晶体结构解析案例75(残余峰严重扭曲结构-孪晶拆分)

DJ_Tokyo

晶体结构解析案例75(残余峰严重扭曲结构-孪晶拆分)

案例来源：CCDC[1] 2348841. Chem. Sci. 2024, 15, 20315‒20327. DOI[2]: 10.1039/d4sc04197f.

案例结构如图1所示（由ChemBioDraw[3]绘制）。

▲图1 案例结构

正常还原得到的数据，解析后金刚烷的一个碳碳键处存在很大残余峰严重扭曲了金刚烷的几何结构，如图2所示（由Olex2[4]呈现），即便在精修中添加了PLATON[5]检测到的孪晶法则也作用不大。

▲图2 残余峰扭曲金刚烷几何结构

使用PLATON生成的HKLF5格式文件精修，用SHELXL[6]指令DFIX（参阅推文“SHELXL指令之DFIX”）限制金刚烷几何结构，残余峰会增大，如图3所示。

▲图3 PLATON生成的HKLF5格式文件精修结果

其衍射图如图4所示（由APEX4[7]呈现），衍射点存在拖尾。

▲图4 衍射图

指标化得到晶胞参数以及三个正方向倒易空间点阵如图5所示。

▲图5 指标化和倒易空间点阵情况

按照推文“APEX4孪晶拆分步骤”方法对其做孪晶拆分，情况有所改善，如图6所示。

▲图6 孪晶拆分结果

视频操作：

单晶结构解析练习505(文献案例-数据还原-孪晶拆分)：https://www.bilibili.com/video/BV1K3PVemEML

数据下载：

论文PDF文档和CIF文件：

链接: https://pan.baidu.com/s/1NrwFAmrWlAddtcybJxX2yg

提取码: aj7h

晶体数据：

链接:https://pan.baidu.com/s/1OehLVjgoRVQ-lRwNp_uq3w

提取码: 76ga

参考文献

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[3]    (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.

[4]    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.

[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.

[6]    (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.

[7]    Bruker (2021). APEX4 (Version 2021.4-1). Program for Data Collection on AreaDetectors. Bruker AXS Inc., Madison, Wisconsin, USA.

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