Disordered Fragments of Chemical Structures Based on Single-crystal X-ray Diffraction

摘要
图/表
参考文献
相关文章 (9)

全文: PDF (3161 KB) HTML (1 KB)
输出: BibTeX | EndNote (RIS)

摘要 For the reported chemical structures, the disordered fragments of the structure acting as hosts and guests are common and unmanageable for crystallographers. How to analyze and treat such disordered assemblies is an important task for crystallographers. It is often difficult for some researchers to refine the disordered structures, even to mechanically justify the refined consequence in the absence of expertise. Herein, some examples of disorder refinements selected from the literature, including the disordered assemblies of nitrate, perchlorate, alkyl, aromatic assemblies, and guest solvent molecules, are summarized and discussed to provide practical advice for investigating the disorders for crystallographic researchers and beginners. The refinement approach for these disordered assemblies is also discussed in detail, which is helpful for crystallographers.

	服务

	把本文推荐给朋友
	加入我的书架
	加入引用管理器
	E-mail Alert
	RSS
	作者相关文章
	张俊
	马晓帆
	轩小朋

关键词 ： single-crystal X-ray diffraction, crystal-structure refinement, disorder, disordered assemblies

Abstract：For the reported chemical structures, the disordered fragments of the structure acting as hosts and guests are common and unmanageable for crystallographers. How to analyze and treat such disordered assemblies is an important task for crystallographers. It is often difficult for some researchers to refine the disordered structures, even to mechanically justify the refined consequence in the absence of expertise. Herein, some examples of disorder refinements selected from the literature, including the disordered assemblies of nitrate, perchlorate, alkyl, aromatic assemblies, and guest solvent molecules, are summarized and discussed to provide practical advice for investigating the disorders for crystallographic researchers and beginners. The refinement approach for these disordered assemblies is also discussed in detail, which is helpful for crystallographers.

Key words： single-crystal X-ray diffraction crystal-structure refinement disorder disordered assemblies

收稿日期: 2019-06-10 出版日期: 2020-04-13

基金资助:This work was supported by the National Natural Science Foundation of China (Nos. 21671003 and 21201005),and the High Performance Computing Center of Henan Normal University and the 111 Project (No. D17007)

通讯作者: zhangjun@ahjzu.edu.cn E-mail: zhangjun@ahjzu.edu.cn

引用本文:

张俊;马晓帆;轩小朋. Disordered Fragments of Chemical Structures Based on Single-crystal X-ray Diffraction[J]. 结构化学, 2020, 39(4): 698-708.
ZHANG Jun;MA Xiao-Fan;XUAN Xiao-Peng. Disordered Fragments of Chemical Structures Based on Single-crystal X-ray Diffraction. CHINESE JOURNAL OF STRUCTURAL CHEMISTRY, 2020, 39(4): 698-708.

链接本文:

http://manu30.magtech.com.cn/jghx/CN/ 或 http://manu30.magtech.com.cn/jghx/CN/Y2020/V39/I4/698

REFERENCES
(1) Mei, J.; Leung, N. L. C.; Kwok, R. T. K.; Lam, J. W. Y.; Tang, B. Z. Aggregation-induced emission: together we shine, united we soar! Chem. Rev. 2015, 115 21, 11718–11940.
(2) Jiang, J.; Yaghi, O. M. Bronsted acidity in metal-organic frameworks. Chem. Rev. 2015, 115 14, 6966–6997.
(3) Chen, Z.; Islamoglu, T.; Farha, O. K. Toward base heterogenization: a zirconium metal-organic framework/dendrimer or polymer mixture for rapid hydrolysis of a nerve-agent simulant. ACS Appl. Nano. Mater. 2019, 1005–1008.
(4) Jin, S.; Xu, F.; Du, W.; Kang, X.; Chen, S.; Zhang, J.; Li, X.; Hu, D.; Wang, S.; Zhu, M. Isomerism in Au-Ag alloy nanoclusters: structure determination and enantioseparation of [Au9Ag12(SR)4(dppm)6X6]3+. Inorg. Chem. 2018, 57 9, 5114–5119.
(5) Wang, S.; Song, Y.; Jin, S.; Liu, X.; Zhang, J.; Pei, Y.; Meng, X.; Chen, M.; Li, P.; Zhu, M. Metal exchange method using Au25 nanoclusters as templates for alloy nanoclusters with atomic precision. J. Am. Chem. Soc. 2015, 137 12, 4018–4021.
(6) Shi, S. Y.; Chen, L. Y.; Li, Y.; He, L. H.; Zhang, J.; Cui, X. B. Three new hybrid compounds constructed from {PSb2Mo12O40} polyoxoanions, TMMC or organic amines. Inorg. Chem. Commun. 2019, 99, 149–155.
(7) Shi, S.; Chen, L.; Zhu, T.; Zhang, J.; Cui, X. Two new compounds of polyoxoanions, transition metal complexes and organic amines. Inorg. Chim. Acta 2018, 477, 292–299.
(8) Jin, M.; Seki, T.; Ito, H. Mechano-responsive luminescence via crystal-to-crystal phase transitions between chiral and non-chiral space groups. J. Am. Chem. Soc. 2017, 139 22, 7452–7455.
(9) Bruker. APEX3. 2014.3 - 0. Ed.; Bruker AXS Inc.: Madison, Wisconsin, USA 2014.
(10) SHELXTL Reference Manual. 5.03 Ed.; Siemens Energy & Automation Inc.: Madison, WI 1996.
(11) Farrugia, L. J. WinGX and ORTEP for Windows: an update. J. Appl. Cryst. 2012, 45 4, 849–854.
(12) 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 2, 339–341.
(13) Bruker. SAINT. 7.68 A ed.; Bruker AXS Inc.: Madison, Wisconsin, USA 2009.
(14) Bruker. SADABS. 2008/1 ed.; Bruker AXS Inc.: Madison, Wisconsin, USA 2008.
(15) Sheldrick, G. M. SHELXT - integrated space-group and crystal-structure determination. Acta Cryst. 2015, A71, 3–8.
(16) Sheldrick, G. M. Crystal structure refinement with SHELXL. Acta Cryst. 2015, C71, 3–8.
(17) Šišak Jung, D.; Baerlocher, C.; McCusker, L. B.; Yoshinari, T.; Seebach, D. Solving the structures of light-atom compounds with powder charge flipping. J. Appl. Cryst. 2014, 47 5, 1569–1576.
(18) Müller, P. Practical suggestions for better crystal structures. Crystallography Reviews 2009, 15 1, 57–83.
(19) Müller, P.; Herbst-Irmer, R.; Spek, A. L.; Schneider, T. R.; Sawaya, M. R. Crystal Structure Refinement: A Crystallographer's Guide to SHELXL. Oxford University Press: Oxford, New York 2006.
(20) Zhang, H.; Wang, H.; Yu, J. 1,4-Bis(4-methyl-2-nitrophenoxy)butane. IUCrData 2017, 2 12, x171734.
(21) Zhang, J. G.; Gong, W. J.; Guan, Y. S.; Li, H. X.; Young, D. J.; Lang, J. P. Carboxylate-assisted assembly of zinc and cadmium coordination complexes of 1,3,5-tri-4-pyridyl-1,2-ethenylbenzene: structures and visible-light-induced photocatalytic degradation of congo red in water. Cryst. Growth Des. 2018, 18 10, 6172–6184.
(22) Jin, F.; Zhang, Y.; Wang, H. Z.; Zhu, H. Z.; Yan, Y.; Zhang, J.; Wu, J. Y.; Tian, Y. P.; Zhou, H. P. Diverse structural Ag(I) supramolecular complexes constructed from multidentate dicyanoisophorone-based ligands: structures and enhanced luminescence. Cryst. Growth Des. 2013, 13 5, 1978–1987.
(23) Hu, L.; Wang, H.; Fang, B.; Hu, Z.; Zhang, Q.; Tian, X.; Zhou, H.; Wu, J.; Tian, Y. A reversible two-photon fluorescence probe for Cu(II) based on Schiff-base in HEPES buffer and in vivo imaging. Sens. Actuators, B 2017, 251, 993–1000.
(24) Zhang, J.; Xue, Y. S.; Liang, L. L.; Ren, S. B.; Li, Y. Z.; Du, H. B.; You, X. Z. Porous coordination polymers of transition metal sulfides with PtS topology built on a semirigid tetrahedral linker. Inorg. Chem. 2010, 49 17, 7685–7691.
(25) Dey, A.; Metrangolo, P.; Pilati, T.; Resnati, G.; Terraneo, G.; Wlassics, I. The disorder of perfluoroalkyl chains in crystals: two case histories of interpretation and refinement. J. Fluorine Chem. 2009, 130 9, 816–823.
(26) Hu, L.; Wang, H.; Xia, T.; Fang, B.; Shen, Y.; Zhang, Q.; Tian, X.; Zhou, H.; Wu, J.; Tian, Y. Two-photon-active organotin(IV) complexes for antibacterial function and superresolution bacteria imaging. Inorg. Chem. 2018, 57 11, 6340–6348.
(27) Feng, X.; Hu, J. Y.; Iwanaga, F.; Seto, N.; Redshaw, C.; Elsegood, M. R.; Yamato, T. Blue-emitting butterfly-shaped 1,3,5,9-tetraarylpyrenes: synthesis, crystal structures, and photophysical properties. Org. Lett. 2013, 15 6, 1318–1321.
(28) Jin, F.; Yang, X. F.; Li, S. L.; Zheng, Z.; Yu, Z. P.; Kong, L.; Hao, F. Y.; Yang, J. X.; Wu, J. Y.; Tian, Y. P.; Zhou, H. P. Role of anions in preparing silver(i) complexes with a new multidentate ligand: polymorphs, structures and nonlinear optical properties. CrystEngComm. 2012, 14 24, 8409–8417.
(29) Tong, Y. Y.; Zhang, H.; Chang, L. L.; Xuan, X. P. pH-Dependent reversible crystal transformation of 1-carboxymethyl-1-methyl-pyrrolidinium bromides and their spectroscopic fingerprint. Spectrochim. Acta, Part A 2018, 193, 197–202.
(30) Rogachev, A. Y.; Liu, S.; Xu, Q.; Li, J.; Zhou, Z.; Spisak, S. N.; Wei, Z.; Petrukhina, M. A. Placing metal in the bowl: does rim alkylation matter? Organometallics 2019, 38 2, 552–566.
(31) Ding, T.; Wang, X. X.; Zhang, M.; Ou, S. M.; Hu, T. J. Four new coordination polymers based on a pyridinetetracarboxylate ligand: syntheses, structures and high CO2/CH4 separation. CrystEngComm. 2017, 19 24, 3313–3321.
(32) Spek, A. L. PLATON, A Multipurpose Crystallographic Tool. Utrecht University: The Netherlands 2006.
(33) Li, J. R.; Yakovenko, A. A.; Lu, W.; Timmons, D. J.; Zhuang, W.; Yuan, D.; Zhou, H. C. Ligand bridging-angle-driven assembly of molecular architectures based on quadruply bonded Mo-Mo dimers. J. Am. Chem. Soc. 2010, 132 49, 17599–17610.
(34) Li, J. R.; Zhou, H. C. Metal-organic hendecahedra assembled from dinuclear paddlewheel nodes and mixtures of ditopic linkers with 120 and 90 degrees bend angles. Angew. Chem. Int. Ed. 2009, 48 45, 8465–8468.
(35) Xu, L.; Zhai, M. K.; Wang, F.; Sun, L.; Du, H. B. A series of robust metal-porphyrinic frameworks based on rare earth clusters and their application in N–H carbene insertion. Dalton Trans. 2016, 45 43, 17108–17112.
(36) Feng, D.; Gu, Z. Y.; Chen, Y. P.; Park, J.; Wei, Z.; Sun, Y.; Bosch, M.; Yuan, S.; Zhou, H. C. A highly stable porphyrinic zirconium metal-organic framework with shp-a topology. J. Am. Chem. Soc. 2014, 136 51, 17714–17717.
(37) Luo, X. M.; Chen, L.; Dong, Y. Y.; Li, J.; Cui, C. H.; Cao, J. P.; Xu, Y. Three new high-nuclear transition-metal-substituted heteropolytungstates: syntheses, crystal structures, magnetic studies and NLO properties. Dalton Trans. 2018, 47 28, 9504–9511.
(38) Wang, Q.; Lin, C.; Zou, G.; Liu, M.; Gao, D.; Bi, J.; Huang, L. K2[B3O3(OH)5]: a new deep-UV nonlinear optical crystal with isolated [B3O3(OH)5]2- anionic groups. J. Alloys Compd. 2018, 735, 677–683.
(39) Hu, Z.; Zhang, Q.; Zhang, M.; Du, W.; Wang, Y.; Zhang, J.; Wu, J.; Tian, Y.; Fang, M. Chiral crystals based on achiral ligand and their framework dependent luminescent properties. Inorg. Chem. Commun. 2018, 97, 149–156.
(40) Luo, X. M.; Hu, Z. B.; Lin, Q. F.; Cheng, W.; Cao, J. P.; Cui, C. H.; Mei, H.; Song, Y.; Xu, Y. Exploring the performance improvement of magnetocaloric effect based Gd-exclusive cluster Gd60. J. Am. Chem. Soc. 2018, 140 36, 11219–11222.
(41) Xu, W. J.; Xie, K. P.; Xiao, Z. F.; Zhang, W. X.; Chen, X. M. Controlling two-step phase transitions and dielectric responses by a-site cations in two perovskite-like coordination polymers. Cryst. Growth Des. 2016, 16 12, 7212–7217.
(42) Baral, M.; Chattopadhyay, M. K.; Jangir, R.; Chakrabarti, A.; Ganguli, T. Presence of atomic disorder and its effect on the magnetic and electronic properties of NiCrGa half Heusler alloy. J. Magn. Magn. Mater. 2019, 475, 675–682.
(43) Trojan-Piegza, J.; Wang, Z.; Kinzhybalo, V.; Zhou, G.; Wang, S.; Zych, E. Spectroscopic reflects of structural disorder in Eu3+/Pr3+-doped La0.4Gd1.6Zr2O7 transparent ceramics. J. Alloys Compd. 2018, 769, 18–26.