定错晶胞则解不出结构3(一个孪晶拆分案例)

DJ_Tokyo

★声明：本文仅代表个人观点，笔者学识有限，资料整理过程中难免存在疏漏谬误，请不吝指正。

定错晶胞则解不出结构3(一个孪晶拆分案例)

案例结构为6-羟基烟酸（6-oxo-1,6-dihydropyridine-3-carboxylic acid, CAS:5006-66-6, CCDC [1]: 2562903, DOI [2]: 10.5517/ccdc.csd.cc2s0x91.），其结构如图1所示（由ChemBioDraw[3]绘制），数据由一位粉丝朋友提供，在此感谢！

▲图1 案例结构

笔者利用APEX6 [4]按照默认设置处理，得到的是错误的晶胞参数，结果如图2所示，解析结果能观察到一些六元环，但是整个不对称单元（ASU, asymmetric unit）中原子众多，且多为非正定（NPD, non positive definite）。

▲图2 错误晶胞结果

按照正确晶胞参数还原数据，结果如图3所示（由Olex2 [5]呈现），R1 = 12.91%，wR2 = 34.54%，残余峰（Max Peak = 1.4）触发一个B级警报PLAT097（参阅推文“CheckCIF-PLAT097”，验证报告由PLATON [6]呈现）。

▲图3 正确晶胞常规数据还原结果

采用“APEX4孪晶拆分步骤”推文方法进行孪晶拆分，拆分成2个晶畴，结果如图4所示，R1 = 12.59%，wR2 = 31.65%，残余峰（MaxPeak = 1.1）触发一个B级警报PLAT097。

▲图4 正确晶胞孪晶拆分2个晶畴结果

利用APEX中的CELL NOW例程进行孪晶拆分（参阅推文“APEX4孪晶拆分步骤(CELL_NOW)”），拆分成4个晶畴，结果如图5所示，R1 = 8.60%，wR2 = 26.70%，残余峰小（MaxPeak = 0.4），无AB级警报。

▲图5 正确晶胞孪晶拆分4个晶畴结果

视频操作：

单晶结构解析练习779(数据还原-孪晶拆分-残余峰-PLAT097)：https://www.bilibili.com/video/BV1FTTr6NEjy

数据下载：

链接:https://pan.baidu.com/s/1EtWmLTAFku94gSppb900ug?pwd=ehkj

提取码: ehkj

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]    Bruker(2024). APEX6 (Version 2025.6-0). Program for Data Collection on AreaDetectors. 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-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.