SQUEEZE for treating severely disordered solvent molecules in the refinement of the otherwise ordered crystal structures of [Cd(C12H10N4)(C15H9O2)2(CH3OH)]·0.5H2O·CH3OH and [Cd(C12H10N4)1.5(C15H9O2)2]·CH3OH

Authors

  • Seik Weng Ng Department of Chemistry University of Malaya 50603 Kuala Lumpur and Chemistry Department, King Abdulaziz University, Jeddah, Saudi Arabia

DOI:

https://doi.org/10.20450/mjcce.2015.628

Keywords:

solvent molecules, voids, SQUEEZE, Crystal Explorer

Abstract

In the refinement of the crystal structure of [Cd(C12H10N4)(C15H9O2)2(CH3OH)].0.5H2O.CH3OH, the lattice water molecule was not located by difference Fourier synthesis but was instead deduced by using SQUEEZE owing to severe disorder of the water molecule in the otherwise ordered crystal structure.  Similarly deduced were the two symmetry-independent methanol molecules in [Cd(C12H10N4)1.5(C15H9O2)2].CH3OH.  The first coordination polymer adopts a chain motif and the second a layer motif; for both, the N-heterocycle functions as a bridge to connect adjacent metal atoms.  The solvent molecules are presumed to reside in voids, which are themselves connected into channels.  The crystallographic program Crystal Explorer was used in the illustration of the channels.  Crystal data C44H37N4O6.5Cd: FW = 838.18, monoclinic, P21/n, a = 16.7871(4) Å, b = 26.5431(5) Å, c = 18.7034(5) Å, b = 111.915(3)°, V = 7731.7(3) Å3.  Crystal data for C49H38N6O5.5Cd: FW = 911.25, monoclinic, P21/c, a = 11.0586(3) Å, b = 23.5007(6) Å, c = 17.3454(5) Å, b = 105.626(3)°, V = 4341.2(2) Å3.

References

A. L. Spek, Structure validation in chemical crystallography, Acta Cryst., D65, 148–155 (2009).

P. van der Sluis, A. L. Spek, BYPASS: an effective method for the refinement of crystal structures containing disordered solvent regions, Acta Cryst., A46, 194–201 (1990).

S. W. Ng, Guessing unknown and disordered solvent molecules with SQUEEZE in the structure validation program PLATON, J. Chem. Soc. Pakistan, 36, 000–000 (2014).

S. S. S. Raj, H.-K. Fun, J. Zhang, R.-G. Xiong, X.-Z. You, Pyridine-4-carbaldehyde azine, Acta Cryst., C56, e274–e275 (2000).

D. M. Ciurtin, Y.-B. Dong, M. D. Smith, T. Barclay, H.-C. zur Loye, Two versatile, N,N’-bipyridine-type ligands for preparing organic-inorganic coordination polymers: new cobalt- and nickel-containing framework materials, Inorg. Chem., 40, 2825–2834 (2001).

G. Zhang, G. Yang, J. S. Ma, Anion control of the self-assembly of one-dimensional molecular ladders vs three-dimensional cross-like arrays based on a bidentate Schiff base ligand, Cryst. Growth Des., 6, 1897–1902 (2006).

C.-S. Liu, J.-J. Wang, Z. Chang, L.-F. Yan, Cadmium(II) complexes with a bulky anthracene‐based carboxylate ligand: syntheses, crystal structures, and luminescent properties, Z. Anorg. Allg. Chem., 636, 1115–1123 (2009).¬¬

Agilent Technologies, Santa Clara, CA, USA. CrysAlisPRO (2014).

R. C. Clark, J. S. Reid, The analytical calculation of absorption in multifaceted crystals, Acta Cryst., A51, 887–897 (1995).

G. M. Sheldrick, A short history of SHELX, Acta Cryst., A64, 112–122 (2008).

A. L. Spek, PLATON/SQUEEZE in the context of twinning and SHELXL2013, Utretcht University, The Netherlands, (2013).

O. V. Dolomanov, A. J. Blake, N. R. Champness, M. Shröder, OLEX: new software for visualization and analysis of extended crystal structures, J. Appl. Cryst., 36, 1283–1284 (2003).

C.-S. Liu, X.-S. Shi, J.-R. Li, J.-J. Wang, X.-H. Bu, Cd(II) coordination architectures with mixed ligands of 3-(2-pyridyl)pyrazole and pendant carboxylate ligands bearing different aromatic skeletons: syntheses, crystal structures, and emission properties, Cryst. Growth Des., 6, 656–663 (2006).

L. J. Farrugia, WINGX and ORTEP for Windows: an update, J. Appl. Cryst., 45, 849–852 (2012).

C. B. Hübschle, G. M. Sheldrick, B. Dittrich, ShelXle: a Qt graphical user interface for SHELXL, J. Appl. Cryst., 44, 1281–1284 (2011).

S. K. Wolff, K. D. Grimwood, J. J., McKinnon, M. J. Turner, D. Jayatilaka, M. A. Spackman, CrystalExplorer (Version 3.1), University of Western Australia (2012).

M. J. Turner, J. J. McKinnon, D. Jayatilaka, M. A. Spackman, Visualisation and characterisation of voids in crystalline materials, CrystEngComm, 13, 1804–1813 (2011).

M. A. Spackman, D. Jayatilaka, Hirshfeld surface analysis, CrystEngComm, 11, 19–32 (2009).

D. Ma, Y. Li, Z. Li, Tuning the moisture stability of metal–organic frameworks by incorporating hydrophobic functional groups at different positions of ligands, Chem. Commun., 47, 7377–7379 (2011).

Li, R.-J., Li, M., Zhou, X.-P., Ng, S.W., O’Keefe, M. & Li, D. (2014). ROD-8, a rod MOF with a pyrene-cored tetracarboxylate linker: framework disorder, derived nets and selective gas absorption. CrystEngComm, 14, 6291–6295.

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Published

2015-05-15

How to Cite

Ng, S. W. (2015). SQUEEZE for treating severely disordered solvent molecules in the refinement of the otherwise ordered crystal structures of [Cd(C12H10N4)(C15H9O2)2(CH3OH)]·0.5H2O·CH3OH and [Cd(C12H10N4)1.5(C15H9O2)2]·CH3OH. Macedonian Journal of Chemistry and Chemical Engineering, 34(1), 57–61. https://doi.org/10.20450/mjcce.2015.628

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Section

Structural Chemistry