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晶体数据审稿意见-空间群案例1 案例来源：CCDC[1] 2350450, 2350452. Molecules 2024, 29, 2523. DOI[2]: 10.3390/molecules29112523. 审稿意见： There is however one potentially serious concern regarding thedetermined crystal structures 5 and 6 (derived from the two enantiomers of(1-chloroethyl)benzene). Both structures have been solved and refined incentrosymmetric space groups (Pī and P21/n), i.e. with both enantiomers present inthe crystal structure, and this is accounted for in the discussion by presumingthat racemisation has occurred upon heating of the reactant mixture. However,there are some indications that these are in fact cases of pseudosymmetry, andthat the structures are in fact non-centric, erroneously refined ascentrosymmetric (i.e. there was noracemisation, but it is only the artefact of the wrongly assigned space group).This is not unlikely to occur if the majority of the atoms (the PTA macrocycle)form an (approximately) centrosymmetric assembly, and only a small portion ofthe structure (the guest molecule) does not. Classic 'symptom' of suchmisassignment of the space group apparent disorder of the part of the structurewhich 'brakes' the symmetry. The disorder in 6 is apparent, but is also present in 5, as evidenced by large and highly elongated (even with ISOR!)displacement ellipsoids of C1 and Cl1. Therefore both 5 and 6 should be solved and refined in non-centric groups (viz P1 and P21), in order to see whether these problems can beresolved. It might be necessary to perform additional measurements (inparticularly for 5, as the wholereflection sphere is needed for proper structure refinement in P1). Structure 6 has anadditional highly suspect feature – a water molecule (of unknown origin)positioned 1.9191 Å (extremely close contact!) from a phenyl carbon (C1BA),with the 'water molecule' hydrogen atoms do not participate in any sensible HBinteractions. This is highly unusual, and implies erroneous assignment of atomtype (possibly the O7 is in fact a chlorine atom with ca 0.25 occupancy from adifferently oriented (1-chloroethyl)benzene molecule). Additional problem forsupposing this to be a water molecule is in the fact that there was no water inthe system upon crystallisation, and, since the both the crystallisation mediumand the binding site in the crystal structure are highly hydrophobic,absorption of water from the atmosphere is extremely unlikely. Therefore, theclaim of the presence of water in this structure should be corroborated by someadditional evidence, such as a TGA curve showing the loss of a stoichiometricamount of water. Both structures therefore, in my opinion, require a moredetailed inspection. 大意： 然而，对于所确定的晶体结构5和6（衍生自(1-氯乙基)苯的两种对映体），存在一个潜在的严重问题。这两种结构都在中心对称空间群（Pī和P21/n）中得到解析和精修，即晶体结构中存在两种对映异构体，这在讨论中是通过假设反应物混合物加热时发生外消旋来解释的。然而，有迹象表明，这些实际上是赝对称的情况，这些结构实际上是非中心的，被错误地精修为中心对称的（即没有外消旋化，但这只是错误分配空间群的产物）。如果大多数原子（PTA大环）形成（近似）中心对称的组装，而只有一小部分结构（客体分子）不形成，则这种情况不太可能发生。这种空间群错误分配的典型“症状”是“制动”对称性的结构部分明显无序。6中的无序是明显的，但也存在于5中，这可以从C1和Cl1的大而高度细长（即使有ISOR约束！）的位移椭球体中得到证明。因此，5和6都应该在非中心群（即P1和P21）中解析和精修，以看看这些问题是否可以解决。可能需要进行额外的测量（特别是对于5，因为P1中的适当结构精修需要整个衍射球）。 结构6还有一个非常可疑的特征——一个水分子（来源不明）位于苯基碳（C1BA）的1.9191 Å处（非常紧密的接触！），与“水分子”氢原子不参与任何明显的氢键相互作用。这是非常不寻常的，意味着原子类型的错误分配（可能O7实际上是一个氯原子，与不同取向的(1-氯乙基)苯分子的占有率约为0.25）。假设这是一个水分子的另一个问题是，在结晶时体系中没有水，而且由于结晶介质和晶体结构中的结合位点都是高度疏水的，因此从大气中吸收水的可能性极小。因此，这种结构中存在水的说法应该得到一些额外证据的证实，例如显示化学计量量的水损失的TGA曲线。 因此，在我看来，这两个结构都需要更详细的检查。 ▲图1 结构5中心对称空间群Pī下解析和精修结果 ▲图2 结构5非中心对称空间群P1下解析和精修结果 ▲图3 结构6中心对称空间群P21/n下解析和精修结果 ▲图4 结构6非中心对称空间群P21下解析和精修结果 在非中心对称空间群下解析时，虽然对客体分子做了适当的无序处理，但发现精修无法收敛。 For5, the refinement cannot convergence when solved in P1 space group. Thus received the following checkCIF A and Balerts. PLAT080_ALERT_2_AMaximum Shift/Error ............................ 1.41 Why ? PLAT340_ALERT_3_BLow Bond Precision on C-C Bonds............... 0.01537 Ang. For6, the refinement cannot convergence when solved in P21 space group. Thus received the following checkCIF Aand B alerts. PLAT080_ALERT_2_AMaximum Shift/Error ............................ 0.42 Why ? PLAT340_ALERT_3_BLow Bond Precision on C-C Bonds............... 0.0153 Ang. Seeattached CIF files. 最后还是以中心对称空间群结果发表的。 如需论文和晶体数据，请从以下链接下载： 提取码: szz5 视频讲解请参阅： 晶体数据审稿意见-空间群案例1：https://www.bilibili.com/video/BV1iA1iY2E3s 参考文献 [1] (a) Allen, F. H. The Cambridge StructuralDatabase: a quarter of a million crystal structures and rising. Acta Cryst. 2002, B58, 380–388. DOI: 10.1107/S0108768102003890. (b) Allen, F. H. TheCambridge Structural Database: a quarter of a million crystal structures andrising. Acta Cryst. 2016, B72, 171–179. DOI:10.1107/S2052520616003954. [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 forStandardization (2022). ISO 26324:2022. Informationand Documentation – Digital Object Identifier System. https://www.iso.org/standard/81599.htmlOlex2: 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. SHELXL: (a) Sheldrick, G. M. SHELXL-2019/3, Program for Crystal Structure Refinement, University of Göttingen,Germany, 2019. (b)Sheldrick, G. M. A Short History of SHELX.Acta Cryst. 2008, A64, 112–122. DOI: 10.1107/S0108767307043930. (c) Sheldrick, G. M. CrystalStructure Refinement with SHELXL. Acta Cryst. 2015, C71, 3–8. DOI: 10.1107/S2053229614024218. (d) Lübben, J.; Wandtke, C. M.;Hübschle, C. B.; Ruf, M.; Sheldrick, G. M.; Dittrich, B. Aspherical scatteringfactors for SHELXL – model,implementation and application. 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：晶体数据审稿意见-空间群案例1.pdf
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