Citation: Jun ZHANG, Xiao-Fan MA, Xiao-Peng XUAN. Disordered Fragments of Chemical Structures Based on Single-crystal X-ray Diffraction[J]. Chinese Journal of Structural Chemistry, ;2020, 39(4): 698-708. doi: 10.14102/j.cnki.0254-5861.2011-2494 shu

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

  • Corresponding author: Jun ZHANG, zhangjun@ahjzu.edu.cn Xiao-Peng XUAN, xpxuan@henannu.edu.cn
  • Received Date: 7 June 2019
    Accepted Date: 8 September 2019

    Fund Project: the National Natural Science Foundation of China 21671003the National Natural Science Foundation of China 21201005the High Performance Computing Center of Henan Normal University and the 111 Project D17007

Figures(12)

  • 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.
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    1. [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.  doi: 10.1021/acs.chemrev.5b00263

    2. [2]

      Jiang, J.; Yaghi, O. M. Bronsted acidity in metal-organic frameworks. Chem. Rev. 2015, 115 14, 6966–6997.  doi: 10.1021/acs.chemrev.5b00221

    3. [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. [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.  doi: 10.1021/acs.inorgchem.8b00183

    5. [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.  doi: 10.1021/ja511635g

    6. [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.  doi: 10.1016/j.inoche.2018.11.005

    7. [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.  doi: 10.1016/j.ica.2018.03.012

    8. [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.  doi: 10.1021/jacs.7b04073

    9. [9]

      Bruker. APEX3. 2014.3 - 0. Ed.; Bruker AXS Inc.: Madison, Wisconsin, USA 2014.

    10. [10]

      SHELXTL Reference Manual. 5.03 Ed.; Siemens Energy & Automation Inc.: Madison, WI 1996.

    11. [11]

      Farrugia, L. J. WinGX and ORTEP for Windows: an update. J. Appl. Cryst. 2012, 45 4, 849–854.  doi: 10.1107/S0021889812029111

    12. [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.  doi: 10.1107/S0021889808042726

    13. [13]

      Bruker. SAINT. 7.68 A ed.; Bruker AXS Inc.: Madison, Wisconsin, USA 2009.

    14. [14]

      Bruker. SADABS. 2008/1 ed.; Bruker AXS Inc.: Madison, Wisconsin, USA 2008.

    15. [15]

      Sheldrick, G. M. SHELXT - integrated space-group and crystal-structure determination. Acta Cryst. 2015, A71, 3–8.

    16. [16]

      Sheldrick, G. M. Crystal structure refinement with SHELXL. Acta Cryst. 2015, C71, 3–8.

    17. [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.  doi: 10.1107/S1600576714016732

    18. [18]

      Müller, P. Practical suggestions for better crystal structures. Crystallography Reviews 2009, 15 1, 57–83.  doi: 10.1080/08893110802547240

    19. [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. [20]

      Zhang, H.; Wang, H.; Yu, J. 1,4-Bis(4-methyl-2-nitrophenoxy)butane. IUCrData 2017, 2 12, x171734.  doi: 10.1107/S2414314617017345

    21. [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.  doi: 10.1021/acs.cgd.8b01040

    22. [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.  doi: 10.1021/cg400025j

    23. [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.  doi: 10.1016/j.snb.2017.05.140

    24. [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.  doi: 10.1021/ic100212q

    25. [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.  doi: 10.1016/j.jfluchem.2009.06.018

    26. [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.  doi: 10.1021/acs.inorgchem.8b00413

    27. [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.  doi: 10.1021/ol4002653

    28. [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.  doi: 10.1039/c2ce26145f

    29. [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.  doi: 10.1016/j.saa.2017.11.054

    30. [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.  doi: 10.1021/acs.organomet.8b00837

    31. [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.  doi: 10.1039/C7CE00535K

    32. [32]

      Spek, A. L. PLATON, A Multipurpose Crystallographic Tool. Utrecht University: The Netherlands 2006.

    33. [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.  doi: 10.1021/ja1080794

    34. [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.  doi: 10.1002/anie.200904722

    35. [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.  doi: 10.1039/C6DT03678C

    36. [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.  doi: 10.1021/ja510525s

    37. [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.  doi: 10.1039/C8DT01613E

    38. [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.  doi: 10.1016/j.jallcom.2017.11.174

    39. [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.  doi: 10.1016/j.inoche.2018.09.016

    40. [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.  doi: 10.1021/jacs.8b07841

    41. [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.  doi: 10.1021/acs.cgd.6b01404

    42. [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.  doi: 10.1016/j.jmmm.2018.10.089

    43. [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.  doi: 10.1016/j.jallcom.2018.07.233

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