Uhlíkové nanostruktury, biomolekuly a simulace

Head of the Division:
Prof. Michal Otyepka, Ph.D.

Scientific focus of the division:

• Synthesis of functionalized carbon-based materials (graphene, nanodiamonds, nanotubes, amorphous carbon, carbogenic quantum dots etc.) and their applications in biosensing, electrochemistry, water purification etc.
• Theoretical design and synthesis of novel carbon-based materials including graphene derivatives
• Development of hybrid carbogenic structures with embedded nanoparticles (Fe, Fe₃O₄,Si)
• Combined experimental and theoretical description of interaction of carbon nanostructures with biomacromolecules and their functional components
• Structure and dynamics of biomacromolecules and their functional components, interaction of biomacromolecules with membrane bilayer, enzyme and RNA catalysis, development of new theoretical tools for description of biomacromolecules, nanomaterials and their mutual interactions
• Molecular dynamics simulations of biomacromolecules, force field development and testing (namely for RNA), quantum chemical and hybrid QM/MM calculations, simulation of lipid bilayer penetration, interaction of metals with graphene.

Results highlights:

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., 2013. 135 (16), 6372-6377.
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Lazar, 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, 2013. 7 (2), 1646-1651. 
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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, 2012. 112 (11), 6156-6214
Link 

Granatier J, Lazar P, Otyepka* M, Hobza* P: The Nature of the Binding of Au, Ag, and Pd to Benzene, Coronene, and Graphene: From Benchmark CCSD(T) to Plane-Wave DFT Calculations. J. Chem. Theor. Comput., 2011. 7(11), 3743-3755.
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Ditzler, M.; Otyepka, M.; Sponer, J.; Walter, N. Molecular Dynamics and Quantum Mechanics of RNA: Conformational and Chemical Change We Can Believe In. Acc. Chem. Res., 2010, 1, 40-47. 
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Georgakilas V, Bourlinos AB, Zboril R, Steriotis TA, Dallas P, Stubos AK, Trapalis Ch. Organic functionalization of graphenes. Chem. Commun., 2010. 46(10), 1766-1768.
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Riley, K. E.; Pitoňák, M.; Jurečka, P.; Hobza, P. Stabilization and Structure Calculations for Noncovalent Interactions in Extended Molecular Systems Based on Wave Function and Density Functional Theories, Chem. Rev. 2010, 110, 5023–5063. 
Link

Zbořil, R.; Karlický, F.; Bourlinos, A. B.; Steriotis, T. A.; Stubos, A. K.; Georgakilas, V.; Šafářová, K.; Jančík, D.; Trapalis, C.; Otyepka, M. Graphene Fluoride: A Stable Stoichiometric Graphene Derivative and Its Chemical Conversion to Graphene, Small 2010, 6, 2885-2891. 
Link

Bourlinos, A. B.; Georgakilas, V.; Zboril, R.; Steriotis, T. A.; Stubos, A. K. Liquid-Phase Exfoliation of Graphite Towards Solubilized Graphenes, Small 2009, 5, 1841-1845. 
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Bourlinos, A.B.; Stassinopoulos, A.; Anglos, D.; Zboril, R.; Karakassides, M.; Giannelis, E.P., Surface functionalized carbogenic quantum dots, Small 2008, 4, 455-458. 
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Banas, P.; Hollas, D.; Zgarbova, M.; Jurecka, P.; Orozco, M.; Cheatham III, T. E.; Sponer, J.; Otyepka, M., Performance of Molecular Mechanics Force Fields for RNA Simulations: Stability of UUCG and GNRA Hairpins, J. Chem. Theory and Comput. 2010, 6, 3836-3849. 
Link

Banas, P.; Walter, N.G.; Šponer, J.; Otyepka, M., Protonation States of the Key Active Site Residues and Structural Dynamics of the glmS Riboswitch As Revealed by Molecular Dynamics, J. Phys. Chem. B  2010, 114, 8701-8712. 
Link

Zgarbova, M.; Otyepka, M.; Sponer, J.; Mladek, A.; Banas, P.; Cheatham, T.E.; Jurecka, P.: Refinement of the Cornell et al. Nucleic Acids Force Field based on Reference Quantum Chemical Calculations of Glycosidic Torsion Profiles. J. Chem. Theory Comput., 2011 
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