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晶体数据审稿意见-CCDC2057105(无序处理) 案例来源：CCDC[1] 2057105. New J. Chem. 2024, 48, 18695–18699.DOI[2]: 10.1039/d4nj03582h. 审稿意见如下： | 审稿意见 | | There are 4 Structures in this paper. We examined this file: 2057102-2063197. | 该论文中有4个结构。我们检查了这些文件：2057102‒2063197。 | The following CIF items are missing from at least one structure: | | _computing_data_collection | _computing_data_collection | In some structures, 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. | 在某些结构中，使用了溶剂遮掩，但CIF中没有关于这一过程的报道。这是不可接受的。您必须提供有关被遮掩部分的估计数量和性质的信息。 | 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. | 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、孔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，导致许多后续量（如密度、分子量、F000和吸收系数μ）的报道不正确。 | "The chemical formula must be consistent with the atomic content specified by the _atom_site_ information, and match the _chemical_formula_weight. If atoms are missing from the atomic model (e.g. unlocated H atoms or solvent molecules suppressed by the 'SQUEEZE' or similar approach), the moiety and sum formulae should state the assumed overall formula." | “化学分子式必须与_atom_site_信息指定的原子内容一致，并与_chemical_formula_weight相匹配。如果原子模型中缺失原子（例如未定位的氢原子，或者由‘SQUEEZE’或类似方法抑制的溶剂分子），单体分子式和总体分子式应指明假定的总体子式。” | | |
上述是总体审稿意见，以下为单独审稿意见： | 审稿意见 | | **4** (CCDC 2057105) The R factors are too high, and the missed disorder is clearly visible from the residual density plot. This is very easy to model in will lower R1 to around 7.3%. Please report what has been masked properly (see above). | **4** (CCDC 2057105) R因子太高，未处理的无序很明显能从残余密度图中看出来。这很容易建模，并且将使R1降低至约7.3%。 请正确报道遮掩的内容（见上文）。 | Structure 4 (CCDC 2057105): C66 H75 Cl Fe2 N3 P3 These CheckCif A and B alerts are raised by this structure: 910_ALERT_3_B Missing # of FCF Reflection(s) Below Theta(Min). 18 Note The crystal size is reported as ? x ? x ? mm. | 结构4（CCDC 2057105）：C66 H75 Cl Fe2 N3 P3 该结构存在以下A和B级警报： 910_ALERT_3_B Missing # of FCF Reflection(s) Below Theta(Min). 15 Note 报道的晶体尺寸是? x ? x ? mm。 | Please ensure that no CheckCif alerts remain, and if any do, please comment on them and explain why it is impossible to address these issues. You will have to re-process your diffraction data carefully. | 请确保没有CheckCif警报（注：此处指的是A级和B级警报），如果有，请对其进行评论，并解释为何无法解决这些问题（请勿忽略这后半句，参与推文“晶体领域中的断章取义”）。您必须仔细重新处理衍射数据。 |
如图1所示，该结构投稿时用Olex2[4]的Solvent Mask[5]例程做了溶剂遮掩，但没有报道遮掩的内容，正如审稿人所说，右边的金刚烷基团从残余密度图来看明显存在无序。 ▲图1 CCDC 2057104（投稿） 笔者帮其取消了溶剂遮掩，并建模了溶剂（四氢呋喃），并对该金刚烷基做了二组分无序，结果如图2所示，残余密度图干净多了，残余峰以及R因子均降低不少。 ▲图2 CCDC 2057104（发表） ▲图3 B级警报PLAT910解释说明 取消溶剂遮掩，将溶剂进行妥善建模后得到如下回复： | Thank you for your comments and corrections and modelling of the solvent. | 感谢您的评论和修正，以及对溶剂的建模。 |
但是不要忘了修改论文中的描述： | The experimental still states that Squeeze was used however the solvent has now been modelled, please remove this and give details of the solvent modelling. Please also add in details of the disorder modelling and twinning once modelled. | 实验部分仍然指出使用了Squeeze，但现已建模溶剂，请删除此描述，并给出溶剂建模的详情。请添加无序建模和孪晶建模的详情。 |
如需数据进行练习，请从以下链接下载： 论文PDF文档和CIF文件： 提取码: 9m39 晶体数据： 提取码: wpza 视频讲解请参阅： 晶体数据审稿意见-CCDC2057105(无序处理)：https://www.bilibili.com/video/BV1roKWeCEY5 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. (c) Mitchell, J.; Robertson, J. H.; Raithby,P. R. Cambridge Crystallographic Data Centre (CCDC). Comprehensive Coordination Chemistry III 2021, 413–437. DOI:10.1016/B978-0-12-409547-2.14829-2. [2] (a) InternationalOrganization for Standardization (2012). ISO 26324:2012. Information and Documentation – Digital Object Identifier System. http://www.iso.org/iso/catalogue_detail.htm?csnumber=43506. (b) McDonald J. D.;Levine-Clark, M. Encyclopedia of Libraryand Information Sciences. Fourth Edition, CRC Press, 2017. DOI: 10.1081/e-elis4. (c) Liu, J. Digital ObjectIdentifier (DOI) and DOI Services: An Overview. Libri 2021, 71, 349‒360. DOI:10.1515/libri-2020-0018. (d) International Organization for Standardization(2022). ISO 26324:2022. Information andDocumentation – Digital Object Identifier System. https://www.iso.org/standard/81599.html[3] (a) Hall, S. R.;Allen, F. H. Brown, I. D. The Crystallographic Information File (CIF): A NewStandard Archive File for Crystallography. ActaCryst. 1991, A47, 655–685. DOI:10.1107/S010876739101067X. (b) Hall, S. R. The STAR File: A New Formatfor Electronic Data Transfer and Archiving. J.Chem. Inf. Comput. Sci. 1991, 31, 326–333. DOI:10.1021/ci00002a020. (c) Hall, S. R.; Spadaccini, N. The STAR File:Detailed Specifications. J. Chem. Inf.Comput. Sci. 1994, 34, 505–508. DOI:10.1021/ci00019a005. [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] Spek, A. L.; vander Sluis, P. BYPASS: An EffectiveMethod for the Refinement of Crystal Structures Containing Disordered SolventRegions. Acta Cryst. 1990, A46, 194–201. DOI:10.1107/S0108767389011189. 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：晶体数据审稿意见-CCDC2057105(无序处理).pdf
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发表于 2025-4-17 07:07:57
