晶体数据还原示例53(完整度和Rint)

DJ_Tokyo

                              

晶体数据还原示例53(完整度和Rint)

案例来源：CCDC[1] 2401441, 2453623. JACS Au 2025, DOI[2]: 10.1021/jacsau.5c00425.

案例结果如图1所示（由ChemBioDraw[3]绘制）。

▲图1 案例结构

该结构发表时的数据状态如图2所示（由Olex2[4]呈现），完整度为99.1%，Rint = 12.01%。

▲图2 CCDC 2401441发表时状态

打开其CIF[5]文件，发现里面没有吸收校正信息，如图3所示，表面该数据可能没有做吸收校正处理，故而导致Rint值偏高。

▲图3 CIF中吸收校正信息条目

该晶体用铜靶测试，总共31轮数据（显然是按照手性策略收集的数据），3143帧衍射照片，总大小为2.32 GB，外加一轮fastscan（180帧衍射照片，136 MB），fastscan曝光时间为1秒，34轮数据曝光时间为10秒，其衍射图如图4所示（由APEX4[6]呈现）。

▲图4 衍射图

如果只对31轮数据进行还原，并做吸收校正，则其结果如图5所示，完整度为97.5%，Rint = 4.05%。

▲图5 31轮数据+吸收校正结果

对于“31轮数据+吸收校正结果”来说，有些离群点，如图6所示。

▲图6 离群点

如果使用SHELXL[7]指令OMIT（参阅推文“SHELXL指令之OMIT”）将这些离群点从精修中删除（参阅推文“CheckCIF-B级警报PLAT934(如何删除衍射点)”或视频“CheckCIF-B级警报PLAT934(如何删除衍射点)：https://www.bilibili.com/video/BV1WJDJYbESq”“Olex2基操-OMIT指令的使用：https://www.bilibili.com/video/BV1av411e7f2”和“Olex2中OMIT指令的使用：https://www.bilibili.com/video/BV1bw411D7Nb”），则结果如图7所示。

▲图7 删除离群点结果

如果对31轮数据+fastscan进行还原，并做吸收校正，则其结果如图8所示，完整度为99.2%，Rint = 3.99%。

▲图8 31轮数据+fastscan+吸收校正结果（CCDC 2453623）

三种情况处理结果对比如下：

1、31轮数据+fastscan

2、31轮数据+吸收校正

3、31轮数据+fastscan+吸收校正

处理	信噪比	Rint	完整度	Max Peak	Min Peak	R1	wR2
1	29.5	12.01%	99.1%	0.2	-0.2	4.28%	10.52%
2	59.5	4.05%	97.5%	0.4	-0.4	3.14%	10.98%
2+OMIT	60.0	4.05%	97.3%	0.1	-0.1	2.95%	8.07%
3	55.2	3.99%	99.2	0.2	-0.1	3.01%	8.12%

处理	Hooft y[8]	Parson's q[9]	Flack x[10]
1	0.01(3)	-0.03(4)	-0.01(16)
2	0.09(2)	0.08(2)	0.10(16)
2+OMIT	0.09(2)	0.08(2)	0.09(14)
3	0.10(2)	0.09(2)	0.09(14)

相关视频：

单晶结构解析练习619(文献案例-数据还原)：https://www.bilibili.com/video/BV1VpNHz1EXk

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 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 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) 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.

[6]    Bruker (2021). APEX4 (Version 2021.4-1). Program for Data Collection on AreaDetectors. Bruker AXS Inc., Madison, Wisconsin, USA.

[7]    (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.

[8]    (a) Hooft, R. W. W.; Straver, L. H.; Spek, A. L.Determination of Absolute Structure using Bayesian Statistics on BijvoetDifferences. J. Appl. Cryst. 2008, 41, 96–103. DOI: 10.1107/S0021889807059870. (b) Hooft, R. W. W.; Straver, L. H.; Spek,A. L. Using the t-Distribution toImprove the Absolute Structure Assignment with Likelihood Calculations. J. Appl. Cryst. 2010, 43, 665–668. DOI: 10.1107/S0021889810018601.

[9]    Parsons, S.; Flack, H. Precise Absolute-StructureDetermination in Light-Atom Crystals. ActaCryst. 2004, A60, s61. DOI:10.1107/S0108767304098800.

[10]  Flack, H. D. OnEnantiomorph-Polarity Estimation. Acta Cryst. 1983,A39, 876–881. DOI: 10.1107/S0108767383001762.

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