Dr. Babak Minofar, PhD


Vedoucí centra
Zamek 136, 37333 Nove Hrady
Tel.: +420 389 033 801

Současné zaměření

The main interests of the lab are computational study of :


  • Solvation structure and dynamics of ions in aqueous solution
  • Solvation structure and dynamics ions of in non-aqueous media
  • Solvation structure and dynamics of proteins in organic solvents
  • Solvation structure and dynamics of proteins in ionic liquids
  • Aggregation of porphyrins and carotenoids in aqueous media
  • Interaction of ions with graphene and graphene oxide
  • Interaction of Polyaromatic Hydrocarbons (PAHs) with humic acid
  • Interaction of graphene and graphene oxide with humic acid
  • Interaction of graphene and graphene oxide with humic acid
  • Interaction of micro-pollutants with soil organic matter
  • Structural and dynamical behavior of biomolecules in organic solvents and ionic liquids as potential media for drug delivery, macromolecular crystallization and bio-remediation of industrial wastes.
  • Application of nano-materials and graphene oxide for removal of micro-pollutants such as drugs, pharmaceutical and personal care products from aquatic environments.
  • Application of ionic liquids supported on of clay materials for removal of micro-pollutants such as drugs, pharmaceutical and personal care products from aquatic environments
  • Interaction of micro-pollutants with aquatic natural organic matter (NOM) for understanding their bioavailability and toxicity to freshwater microalgae.
  • Application of graphene oxide and nanomaterials for energy related materials such as fuel cells and lithium ion batteries
  • Application of ionic liquids and polymers such as nafion membrane for developing and modification of electrolytes for fuel cells.
  • Solvation structure and dynamics of Li+ ion in ionic liquids for increasing the performance lithium ion batteries by molecular dynamics simulations.
  • Solvation structure and dynamics of pure ionic liquids as a new candidate as electrolyte solution for lithium ion batteries by molecular dynamics simulations and x-ray scattering.
  • Solvation structure and dynamics of pure protic and aprotic ionic liquids as a new candidates from removal of CO2 and SO2 gases from natural gas by molecular dynamics simulations.
  • Adsorption of micro-pollutants on metal oxide surfaces


Dřívější výsledky

During my PhD study in Charles University in Prague under supervision of professor Pavel Jungwirth I have beeing working on “Structure and Dynamics of Ions at the Air/Water Interface ",from 2003 to 2007. In this study my main focus was understanding the processes which happen at the air-water interface in order to understand its effect on the atmospheric chemistry. I have been using molecular dynamics simulations to understand the solvation, dynamics and properties of ions at the aqueous interfaces in molecular level.

In my first postdoctoral fellowship in Academy of Sciences of the Czech Republic and Institute of Physical Biology of University of South Bohemia from 2007 to 2010 I have been involved in studying the dynamics of ions in Transient Receptor Potential cation channel, subfamily A, member 1 (TRPA1) which is an ion channel and known as a sensor for environmental irritants giving rise to somatosensory modalities such as pain and cold.

  In my second postdoc position in Japan as Postdoctoral Fellowship for Foreign Researchers from Japan Society for Promotion the of Science (JSPS) in Kyushu University and Niigata University from 2010 to 2012 I have been involved in studying the solvation and dynamics of ionic liquids.

Also I have been involved in studying the solvation and dynamics of ions and gases in ionic liquids and surface properties of ionic liquids. One of the outcome of studying the solvation of gases such as SO2 and CO2 in ionic liquids was presented in First Ionic Liquid Symposium in Japan, Tottori collaborated with Prof Fehrmann and Prof Riisager from the Centre for Catalysis and Sustainable Chemistry in Danish Technical University in Copenhagen.


  1. Minofar B., Self assembly of ionic liquids at the air/water interface, the Journal of Self-Assembly and Molecular Electronics,(2015) doi: 10.13052/jsame2245-4551.2015005


  2. Kroutil O., Minofar B., Kabeláč M., Structure and Dynamics of Solvated Hydrogenoxalate and Oxalate Anions: a Theoretical Study, Journal of Molecular Modeling, 2016, 22(9), 1-10 DOI 10.1007/s00894-016-3075-0


  3. Priyakshree Borthakur, Purna K. Boruaha,, Najrul Hussaina,, Bhagyasmeeta Sharma, Babak Minofar, Manash R., Das, An experimental and theoretical study of specific ion effect on the graphene oxide surface and investigation of their influence in reactive extraction of model dye molecule at water/organic interface, J. Phys. Chem. C, 2016, 120 (26), pp 14088–14100


  4. Kesan G., Durchan M., Tichy J., Minofar B., Kuznetsova V. Fuciman M. Slouf V. Parlak, C., Polivka T., Different Response of Carbonyl Carotenoids to Solvent Proticity Helps to Estimate Structure of the Unknown Carotenoid From Chromera Velia, J. Phys. Chem. B, 2015, 119 (39), pp 12653–12663


  5. Harifi-Mood AR., Minofar B., Solvatochromic propensities of para nitroaniline and para nitroanisole dyes in mixture of deep eutectic solvents and molecular solvents a combined spectroscopy and molecular dynamics simulation study, Journal of Molecular Liquids, (222),2016, 845–853 http:// dx.doi.org/ 10.1016/j. molliq.2016.07.036


  6. Harifi-Mood AR., Aryafard M., Minofar B., Ziyaei-Halimehjani A., Specific spectroscopic behavior of Reichardt's betaine dye in binary mixtures of tetra-n-butylammonium glycinate and tetra-n-butylammonium l- alaninate with molecular solvents. Journal of Molecular Liquids, (197), 2014, 315–321, DOI: 10.1016/j.molliq.2014.05.010


  7. Habartova, A.; Obisesan, A; Minofar, B; Roeselova, M. ; Partial hydration of n-alkyl halides at the water-vapor interface: a molecular simulation study with atmospheric implications; THEORETICAL CHEMISTRY ACCOUNTS, 2014,133,(3); 10.1007/s00214-014-1455-z


  8. Doi H.; Song XD.; Minofar B.; Kanzaki R.; Takamuku T.; Umebayashi Y.; A New Proton Conductive Liquid with No Ions: Pseudo-Protic Ionic Liquids; CHEMISTRY-A EUROPEAN JOURNAL, 2013, 19 (35);11522- 11526; DOI: 10.1002/chem.201302228


  9. Kurisaki T., Tanaka D., Inoue Y., Wakita H., Minofar B., Fukuda S., Ishiguro H., Umebayashi, Y.Surface Analysis of Ionic Liquids with and without Lithium Salt Using X-ray Photoelectron Spectroscopy; J. Phys. Chem. B, 2012,116 (35), pp 10870–10875


  10. Zayats V., Samad A., Minofar B., Roelofs K., Stockner T., Ettrich R.; (2012) Regulation of the transient receptor potential channel TRPA1 by itsN-terminal ankyrin repeat domain. Journal of Molecular Modeling, online 3.7.2012, DOI:10.1007/s00894-012-1505-1


  11. Song X., Hamano H., Minofar B., Kanzaki R., Fujii K., Kameda Y. Kohara, Watanabe M., Ishiguro S., Umebayashi Y.; Structural Heterogeneity and Unique Distorted Hydrogen Bonding in Primary Ammonium Nitrate Ionic Liquids Studied by High-Energy X-ray Diffraction Experiments and MD Simulations. Journal of Physical Chemistry B,2012, 116(9) 2801- 2813


  12. Khabiri M., Minofar B., Brezovský J., Damborský J., Ettrich R.; (2012) Interaction of Organic Solvents with Protein Structures at Protein Solvent Interface. Journal of Molecular Modeling, online 2012,DOI:10.1007/s00894-012-1507-z


  13. Reshak AH., Kamarudin H., Auluck. S, Minofar B., Kityk I.; Electronic structure, chemical bonding features, and electron charge density of the double-cubane single crystal [Sb(7)S(8)Br(2)](AlCl(4))(3); Appl. Phys. Lett.98, 201903 (2011); doi:10.1063/1.3583674


  14. Umebayashi, Y; Harnano, H;Seki, S.; Minofar, B.; Fujii, K; Hayamizu, K ; Tsuzuki, S; meda,Y.;Kohara, S;Watanabe, M; Liquid Structure of and Li(+) Ion Solvation in Bis(trifluoromethanesulfonyl)amide Based Ionic Liquids Composed of 1-Ethyl-3-methylimidazolium and N-Methyl-N-propylpyrrolidinium Cations; Journal of Physical Chemistry B;15; 42;12179-12191


  15. Takeuchi M., Matubayasi N., Kameda Y., Minofar B., Umebayashi Y., Ishiguro S.; Free-energy and structural analysis of ion solvation and contact ion pair formation of Li+ with BF4– and PF6– in water and carbonate solvents. J. Phys. Chem. B,2012, 116 (22), pp 6476–6487


  16. Štěpánková,V.; Khabiri,M.; Minofar, B.; Ettrich, R.; Damborský, J.; Brezovský, J; Pavelka, A; Minofar, B.; Prokop, Z.; Ettrich, R.; Chaloupková, R.; Damborský, J.; Expansion of Access Tunnels and Active-Site Cavities Influence Activity of Haloalkane Dehalogenases in Organic Cosolvents, Chembiochem. 2013 May 10;14(7):890-7. doi: 10.1002/cbic.


  17. Chen XK, Minofar B, Jungwirth P, et al. Interfacial Molecular Organization at Aqueous Solution Surfaces of Atmospherically Relevant Dimethyl Sulfoxide and Methanesulfonic Acid Using Sum Frequency Spectroscopy and Molecular Dynamics Simulation; Journal of Physical Chemistry B, 2010, 114 (47), 15546-15553


  18. Samad A, Sura L, Benedikt J, Ettrich R, Minofar B, Teisinger J, Vlachova V, The C-terminal basic residues contribute to the chemical- and voltage-dependent activation of TRPA1; BIOCHEMICAL JOURNAL, 2011, 433, 197-204


  19. Lauw, Y.; Horne, M. D.; Rodopoulos, T.; Webster, N. A. S.; Minofar, B.; Nelson, A. X-Ray reflectometry studies on the effect of water on the surface structure of [C(4)mpyr][NTf2] ionic liquid; Phys. Chem. Chem. Phys., 2009, 11, 11507 - 11514


  20. Kandice Harper, Babak Minofar, M. Roxana Sierra Hernandez, Nadia N. Casillas-Ituarte, Martina Roeselova, Heather C. Allen; Surface residence and uptake of methyl chloride and methyl alcohol at the air/water interface studied by vibrational sum frequency spectroscopy and molecular dynamics. Journal of Physical Chemistry A, 113 (2009) 2015


  21. Mahiuddin, S.; Minofar, B.; Borah, J. M.; Das, M. R.; Jungwirth, P.: Propensities of Oxalic, Citric, Succinic, and Maleic Acids for the Aqueous Solution/Vapour Interface: Surface Tension Measurements and Molecular Dynamics Simulations. Chemical Physics Letters, 462 (2008) 217


  22. Picalek, J.; Minofar, B.; Kolafa, J.; Jungwirth, P.: Aqueous solutions of ionic liquids: Study of the solution/vapor interface using molecular dynamics simulations. Physical Chemistry Chemical Physics, 10 (2008) 5765.


  23. Minofar, B.; Jungwirth, P.; Ras, M. R.; Kunz, W.; Mahiuddin, S.: Jungwirth, P.: Propensity of Formate, Acetate, Benzoate, and Phenolate for the Aqueous Solution/Vapour Interface: Surface Tension Measurements and Molecular Dynamics Simulations. Journal of Physical Chemistry C, 111 (2007) 8242


  24. Minofar, B.; Vacha, R.; Wahab, A.; Mahiuddin, S.; Kunz, W.; Jungwirth, P.: Propensity for the air/water interface and ion pairing in magnesium acetate vs. magnesium nitrate solutions: Molecular dynamics simulations and surface tension measurements. Journal of Physical Chemistry B, 110 (2006) 15939


  25. Wang, X.-B.; Woo, H.-K.; Wang, L.-S.; Minofar, B.; Jugwirth, P.: Determination of the Electron Affinity of the Acetyloxyl Radical (CH3COO) by Low Temperature Anion Photoelectron Spectroscopy and ab initio Calculations. Journal of Physical Chemistry A, 110 (2006) 5047


  26. Petrov, M.; Minofar, B.; Vrbka, L.; Jugwirth, P.; Koelsch, P.; Motschmann, H.: Aqueous ionic and complementary zwitterionic soluble surfactants: Molecular dynamics simulations and sum frequency generation spectroscopy of the surfaces. Langmuir, 22 (2006) 2498


  27. Wahab, A.; Mahiuddin, S.; Hefter, G.; Kunz, W.; Minofar, B.; Jungwirth, P.: Ultrasonic velocities, densities, viscosities, electrical conductivities, Raman spectra, and molecular dynamics simulations of aqueous solutions of Mg(OAc)2 and Mg(NO3)2: Hofmeister effects and ion pair formation. Journal of Physical Chemistry B, 109 (2005) 24108


  28. Minofar, B.; Vrbka, L.; Mucha, M.; Jungwirth, P.; Yang, X.; Wang, X.-B.; Fu, Y.-J.; Wang, L.-S.: Interior and Interfacial Aqueous Solvation of Benzene Dicarboxylate Dianions and Their Methylated Analogues: A Combined Molecular Dynamics and Photoelectron Spectroscopy Study. Journal of Physical Chemistry A, 109 (2005) 5042


  29. Minofar, B.; Mucha, M.; Jungwirth, P.; Yang, X.; Fu, Y.-J.; Wang, X.-B.; Wang, L.-S.: Bulk vs. Interfacial Aqueous Solvation of Dicarboxylate Dianions. Journal of the American Chemical Society, 126 (2004) 11691


  30. Vrbka, L.; Mucha, M.; Minofar, B.; Jungwirth, P.; Brown, E. C.; Tobias, D. J.: Propensity of Soft Ions for the Air/Water Interface. Current Opinion in Interface and Colloid Science, 9 (2004) 67


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