CheckCIF-PLAT395警报会是问题吗

DJ_Tokyo

CheckCIF-PLAT395警报会是问题吗

案例来源：CCDC[1] 2413561. DOI[2]:10.5517/ccdc.csd.cc2m0htz.

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）为其晶体结构，验证报告（由PLATON[5]呈现）表明有4个G级警报PLAT395（参阅推文“CheckCIF-PLAT395”）。

▲图2 案例结构及其验证报告

PLAT395是说X‒O‒Y角度偏离120°，上述结构中的X‒O‒Y角度6个，如下：

X‒O‒Y	数值	PLAT395
B1‒O1‒C1	121.61(13)°	‒
B1‒O2‒C7	104.14(13)°	G level
B1‒O3‒C8	103.93(13)°	G level
B2‒O4‒C2	126.22(14)°	‒
B2‒O5‒C13	104.10(13)°	G level
B2‒O6‒C16	104.03(13)°	G level

O2、O3、O5和O6是五元环的构建原子，因此它们的X‒O‒Y偏离120°较大从而触发了G级警报PLAT395，这只是一种提醒，而不是说存在错误。

类似的案例还有论文“Chem. Sci. 2020, 11, 126–131. DOI: 10.1039/c9sc04053f.”中CCDC 1943000结构，作者在CIF[6]中对此做了解释说明（This is due to thestrained geometry of the structure.），如图3所示。

▲图3 CCDC 1943000结构

如图4所示为论文“Chem. Commun. 2018, 54, 6808‒6811. DOI: 10.1039/c8cc01529e.”中CCDC 1819494结构，很显然，磷上的乙基与大环之间存在位阻作用使得B‒O‒P角度远大于120°从而触发了G级警报PLAT295，作者在CIF中对此做了解释说明（The deviation isdue to the nature of the adduct bond between the boron atom and oxygen atom ofthe molecule.）。

▲图4 CCDC 1819494结构

视频讲解请参阅：

CheckCIF-PLAT395警报会是问题吗：https://www.bilibili.com/video/BV1m5rEY6EWf

相关视频：

单晶结构解析练习386(数据还原-未知化合物)：https://www.bilibili.com/video/BV1aZ6DYqE54

数据下载：

链接:https://pan.baidu.com/s/10WoARmgYHoyiACVwZpXKlQ

提取码: 7bk3

后两个案例论文PDF和CIF文件请从以下链接下载：

链接: https://pan.baidu.com/s/16NJJmtjEkMc1vWs2Aqjuzg

提取码: 4qr2

参考文献

[1]    (a) Allen, F. H.The Cambridge Structural Database: A Quarter of a Million Crystal Structuresand 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) 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) 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) Hall, S. R.;Allen, F. H. Brown, I. D. The Crystallographic Information File (CIF): A NewStandard Archive File for Crystallography. ActaCryst. 1991, A47, 655–685. DOI:10.1107/S010876739101067X. (b) Hall, S. R. The STAR File: A New Formatfor Electronic Data Transfer and Archiving. J.Chem. Inf. Comput. Sci. 1991, 31, 326–333. DOI:10.1021/ci00002a020. (c) Hall, S. R.; Spadaccini, N. The STAR File:Detailed Specifications. J. Chem. Inf.Comput. Sci. 1994, 34, 505–508. DOI:10.1021/ci00019a005.

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：CheckCIF-PLAT395警报会是问题吗.pdf

链接: https://pan.baidu.com/s/1Ame7Sfoh_gk1uu3xYunNkQ 提取码: q3g5