CheckCIF-B级警报PLAT987(审稿意见)

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CheckCIF-B级警报PLAT987(审稿意见)

前段时间，在布鲁克晶体群中有小伙伴遇到B级警报PLAT987（参阅推文“CheckCIF-PLAT978”），并在群里询问，如图1所示。

▲图1 问题描述

对此，群主张老师做了解答，如图2所示。

▲图2 问题解答

以下是一个案例，仅供参考。

案例来源：CCDC[1] 1590039, 1590042. Inorg. Chem. Commun. 2018, 97, 149‒156. DOI[2]: 10.1016/j.inoche.2018.09.016.

审稿意见	大意
In the manuscript, the authors wrote:  "flack parameter of complex 1  is 0.066(13), and that of complex 2  is 0.053(7). The flack parameter value tends to zero, which indicates that  the chiral space group is chosen correctly and the crystals are chiral".      Expected values are 0 (within 3 esd's) for  correct absolute structure, but from checkCIF/PLATON report:    Datablock: complex1	在手稿中，作者写道“配合物1的flack参数为0.066(13)，配合物2的flack参数为0.053(7)。Flack参数趋近于零，表明手性空间群选择正确，晶体是手性”。对于正确绝对结构，Flack参数期望值为0（在3倍估计标准不确定度范围内），但checkCIF/PLATON[3]报告存在如下B级警报PLAT987（参阅推文“CheckCIF-PLAT978”）和G级警报PLAT033（参阅推文“CheckCIF-PLAT033”）：
Alert level B PLAT987_ALERT_1_B The Flack x  is >> 0 Do a BASF/TWIN Refinement Please Check    Alert level G PLAT033_ALERT_4_G Flack x  Value Deviates > 3.0 * sigma from Zero . 0.066 Note

配合物1和2的结构如图3‒4所示，两者均结晶于四方晶系，前者为第92号空间群P41212，后者为第96号空间群P43212，晶体结构由Olex2[4]呈现，平面结构由ChemBioDraw[5]绘制。

▲图3 配合物1（CCDC 1590039）结构

▲图4 配合物2（CCDC 1590042）结构

该论文中支持信息（SupportingInformation）中对此说明如下：

说明

大意

The  checkcif program of Platon considers that the structures of complex 1 and 2 are both twinning, not chiral, so the report gives the alerts  bout flack parameters. But we analyze the two structures and find that the  two complexes are both chiral, and the CD spectrum support the chirality of  the complexes. Therefore, the alerts given by checkcif report about cif files  of complex 1 and 2 are incorrect and could be  accepted, the twin/basf order was not applied during the final circles of  refinement. To remove the alerts by refinement is very easy, but it is  generally known that the alert does not mean incorrect structure.

CheckCIF程序PLATON认为配合物1和2均为孪晶，而非手性，因此报告给出有关Flack参数的警报。但我们分析两个结构，发现均为手性，并且圆二色光谱CD（circular dichroism）支持配合物的手性。因此，CheckCIF报告给出的关于配合物1和2的CIF文件的警报是不正确的，这些警报是可接受的，在最终的精修循环中没有应用TWIN/BASF命令。通过精修消除警报非常容易，但总所周知，警报并不意味着结构不正确。

就上述张老师的解答和文献案例，对于遇到PLAT987警报时，笔者个人认为可分两种情况：

（1）如果结构为非手性，并且也不关心和研究晶体手性，则可以按照推文“CheckCIF-B级警报处理示例(PLAT342,926,927和987)”“审稿意见-B级警报PLAT987的解决示例”或视频“CheckCIF警告解决1(PLAT790和PLAT987)：https://www.bilibili.com/video/BV1yo4y197V1”“CheckCIF-B类警报解决示例(PLAT342,926,927和987)：https://www.bilibili.com/video/BV1kw411U7NU”“审稿意见-B级警报PLAT241和PLAT250以及PLAT987的解决示例：https://www.bilibili.com/video/BV1w**1Q7ei”中方法在ins中添加“TWIN”和“BASF 0.5”（0.5为初始值，可以填0和1之间的任意数值）两条指令，精修重新生成CIF文件来消除PLAT987警报；

（2）如果关心和研究晶体手性（不论结构是否为手性），则可参照上述文献案例，辅以其他能够证明手性的表征（如圆二色光谱等）对PLAT987警报进行说明即可。

视频讲解请参阅：

CheckCIF-B级警报PLAT987(审稿意见)：https://www.bilibili.com/video/BV1uNwYeiEJC

案例论文PDF及其CIF文件可从如下链接下载：

链接: https://pan.baidu.com/s/1TEgjYC7T4yTuYzK5LP6nFw

提取码: iity

参考文献

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[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.html

[3]    (a) Spek, A. L. Single-CrystalStructure Validation with the Program PLATON.J. Appl. Cryst. 2003, 36, 7–13. DOI: 10.1107/S0021889802022112.(b) Spek, A. L. StructureValidation in Chemical Crystallography. ActaCryst. 2009, D65, 148–155. DOI:10.1107/S090744490804362X. (c) Spek, A. L. What Makes a Crystal Structure Report Valid? Inorg. Chim. Acta 2018, 470, 232–237. DOI:10.1016/j.ica.2017.04.036. (d) Spek, A. L. checkCIFValidation ALERTS: What They Mean and How to Respond. Acta Cryst. 2020, E76, 1–11. DOI: 10.1107/S2056989019016244.

[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.

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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。

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链接: https://pan.baidu.com/s/1h555QeblDtPT9Vto9Jp3NA 提取码: qfth