晶体结构扣除溶剂后在论文中的描述

有小伙伴向笔者提了如下问题：

想请教您一个问题，我们单晶包裹溶剂的话，用的都是squeeze，讨论的结构都是去溶剂之后的，但是审稿人给出这个意见是什么意思呢？

The word 'squeeze' or 'mask' also does not appear in the MS. The chemical formula for this material (and the other one) is also missing from the MS.

从问题描述来看，提问者的晶体数据，用软件将结构中的溶剂去除了，也就是“squeeze”（挤出）或“mask”（遮掩），然而并没有在论文中对这一操作进行说明。

与此相关的还有审稿意见：

For the solvent masking, you must report the masked species in the moiety formula and add their atoms to the sum formula. [ solvents] is not acceptable, the square brackets should contain the solvents that were masked.

该审稿意见处理相关视频：https://www.bilibili.com/video/BV1Td4y1475w

上述两个审稿意见所表达的意思差不多，作者提交的晶体数据做了去除溶剂贡献的操作，但无论是在论文正文、支撑信息还是晶体数据中，均未对这一操作做任何相关说明。如果晶体数据执行了去除溶剂贡献的操作，则通常需要回答这些问题：

（1）溶剂贡献的扣除原因？

（2）溶剂贡献的扣除种类？

（3）溶剂贡献的扣除数量？

此处的溶剂不单单特指溶剂，也可以是离子等。

扣除溶剂可采用PLATON[1]中的SQUEEZE[2]程序或Olex2[3]中的Solvent Mask[4]程序来执行。操作步骤可参阅推文“去除无序溶剂对计算结构因子的贡献”。

案例1：CrystEngComm, 2017, 19, 4709–4712. (DOI: 10.1039/C7CE00849J. CCDC: 1545666)

该案例中，在论文正文对此做了说明，由于抗衡离子质子化的胺（3,5-dimethylpiperidine(3,5-二甲基哌啶)——扣除物种）无序严重（扣除原因），故而使用SQUEEZE将其扣除，最后在确定的分子式中给出了扣除数量（且补充了另外的物种水分子及其数量），如图1.1所示。（此处扣除的不是溶剂，而是抗衡离子。）

其不对称单元（ASU）如图1.2所示，ASU中没有任何CHNO等原子，应是手动在CIF文件中“_chemical_formula_sum”项添加了这些原子及其数量，不过并未编辑“_chemical_formula_moiety”项，如图1.3所示。

案例2：Sci. China Chem. 2023, 66, 117–126. (DOI: 10.1007/s11426-022-1396-x. CCDC: 2152634)

该案例中，在支撑信息中对此做了说明，如图2.1所示，由于一个（扣除数量）游离的溶剂分子甲苯（扣除种类）严重无序（扣除原因），故使用Solvent Mask将其扣除。

案例3：Dalton Trans. 2020, 49, 8933–8948. (DOI: 10.1039/D0DT00729C. CCDC: 1936173)

该案例中，在论文正文对此做了说明，如图3.1所示，由于抗衡离子K+和水分子（扣除种类）无序严重（扣除原因），故使用Solvent Mask将其扣除，并将12个K+和44个水（扣除数量）添加到分子式中。

其结构和Solvent Mask情况如图3.2所示，Solvent Mask计算结果是在约3498 Å3体积中扣除了约617个电子，作者根据电荷平衡、元素分析、热重分析等，推测扣除的物种是44个水（电子数：44 × 10 = 440）和12个K+（电子数：12 × 18 = 216），总计为440 + 216 = 656。

其CIF文件中分子式如图3.3所示，“_chemical_formula_moiety”项中有2个K，加上推测的12个K，共14个K，这和“_chemical_formula_sum”中K的数量对应；“_chemical_formula_moiety”项中的15(O)，应该是15个水，加上推测的44个水，共计59个水，也就是118个H和59个O，氧的数量为177 + 59 = 236，这和“_chemical_formula_sum”中O的数量对应，然而氢的数量为31 + 118 = 149，这和“_chemical_formula_sum”中H的数量170无法对应，不知是作者手动编辑输入错误，还是其他原因。

一些相关审稿意见：

例1：

1. The investigation shows that there is not ethanol/water solvent, but most likely two disordered ethanol molecules. However, exact localization of these molecules at room temperature is very problematic even for experts.

I obtained R-factor 5.4% with two disordered ethanol molecules.

2. I generally do not support use of SQUEEZE procedure, but in this particular case I would recommend you to do so and use solvent mask.

This way, I obtained R-factor 4.5%

3. Please, re-refine the structure either using disordered solvent model or using solvent mask procedure.

4. The structure represents bis-ethanol solvate, no water here, please make corrections.

5. If you decide to go with the solvent mask, this must be explicitly stated in the paper

6. I see your description of hydrogen bonds is wrong. Please, check carefully and make corrections.

7. The rest of my criticisms from the previous letter applies. I apologize for losing your res and hkl files.

例2：

There are two cyanide ions in the solvent sphere -- but these are not mentioned in the text. Where do they come from?

If you are not particularly interested in the solvent sphere, I recommend using a solvent mask for these moieties and concentrate on getting the best model of the main molecule.

I attach a refinement with an R1 of 4.17% (down from 8.22%). I have masked everything in the solvent sphere (and assumed it is all water) and have modelled the disorder that is obvious in one part of the main molecule. Please have a look at this structure and take it from there.

参考文献

[1] (a) Spek, A. L. Single-crystal structure validation with the program PLATON. J. Appl. Cryst. 2003, 36, 7–13. (b) Spek, A. L. Structure validation in chemical crystallography. Acta Cryst. 2009, D65, 148–155. (c) Spek, A. L. What makes a crystal structure report valid? Inorg. Chim. Acta 2018, 470, 232–237. (d) Spek, A. L. checkCIF validation ALERTS: what they mean and how to respond. Acta Cryst. 2020, E76, 1–11.

[2] Spek, A. L. PLATON SQUEEZE: a tool for the calculation of the disordered solvent contribution to the calculated structure factors. Acta Cryst. 2015, C71, 9−18.

[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.

[4] Rees, B.; Jenner, L.; Yusupov, M. Bulk-solvent correction in large macromolecular Structures. Acta Cryst. 2005, D61, 1299−1301.