Molecular mechanics studies of thionin blue in zeolite mordenite

Suraj Deore, Petra Simoncic, Alexandra Navrotsky

Research output: Contribution to journalArticlepeer-review

12 Scopus citations


The localization and arrangement of thionin blue (C12H10N3S+) dye molecules in the zeolite mordenite framework is studied by molecular mechanics (MM) simulations. The computational results for dye molecule localization are compared to those from single crystal X-ray diffraction. Two low energy thionin orientations are observed. In both, the thionin molecules are inclined within the large 12-membered ring channels and indicate electrostatic interaction with the framework and with the extra-framework Na+ ions. Molecule orientation and the determined S⋯O (3.12 and 3.13 Å), N⋯O (3.22 and 3.33 Å) and C⋯O (3.45 and 3.41 Å) distances from the dye molecule to the channel wall are in reasonable agreement with the values found by single crystal X-ray diffraction (S⋯O = 3.084 Å, N⋯O = 3.087 Å and C⋯O = 3.235 Å). Clustering of thionin molecules in the 12-membered ring channels is not observed. The calculated potential energies for these two low energy configurations are essentially the same (∼-2236 kJ/mol) The global minimum was confirmed by multiple simulation runs, using different starting orientations of the thionin molecules in the mordenite framework. Quench simulations were also performed to understand the energetics of diffusion of thionin molecules in mordenite. The calculated activation energy of diffusion, ∼12-15 kJ, is comparable to values reported in literature for molecular diffusion in zeolites.

Original languageEnglish (US)
Pages (from-to)342-349
Number of pages8
JournalMicroporous and Mesoporous Materials
Issue number1-3
StatePublished - Mar 1 2008
Externally publishedYes


  • Diffusion
  • Guest molecule
  • Molecular mechanics
  • Mordenite

ASJC Scopus subject areas

  • Chemistry(all)
  • Materials Science(all)
  • Condensed Matter Physics
  • Mechanics of Materials


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