原子非正定处理案例2(A级警报PLAT211)

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原子非正定处理案例2(A级警报PLAT211)

案例来源：CCDC[1] 2451886.DOI[2]:10.5517/ccdc.csd.cc2n9d3h.

案例结构如图1所示（由ChemBioDraw[3]绘制）。

▲图1 案例结构

如图2所示（由Olex2[4]呈现）原子编号为C16的碳原子其椭球形状为接近2维（2D）的扁平形状，由此触发了一个A级警报PLAT211（参阅推文“CheckCIF-PLAT211”）“ADP of Atom C16 is N.P.D. or (nearly) 2D.Please Check”（原子C16的原子位移参数（ADP, atomic displacement parameter）是非正定（N.P.D., non-positive definite）或（近乎）2维（2D）。请检查。）（验证报告由PLATON[5]呈现。）

▲图2 数据情况和验证报告

对于这种情况，整个结构中仅有一个原子非正定，可以用SHELXL[6]指令ISOR（参阅推文“SHELXL指令之ISOR”）进行限制，具体操作就是在ins文件中添加一条指令“ISOR 0.01 0.02 C16”，精修后C16的源自椭球不再薄如蝉翼，而是鼓囊了一些，因此上述A级警报PLAT211就被消除了，如图3所示。

▲图3 消除A级警报PLAT211后的结果

有关非正定（NPD, non-positivedefinite），以下英文内容摘自“CrystalStructure Refinement: A Crystallographer’s Guide to SHELXL.”[7]，中文内容摘自其中译版《晶体结构精修——晶体学者的SHELXL软件指南》[8]：

NPD stands for "non-positive definite"  and refers to a thermal ellipsoid with one or more of the three half-axes of  the anisotropic displacement ellipsoid possessing a negative value. This is  physically meaningless and a model containing an atom of this kind is not  publishable. (At least it should not be published—sometimes it is surprising what seems to be  "publishable" to referees and editors.)

NPD代表“非正定”，它对应这样的热振动椭球——各向异性位移椭球的三个半轴有一个或多个取值为负。这种结果毫无物理意义，且包含这种原子的模型是不能发表的。（至少是不应当被发表——令人惊讶的是一些例子在审稿人和编辑看来却是可以发表的。）

视频操作演示请参阅：

单晶结构解析练习606(非正定-AB级警报处理)：https://www.bilibili.com/video/BV1cmTpzNE3s

如需数据进行练习，请从以下链接下载：

链接:https://pan.baidu.com/s/1d_EV8B2x_uoGm5vKNTmriQ

提取码: w7rm

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. DOI:10.1107/S2052520616003954. (c) Mitchell, J.; Robertson, J. H.; Raithby,P. R. Cambridge Crystallographic Data Centre (CCDC). Comprehensive Coordination Chemistry III 2021, 413–437. DOI: 10.1016/B978-0-12-409547-2.14829-2.

[2]    (a)International Organization for Standardization (2012). ISO 26324:2012. Information and Documentation – DigitalObject 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)Klein, F. M. CS ChemDraw Pro,1 Version 3.1 for Windows. J. Chem. Inf. Comput.Sci. 1995, 35, 166–167. DOI: 10.1021/ci00023a026. (b)Cousins, K. R. ChemDraw 6.0 Ultra CambridgeSoft Corporation, 100 Cambridge ParkDrive, Cambridge, MA 02140. http://www.camsoft.com. Commercial Price:  $1395.Academic Price:  $699. J. Am. Chem. Soc. 2000, 122, 10257–10258. DOI: 10.1021/ja0047572.(c) Buntrock, R. E. ChemOffice Ultra 7.0. J.Chem. Inf. Comput. Sci. 2002, 42, 1505–1506. DOI: 10.1021/ci025575p. (d) Li, Z.; Wan, H.; Shi, Y.;Ouyang, P. Personal Experience with Four Kinds of Chemical Structure DrawingSoftware: Review on ChemDraw, ChemWindow, ISIS/Draw, and ChemSketch. J. Chem.Inf. Comput. Sci. 2004, 44, 1886–1890. DOI: 10.1021/ci049794h.(e) Mendelsohn, L. D. ChemDraw8 Ultra, Windows and Macintosh Versions. J.Chem. Inf. Comput. Sci. 2004, 44, 2225–2226. DOI: 10.1021/ci040123t. (f) Cousins, K. R. ChemDrawUltra 9.0. CambridgeSoft, 100 CambridgePark Drive, Cambridge, MA 02140. www.cambridgesoft.com. See Web site for pricing options. J. Am. Chem. Soc. 2005, 127, 4115–4116. DOI:10.1021/ja0410237. (g) Zielesny, A. Chemistry Software PackageChemOffice Ultra 2005. J. Chem. Inf.Model. 2005, 45, 1474–1477. DOI:10.1021/ci050273j. (h) Mills, N. ChemDraw Ultra 10.0 CambridgeSoft, 100CambridgePark Drive, Cambridge, MA 02140. www.cambridgesoft.com. CommercialPrice:  $1910 for download, $2150 for CD-ROM; Academic Price:  $710 fordownload, $800 for CD-ROM. J. Am. Chem.Soc. 2006, 128, 13649–13650. DOI: 10.1021/ja0697875. (i) Kerwin, S. M.ChemBioOffice Ultra 2010 Suite. J. Am. Chem.Soc. 2010, 132, 2466–2467. DOI: 10.1021/ja1005306. (j) Milne, G. W. A. SoftwareReview of ChemBioDraw 12.0. J. Chem. Inf.Model. 2010, 50, 2053. DOI:10.1021/ci100385n. (k) Narayanaswamy, V. K.; Rissdörfer, M.; Odhav, B.Review on CambridgeSoft ChemBioDraw Ultra 13.0v. Int. J. Theor. Appl. Sci. 2013,5, 43–49.

[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.

[5]    (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.

[6]    (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. Crystal Structure 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.

[7]    Müller, P.;Herbst-Irmer, R.; Spek, A. L.; Schneider, T. R.; Swaya, M. R. Crystal Structure Refinement: ACrystallographer’s Guide to SHELXL. Oxford University Press Inc. New York,2006.

[8]    Müller, P.; Herbst-Irmer, R.; Spek, A.L.; Schneider, T. R.; Swaya, M. R. 著;Müller, P. 编; 陈昊鸿 译; 赵景泰 校. 晶体结构精修——晶体学者的SHELXL软件指南. 北京: 高等教育出版社, 2010.

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