University of Göttingen, Germany, 2019. (b) Sheldrick, G. M. A Short History of SHELX. Acta Cryst. 2008, A64, 112–122. DOI: 10.1107/S0108767307043930. (c) Sheldrick, G. M. Crystal Structure Refinement with SHELXL. Acta Cryst. 2015, C71, 3–8. DOI: 10.1107/S2053229614024218. (d) Lübben, J.; Wandtke, C. M.; Hübschle, C. B.; Ruf, M.; Sheldrick, G. M.; Dittrich, B. Aspherical scattering factors for SHELXL – model, implementation and application. Acta Cryst. 2019, A75, 50–62. DOI: 10.1107/S2053273318013840. [5] Bruker (2014). XPREP (Version 2014/2), Program for Space Group Determination. Bruker AXS Inc., Madison, Wisconsin, USA. [7] (a) Allen, F. H. The Cambridge Structural Database: a quarter of a million crystal structures and rising. Acta Cryst. 2002, B58, 380–388. DOI: 10.1107/S0108768102003890. (b) Allen, F. H. The Cambridge Structural Database: a quarter of a million crystal structures and rising. Acta Cryst. 2016, B72, 171–179. DOI: 10.1107/S2052520616003954. |
| 声明：本文仅代表个人观点，笔者学识有限，资料整理过程中可能存在疏漏错误，请不吝指正。 |
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