Carbon nanostructures, biomacromolecules and simulations

Head of the Division:

Prof. Michal Otyepka, Ph.D.

 About the group:

Graphene and its derivatives (fluorographene, graphene oxide) belong to extensively studied compounds within the framework of our research. The research includes the development of novel methods for the functionalization and chemical modification of graphene and its derivatives. We benefit from a tight connection between both theoretical and experimental approaches. Other research directions include explorations of fluorescent carbon quantum dots and their application for cell imaging, along with the study of porous carbon nanostructures for environmental and catalytic applications. The group develops theoretical methods and tools for the study of biomacromolecules and nanomaterials. The focus is on the structure and dynamics of biomacromolecules and their functional components, on the interaction of biomacromolecules with membrane bilayers, on enzyme and RNA catalysis.


Results highlights:

P. Trouillas, J. C. Sancho-García, V. De Freitas, J. Gierschner, M. Otyepka, O. Dangles: Stabilizing and Modulating Color by Copigmentation: Insights from Theory and Experiment,CHEMICAL REVIEWS vol. 116, iss. 9, pp. 4937-4982, 2016.
DOI: 10.1021/acs.chemrev.5b00507, IF = 46.568

M. H. Kolář, P. Hobza: Computer Modeling of Halogen Bonds and Other σ-Hole Interactions, CHEMICAL REVIEWS vol. 116, iss. 9, pp. 5155-5187, 2016.
DOI: 10.1021/acs.chemrev.5b00560, IF = 46.568

M. Dubecký, L. Mitas, P. Jurečka: Noncovalent Interactions by Quantum Monte Carlo, CHEMICAL REVIEWS vol. 116, iss. 9, pp. 5188-5215, 2016.
DOI: 10.1021/acs.chemrev.5b00577, IF = 46.568

cover-11-05-2016-14-34-58X. Chia, A. Adriano, P. Lazar, Z. Sofer, J. Luxa, M. Pumera: Layered Platinum Dichalcogenides (PtS 2 , PtSe 2 , and PtTe 2 ) Electrocatalysis: Monotonic Dependence on the Chalcogen Size , ADV. FUNCT. MATER.,  2016.
DOI: 10.1002/adfm.201505402, IF = 10.4

C. C. Givelet, P. I. Dron, J. Wen, T. F. Magnera, M. Zamadar, K. Čépe, H. Fujiwara, Y. Shi, M. R. Tuchband, N. Clark, R. Zboril, J. Michl: Challenges in the Structure Determination of Self-Assembled Metallacages. What Do Cage Cavities Contain, Solvent or Internal Vapor Bubbles?, J. AM. CHEM. SOC., ASAP, 2016.
DOI: 10.1021/jacs.5b12050, IF = 12.113

V. Georgakilas, A. Demeslis, E. Ntararas, A. Kouloumpis, K. Dimos, D. Gournis, M. Kocman, M. Otyepka, R. Zbořil: Hydrophilic Nanotube Supported Graphene-Water Dispersible Carbon Superstructure with Excellent Conductivity, ADVANCED FUNCTIONAL MATERIALS vol. 25, iss. 10, pp. 1481-1487, 2015.
DOI: 10.1002/adfm.201403801, IF = 10.4

V. Urbanová, K. Holá, A. B. Bourlinos, K. Čépe, A. Ambrosi, A. H. Loo, M. Pumera, F. Karlický, M. Otyepka, R. Zbořil: Thiofluorographene-Hydrophilic Graphene Derivative with Semiconducting and Genosensing Properties, ADV. MATER., vol. 27, iss. 14, pp. 2305-2310, 2015.
DOI: 10.1002/adma.201500094, IF = 15.409

K. Hola, Y. Zhang, Y. Wang, E. P. Giannelis, R. Zboril, A. L. Rogach: Carbon dots—Emerging light emitters for bioimaging, cancer therapy and optoelectronics, NANO TODAY 9, 5, (2014).
DOI: 10.1016/j.nantod.2014.09.004, IF=18.432

J. Fanfrlík, A. Přáda, Z. Padělková, A. Pecina, J. Macháček, M. Lepšík, J. Holub, A. Růžička, D. Hnyk and P. Hobza: “The Dominant Role of Chalcogen Bonding in the Crystal Packing of 2D/3D Aromatics”, ANGEW. CHEM. INT. ED., vol. 53, iss. 38, pp. 10139-10142, 2014.
DOI: 10.1002/anie.201405901, IF=11.336

P. Lazar, C. K. Chua, K. Holá, R. Zbořil, M. Otyepka, M. Pumera: Dichlorocarbene-Functionalized Fluorographene: Synthesis and Reaction Mechanism, SMALL, 2015.
DOI: 10.1002/smll.201500364

J. Sponer, P. Banáš, P. Jurecka, M. Zgarbova, P. Kührová, M. Havrila, M. Krepl, P. Stadlbauer and M. Otyepka: “Molecular Dynamics Simulations of Nucleic Acids. From Tetranucleotides to the Ribosome.”, J. PHYS. CHEM. LETT., vol. 5, iss. 10, pp. 1771-1782, 2014.
DOI: 10.1021/jz500557y, IF=6.687

P. Lazar, E. Otyepková, P. Banáš, A. Fargašová, K. Šafářová, L. Lapčík, J. Pechoušek, R. Zbořil and M. Otyepka: “The nature of high surface energy sites in graphene and graphite”, CARBON, vol. 73, pp. 448-453, 2014.
DOI: 10.1016/j.carbon.2014.03.010, IF=6.160

K. Hola, A. Bourlinos, O. Kozak, K. Berka, K. Siskova, M. Havrdova, J. Tucek, K. Safarova, M. Otyepka, E. Giannelis and R. Zboril: “Photoluminescence effects of graphitic core size and surface functional groups in carbon dots: COO− induced red-shift emission”, CARBON, vol. 70, pp. 279-286, 2014.
DOI: 10.1016/j.carbon.2014.01.008, IF=6.160

X. Chia, A. Ambrosi, M. Otyepka, R. Zbořil and M. Pumera: “Fluorographites (CFx)n Exhibit Improved Heterogeneous Electron-Transfer Rates with Increasing Level of Fluorination: Towards the Sensing of Biomolecules “, CHEMISTRY – A EUROPEAN JOURNAL, vol. 20, iss. 22, pp. 6665-6671, 2014.
DOI: 10.1002/chem.201402132, IF=5.696

M. Paloncýová, G. Fabre, R. H. DeVane, P. Trouillas, K. Berka and M. Otyepka: “Benchmarking of Force Fields for Molecule–Membrane Interactions”,J. CHEM. THEORY COMPUT., 10 (9), pp. 4143-4151, 2014.
DOI: 10.1021/ct500419b, IF=5.310

M. Paloncýová, R. H. DeVane, B. P. Murch, K. Berka and M. Otyepka: “Rationalization of Reduced Penetration of Drugs through Ceramide Gel Phase Membrane”, LANGMUIR, 30 (46), pp 13942–13948, 2014.

DOI: 10.1021/la503289v, IF=4.384

ancac3_v007i002.inddLazar, P; Zhang, S; Safarova, K; Li, Q; Froning, JP; Granatier, J; Hobza, P; Zboril, R; Besenbacher, F; Dong, MD; Otyepka, M: “Quantification of the Interaction Forces between Metals and Graphene by Quantum Chemical Calculations and Dynamic Force Measurements under Ambient Conditions”, ACS NANO, 7 (2), 1646-1651, 2013.
DOI: 10.1021/nn305608a, IF=12.062

F. Karlický, K. K. R. Datta, M. Otyepka and R. Zbořil: “Halogenated Graphenes: Rapidly Growing Family of Graphene Derivatives” ACS NANO, 7 (8), pp 6434–6464, 2013.

DOI: 10.1021/nn4024027, IF=12.062

Lazar, P; Karlicky, F; Jurecka, P; Kocman, M; Otyepkova, E; Safarova, K; Otyepka, M; “Adsorption of Small Organic Molecules on Graphene”, J. AM. CHEM. SOC., 135 (16), 6372-6377, 2013.

DOI: 10.1021/ja403162r, IF=11.444

Vasilios Georgakilas, Michal Otyepka, Athanasios B. Bourlinos, Vimlesh Chandra, Namdong Kim, K. Christian Kemp, Pavel Hobza, Radek Zboril, and Kwang S. Kim: Functionalization of Graphene: Covalent and Non-Covalent Approaches, Derivatives and Applications CHEMICAL REVIEWS, 112 (11), 6156-6214, 2012.

DOI: 10.1021/cr3000412 , IF=45.661

High-resolution transmission electron microscop

High-resolution Transmission Electron Microscope

Scanning Electron Microscope

Scanning Electron Microscope

Transmission Electron Microscope

Transmission Electron Microscope


AFM Raman


TOC image: “Functionalization of Graphene: Covalent and Non-Covalent Approaches, Derivatives and Applications,” Chem. Reviews (2012) 112(11)

Biomolecular simulation

Model of membrane bound Cytochrome P450 2C9. The arrows show binding of ibuprofen and release of 3-hydroxyibuprofen

Visiting scientists – Team leaders:

Athanasios B. Bourlinos, Ph.D. (Home institution: Institute of Materials Science (IMS) of the National Center for Scientific Research “Demokritos”, Greece) Institute of Materials Science (IMS) of the National Center for Scientific Research “Demokritos” is the major National Research Center in Greece. IMS is the succession of the Direction of Physics, one of the historical departments of Demokritos, which was established in year 1961. The combination of high quality scientific personnel and very good infrastructure has contributed to the achievement of excellent scientific work and substantial external funding of the order of 1 MEuro/year. In year 2000 IMS was awarded funds for the establishment of the Center of Excellence for Nanostructured Materials in Greece.


Assoc. Prof. Michael A. Karakassides (Home institution: University of Ioannina, Department of Materials Science & Engineering, Greece) Biomaterials, Hybrids and Mesoporous Materials Group group (group is led by Assoc. Prof. Michael A. Karakassides) was established in 2001 and currently gathers more than 15 researchers, including post-graduate students. It aims at a variety of topics in inorganic porous and hybrids solids, ceramics and glasses and nanomaterials, either in pure or in composite form. Advance applications, such as, biomaterials, carbon nanotubes, graphene, nanocomposites, and traditional ones, such as clay materials, vitrification and ceramization processing of industrially produced ceramics, water cleaning processing with the aid of hybrid nano-ceramic etc., are both included in the activities of BHMM group. High-importance objectives of the group, are the design and the development of new functional materials, including synthesis and processing optimization and characterization up to commercialization level.