晶体数据还原示例46(孪晶拆分-B级警报PLAT973) 案例来源:CCDC[1] 2409825‒2409826. DOI[2]: 10.5517/ccdc.csd.cc2lwm9f;10.5517/ccdc.csd.cc2lwmbg. 案例结构如图1所示(由ChemBioDraw[3]绘制)。 ▲图1 案例结构 该结构的晶体衍射图如图2所示(由APEX4[4]呈现),由钼靶测试,曝光时间为2秒。 ▲图2 衍射图 按默认设置(信噪比阈值为10.00,从3轮数据,每轮20帧sfrm中收集衍射点)收集到865个衍射点,添加限制条件后剩下289个衍射点用于中指标化,结果如图3所示,指标化率在60%左右。 ▲图3 指标化结果 按此默认结果进行数据还原,结果如图4所示(由Olex2[5]呈现,验证报告由PLATON[6]呈现),精修指标都还不错,但金属附近的残余峰触发了一个B级警报PLAT973(参阅推文“CheckCIF-PLAT973”)。 ▲图4 CCDC 2409826结果 其倒易空间点阵的3个正方向如图5所示。 ▲图5 倒易空间点阵 对其做孪晶拆分,将865个衍射点分为两组,分别为408和457个衍射点,如图6所示。 ▲图6 衍射点分组 这2组衍射点指标化结果如图7所示。 ▲图7 拆分的衍射点的指标化结果 孪晶拆分后,结果如图8所示,无AB级警报,虽然R因子比上面略高。 ▲图8 CCDC 2409825结果 视频操作演示请参阅: 单晶结构解析练习364(孪晶拆分-文献案例): 如需数据进行练习,请从以下链接下载: 提取码: r5uv 参考文献 [1] (a) Allen, F. H. The Cambridge StructuralDatabase: A Quarter of a Million Crystal Structures 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 III2021, 413–437. DOI: 10.1016/B978-0-12-409547-2.14829-2. [2] (a) International Organization forStandardization (2012). ISO 26324:2012. Informationand 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 for Standardization(2022). ISO 26324:2022. Information andDocumentation – Digital Object Identifier System. https://www.iso.org/standard/81599.html[3] (a) Klein, F. M. CS ChemDraw Pro,1 Version3.1 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] Bruker (2021). APEX4 (Version 2021.4-1).Program for Data Collection on Area Detectors. Bruker AXS Inc., Madison,Wisconsin, USA. [5] 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. [6] (a) Spek, A. L. Single-Crystal Structure Validation with theProgram 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. 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:晶体数据还原示例46(孪晶拆分-B级警报PLAT973).pdf
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