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晶体数据审稿意见-非谐波精修(残余峰导致A级警报PLAT971) 案例来源：CCDC[1]:2441907. Dalton Trans. 2025, DOI[2]: 10.1039/d5dt01347j. 案例结构如图1所示（由ChemBioDraw[3]绘制）。 ▲图1 CCDC 2441907结构 审稿意见如下： **2_CCDC2** (CCDC 2441907) 4-400K The 'disorder' refinement involving theRe atom is incorrect. This is not disorder, but anharmonicity. When refiningthis, the residual peak will be of magnitude 0.6 and R1 willbe 1.87% 大意如下： 铼原子的“无序”精修不正确。这不是无序，而是非简谐振动。当对此进行精修，残余峰会降为0.6，而R1会降为1.87%。 用Olex2[4]打开投稿时的晶体数据，如图2所示，原先对高铼酸根中铼原子做了二组分无序处理，第一组分铼原子编号为Re1，第二组分铼原子编号为Re2，使用自由变量精修两者占有率，其比例大约为0.85716:0.14284，R1 = 2.10%，wR2 = 5.69%，Max Peak = 0.5 eÅ–3，Min Peak = -0.8 0.5 eÅ–3。 ▲图2 CCDC 2441907投稿时状态 取消该铼原子的无序处理，如图3所示，铼原子旁边有一个很大的残余峰Q1，此时Max Peak = 4.0 eÅ–3，Min Peak = -2.4 eÅ–3，R1 = 4.41%，wR2 = 11.78%。 ▲图3 铼原子不做无序处理时的状态 ▲图4 级警报PLAT971 按照审稿人建议，对其做非简谐振动精修，结果如图5所示，R1 = 1.73%，wR2 = 4.32%，Max Peak = 0.3 eÅ–3，Min Peak = -0.7 eÅ–3。 ▲图5 CCDC 2441907发表时状态 以上是审稿意见处理结果，那么如何对特定原子进行非谐波精修呢？Olex2官网（https://www.olexsys.org/）对此已有说明，相关内容如下（参阅推文“Olex2官网内容中英文对照”）： | Anharmonic Refinement Refining atoms anharmonically It is possible to refine the displacements of selected atoms anharmonically in olex2.refine. Here's how it is done. Warning: This is an experimental feature – it works, but please use it at your own disgression. You must be aware that this technique is open to abuse. Select the atom(s) you want to refine anharmonically and type anis -a. If you don't want to refine atoms anharmonically any longer, please select these atoms (or all!) and just type anis – this will remove the anharmonic flag for all. You can visualise the resulting 'shape' in terms of mean square displacement of the atoms by switching on an alternative display style for all atoms, type MSDSView -a=anh -s=1.5 Please keep in mind that the scale of 1.5 will apply and that for the anharmonic atoms only the contribution of the anharmonic terms is shown. You can disable this view by typing kill MSDS. A judgement whether it might be reasonable to refine anharmonic motion can be made according to Kuhs' rule: Kuhs Aust. J. Phys. 1988, 41, 369-82. 0.074758 sqrt(n/U^2) might give an estimate what resolution in sinus theta over lambda is required to have a significant difference between anharmonic and harmonic motion. | 非谐波精修 非谐波精修原子 在olex2.refine中可对所选原子的位移参数进行非谐波精修。此处是其操作过程。 警告：这是一个实验性功能——它可以工作，但请自行使用。您必须意识到，这种技术容易被滥用。 选择想要非谐波精修的原子并键入anis -a。若不想再对原子进行非谐波精修，请选择这些原子(或所有！)，只需键入anis——这将移除所有非谐波标记。 通过为所有原子打开另一种显示样式，键入MSDSView -a=anh -s=1.5，您可根据原子的均方位移来可视化生成的"形状"。请记住，1.5的比例将适用，对于非谐波原子，仅显示非谐波项的贡献。您可以通过键入kill MSDS来禁用此视图。 可以根据Kuhs的规则：Kuhs Aust. J. Phys. 1988, 41, 369–382来判断精修非谐波振动是否合理。0.074758 sqrt(n/U^2)可能会给出一个估计值，即sinθ与λ之间的分辨率需要多少才能在非谐波运动与谐波运动之间产生显著差异。 |
根据上述信息，以下介绍对铼原子进行非谐波精修的具体操作，如图6所示，在Work>>Refine下将Program由ShelXL[6]（即shelxl.exe，SHELX结构精修程序）改为olex2.refine[4]（Olex2程序自带的结构精修程序）。 ▲图6 选择Olex2结构精修程序olex2.refine 随后，点击选择铼原子，并在主界面左下角输入指令“anis -a”（注意：“anis”和“-a”之间有一个空格），如图7所示。 ▲图7 选择原子并输入anis -a 回车使程序读入指令“anis -a”，然后精修即可，结果如图8所示，此时R1 = 2.03%。 ▲图8 对铼原子进行非谐波精修的结果 对整个高铼酸根所有原子做非谐波精修，结果如图9所示，R1降到2%以下。 ▲图9 整个高铼酸根做非谐波精修的结果 请注意，对原子做非谐波精修会增加参数的数量，对于本案例来说，没有做非谐波精修时，数据参数比为14.6，对铼原子做非谐波精修后，数据参数比降为13.6，而对整个高铼酸根五个原子都做非谐波精修后，数据参数比降为10.5。非谐波精修通常要求高分辨率数据，本案例数据为钼靶光源数据，分辨率0.82 Å并不算高。 视频讲解和操作演示请参阅： 晶体数据审稿意见-非谐波精修(残余峰导致A级警报PLAT971)：https://www.bilibili.com/video/BV1vzbxzXEVq 如需文献“Aust. J. Phys. 1988, 41, 369–382. DOI: 10.1071/PH880369.”，可从以下链接下载： 提取码: bi2n 参考文献 [1] (a)Allen, F. H. The Cambridge Structural Database: A Quarter of a Million CrystalStructures and 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. 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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-非谐波精修(残余峰导致A级警报PLAT971).pdf
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发表于 2025-8-16 07:05:52
