|
相关软件或概念：Olex2[1] (Version: Olex2-1.5); SHELXL[2] (Version: SHELXL-2019/3); PLATON[3] (Version: 60124) 案例来源：Dalton Trans. 2024, 53, 5917–5921. DOI：10.1039/d3dt04001a 年初的时候，有小伙伴晶体数据审稿意见回来，求助处理晶体数据，如图1–2所示。 ▲图1 问题诉求 ▲图2 问题诉求 其审稿意见如下： **112004_sq** (CCDC 2311191) The R factors are too large to contemplate publication of thisstructure. The fit between your model and the measured data is very bad, andthis can be seen also from the residual density plot and the Fractal DimensionPlot. Sometimes there are good reasons why it is very difficult to obtaingood data of a given material, but in those cases I would expect a detaileddescription of the problems and a valid justification as to why it isimpossible to avoid these. Here, there is nothing at all in the CIF or the manuscript, wherethere are no structural details at all. The structure 'looks' ok by virtue of these inappropriateconstraints: EADP O1 O2 O3 O4 O7 O8 O12 O11 O14 O13 O9 O10 O15 O19 O18 O17 O21O16 C20 = O6 O5 O22 O23 EADP C12 C8 C2 C5 C4 C9 C7 C1 C6 C11 C3 C10 C13 C15 C14 C17 C16 C28C27 C26 = C29 C33 C35 C36 C34 C37 C38 C39 C46 C47 C49 C48 C50 C55 C25 C19 C54C18 C21 = C22 C52 C60 C32 C31 C30 C44 C40 C43 C41 C42 C45 C23 C24 C51 C53 O54 Removing these, will lower R1 to ~7.8% with almost acceptable ADPs. There is clearly disorder here that can and must be modelled. An R1of ~6.5% will probably result. A solvent mask has been used, but that mask has been produced usinga long deprecated version of PLATON. Somehow, an (empty) fab file has *also*been included in the CIF. This is a very strange thing to have happened here: -20 0 2 0.0000 0.0000 -20 0 4 0.0000 0.0000 -20 0 6 0.0000 0.0000 -20 0 8 0.0000 0.0000 -20 0 10 0.0000 0.0000 -20 1 3 0.0000 0.0000 [...] Please revise this structure thoroughly and according to standardcrystallographic practices. The data this structure are based on are not great, but they aresufficient to obtain a sensible and likely correct model of your material. Thank you. Structure 112004_sq (CCDC 2311191): C56 H45 Mg4 N0 O23 These CheckCif A and B alerts are raised by this structure. This isfor your information only - you may wish to address these issues beforere-submitting your cif file to the CCDC. 084_ALERT_3_B High wR2 Value (i.e. > 0.25) ...................0.45 Report 340_ALERT_3_B Low Bond Precision on C-C Bonds ............... 0.012Ang. 420_ALERT_2_B D—H Bond Without Acceptor O17 --H17D . Please Check 420_ALERT_2_B D—H Bond Without Acceptor O17 --H17E . Please Check 420_ALERT_2_B D—H Bond Without Acceptor O21 --H21 . Please Check 922_ALERT_1_B wR2 in the CIF and Differ by ............... 0.0200Check 972_ALERT_2_B Check Calcd Resid. Dens. 0.08Ang From O54 -2.59 eA-3 主要是一些建模和AB级警报的处理，如图3所示，结构中乙酸片段椭球异常，其附近差值电子密度图表明该处存在很大问题。 ▲图3 待处理数据 随后对该乙酸片段做二组分无序处理，另外建模了与金属配位的甲醇溶剂以及水分子，最终结果如图4所示。 ▲图4 数据处理结果 最终结果还剩下有一些AB级警报，对其做了解释说明，如图5所示。 ▲图5 对AB级警报的解释 视频操作请参阅： 晶体数据审稿意见-建模和AB级警报处理：https://www.bilibili.com/video/BV1pr421t7by 如需论文及数据，请从以下链接下载： （1） 链接：https://pan.quark.cn/s/879f28b55fc3 提取码：hsvA （2） 链接：https://pan.baidu.com/s/1XKRApowa8xCPabCI4JvxRw 提取码：7e4f 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. [2](a) Sheldrick, G. M. SHELXL-2019/3, Program for Crystal Structure Refinement,University of Göttingen, Germany, 2019. (b) Sheldrick, G. M. A short history ofSHELX. Acta Cryst. 2008, A64, 112–122. (c) Sheldrick, G. M.Crystal structure refinement with SHELXL.Acta Cryst. 2015, C71, 3–8. (d)Lübben, J.; Wandtke, C. M.; Hübschle, C. B.; Ruf, M.; Sheldrick, G. M.;Dittrich, B. Aspherical scattering factors for SHELXL – model, implementation and application. Acta Cryst. 2019, A75, 50–62. [3] (a) Spek, A. L. Single-crystal structure validationwith the program PLATON. J. Appl.Cryst. 2003, 36, 7–13. (b) Spek,A. L. Structure validation in chemical crystallography. Acta Cryst. 2009, D65, 148–155. (c) Spek, A. L. What makes a crystal structure reportvalid? Inorg. Chim. Acta 2018, 470, 232–237. (d) Spek, A. L. checkCIFvalidation ALERTS: what they mean and how to respond. Acta Cryst. 2020, E76, 1–11.
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-建模和AB级警报处理.pdf --来自百度网盘超级会员v1的分享
| 
发表于 
