无序示例-羧基和醛基共占据混合无序(无序代表的化学意义)

DJ_Tokyo

相关软件或概念：Olex2[1] (Version: Olex2-1.5); SHELXL[2] (Version: SHELXL-2019/3); Mercury[3] (Version: Mercury 2023.2.0 (build 382240));CCDC[4]; CIF[5]

案例来源：CCDC2338815, DOI: 10.5517/ccdc.csd.cc2jhqnf.

该分子中羧基的羟基氧（O1）处差值电子密度表明该原子定大了，要么是比氧更小的原子，要么不是全占位，如图1所示。

▲图1 原子O1处差值电子密度

将O1的占有率放开精修（即自由精修），结果为0.78903，如图2所示。

▲图2 O1占有率自由精修结果

结合化合物原料推测，该处应为醛基或羧基，而从O1占有率自由精修结果看，显然此处应是醛基和羧基的共占据混合无序，将该羟基用PART 1分组，并赋予其自由变量，加氢后，精修至收敛后，羧基和醛基的比例为0.769:0.231，如图3所示。

▲图3 无序处理结果

上述无序结果代表该晶体结构为如图4所示两个化合物的混合物，其比例为76.9%和23.1%。

▲图4 无序代表的结构

视频操作演示请参阅：

单晶结构解析练习78：https://www.bilibili.com/video/BV1qi421o7R7

参考文献

[1]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.

[2](a) Sheldrick, G. M. SHELXL-2019/3, Program for Crystal Structure Refinement,University of Göttingen, Germany, 2019. (b) Sheldrick, G. M. A short history ofSHELX. Acta Cryst. 2008, A64, 112–122. (c) Sheldrick, G. M.Crystal structure refinement with SHELXL.Acta Cryst. 2015, C71, 3–8. (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.

[3]Macrae, C. F., Edgington, P. R., McCabe, P., Pidcock, E., Shields, G. P.,Taylor, R., Towler, M. & van de Streek, J. (2006). J. Appl. Cryst. 39,453-457.

[4](a) Allen, F. H. The Cambridge Structural Database: a quarter of a millioncrystal structures and rising. ActaCryst. 2002, B58, 380–388. (b) Allen, F. H. TheCambridge Structural Database: a quarter of a million crystal structures andrising. Acta Cryst. 2016, B72, 171–179.

[5](a) Hall, S. R.; Allen, F. H. Brown, I. D. The Crystallographic InformationFile (CIF): a New Standard Archive File for Crystallography. Acta Cryst. 1991, A47, 655–685. (b)Hall, S. R. The STAR File: A New Format for Electronic Data Transfer andArchiving. J. Chem. Inf. Comput. Sci.1991, 31, 326–333. (c) Hall, S. R.; Spadaccini, N. The STAR File:Detailed Specifications. J. Chem. Inf.Comput. Sci. 1994, 34, 505–508.

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