数据还原导向不同空间群案例1

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数据还原导向不同空间群案例1

案例来源：CCDC[1] 2402575‒2452576. DOI[2]:10.5517/ccdc.csd.cc2ln2fs; 10.5517/ccdc.csd.cc2ln2gt.

其结构如图1所示（由ChemBoiDraw[3]绘制）。

▲图1 案例结构

两个晶体的衍射图如图2所示（由APEX4[4]呈现），CCDC 2402575的曝光时间为8秒，CCDC 2402576的曝光时间为4秒，明显后者衍射更强。

▲图2 两个晶体的衍射图

按默认设置（信噪比阈值10.00，3轮数据每轮20幅sfrm）收集衍射点进行指标化，CCDC 2402575收集到246个衍射点，三个方法得到的晶胞参数Score值几乎相同，程序默认选择体积更小的晶胞（Score值更高一点），CCDC 2402576收集到344个衍射点，程序选择Score值更高的大体积晶胞，如图3所示。

▲图3 两个数据指标化结果

到了BravaisLattice步骤时，两者晶胞参数变成相同的，但CCDC 2402575是Monoclinic C而CCDC 2402576是Monoclinic P，如图4所示。

▲图4 两个数据Bravais Lattice结果

在XPREP[5]中，CCDC2402575确定为第15号空间群C2/c，CCDC 2402576确定为第14号空间群P21/c，如图5所示。

▲图5 两个数据空间群确定情况

如图6−7所示（由Olex2[6]呈现），CCDC 2402575不对称单元ASU（asymmetry unit）中为半个分子结构，需要对此操作得到完整分子结构，CCDC 2402576 ASU中为完整的一个分子结构。

▲图6 CCDC 2402575 ASU结构

▲图7 CCDC 2402576 ASU结构

视频操作演示请参阅：

单晶结构解析练习301(数据还原-无序建模)：https://www.bilibili.com/video/BV1doUbYTEn7

如需数据进行练习，请从以下链接下载：

链接: https://pan.baidu.com/s/1ZI4N6LjKyRrt-PAXL80cvw

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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]    Bruker (2014). XPREP (Version 2014/2), Programfor Space Group Determination. Bruker AXS Inc., Madison, Wisconsin, USA.

[6]    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.

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