文献晶体数据改进示例26(THF占有率)

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文献晶体数据改进示例26(THF占有率)

案例来源：CCDC[1]: 2172922. Chem. Eur. J. 2022, 28, e202201897. DOI[2]: 10.1002/chem.202201897.

案例结构为四(四氢呋喃)双吲哚钙[(THF)4Ca(Ind)2]，如图1所示（由ChemBioDraw[3]绘制）。

▲图1[(THF)4Ca(Ind)2]结构

从CCDC下载其CIF[4]文件（2172922.cif）（参与推文“通过CCDC号下载CIF文件”“通过DOI号下载CIF文件”或视频“CCDC-Access Structures-根据CCDC号查找CIF文件：https://www.bilibili.com/video/BV1ZM4y1f7BJ”“CCDC-Access Structures-根据DOI查找CIF文件：https://www.bilibili.com/video/BV1Lb41197UH”）用Olex2[5]提取并打开CIF中嵌入的res和hkl文件（参与推文“提取CIF中的hkl和res文件”或视频“Olex2视频教程——从合并CIF文件中提取hkl文件进行精修：https://www.bilibili.com/video/BV1sb411W7MP”），在Work选项卡下Toolbox Work的Labels下拉菜单中选择Crystallographic Occupancy，如图2所示，其溶剂四氢呋喃（THF, , tetrahydrofuran, CAS: 109-99-9）的占有率为0.5，即不对称单元ASU（asymmetric unit）中含有0.5个THF，主体结构[(THF)4Ca(Ind)2]为1个，故而整体结构为[(THF)4Ca(Ind)2]·0.5THF，这与CIF中_chemical_formula_moiety（参阅推文“CIF核心词典-CHEMICAL_FORMULA”）条目值'2(C32 H44 Ca N2 O4), C4 H8 O'一致（结构式和分子式本质上是片段或原子数量比例）。

▲图2CCDC 2172922不对称单元结构

在Olex2中按下Ctrl+M查看差值电子密度图，如图3所示，溶剂THF处明显有绿色电子云密度，这表明THF的数量显然大于0.5个。

▲图3THF处差值电子密度图

可以对该THF的占有率使用自由变量进行整体统一自由精修，具体操作如下：选中整个THF，然后输入指令“part 1 41”（因为[(THF)4Ca(Ind)2]中配位的THF的无序已经占用了第2个和第3个自由变量，因此这里使用第4个自由变量，置于分组序号则随便，此处采用1），如图4所示。

▲图4设置THF占有率整体统一自由精修

精修后，该THF的占有率为0.98589（接近1），且THF处差值电子密度图变得十分干净，如图5所示，R1从8.61%降为6.53%，wR2从31.68%降为20.77%，很显然，单从晶体数据来看，该THF定为0.5个是不合理的。

▲图5THF占有率整体统一自由精修结果

把溶剂THF占有率定为1，并对结构中的一些无序进行处理，用SHELXL[6]指令OMIT（参阅推文“SHELXL指令之OMIT”）删除一些离群点（参阅推文“CheckCIF-B级警报PLAT934(如何删除衍射点)”或视频“CheckCIF-B级警报PLAT934(如何删除衍射点)：https://www.bilibili.com/video/BV1WJDJYbESq”“Olex2基操-OMIT指令的使用：https://www.bilibili.com/video/BV1av411e7f2”“Olex2中OMIT指令的使用：https://www.bilibili.com/video/BV1bw411D7Nb”），最终结果如图6所示，R1降为5.97%，wR2降为16.65%。

▲图6改进后的最终结果

综上所述，显然该结构建模为[(THF)4Ca(Ind)2]·THF比[(THF)4Ca(Ind)2]·0.5THF更加合理。

视频操作演示请参阅：

文献晶体数据改进示例26(THF占有率)：https://www.bilibili.com/video/BV1W1KTz4EYR

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参考文献

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