Hydrogen bonding and vibrational spectra in kaolinite-dimethylsulfoxide and -dimethylselenoxide intercalates - A solid-state computational study

Clays and Clay Minerals

Volumn 57, Issue 1, 2009, Pages 54-71

  Scholtzová, Eva ^a   Smrĉok, L'Ubomír ^a  

^a INSTITUTE OF CHEMISTRY   (Slovakia)

Author keywords

DFT; DMSeO; DMSO; Hydrogen bonds; Kaolinite; Vibrational spectra

Indexed keywords

AB-INITIO CALCULATIONS; ATOMIC COORDINATES; BENDING MODES; BOND DISTANCES; COMPUTATIONAL STUDIES; CRYSTAL REFINEMENTS; DENSITY-FUNCTIONAL THEORIES; DFT; DIFFRACTION DATUM; DMSEO; DMSO; DOMINANT CONTRIBUTIONS; HIGH QUALITIES; HYDROGEN BONDINGS; HYDROGEN-BOND GEOMETRIES; INFRARED AND RAMAN SPECTRUM; INTERLAYER SPACES; ORGANIC MOLECULES; RED SHIFTS; STRETCHING MODES; STRUCTURAL INFORMATIONS; SUPPORTING ROLES; TOTAL ENERGIES; VIBRATIONAL MODES;

ALUMINUM; ATOMS; BINDING SITES; CRYSTAL ATOMIC STRUCTURE; DENSITY FUNCTIONAL THEORY; DIMETHYL SULFOXIDE; HYDROGEN; INFRARED SPECTROSCOPY; KAOLINITE; MOLECULAR SPECTROSCOPY; PROBABILITY DENSITY FUNCTION; VIBRATIONAL SPECTRA;

HYDROGEN BONDS;

CHEMICAL BONDING; CRYSTAL STRUCTURE; KAOLINITE; RAMAN SPECTROSCOPY; X-RAY DIFFRACTION;

EID: 65549126011     PISSN: 00098604     EISSN: None     Source Type: Journal    
DOI: 10.1346/CCMN.2009.0570106     Document Type: Article

References (41)

1. 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.
2. 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.
3. Blöchl, P.E., (1994) Projector augmented-wave method. Physical Review B, 50, 17953-17979.
4. Brandenburg, K. (2006) Diamond.. Version 3.1d. Crystal Impact GbR, Bonn, Germany.
5. 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.
6. Castellano, R.K. (2004) Progress toward understanding the nature and function of C-H...O interactions. Current Organic Chemistry, 8, 845-865.
7. 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.
8. Desiraju, G.R. (1991) The C-H...O hydrogen bond in crystals: what is it? Accounts of Chemical Research, 24, 290-296.
9. 3; X=O, S, Se; Z=O,S) compounds. Journal of the American Chemical Society, 121, 3156-3164.
10. Fang, Q., Huang, S., and Wang, W. (2005) Intercalation of dimethysulfoxide in kaolinite: molecular dynamics study. Chemical Physics Letters, 411, 233-237.
11. Filatov, A.S., Block, E., and Petrukhina, M.A. (2005) Dimethyl selenoxide. Acta Crystallographica, C61, 596-598.
12. Frost, R.L., Kristof, J., Horvath, E., and Kloprogge, J.T. (2000) Kaolinite hydroxyls in dimethylsulfoxide-intercalated kaolinites at 77K a a Raman spectroscopic study. Clay Minerals, 35, 443-454.
13. 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.
14. Hafner, J. (2003) Vibrational spectroscopy using ab initio density-functional techniques. Journal of Molecular Structure, 651-653, 3-17.
15. Hayashi, S. (1995) NMR study of dynamics of dimethyl sulfoxide molecules in kaolinite/dimethyl sulfoxide intercalation compounds. Journal of Physical Chemistry, 99, 7120-7129.
16. 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.
17. 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.
18. Ibberson, R.M. (2005) Neutron powder diffraction studies of dimethyl sulfoxide. Acta Crystallographica, C61, 571-573.
19. 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.
20. 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.
21. 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.
22. 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.
23. Kresse, G. and Hafner, J. (1993) Ab initio molecular dynamics for open-shell transition metals. Physical Review B, 48, 13115-13118.
24. 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.
25. Kresse, G. and Joubert, J. (1999) From ultrasoft potentials to the projector augmented wave method. Physical Review B, 59, 1758-1775.
26. 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.
27. Michalková, A. and Tunega, D. (2007) Kaolinite, dimethylsulfoxide intercalate - a theoretical study. Journal of Physical Chemistry, C111, 11259-11266.
28. 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.
29. 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.
30. Olejnik, S., Posner, A.M., and Quirk, J.P. (1970) The intercalation of polar organic compounds into kaolinite. Clay Minerals, 8, 421-434.
31. Perdew, J.P. and Wang, Y. (1992) Accurate and simple analytic representation of the electron-gas correlation energy. Physical Review, B45, 13244-13249.
32. Perdew, J.P. and Zunger, A. (1981) Self-interaction correction to density-functional approximations for many-electron systems. Physical Review, B23, 5048-5079.
33. Portmann, S. and Luthi, H.P. (2000) MOLEKEL: an interactive molecular graphics tool, Chimia, 54, 766-769.
34. 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.
35. 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.
36. Smrčok, L'. (1995) A comparison of powder diffraction studies of kaolin group minerals. Zeitschrift fûr Kristallographie, 210, 177-183.
37. Spek, A.L. (2002) PLATON. A Multipurpose Crystallographic Tool. Utrecht University, The Netherlands. (www.cryst.chem.uu.nl/ platon).
38. 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.
39. Steiner, T. (2002) The hydrogen bond in the solid state. Angewandte Chemie - International Edition, 41, 48-76.
40. Teter, M.P., Payne, M.C., and Allan, D.C (1989) Solution of Schrodinger's equations for large systems. Physical Review, B40, 12255-12263.
41. Thompson, J.G. and Cuff, C. (1985) Crystal structure of kaolinite:dimethylsulfoxide intercalate. Clays and Clay Minerals, 11, 490-500.