X射线晶体学结合电子晶体学在复杂无机晶体结构解析中的应用

doi:10.3866/PKU.WHXB201907052

摘要/Abstract

摘要：

自然界中的材料，比如无机材料，有机材料，生物材料等等，均有其独特的物理和化学性质。而材料的性能又与材料的结构息息相关，只有充分了解了材料的结构，才能更加深入的研究材料性质。因此，材料结构的确定在化学、物理、生物等学科中的显得尤为重要。X射线晶体学作为传统的结构解析技术仍然是目前最重要的结构解析手段，但是对于复杂结构，X射线衍射晶体学解析结构也存在一些不足，往往需要其他技术手段相补充才能完成复杂结构的结构解析。电子晶体学虽然起步比X射线晶体学晚，但是，经过近几十年的发展，已经是结构解析领域一个非常重要的手段。本文将主要介绍X射线晶体学结合电子晶体学在复杂无机晶体结构解析中的应用。

关键词: 结构确定, X射线衍射, 电子晶体学, 三维电子衍射, 复杂无机晶体结构

Abstract:

Inorganic, organic, and biological materials have specific natural properties which mostly depend on their atomic structures. The properties of novel materials can be predicted based solely on knowing the structure fully. Thus, structure determination plays a very important role in chemistry, physics, and materials science. X-ray crystallography, including single-crystal X-ray diffraction (SCXRD) and powder X-ray diffraction (PXRD), remains an important technique for studying structures. However, SCXRD can only be applied to high-quality large single crystals without disorders/defects, whereas PXRD provides only one-dimensional information and reflections with the similar d-values will overlap, which makes it difficult to determine the unit-cell parameters, space groups, and accurate intensities. Another important technique for structural determination is electron crystallography (EC). As the electron is the probe, EC alone can be used for those crystals which are too small to be studied by SCXRD or too complex to be studied by PXRD. Electrons interact much more strongly with matter than X-rays; therefore, both electron diffractions (ED) patterns and high-resolution transmission electron microscopy (HRTEM) images can be obtained from nano-sized crystals. Although electron crystallography started later than X-ray crystallography, it has become a very important technique for structural analysis after several decades of development. Especially, three dimensional (3D) ED techniques have been developed, automated electron diffraction tomography (ADT) and rotation electron diffraction (RED), which allow for automated data collection without requiring considerable expertise on the operation of electron microscopes. In addition, the intensities of 3D ED data can be extracted and used for structure determination using specialized software developed for SCXRD. However, the strong interactions between electrons and materials also result in dynamic effects and beam damage. Although the dynamic effects in 3D electron diffraction techniques (ADT and RED) can be significantly reduced, some structures still pose problems for obtaining an initial model due to beam damage. Therefore, EC and X-ray crystallography have significant limitations. For many complicated crystals, a single technique is insufficient to solve the crystal structure and different techniques that supply complementary structural information must be used to obtain a complete structural determination. Herein, the application of X-ray crystallography combined with EC for the analysis of complex inorganic crystal structures will be introduced, covering issues associated with peak overlap, impurities, pseudo-symmetry and twinning, disordered frameworks, location guests, and aperiodic structures.

Key words: Structure determination, X-ray diffraction, Electron crystallography, Three-dimensional electron diffraction, Complex inorganic crystal structure

黎建,林聪,林建华,孙俊良. X射线晶体学结合电子晶体学在复杂无机晶体结构解析中的应用[J]. 物理化学学报, 2020, 36(1), 1907052. doi: 10.3866/PKU.WHXB201907052

Jian Li,Cong Lin,Jianhua Lin,Junliang Sun. Application of Combining X-ray Diffraction and Electron Crystallography for Determination of Complex Inorganic Crystal Structure[J]. Acta Physico-Chimica Sinica 2020, 36(1), 1907052. doi: 10.3866/PKU.WHXB201907052

链接本文: https://www.whxb.pku.edu.cn/CN/10.3866/PKU.WHXB201907052

https://www.whxb.pku.edu.cn/CN/Y2020/V36/I1/1907052

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参考文献 67

1	Chen X. M. ; Cai J. W. Principle and Practice of Single Crystal Structure Analysis Science Press: Beijing, 2007, p. 15.
	陈小明; 蔡继文. 单晶结构分析的原理与实践, 北京: 科学出版社, 2007, 15.
2	Zou X. D. ; Hovmoller S. ; Oleynikov P. Electron Crystallography Electron Microscopy and Electron Diffraction Oxford University Press: UK, 2011, p. 86.
3	Patterson A. L. Phys. Rev. 1934, 46, 372. doi: 10.1103/PhysRev.46.372
4	Sheldrick G. M. Acta Crystallogr. A 1990, 46, 467. doi: 10.1107/S0108767390000277
5	Oszlányi G. ; Sütő A. Acta Crystallogr. A 2004, 60, 134. doi: 10.1107/S0108767303027569
6	De Vries R. Y. ; Briels W. J. ; Feil D. Acta Crystallogr. A 1994, 50, 383. doi: 10.1107/S0108767393012802
7	Mitchell M. An Introduction to Genetic Algorithms MIT Press Cambridge: MA, USA, 1998.
8	Deem M. W. ; Newsam J. M. J. Am. Chem. Soc. 1992, 114, 7189. doi: 10.1021/ja00044a035
9	Tang L. Q. ; Shi L. ; Bonneau C. ; Sun J. L. ; Yue H. J. ; Ojuva A. ; Lee B. L. ; Kritikos M. ; Bell R. G. . Bacsik Z. ; et al Nat. Mater. 2008, 7, 381. doi: 10.1038/nmat2169
10	Su J. ; Wang Y. X. ; Wang Z. M. ; Lin J. H. J. Am. Chem. Soc 2009, 131, 6080. doi: 10.1021/ja901330u
11	Baerlocher Ch. ; Gramm F. ; Massguer L. ; McCusker L. B. ; He Z. ; Hovmoller S. ; Zou X. Science 2007, 315, 1113. doi: 10.1126/science.1137920
12	Lorgouilloux Y. ; Dodin M. ; Paillaud J. L. ; Caullet P. ; Michelin L. ; Josien L. ; Ersen O. ; Bats N. J. Solid State Chem 2009, 182, 622. doi: 10.1016/j.jssc.2008.12.002
13	Inge A. ; Huang S. L. ; Chen H. ; Moraga F. ; Sun J. L. ; Zou X. D. Cryst. Growth Des. 2012, 12, 4853. doi: 10.1021/cg300647s
14	Ju J. ; Lin J. H. ; Li G. B. ; Yang T. ; Li H. M. ; Liao F. H. ; Loong C. K. ; You L. P. Angew. Chem. Int. Ed. 2003, 42, 5607. doi: 10.1002/anie.200352263
15	Yang T. ; Bartoszewicz A. ; Ju J. ; Sun J. L. ; Liu Z. ; Zou X. D. ; Wang Y. X. ; Li G. B. ; Liao F. H. ; Martín M. B. ; et al Angew. Chem. Int. Ed 2011, 50, 12555. doi: 10.1002/anie.201106310
16	Estermann M. A. ; McCusker L. B. ; Baerlocher C. J. Appl. Cryst. 1992, 25, 539. doi: 10.1107/S0021889892004862
17	Baerlocher Ch. ; McCusker L. B. ; Palatinus L. Z. Kristallogr. 2007, 222, 47. doi: 10.1524/zkri.2007.222.2.47
18	Kolb U. ; Mugnaioli E. ; Gorelik T. E. Cryst. Res. Technol. 2011, 46, 542. doi: 10.1002/crat.201100036
19	Zhang D. ; Oleynikov P. ; Hovmoller S. ; Zou X. D. Z. Kristallogr 2010, 225, 94. doi: 10.1524/zkri.2010.1202
20	Xu L. ; Zhang L. ; Li J. ; Koki M. ; Peng F. ; Xu H. ; Lin C. ; Gao L. ; Jiang J. G. ; Watcharop C. ; et al Chem. Eur. J. 2018, 24, 9247. doi: 10.1002/chem.201802087
21	Hua W. ; Chen H. ; Yu Z. B. ; Zou X. D. ; Lin J. H. ; Sun J. L. Angew. Chem. Int. Ed. 2014, 53, 5868. doi: 10.1002/anie.201309766
22	Huang S. L. ; Su J. ; Kirsten C. ; Ken I. ; Liang J. ; Zou X. D. ; Sun J. L. Inorg. Chem. Front 2014, 1, 278. doi: 10.1039/C3QI00088E
23	Zhang Y. B. ; Su J. ; Hiroyasu F. ; Yun Y. F. ; Felipe G. ; Adam D. ; Zou X. D. ; Omar M. Y. J. Am. Chem. Soc. 2013, 135, 16336. doi: 10.1021/ja409033p
24	Ding H. ; Li J. ; Xie G. H. ; Lin G. Q. ; Chen R. F. ; Peng Z. K. ; Yang C. L. ; Wang B. S. ; Sun J. L. ; Wang C. Nat. Commun. 2018, 9, 5234. doi: 10.1038/s41467-018-07670-4
25	Ma T. ; Li J. ; Niu J. ; Zhang L. ; Ahmed S E. ; Lin C. ; Shi D. ; Chen P. H. ; Li L. H. ; Du X. ; et al Am. Chem. Soc. 2018, 40, 6763. doi: 10.1021/jacs.8b03169
26	Gramm F. ; Baerlocher C. ; McCusker L. B. ; Warrender S. J. ; Wright P. A. ; Han B. ; Hong S. B. ; Liu Z. ; Ohsuna T. ; Terasaki O. Nature 2006, 444, 79. doi: 10.1038/nature05200
27	Willhammar T. ; Sun J. L. ; Wan W. ; Oleynikov P. ; Zhang D. L. ; Zou X. D. ; Moliner M. ; Gonzalez J. ; Martínez C. ; Rey F. ; et al Nat. Chem 2012, 3, 188. doi: 10.1038/nchem.1253
28	Han Y. ; Zhang D. ; Chng L. L. ; Sun J. ; Zhao L. ; Zou X. ; Ying J. Y. Nat. Chem. 2009, 1, 123. doi: 10.1038/nchem.166
29	Baerlocher C. ; Xie D. ; McCusker L. B. ; Hwang S. J. ; Chan I. Y. ; Ong K. ; Burton A. W. ; Zones S. I. Nat. Mater 2008, 7, 631. doi: 10.1038/nmat2228
30	Xu L. ; Ji X. ; Jiang J. ; Han L. ; Che S. ; Wu P. Chem. Mater 2015, 27, 7852. doi: 10.1021/acs.chemmater.5b03658
31	Grosse-Kunstleve R. W. ; McCusker L. B. ; Baerlocher C. J. Appl. Cryst. 1999, 32, 536. doi: 10.1107/S0021889899003453
32	Sun J. L. ; Bonneau C. ; Cantin A. ; Corma A. ; Diaz-Cabanas M. J. ; Moliner M. ; Zhang D. L. ; Li M. R. ; Zou X. D. Nature 2009, 458, 1154. doi: 10.1038/nature07957
33	Chen H. ; Ju J. ; Meng Q. ; Su J. ; Lin C. ; Zhou Z. Y. ; Li G. ; Wang W. ; Gao W. ; Zeng C. ; et al J. Am. Chem. Soc 2015, 137, 7047. doi: 10.1021/jacs.5b03685
34	Li J. ; Lin C. ; Min Y. X. ; Yuan Y. Y. ; Li G. B. ; Yang S. H. ; Pascal M. ; Lin J. H. ; Sun J. L. J. Am. Chem. Soc. 2019, 141, 12,4990. doi: 10.1021/jacs.9b00093
35	Yu Z. B. ; Han Y. ; Zhao L. ; Huang S. L. ; Zheng Q. Y. ; Lin S. Z. ; Córdova A. ; Zou X. D. ; Sun J. L. Chem. Mater 2012, 24, 3701. doi: 10.1021/cm301654d
36	Nnewsam J. M. ; Treacy M. M. J. ; Koetsier W. T. ; de Gruyter C. B. Proc. R. Soc. London Ser. A 1988, 420, 375. doi: 10.1098/rspa.1988.0131
37	Conradsson T. ; Zou X. D. ; Dadachov M. Inorg. Chem 2000, 39, 1716. doi: 10.1021/ic9911217
38	Corma A. ; Moliner M. ; Cantín Á. ; Díaz-Cabañas M. ; Jordá J. ; Zhang D. ; Sun J. L. ; Jansson K. ; Hovmöller S. ; Zou X. D. Chem. Mater. 2008, 20, 3218. doi: 10.1021/cm8002244
39	Willhammar T. ; Zou X. D. Z. Kristallogr 2013, 228, 11. doi: 10.1524/zkri.2012.1564
40	Liu L. F. ; Yu Z. B. ; Chen H. ; Deng Y. ; Lee B. ; Sun J. L. Cryst. Growth Des. 2013, 13, 4168. doi: 10.1021/cg400880a
41	Wadlinger, R. L.; Kerr, G. T.; Rosinski, E. J. Catalytic Composition of a Crystalline Zeolite. US Patent 3308069, 1967.
42	Xu Y. ; Liu L. F. ; Daniel M. ; Sun J. L. ; Zhang P. ; Yu J. H. Inorg. Chem 2013, 52, 10238. doi: 10.1021/ic302705f
43	Yang S. H. ; Sun J. L. ; Ramirez-Cuesta A. ; Callear S. ; David W. ; Anderson D. ; Newby R. ; Blake A. ; Parker J. ; Tang C. ; et al Nat. Chem. 2012, 4, 887. doi: 10.1038/nchem.1457
44	Lo B. ; Ye L. ; Qu J. ; Sun J. L. ; Zheng J. ; Kong D. ; Murray C. ; Tang C. ; Tsang S. Angew. Chem. Int. Ed 2016, 55, 1. doi: 10.1002/anie.201600487
45	Liang J. ; Su J. ; Wang Y. ; Chen Y. ; Zou X. ; Liao F. ; Lin J. ; Sun J. L. Chem. Eur. J. 2014, 20, 16097. doi: 10.1002/chem.201405449
46	Inge A. K. ; Fahlquist H. ; Willhammar T. ; Huang Y. ; McCusker L. B. ; Zou X. J. Appl. Crystallogr 2013, 46, 1094. doi: 10.1107/S0021889813013101
47	Yamamoto A. Acta Crystallogr. A 1993, 49, 831. doi: 10.1107/S0108767393004404
48	Li M. ; Sun J. L. ; Peter O. ; Sven H. ; Zou X. D. ; Benjamin G. Acta Crystallogr. B 2010, 66, 17. doi: 10.1107/S0108768109053804
49	Li J. ; Sun J. L. Acc. Chem. Res 2017, 50, 2737. doi: 10.1021/acs.accounts.7b00366
50	Sun J. L. ; Lee S. ; Lin J. H. Chem. Asian J. 2007, 2, 1204. doi: 10.1002/asia.200700088
51	Sun J. L. ; Li G. B. ; Li Z. F. ; You L. P. ; Lin J. H. Inorg. Chem. 2006, 45, 8394. doi: 10.1021/ic060862m
52	Zhou Z. ; Xu X. ; Fei R. ; Mao J. ; Sun J. L. Acta Crystallogr. B 2016, 72, 194. doi: 10.1107/S2052520615019733
53	Schmidt J. ; Lee S. ; Fredrickson D. ; Conrad M. ; Sun J. L. ; Harbrecht B. Chem. Eur. J 2007, 13, 1394. doi: 10.1002/chem.200600135
54	Sun Z. H. ; Li J. ; Ji C. M. ; Sun J. L. ; Hong M. C. ; Luo J. H. J. Am. Chem. Soc. 2017, 139, 44,15900. doi: 10.1021/jacs.7b08950
55	Lin K. ; Zhou Z. ; Liu L. ; Ma H. ; Chen J. ; Deng J. ; Sun J. ; You L. ; Kasai H. ; Kato K. ; et al J. Am. Chem. Soc 2015, 137, 13468. doi: 10.1021/jacs.5b08230
56	Wang Y. ; Yang T. ; Xu H. ; Zou X. D. ; Wan W. J. Appl. Cryst 2018, 51, 1094. doi: 10.1107/S1600576718007604
57	Wang Y. ; Takki S. ; Cheung O. ; Xu H. ; Wan W. ; Ohrstrom L. ; Inge A. K. Chem. Commun. 2017, 53, 7018. doi: 10.1039/C7CC03180G
58	Wang B. ; Timo R. ; Inge A. K. ; Xu H. Y. ; Yang T. M. ; Huang Z. H. ; Norbert S. ; Zou X. D. Chem. Eur. J 2018, 24, 17429. doi: 10.1002/chem.201804133
59	Xu H. ; Lebratte H. ; Yang T. ; Srinivas V. ; Hovmoller S. ; Hogbom M. ; Zou X. Structure 2018, 26, 667. doi: 10.1016/j.str.2018.02.015
60	Nannenga B. L. ; Shi D. ; Hattne J. ; Reyes F. E. ; Gonen T. eLife 2014, 3, e03600. doi: 10.7554/eLife.03600
61	de la Cruz M. J. ; Hattne J. ; Shi D. ; Seidler P. ; Rodriguez J. ; Reyes F. E. ; Sawaya M. R. ; Cascio D. ; Weiss S. C. ; Kim S. K. ; et al Nat. Methods 2017, 14, 399. doi: 10.1038/nmeth.4178
62	Rodriguez J. A. ; Ivanova M. I. ; Sawaya M. R. ; Cascio D. ; Reyes F. E. ; Shi D. ; Sangwan S. ; Guenther E. L. ; Johnson L. M. ; Zhang M. ; et al Nature 2015, 525, 486. doi: 10.1038/nature15368
63	Christopher G. J. ; Michael W. M. ; Johan H. ; Tyler J. F. ; Brian M. S. ; Jose A. R. ; Hosea M. N. ; Gonen T. ACS Cent. Sci. 2018, 4, 1587. doi: 10.1021/acscentsci.8b00760
64	Gruene T. ; Wennmacher J. ; Zaubitzer C. ; Holstein J. J. ; Heidler J. ; Fecteau-Lefebvre A. ; De Carlo S. ; Müller E. ; Goldie K. N. ; Regeni I. ; et al Angew. Chem. Int. Ed 2018, 57, 16313. doi: 10.1002/anie.201811318
65	Palatinus L. ; Brazda P. ; Boullay P. ; Perez O. ; Klementova M. ; Petit S. ; Eigner V. ; Zaarour M. ; Mintova S. Science 2017, 335, 166. doi: 10.1126/science.aak9652
66	Xu H. Y. ; Zou X. D. Science 2019, 364, 632. doi: 10.1126/science.aax5385
67	Brázda P. ; Palatinus L. ; Babor M. Science 2019, 364, 667. doi: 10.1126/science.aaw2560

	SCXRD	PXRD	ED (2D/3D)	HRTEM
Unit cell	Easy	Difficult	Require expertise /Easy	Difficult
Space group	Easy	Difficult	Require expertise /Easy	Difficult
Peak overlapping	No	Yes	No/No	No
Completeness	High	High	Low/High	Low
Beam damage	Low	Low	Medium/Medium	Strong
Phase	No	No	No/No	Yes
Information of sample	Single crystal	over	Single crystal	Single crystal
Intensities	Kinematic	Kinematic	Dynamic/Dynamic	Dynamic
Data collection	Easy	Easy	Difficult /Difficult	Difficult
Structure solution	Easy	Difficult	Difficult/easy	Difficult
Refinement	Accurate	Accurate	Less accurate/ Less accurate	Less accurate/ Less accurate
Crystal size	> 1 μm	> 50 nm	> 50 nm	> 5 nm

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