Hostname: page-component-7479d7b7d-qlrfm Total loading time: 0 Render date: 2024-07-11T17:37:39.645Z Has data issue: false hasContentIssue false
  • English
  • Français

Crystal structure of 1-propanethiol–Co2(dobdc) from laboratory X-ray powder diffraction data

Published online by Cambridge University Press:  10 February 2020

Jonathan B. Lefton ,
Kyle B. Pekar ,
Daniel Sethio ,
Elfi Kraka  and
Tomče Runčevski Open the ORCID record for Tomče Runčevski [Opens in a new window]
Jonathan B. Lefton
Affiliation:
Department of Chemistry, Southern Methodist University, Dallas, TX75275, USA
Kyle B. Pekar
Affiliation:
Department of Chemistry, Southern Methodist University, Dallas, TX75275, USA
Daniel Sethio
Affiliation:
Department of Chemistry, Southern Methodist University, Dallas, TX75275, USA
Elfi Kraka
Affiliation:
Department of Chemistry, Southern Methodist University, Dallas, TX75275, USA
Tomče Runčevski*
Affiliation:
Department of Chemistry, Southern Methodist University, Dallas, TX75275, USA
*
a)Author to whom correspondence should be addressed. Electronic mail: truncevski@smu.edu
Get access Rights & Permissions [Opens in a new window]

Abstract

Laboratory X-ray powder diffraction was used to solve and refine the crystal structures of appended guest molecules within the pores of metal–organic frameworks (MOFs). Herein, we report the crystal structure of 1-propanethiol adsorbed in the pores of Co2(dobdc) (dobdc4– = 2,5-dioxido-1,4-benzenedicarboxylate, MOF-74). Soaking the activated MOF in neat 1-propanethiol resulted in the formation of 1-propanethiol–Co2(dobdc). The thiol appendant MOF maintained the crystal symmetry, with a rhombohedral space group R-3 and unit-cell parameters a = 25.9597(9) Å, c = 6.8623(5) Å, and V = 4005.0(4) Å3. As expected, the thiol sulfur formed a bond with the open cobalt metal site. The alkane chain was directed toward the center of the pore, participating in numerous van der Waals weak interactions with neighboring molecules. For the final Rietveld refinement, soft restrains were applied using bond distances obtained by periodic density functional theory (DFT) geometry optimization.

Keywords

MOFX-ray powder diffractioncrystal structureRietveld refinementgeometry optimization
Type
Invited Paper
Information
Powder Diffraction , Volume 35 , Issue 1 , March 2020 , pp. 3 - 6
Copyright
Copyright © International Centre for Diffraction Data 2020

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

References

Andreev, Y. G., MacGlashan, G. S., and Bruce, P. G. (1997). “Ab initio solution of a complex crystal structure from powder-diffraction data using simulated-annealing method and a high degree of molecular flexibility,” Phys. Rev. B 55, 12011–12017.CrossRefGoogle Scholar
Bloch, E. D., Murray, L. J., Queen, W. L., Chavan, S., Maximoff, S. N., Bigi, J. P., Krishna, R., Peterson, V. K., Grandjean, F., Long, G. J., Smit, B., Bordiga, S., Brown, C. M., and Long, J. R. (2011). “Selective binding of O2 over N2 in a redox-active metal-organic framework with open iron(II) coordination sites,” J. Am. Chem. Soc. 133, 14814–14822.CrossRefGoogle Scholar
Bloch, E. D., Queen, W. L., Krishna, R., Zadrozny, J. M., Brown, C. M., and Long, J. R. (2012). “Hydrocarbon separations in a metal-organic framework with open iron(II) coordination sites,” Science 335, 1606–1610.CrossRefGoogle Scholar
Dietzel, P. D. C., Panella, P., Hirscher, M., Blom, R., and Fjellvag, H. (2006). “Hydrogen adsorption in a nickel based coordination polymer with open metal sites in the cylindrical cavities of the desolvated framework,” Chem. Commun. 959–961.CrossRefGoogle Scholar
Dietzel, P. D. C., Johnsen, R. E., Fjellvag, H., Bordiga, S., Groppo, E., Chavan, S., and Blom, R. (2008). “Adsorption properties and structure of CO2 adsorbed on open coordination sites of metal–organic framework Ni2(dhtp) from gas adsorption, IR spectroscopy and X-ray diffraction,” Chem. Commun. 5125–5127.CrossRefGoogle ScholarPubMed
Dovesi, R., Erba, A., Orlando, R., Zicovich-Wilson, C. M., Civalleri, B., Maschio, L., Rèrat, M., Casassa, S., Baima, J., Salustro, S., and Kirtman, B. (2017). “Quantum-mechanical condensed matter simulations with CRYSTAL,” WIREs Comput. Mol. Sci. 8, 1360.CrossRefGoogle Scholar
Geier, S. J., Mason, J. A., Bloch, E. D., Queen, W. L., Hudson, M. R., Brown, C. M., and Long, J. R. (2013). “Selective adsorption of ethylene over ethane and propylene over propane in the metal–organic frameworks M 2(dobdc) (M = Mg, Mn, Fe, Co, Ni, Zn),” Chem. Sci. 4, 2054–2061.CrossRefGoogle Scholar
Gilat, G. (1972). “Analysis of methods for calculating spectral properties in solids,” J. Comp. Phys. 10, 432.CrossRefGoogle Scholar
Gonzalez, M. I., Mason, J. A., Bloch, E. D., Teat, S. J., Gagnon, K. J., Morrison, G. Y., Queen, W. L., and Long, J. R. (2017). “Structural characterization of framework–gas interactions in the metal–organic framework Co2(dobdc) by in situ single-crystal X-ray diffraction,” Chem. Sci. 8, 4387–4398.CrossRefGoogle ScholarPubMed
Gonzalez, M. I., Kapelewski, M. T., Bloch, E. D., Milner, P. J., Reed, D. A., Hudson, M. R., Mason, J. A., Barin, G., Brown, C. M., and Long, J. R. (2018). “Separation of xylene isomers through multiple metal site interactions in metal−organic frameworks,” J. Am. Chem. Soc. 140, 3412–3422.CrossRefGoogle ScholarPubMed
Grimme, S., Ehrlich, S., and Goerigk, L. (2011). “Effect of the damping function in dispersion corrected density functional theory,” J. Comput. Chem. 21, 1456–1465.CrossRefGoogle Scholar
Kizzie, A. C., Wong-Foy, A. G., and Matzger, A. J. (2011). “Effect of humidity on the performance of microporous coordination polymers as adsorbents for CO2 capture,” Langmuir 27, 6368–6373.CrossRefGoogle ScholarPubMed
Liu, Y., Kabbour, H., Brown, C. M., Neumann, D. A., and Ahn, C. C. (2008). “Increasing the density of adsorbed hydrogen with coordinatively unsaturated metal centers in metal−organic frameworks,” Langmuir 24, 4772–4777.CrossRefGoogle ScholarPubMed
Magdysyuk, O. V., Adams, F., Liermann, H.-P., Spanopoulos, I., Trikalitis, P. N., Hirscher, M., Morris, R. E., Duncan, M. J., McCormick, L. J., and Dinnebier, R. E. (2014). “Understanding the adsorption mechanism of noble gases Kr and Xe in CPO-27-Ni, CPO-27-Mg, and ZIF-8,” Phys. Chem. Chem. Phys. 16, 23908–23914.CrossRefGoogle ScholarPubMed
Pawley, G. S. (1981). “Unit-cell refinement from powder diffraction scans,” J. Appl. Crystallogr. 14, 357–361.CrossRefGoogle Scholar
Peintinger, M. P., Oliveira, D. V., and Bredow, T. (2013). “Consistent Gaussian basis sets of triple-zeta valence with polarization quality for solid-state calculations,” J. Comput. Chem. 34, 451.CrossRefGoogle ScholarPubMed
Perdew, J. P., Burke, K., and Ernzerhof, M. (1996). “Generalized gradient approximation made simple,” Phys. Rev. Lett. 77, 3865–3868.CrossRefGoogle ScholarPubMed
Queen, W. L., Hudson, M. R., Bloch, E. D., Mason, J. A., Gonzalez, M. I., Lee, J. S., Gygi, D., Howe, J. D., Lee, K., Darwish, T. A., James, M., Peterson, V. K., Teat, S. J., Smit, B., Neaton, J. B., Long, J. R., and Brown, C. M. (2014). “Comprehensive study of carbon dioxide adsorption in the metal–organic frameworks M 2(dobdc) (M = Mg, Mn, Fe, Co, Ni, Cu, Zn),” Chem. Sci. 5, 4569–4581.CrossRefGoogle Scholar
Rietveld, H. M. (1969). “A profile refinement method for nuclear and magnetic structures,” J. Appl. Crystallogr. 2, 65–71.CrossRefGoogle Scholar
Sumida, K., Brown, C. M., Herm, Z. R., Chavan, S., Bordiga, S., and Long, J. R. (2011). “Hydrogen storage properties and neutron scattering studiesof Mg2(dobdc)—a metal–organic framework with open Mg2+ adsorption sites,” Chem. Commun. 47, 1157–1159.CrossRefGoogle Scholar