文献晶体数据改进示例27(原子定错)

DJ_Tokyo

★声明：本文仅代表个人观点，笔者学识有限，资料整理过程中难免存在疏漏谬误，请不吝指正。

文献晶体数据改进示例27(原子定错)

案例来源：CCDC [1]: 2417860. DOI [2]: 10.5517/ccdc.csd.cc2m4zh8.(Inorg. Chem. Front. 2025, 12, 4606–4612. DOI: 10.1039/d5qi00735f.)

如图1所示（晶体结构由Olex2 [3]呈现，平面结构由ChemBioDraw [4]绘制，验证报告由PLATON [5]呈现），文献中将其结构解析为[(Ph3P)2CuOH]，在Olex2中查看差值电子密度发现，氧上明显的负差值电子密度（红色），表明该原子定为氧太大了（实际应当是比氧更小的原子），而且氧原子椭球比结构中铜和碳大很多，这些迹象都表明该处定为羟基不正确，而该羟基由于没有氢键受体从而触发了B级警报PLAT420（参阅推文“CheckCIF-PLAT420”）。

▲图1 文献报道结构

查看论文支持材料，可知其合成过程如图2所示。

▲图2 化合物合成过程

从上述分析可知，通过差值电子密度图可以判断，氧原子红色差值电子密度表明氧定大了，而氧周围4处绿色差值电子密度呈四面体四个顶点方向分布，再结合其合成反应式，笔者认为该处不是氢氧根离子，而是四氢硼酸根离子，修正后如图3所示，四氢硼酸根离子周围差值电子密度非常干净，硼原子椭球大小与铜和碳相当，此外R1由3.79%降为2.78%，wR2由10.25%降为6.52%，Max Peak由0.7降为0.3，Min Peak由-0.9降为-0.3，也没有AB级警报。

▲图3 修正结果

视频操作演示请参阅：

文献晶体数据改进示例27(原子定错)：https://www.bilibili.com/video/BV1vrqiBDEBZ

如需论文PDF文档和CIF文件，请从以下链接下载：

链接:https://pan.baidu.com/s/1OZ5pCtmwh-YaRzB-BbTcYw?pwd=22r7

提取码: 22r7

参考文献

[1]    (a) Allen, F. H.The Cambridge Structural Database: A Quarter of a Million Crystal Structuresand Rising. Acta Cryst. 2002, B58, 380–388. DOI:10.1107/S0108768102003890. (b) Groom, C. R.; Bruno, I. J.; Lightfoot, M.P.; Ward, S. C. The Cambridge Structural Database. Acta Cryst. 2016, B72, 171–179. DOI:10.1107/S2052520616003954. (c) Mitchell, J.; Robertson, J. H.; Raithby,P. R. Cambridge Crystallographic Data Centre (CCDC). Comprehensive Coordination Chemistry III 2021, 413–437. DOI:10.1016/B978-0-12-409547-2.14829-2.

[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 for Standardization(2022). ISO 26324:2022. Information andDocumentation – 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) Klein, F. M.CS ChemDraw Pro,1 Version 3.1 for Windows. J.Chem. Inf. Comput. Sci. 1995, 35, 166–167. DOI: 10.1021/ci00023a026. (b)Cousins, K. R. ChemDraw 6.0 Ultra CambridgeSoft Corporation, 100 Cambridge ParkDrive, Cambridge, MA 02140. http://www.camsoft.com. Commercial Price:  $1395.Academic Price:  $699. J. Am. Chem. Soc. 2000, 122, 10257–10258. DOI: 10.1021/ja0047572.(c) Buntrock, R. E. ChemOffice Ultra 7.0. J.Chem. Inf. Comput. Sci. 2002, 42, 1505–1506. DOI: 10.1021/ci025575p. (d) Li, Z.; Wan, H.; Shi, Y.;Ouyang, P. Personal Experience with Four Kinds of Chemical Structure DrawingSoftware: Review on ChemDraw, ChemWindow, ISIS/Draw, and ChemSketch. J. Chem.Inf. Comput. Sci. 2004, 44, 1886–1890. DOI: 10.1021/ci049794h.(e) Mendelsohn, L. D. ChemDraw8 Ultra, Windows and Macintosh Versions. J.Chem. Inf. Comput. Sci. 2004, 44, 2225–2226. DOI: 10.1021/ci040123t. (f) Cousins, K. R. ChemDrawUltra 9.0. CambridgeSoft, 100 CambridgePark Drive, Cambridge, MA 02140. www.cambridgesoft.com. See Web site for pricing options. J. Am. Chem. Soc. 2005, 127, 4115–4116. DOI:10.1021/ja0410237. (g) Zielesny, A. Chemistry Software PackageChemOffice Ultra 2005. J. Chem. Inf.Model. 2005, 45, 1474–1477. DOI:10.1021/ci050273j. (h) Mills, N. ChemDraw Ultra 10.0 CambridgeSoft, 100CambridgePark Drive, Cambridge, MA 02140. www.cambridgesoft.com. CommercialPrice:  $1910 for download, $2150 for CD-ROM; Academic Price:  $710 fordownload, $800 for CD-ROM. J. Am. Chem.Soc. 2006, 128, 13649–13650. DOI: 10.1021/ja0697875. (i) Kerwin, S. M.ChemBioOffice Ultra 2010 Suite. J. Am. Chem.Soc. 2010, 132, 2466–2467. DOI: 10.1021/ja1005306. (j) Milne, G. W. A. SoftwareReview of ChemBioDraw 12.0. J. Chem. Inf.Model. 2010, 50, 2053. DOI:10.1021/ci100385n. (k) Narayanaswamy, V. K.; Rissdörfer, M.; Odhav, B.Review on CambridgeSoft ChemBioDraw Ultra 13.0v. Int. J. Theor. Appl. Sci. 2013,5, 43–49.

[5]    (a) Spek, A. L. Single-CrystalStructure Validation with the Program PLATON.J. Appl. Cryst. 2003, 36, 7–13. DOI: 10.1107/S0021889802022112.(b) Spek, A. L. StructureValidation in Chemical Crystallography. ActaCryst. 2009, D65, 148–155. DOI:10.1107/S090744490804362X. (c) Spek, A. L. What Makes a Crystal Structure Report Valid? Inorg. Chim. Acta 2018, 470, 232–237. DOI:10.1016/j.ica.2017.04.036. (d) Spek, A. L. checkCIFValidation ALERTS: What They Mean and How to Respond. Acta Cryst. 2020, E76, 1–11. DOI: 10.1107/S2056989019016244.