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晶体数据审稿意见-原子指认错误or数据处理问题 案例来源：CCDC[1] 2371872. RSCAdv. 2024, 14, 27697–27702. DOI[2]: 10.1039/d4ra05219f. 审稿意见： Pleaseexamine the attached residual density plot and othergraphs. The Cd atom refines freely to an occupancy of only 85%—this iseither not a Cd atom, there is something else on this site, or it is due toissues in your data processing pipeline. Either way, you must identify the cause of this and eliminateit. The reported R1 is 3.53%. The attached residual density plot clearly shows that atom Cd1 appears to be over-assigned. The Fractal Dimension Plot (according to K. Meindl and J. Henn (2008), Acta Cryst. A64, 404-418) is another way to visualise the problem. When refined freely, Cd1 will refine to an occupancy of ~85%, with a drop in R1 to 2.82%. Alternatively, this atom could be refined as a fully occupied Ru (!) with similarly low R values (but the bond distances are not compatible with such an assignment). Whateverthe reason, it must be found and eliminated. The best way forward is to collectnew data on this material. 大意： 请检查随附的残余密度图和其他图表。 Cd原子自由精修只有85%的占有率——这要么不是Cd原子，这个位点上是其他东西，要么是数据处理存在问题。无论哪种情况，都必须找出原因并将其消除。 报告的R1为3.53%。所附的残余密度图清楚地表明，原子Cd1似乎被过度分配了。分形维数图（根据K. Meindl and J. Henn (2008), Acta Cryst.A64, 404-418）是可视化该问题的另一种方式。 当自由精修时，Cd1将精修至约85%的占有率，R1降至2.82%。或者，这个原子可以被精修为具有类似低R值的全占据的Ru（！）（但键距离与这种分配不兼容）。 无论出于什么原因，都必须找出并将其消除。最好的办法是收集有关这种材料的新数据。 用Olex2[3]打开其数据，按快捷组合键Ctrl+M打开差值电子密度图，如图1所示，金属Cd1附近是负的差值电子密度（红色）。
▲图1 数据情况 将金属Cd1的占有率自由精修（精修程序为SHELXL[4]），结果大约为91.37%（投稿时的数据自由精修后约为85%，当前发表的这个数据是重新测试得到的），R因子也降低不少，如图2所示。
▲图2 金属占有率自由精修结果 视频讲解请参阅： 晶体数据审稿意见-原子指认错误or数据处理问题：https://www.bilibili.com/video/BV1nt1RYGEvh 如需论文和已发表CIF[5]文件，请从以下链接下载： 提取码: yz45 参考文献： [1] (a) Allen, F. H. The Cambridge StructuralDatabase: a quarter of a million crystal structures and rising. Acta Cryst. 2002, B58, 380–388. DOI: 10.1107/S0108768102003890. (b) Allen, F. H. TheCambridge Structural Database: a quarter of a million crystal structures andrising. Acta Cryst. 2016, B72, 171–179. DOI:10.1107/S2052520616003954. [2] (a) InternationalOrganization for Standardization (2012). ISO 26324:2012. Information and Documentation – Digital Object Identifier System. http://www.iso.org/iso/catalogue_detail.htm?csnumber=43506. (b) McDonald J. D.;Levine-Clark, M. Encyclopedia of Libraryand Information Sciences. Fourth Edition, CRC Press, 2017. DOI: 10.1081/e-elis4. (c) Liu, J. Digital ObjectIdentifier (DOI) and DOI Services: An Overview. Libri 2021, 71, 349‒360. DOI:10.1515/libri-2020-0018. (d) International Organization forStandardization (2022). ISO 26324:2022. Informationand Documentation – Digital Object Identifier System. https://www.iso.org/standard/81599.html[3] 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. [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 scatteringfactors for SHELXL – model,implementation and application. ActaCryst. 2019, A75, 50–62. DOI:10.1107/S2053273318013840. [5] (a) Hall, S. R.; Allen, F. H. Brown, I. D.The Crystallographic Information File (CIF): a New Standard Archive File forCrystallography. Acta Cryst. 1991, A47, 655–685. DOI:10.1107/S010876739101067X. (b) Hall, S. R. The STAR File: A New Formatfor Electronic Data Transfer and Archiving. J.Chem. Inf. Comput. Sci. 1991, 31, 326–333. DOI:10.1021/ci00002a020. (c) Hall, S. R.; Spadaccini, N. The STAR File:Detailed Specifications. J. Chem. Inf.Comput. Sci. 1994, 34, 505–508. DOI:10.1021/ci00019a005. 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。 如需PDF文档，请从以下链接下载： 通过网盘分享的文件：晶体数据审稿意见-原子指认错误or数据处理问题.pdf
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发表于 2025-8-13 07:13:53
