晶体结构分子式非整数文献案例1

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。

晶体结构分子式非整数文献案例1

案例来源：CCDC [1]: 2329160. Angew.Chem. Int. Ed. 2024, 63, e202402093. DOI [2]: 10.1002/anie.202402093.

其反应如图1所示（由ChemBioDraw [3]绘制），利用MsFluid*-Pb（CCDC: 2329154）与环戊二烯基三羰基钼二聚体（[CpMo(CO)3]2,(Cyclopentadienyl)tricarbonylmolybdenum dimer, CAS: 12091-64-4）在氮气（N2,nitrogen, CAS: 7727-37-9）氛围下以四氢呋喃 [4]（THF,tetrahydrofuran, CAS: 109-99-9, CCDC: 1116822–1116823 [4a], 1116824–1116825 [4b]）为溶剂于室温下反应3小时合成目标产物MsFluid*-PbMo(CO)3Cp。

▲图1 案例结构合成反应式

用Olex2 [5]打开CIF[6]文件2329160.cif，并打开Work选项卡下Toolbox Work下Labels下拉菜单中的Crystallographic Occupancy，如图2所示，无序第一组分PbMo(CO)3Cp占有率为0.899，无序第二组分Pb占有率为0.101。

▲图2 无序组分占有率

该无序代表的含义是，这个晶体结构为MsFluid*-PbMo(CO)3Cp和MsFluid*-Pb的混合物，二者比例为0.899:0.101，即前者大约为90%，后者大约为10%，换句话说，原料MsFluid*-Pb未反应完全，因此在结晶时与产物形成了共晶（此类化合物不像普通有机物，可以经柱层析分离得到纯化合物再进行结晶），晶体结构中含有一个游离的正己烷 [7]（C6H14, n-hexane,CAS: 110-54-3, CCDC: 103189），因此其分子式为0.899 × (C80H94MoO3Pb) + 0.101 × (C72H89Pb) + C6H14= C85.192H107.495Mo0.899O2.697Pb，四舍五入即为C85.19H107.49Mo0.90O2.70Pb，与CIF中一致，如图3所示。

▲图3 CIF中分子式

你可能注意到上述笔者计算的C、H和O数量小数点后第三位与CIF中分子式不一致，这是因为笔者计算时采用的是Olex2中CrystallographicOccupancy标签显示的占有率0.899和0.101，该数值已经经过四舍五入保留三位小数，实际上打开ins文件，其占有率为0.89883和(1 - 0.89883) = 0.10117，如图4红色箭头所指，CIF中当然是根据后者计算所得。

▲图4 ins文件中原子参数是五位小数

视频讲解请参阅：

晶体结构分子式非整数文献案例1：https://www.bilibili.com/video/BV14TXKB4Evd

如需论文PDF和晶体数据CIF文件，请从以下链接下载：

链接:https://pan.baidu.com/s/1BehNx1idFiZnLIxtHIRG9w?pwd=an7y

提取码: an7y

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 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]    (a) Luger, P.; Buschmann, J. TwistConformation of Tetrahydrofuran in the Crystal. Angew. Chem. Int. Ed. 1983,22, 410. DOI: 10.1002/anie.198304101. (b) David, W. I. F.; Ibberson, R. M. AReinvestigation of the Structure of Tetrahydrofuran by High-Resolution NeutronPowder Diffraction. Acta Cryst. 1992, C48, 301–303. DOI: 10.1107/S0108270191008582.

[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)Hall, S. R.; Allen, F. H. Brown, I. D. The Crystallographic Information File(CIF): A New Standard Archive File for Crystallography. Acta Cryst. 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.

[7]    Boese, R.; Weiss, H.-C.; Bläser, D. TheMelting Point Alternation in the Short-Chain n-Alkanes: Single-CrystalX-Ray Analyses of Propane at 30 K and of n-Butane to n-Nonane at90 K. Angew. Chem. Int. Ed. 1999, 38, 988–992. DOI: 10.1002/(SICI)1521-3773(19990401)38:7<988::AID-ANIE988>3.0.CO;2-0.