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Olex2中如何把溶剂遮掩内容添加到总分子式中(审稿意见) 案例来源：CCDC[1] 2067415. New J. Chem. 2022, 46, 2465–2471. DOI[2]: 10.1039/d1nj05548h. 案例结构如图1所示（由ChemBioDraw[3]绘制）完整结构（C47H66Cl2N3O4Yb）由主体结构分子（C43H58Cl2N3O3Yb）和溶剂分子（C4H8O）构成。 ▲图1 案例结构 | 审稿意见 | | A solvent mask has been used, but nothing regarding this process has been reported in the CIF. This is not acceptable. You must provide information regarding the estimated number and nature of the masked moieties. The relevant information should be readily available from the TGA/DSC results, the knowledge of the crystallisation conditions and, finally, from the number of masked electrons, the size of the void and the relative position of electron density peaks before the mask was applied. | 已使用溶剂遮掩，但CIF中没有关于该过程的任何报道。这是不可接受的。您必须提供有关遮掩部分的估计数量和性质的信息。相关信息应易于从热重分析/差示扫描量热法结果、结晶条件信息以及最后从遮掩电子的数量、空隙的大小和施加遮掩之前电子密度峰的相对位置获得。 | The reported formulae must contain the masked moieties, leading to the incorrect reporting of many follow-on quantities like the density, molecular mass, F000 and absorption coefficient μ. | 所报道的分子式必须包含遮掩部分，否则会导致许多后续量（如密度、分子量、F000和吸收系数μ）的报告不正确。 |
当采用Olex2中的Solvent Mask将结构模型中的四氢呋喃删去，在176立方埃体积中恢复了49个电子，1个四氢呋喃的电子数为40个，因此删除的如果都是四氢呋喃，则其数量为49/40 = 1.225个，在Content/Asymmetric Unit中填入内容“1.225 C4H8O”（或“1.225 THF”，程序可以识别THF），在该列表下方有两个按钮“Formula +”和“Moiety +”，点击“Formula +”可以将删除的1.225个四氢呋喃分子式添加到CIF的“_chemical_formula_sum”条目中，而点击“Moiety +”可以将删除的1.225个四氢呋喃分子式添加到CIF的“_chemical_formula_moiety”条目（参阅推文“CIF核磁词典-CHEMICAL_FORMULA”）中。点击“Formula +”后，Olex2中分子式由“C43H58Cl2N3O3Yb”更新为“C47.9Cl2H67.8N3O4.2Yb”，并且分子式后有一个刷新分子式按钮，且有SHELXL[9]输出提示“Cell contents from UNIT instruction and atomlist do not agree”（参阅推文“SHELXL提示Cell contents fromUNIT instruction and atom list do not agree何意”或视频“结构精修中Cell contents from UNIT instruction and atomlist do not agree提示何意：https://www.bilibili.com/video/BV1iZ421N7tB”），如图2右图所示，这些提示不要理会，也不要点击分子式后面的刷新按钮，因为点击该按钮就使得“_chemical_formula_sum”条目中只有已建模模型的分子式，如图2左图所示。 ▲图2 溶剂遮掩结果 是否将溶剂遮掩内容添加到总分子式中造成的CIF条目变化如下： | CIF条目 | | | | | 'C47.90 H67.80 Cl2 N3 O4.23 Yb' | | | | _exptl_absorpt_coefficient_mu | | | _exptl_crystal_density_diffrn | | | | | |
对于checkCIF/PLATON验证报告，如图3‒4所示，只要做了溶剂遮掩，分子式的计算值（Calculated）中均有“[+ solvent]”字样，而是否将溶剂遮掩的部分添加到总分子式中则会使得验证报告中分子量（Mr）、密度（Dx, g cm‒3）和F000的计算值和报道值（Reported）存在差异。 ▲图3 验证报告（总分子式 = 主体结构分子） ▲图4 验证报告（总分子式 = 主体结构分子 + 遮掩掉的溶剂） ▲图5 验证报告（总分子式 = 主体结构分子） ▲图6 验证报告（总分子式 = 主体结构分子 + 遮掩掉的溶剂） 造成上述验证报告差异原因如下： CIF中只记录已建模模型的原子列表信息，不记录未建模结构的原子列表信息（因为没建模，所以没有），而通过溶剂遮掩删去的未建模结构部分只是从数据处理上抹去了，实际上这部分抹去的结构也是晶体样品的结构组成部分（参阅推文“晶体(CIF)结构与实际结构之间的差别”），不论从实事求是，尊重客观事实的角度还是从数据处理规范的角度来说，通过数据处理抹去的结构应当添加到总分子式中（所以如果没有这么做，就会出现开头的审稿意见），并在论文中进行说明，而checkCIF/PLATON系统的计算值（Calculated）只统计已建模的结构信息。 视频操作和讲解请参阅： Olex2中如何把溶剂遮掩内容添加到总分子式中(审稿意见)：https://www.bilibili.com/video/BV1wafnYUEXX 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. 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ActaCryst. 2019, A75, 50–62. DOI:10.1107/S2053273318013840. 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：Olex2中如何把溶剂遮掩内容添加到总分子式中(审稿意见).pdf
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发表于 2025-6-17 06:59:48
