Abstract
The aims of this study were to obtain accurate structural information on the dimethyl sulfoxide (DMSO) and dimethylselenoxide (DMSeO) kaolinite intercalates, paying close attention to the hydrogen-bond geometries, and to provide a detailed interpretation of the individual vibrational modes of intercalates under study and relate their energies to the formation of the hydrogen bonds. Accurate positions of all the atoms in the structures of kaolinite:dimethylsulfoxide (K:DMSO) and kaolinite:dimethylselenoxide (K:DMSeO) intercalates have been obtained by the total energy minimization in solid state at density functional theory (DFT) level of the theory. The bond distances and angles in the kaolinite 1:1 layer are in good agreement with those reported in the most recent single-crystal refinement of kaolinite. Computed geometries of DMSO and DMSeO agree well with the high-quality diffraction data and independent theoretical ab initio calculations. The organic molecules are fixed in the interlayer space mainly by three moderately strong O-H⋯O hydrogen bonds, of different strengths, with the O⋯O contact distances being within 2.739–2.932 Å (K:DMSO) and 2.681–2.849 Å (K:DMSeO). Substantially weaker C-H⋯O and O-H⋯S(Se) contacts play only a supporting role. The optimized atomic coordinates were used to calculate the individual vibrational modes between 0 and 4000 cm−1. The maximum red shifts of the OH-stretching modes caused by the formation of the O-H⋯O hydrogen bonds were 407 cm− (K-DMSO) and 537 cm−1 (K-DMeSO), respectively. The Al-O-H bending modes are spread over the large interval of 100–1200 cm−1, but the dominant contributions are concentrated between 800 and 1200 cm−1. Theoretically calculated energies of the OH- and CH-stretching modes show good agreement with the previously published figures obtained from the infrared and Raman spectra of these intercalates.
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References
Balan, E., Marco Saitta, A., Mauri, F., and Calas, G. (2001) First-principles modelling of the infrared spectrum of kaolinite. American Mineralogist, 86, 1321–1330.
Balan, E., Marco Saitta, A., Mauri, F., Lemaire, C., and Guyot, F. (2002) First-principles calculations of the infrared spectrum of lizardite. American Mineralogist 87, 1286–1290.
Blöchl, P.E., (1994) Projector augmented-wave method. Physical Review B, 50, 17953–17979.
Brandenburg, K. (2006) Diamond.. Version 3.1d. Crystal Impact GbR, Bonn, Germany.
Bylander, D.M., Kleinman, L., and Lee, S. (1990) Self-consistent calculations of the energy bands and bonding properties of B-12(C-3). Physical Review B, 42, 1394–1403.
Castellano, R.K. (2004) Progress toward understanding the nature and function of C-H⋯O interactions. Current Organic Chemistry, 8, 845–865.
Ceccarelli, C., Jeffrey, G.A., and Taylor, R. (1981) A survey of O-H⋯O hydrogen bonds geometries determined by neutron diffraction. Journal of Molecular Structure, 70, 255–271.
Desiraju, G.R. (1991) The C-H⋯O hydrogen bond in crystals: what is it? Accounts of Chemical Research, 24, 290–296.
Dobado, J.A., Martinez-Garcia, H., Molina, J.M., and Sundberg, M.R. (1999) Chemical bonding in hypervalent molecules revised. 2. Application of the atoms in molecules theory to Y2XZ and Y2XZ2 (Y=H, F, CH3; X=O, S, Se; Z=O,S) compounds. Journal of the American Chemical Society, 121, 3156–3164.
Fang, Q., Huang, S., and Wang, W. (2005) Intercalation of dimethysulfoxide in kaolinite: molecular dynamics study. Chemical Physics Letters, 411, 233–237.
Filatov, A.S., Block, E., and Petrukhina, M.A. (2005) Dimethyl selenoxide. Acta Crystallographica, C61, 596–598.
Frost, R.L., Kristof, J., Horvath, E., and Kloprogge, J.T. (2000) Kaolinite hydroxyls in dimethylsulfoxide-intercalated kaolinites at 77K — a Raman spectroscopic study. Clay Minerals, 35, 443–454.
Gu, Y., Kar, T., and Scheiner, S. (1999) Fundamental properties of the C-H⋯O interaction: is it a true hydrogen bond? Journal of the American Chemical Society, 121, 9411–9422.
Hafner, J. (2003) Vibrational spectroscopy using ab initio density-functional techniques. Journal of Molecular Structure, 651–653, 3–17.
Hayashi, S. (1995) NMR study of dynamics of dimethyl sulfoxide molecules in kaolinite/dimethyl sulfoxide intercalation compounds. Journal of Physical Chemistry, 99, 7120–7129.
Hayashi, S. (1997) NMR study of dynamics and evolution of guest molecules in kaolinite/dimethyl sulfoxide intercalation compounds. Clays and Clay Minerals, 45, 724–732.
Hobbs, J.D., Cygan, R.T., Nagy, K.L., Schultz, P.A., and Sears, M. (1997) All-atom ab initio energy minimization of the kaolinite structure. American Mineralogist, 82, 657–662.
Ibberson, R.M. (2005) Neutron powder diffraction studies of dimethyl sulfoxide. Acta Crystallographica, C61, 571–573.
Johnston, C.T., Sposito, G., Bocian, D.F., and Birge, R.R. (1984) Vibrational spectroscopic study of the interlamellar kaolinite-dimethylsulfoxide complex. Journal of Physical Chemistry, 88, 5959–5964.
Kirkpatrick, R.J., Kalinchev, A.G., Wang, J., Hou, X., and Amonette, J. (2005) Molecular modeling of the vibrational spectra of interlayer and surface species of layered double hydroxides. Pp. 239–285 in: The Application of Vibrational Spectroscopy to Clay Minerals and Layered Double Hydroxides (J.T. Kloprogge, Editor). CMS Workshop Lecture Series, 13, The Clay Minerals Society, Aurora, CO, USA.
Kresse, G. and Furthmüller, J. (1996a) Efficient iterative scheme for ab initio total energy calculations using a plane-wave basis set. Physical Review B, 54, 11169–11186.
Kresse, G. and Furthmüller, J. (1996b) Efficiency of ab-initio total energy calculations for metals and semiconductors using a plane-wave basis set. Computational Materials Science, 6, 15–50.
Kresse, G. and Hafner, J. (1993) Ab initio molecular dynamics for open-shell transition metals. Physical Review B, 48, 13115–13118.
Kresse, G. and Hafner, J. (1994) Norm-conserving and ultrasoft pseudopotentials for first-row and transition elements. Journal of Physics: Condensed Matter, 6, 8245–8527.
Kresse, G. and Joubert, J. (1999) From ultrasoft potentials to the projector augmented wave method. Physical Review B, 59, 1758–1775.
Martens, W.N., Frost, R.L., Kristof, J., and Horvath, E. (2002) Modification of kaolinite surfaces through intercalation with deuterated dimethylsulfoxide. Journal of Physical Chemistry, B106, 4162–4171.
Michalková, A. and Tunega, D. (2007) Kaolinite, dimethylsulfoxide intercalate — a theoretical study. Journal of Physical Chemistry, C111, 11259–11266.
Neder, R.B., Burghammer, M., Grasl, Th., Schulz, H., Bram, A., and Fiedler, S. (1999) Refinement of the kaolinite structure from single crystal synchrotron data. Clays and Clay Minerals, 47, 487–494.
Olejnik, S., Aylmore, L.A.G., Posner, A.M., and Quirk, J.P. (1968) Infrared spectra of kaolin mineral-dimethylsulfoxide complexes. The Journal of Physical Chemistry, 72, 241–249.
Olejnik, S., Posner, A.M., and Quirk, J.P. (1970) The intercalation of polar organic compounds into kaolinite. Clay Minerals, 8, 421–434.
Perdew, J.P. and Wang, Y. (1992) Accurate and simple analytic representation of the electron-gas correlation energy. Physical Review, B45, 13244–13249.
Perdew, J.P. and Zunger, A. (1981) Self-interaction correction to density-functional approximations for many-electron systems. Physical Review, B23, 5048–5079.
Portmann, S. and Luthi, H.P. (2000) MOLEKEL: an interactive molecular graphics tool, Chimia, 54, 766–769.
Raupach, M., Barron, P.F., and Thompson, J.G. (1987) Nuclear magnetic resonance, infrared, and X-ray powder diffraction study of dimethylsulfoxide and dimethylselenoxide intercalates with kaolinite. Clays and Clay Minerals, 35, 208–219.
Renault, E. and Le Questel, J.-Y. (2004) Selenoxides are better hydrogen-bond acceptors than sulfoxides: a crystallographic database and theoretical investigation. Journal of Physical Chemistry, A108, 7232–7240.
Smrčok, L’. (1995) A comparison of powder diffraction studies of kaolin group minerals. Zeitschrift fûr Kristallographie, 210, 177–183.
Spek, A.L. (2002) PLATON. A Multipurpose Crystallographic Tool. Utrecht University, The Netherlands, (https://doi.org/www.cryst.chem.uu.nl/platon).
Steiner, T. (1998) Lengthening of the covalent X—H bond in heteronuclear hydrogen bonds quantified from organic and organometalic neutron crystal structures. Journal of Physical Chemistry, A102, 7041–7052.
Steiner, T. (2002) The hydrogen bond in the solid state. Angewandte Chemie — International Edition, 41, 48–76.
Teter, M.P., Payne, M.C., and Allan, D.C (1989) Solution of Schrodinger’s equations for large systems. Physical Review, B40, 12255–12263.
Thompson, J.G. and Cuff, C. (1985) Crystal structure of kaolinite:dimethylsulfoxide intercalate. Clays and Clay Minerals, 11, 490–500.
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Scholtzová, E., Smrčok, L. Hydrogen bonding and vibrational spectra in kaolinite-dimethylsulfoxide and -dimethylselenoxide intercalates — A solid-state computational study. Clays Clay Miner. 57, 54–71 (2009). https://doi.org/10.1346/CCMN.2009.0570106
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DOI: https://doi.org/10.1346/CCMN.2009.0570106