晶体数据审稿意见-溶剂遮掩说明和游离水加氢

DJ_Tokyo

晶体数据审稿意见-溶剂遮掩说明和游离水加氢

文本所用软件/程序

GUI: Olex2[1]

案例来源：Chem. Commun. 2024, 60, 8888–8891. DOI[2]: 10.1039/D4CC02720E. CCDC[3]: 2344496.

审稿意见

大意

I sent  your revised manuscript to one of the initial reviewers and I have now  received their report which is copied below. After careful evaluation of your  manuscript and the reviewer's report, I will be pleased to accept your  revised manuscript for publication after further minor revisions. Please  revise your manuscript to fully address the reviewer's comments which concern  use of SQUEEZE, inclusion of hydrogen atoms on water molecules where possible  and ensuring the formula used includes "squeezed" solvent  molecules. When you submit your revised manuscript please include a point by  point response to the reviewer's comments and highlight the changes you have  made.       1 Recommendation:  Major Revision: may be suitable for publication, but only after substantial  changes Comments: There is 1 Structure in this paper. We examined this file:  2344496**a_sq** (CCDC 2344496) 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. 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. "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 only are the solvent water molecules missing from the sum and  moiety formuale, but the water molecules that *are* in the structure are also  missing all hydrogen atoms. Even ligand water molecules are missing their  hydrogen atoms! Please add as many hydrogen atoms to the model as possible.  Those that can not be added, or that are part of the solvent mask, must be  accounted for. I estimate something like this: _chemical_formula_moiety 'H100  K25 Mn11 Nb62 O290.25 Te15, 6.5(H4 O2), O1.75, 27[H2O]' _chemical_formula_sum  'H100 K25 Mn11 Nb62 O332 Te15'_chemical_formula_weight 14748.747. Currently  you are reporting this: _chemical_formula_moiety 'K25 Mn11 Nb62 O281.5 Te15,  23.5(O)' _chemical_formula_sum 'K25 Mn11 Nb62 O305 Te15' _chemical_formula_weight  14136.26. Thank you.       Structure  a_sq (CCDC 2344496): K25 Mn11 Nb62 O305 Te15 These CheckCif A and B alerts  are raised by this structure. This is for your information only - you may  wish to address these issues before re-submitting your cif file to the CCDC.    306_ALERT_2_B  Isolated Oxygen Atom (H-atoms Missing ?) ....... O1W Check306_ALERT_2_B  Isolated Oxygen Atom (H-atoms Missing ?) ....... O2W Check306_ALERT_2_B  Isolated Oxygen Atom (H-atoms Missing ?) ....... O5W Check306_ALERT_2_B  Isolated Oxygen Atom (H-atoms Missing ?) ....... O6W Check306_ALERT_2_B  Isolated Oxygen Atom (H-atoms Missing ?) ....... O8W Check306_ALERT_2_B  Isolated Oxygen Atom (H-atoms Missing ?) ....... O9W Check306_ALERT_2_B  Isolated Oxygen Atom (H-atoms Missing ?) ....... O14W Check306_ALERT_2_B  Isolated Oxygen Atom (H-atoms Missing ?) ....... O18W Check306_ALERT_2_B  Isolated Oxygen Atom (H-atoms Missing ?) ....... O21W Check306_ALERT_2_B  Isolated Oxygen Atom (H-atoms Missing ?) ....... O22W Check306_ALERT_2_B  Isolated Oxygen Atom (H-atoms Missing ?) ....... O23W Check306_ALERT_2_B  Isolated Oxygen Atom (H-atoms Missing ?) ....... O24W Check306_ALERT_2_B  Isolated Oxygen Atom (H-atoms Missing ?) ....... O26W Check306_ALERT_2_B  Isolated Oxygen Atom (H-atoms Missing ?) ....... O27W Check306_ALERT_2_B  Isolated Oxygen Atom (H-atoms Missing ?) ....... O28W Check306_ALERT_2_B  Isolated Oxygen Atom (H-atoms Missing ?) ....... O29W Check306_ALERT_2_B  Isolated Oxygen Atom (H-atoms Missing ?) ....... O30W Check306_ALERT_2_B  Isolated Oxygen Atom (H-atoms Missing ?) ....... O31W Check306_ALERT_2_B  Isolated Oxygen Atom (H-atoms Missing ?) ....... O33W Check306_ALERT_2_B  Isolated Oxygen Atom (H-atoms Missing ?) ....... O34W Check306_ALERT_2_B  Isolated Oxygen Atom (H-atoms Missing ?) ....... O35W Check306_ALERT_2_B  Isolated Oxygen Atom (H-atoms Missing ?) ....... O37W Check306_ALERT_2_B  Isolated Oxygen Atom (H-atoms Missing ?) ....... O38W Check306_ALERT_2_B  Isolated Oxygen Atom (H-atoms Missing ?) ....... O39W Check306_ALERT_2_B  Isolated Oxygen Atom (H-atoms Missing ?) ....... O42W Check306_ALERT_2_B  Isolated Oxygen Atom (H-atoms Missing ?) ....... O44W Check306_ALERT_2_B  Isolated Oxygen Atom (H-atoms Missing ?) ....... O48W Check306_ALERT_2_B  Isolated Oxygen Atom (H-atoms Missing ?) ....... O49W

我已将您的修订稿发送给一位初评人，我现在收到了他们的报告，副本如下。在仔细评估了您的手稿和审稿人的报告后，我很乐意接受你的修改稿，以便在进一步的小幅修改后发表。请修改您的手稿，以充分回应审稿人的意见，这些意见涉及使用SQUEEZE、在可能的情况下在水分子上加入氢原子，并确保使用的分子式包括“挤压的”溶剂分子。当您提交修改后的手稿时，请对审稿人的评论进行逐点回应，并高亮显示您所做的更改。                            1建议：主要修订：可能适合发表，但只有在发生重大更改后才能发表评论：本文有1个结构。我们检查了这个文件：2344496**a_sq**（CCDC 2344496）使用了溶剂掩模，但CIF中没有关于这个过程的任何报告。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。相关信息应易于从TGA/DSC结果、结晶条件的知识中获得，最后从施加掩模前的掩模电子数量、孔隙大小和电子密度峰的相对位置中获得。报告的分子式必须包含遮掩部分，导致许多后续量的报告不正确，如密度、分子量、F000和吸收系数μ。“化学式必须与_atom_site_信息指定的原子含量一致，并与_chemical_formula_weight匹配。如果原子模型中缺少原子（例如，未定位的H原子或被‘SQUEEZE’或类似方法抑制的溶剂分子），则部分及总和式应说明假设的总体式。只有溶剂水分子从总和及部分式中缺少，但结构中的水分子也缺少所有氢原子。甚至配体水分子也缺失氢原子！请在模型中添加尽可能多的氢原子。不能添加的或溶剂掩模的一部分必须考虑在内。我估计大致如下：_chemical_formula_moiety 'H100 K25 Mn11  Nb62 O290.25 Te15, 6.5(H4 O2), O1.75, 27[H2O]' _chemical_formula_sum 'H100  K25 Mn11 Nb62 O332 Te15'_chemical_formula_weight 14748.747。当前您报告的是：_chemical_formula_moiety 'K25 Mn11 Nb62  O281.5 Te15, 23.5(O)' _chemical_formula_sum 'K25 Mn11 Nb62 O305 Te15'  _chemical_formula_weight 14136.26。谢谢！                                                                      结构2344496**a_sq**（CCDC 2344496）K25 Mn11 Nb62 O305 Te15，该结构有如下CheckCif A和B警报。这仅供您参考，您可能希望在将CIF文件重新提交给CCDC之前解决这些问题。          306_ALERT_2_B Isolated Oxygen Atom  (H-atoms Missing ?) ....... O1W Check306_ALERT_2_B Isolated Oxygen Atom  (H-atoms Missing ?) ....... O2W Check306_ALERT_2_B Isolated Oxygen Atom  (H-atoms Missing ?) ....... O5W Check306_ALERT_2_B Isolated Oxygen Atom  (H-atoms Missing ?) ....... O6W Check306_ALERT_2_B Isolated Oxygen Atom  (H-atoms Missing ?) ....... O8W Check306_ALERT_2_B Isolated Oxygen Atom  (H-atoms Missing ?) ....... O9W Check306_ALERT_2_B Isolated Oxygen Atom  (H-atoms Missing ?) ....... O14W Check306_ALERT_2_B Isolated Oxygen Atom  (H-atoms Missing ?) ....... O18W Check306_ALERT_2_B Isolated Oxygen Atom  (H-atoms Missing ?) ....... O21W Check306_ALERT_2_B Isolated Oxygen Atom  (H-atoms Missing ?) ....... O22W Check306_ALERT_2_B Isolated Oxygen Atom  (H-atoms Missing ?) ....... O23W Check306_ALERT_2_B Isolated Oxygen Atom  (H-atoms Missing ?) ....... O24W Check306_ALERT_2_B Isolated Oxygen Atom  (H-atoms Missing ?) ....... O26W Check306_ALERT_2_B Isolated Oxygen Atom  (H-atoms Missing ?) ....... O27W Check306_ALERT_2_B Isolated Oxygen Atom  (H-atoms Missing ?) ....... O28W Check306_ALERT_2_B Isolated Oxygen Atom  (H-atoms Missing ?) ....... O29W Check306_ALERT_2_B Isolated Oxygen Atom  (H-atoms Missing ?) ....... O30W Check306_ALERT_2_B Isolated Oxygen Atom  (H-atoms Missing ?) ....... O31W Check306_ALERT_2_B Isolated Oxygen Atom  (H-atoms Missing ?) ....... O33W Check306_ALERT_2_B Isolated Oxygen Atom  (H-atoms Missing ?) ....... O34W Check306_ALERT_2_B Isolated Oxygen Atom  (H-atoms Missing ?) ....... O35W Check306_ALERT_2_B Isolated Oxygen Atom  (H-atoms Missing ?) ....... O37W Check306_ALERT_2_B Isolated Oxygen Atom  (H-atoms Missing ?) ....... O38W Check306_ALERT_2_B Isolated Oxygen Atom  (H-atoms Missing ?) ....... O39W Check306_ALERT_2_B Isolated Oxygen Atom  (H-atoms Missing ?) ....... O42W Check306_ALERT_2_B Isolated Oxygen Atom  (H-atoms Missing ?) ....... O44W Check306_ALERT_2_B Isolated Oxygen Atom  (H-atoms Missing ?) ....... O48W Check306_ALERT_2_B Isolated Oxygen Atom  (H-atoms Missing ?) ....... O49W

如图1所示，该结构是一个多酸结构，里面有很多的游离水以及配位水，投稿时这些水分子没有加氢，因此审稿人提出让对水分子尽可能进行加氢处理。

▲图1 CCDC 2344496投稿时状态

其checkCIF报告共179页，有7个A级警报，52个B级警报，4821个C级警报和264个G级警报，如图2所示。

▲图2 CCDC 2344496投稿时checkCIF报告

后来作者按照审稿意见对尽可能多的水分子进行加氢，结果如图3所示。

▲图3 CCDC 2344496发表时状态

其checkCIF报告共207页，有45个A级警报，108个B级警报，4856个C级警报和256个G级警报，如图4所示。

▲图4 CCDC 2344496发表时checkCIF报告

相关视频：

晶体数据审稿意见-溶剂遮掩说明和游离水加氢：https://www.bilibili.com/video/BV1wx4y1s7T9

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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. DOI: 10.1107/S0021889808042726.    [2] (a) International Organization for Standardization  (2012). ISO 26324:2012. Information and  Documentation – Digital Object Identifier System.  http://www.iso.org/iso/catalogue_detail.htm?csnumber=43506. (b) International  Organization for Standardization (2022). ISO 26324:2022. Information and Documentation – Digital Object Identifier System.  https://www.iso.org/standard/81599.html    [3] (a) Allen, F.  H. The Cambridge Structural Database: a quarter of a million crystal  structures and rising. Acta Cryst. 2002, B58, 380–388. DOI:  10.1107/S0108768102003890.  (b) Allen, F. H. The Cambridge Structural Database: a quarter of a million  crystal structures and rising. Acta  Cryst. 2016, B72, 171–179. DOI:  10.1107/S2052520616003954.    [4] (a) Hall, S.  R.; Allen, F. H. Brown, I. D. The Crystallographic Information File (CIF): a  New Standard Archive File for Crystallography. Acta Cryst. 1991, A47, 655–685. DOI:  10.1107/S010876739101067X.  (b) Hall, S. R. The STAR File: A New Format for 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.

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