> 2015 (CFN Karlsruhe)

  • Coupled-Perturbed DFTB-QM/MM Metadynamics: Application to Proton-Coupled Electron Transfer
    N. Gillet, M. Elstner, T. Kubař. J Chem Phys accepted, 2018.
  • On the Mechanism of Spontaneous ThiolDisulfide Exchange in Proteins
    M. Putzu, F. Gräter, M. Elstner, T. Kubař. Phys Chem Chem Phys in press, 2018. link
  • Molecular insights into variable electron transfer in amphibian cryptochrome
    E. Sjulstok, G. Lüdemann, T. Kubař, M. Elstner, I.A. Solov'yov. Biophys J 114(11):2563
  • A Molecular Dynamics-Quantum Mechanics Theoretical Study of DNA-Mediated Charge Transport in Hydrated Ionic Liquids.
    Z. Meng, T. Kubař, Y. Mu, F. Shao. J Chem Theory Comput 14(5):2733
  • "siRNA traffic lights": Arabino-configured 2'-anchors for fluorescent dyes are key for dual color readout in cell imaging.
    J. Steinmeyer, H.-K. Walter, M.A. Bichelberger, V. Schneider, T. Kubař, F. Rönicke, B. Olshausen, K. Nienhaus, G.U. Nienhaus, U. Schepers, M. Elstner, H.-A. Wagenknecht. Org Biomol Chem 16(20):37263731, 2018. link
  • Orthogonal 19F-labeling for solid-state NMR reveals the conformation and orientation of short peptaibols in membranes.
    S.L. Grage, S. Kara, A. Bordessa, V. Doan, F. Rizzolo, M. Putzu, T. Kubař, A.M. Papini, G. Chaume, T. Brigaud, S. Afonin, A.S. Ulrich. Chem Eur J 24(17):4328
  • Cation solvation with quantum chemical effects modeled by size-consistent multi-partitioning quantum mechanics/molecular mechanics method.
  • Structural behavior of the peptaibol harzianin HK VI in a DMPC bilayer – insights from MD simulations.
    M. Putzu, S. Kara, S. Afonin, S.L. Grage, A. Bordessa, G. Chaume, T. Brigaud, A.S. Ulrich, and T. Kubař. Biophys J 112(12):2602–2614, 2017. link
  • Reaction Path Averaging: Characterizing structural response of the DNA double helix to electron transfer.
    M.H. Kolář, and T. Kubař. J Phys Chem B 121(7):1520–1532, 2017. link
  • Microsecond simulation of electron transfer in DNA: bottom-up parametrization of an efficient electron transfer model based on atomistic details.
    M. Wolter, M. Elstner, U. Kleinekathöfer, and T. Kubař. J Phys Chem B 121(3):529–549, 2017. link
  • Polaron Effects on Charge Transport through Molecular Wires: A Multi-scale Approach.
    T. Kubař, M. Elstner, B. Popescu, and U. Kleinekathöfer. J Chem Theory Comput 13(1):286–296, 2017. link
  • The effect of the environment on the methyl transfer reaction mechanism between trimethylsulfonium and phenolate.
    D. A. Saez, S. Vogt-Geisse, R. Inostroza-Rivera, T. Kubař, M. Elstner, A. Toro-Labbé, and E. Vöhringer-Martinez. Phys Chem Chem Phys 18(34):2403324042, 2016. link
  • Semiempirical Quantum Mechanical Methods for Noncovalent Interactions for Chemical and Biochemical Applications.
    A.S. Christensen, T. Kubař, Q. Cui, and M. Elstner
    . Chem Rev 116(9):53015337, 2016. link
  • Multi-scale approach to non-adiabatic charge transport in high-mobility organic semiconductors.
    A. Heck, J.J. Kranz, T. Kubař, and M. Elstner. J Chem Theory Comput 11(11):50685082, 2015. link

2011 – 2015 (Karlsruhe)

  • Molecular dynamics investigation of gluazo, a photo-switchable ligand for the glutamate receptor GluK2.
    Y. Guo, T. Wolter, T. Kubař, M. Sumser, D. Trauner, and M. Elstner. PLoS ONE 10(8): e0135399, 2015. link
  • New QM/MM implementation of the DFTB3 method in the Gromacs package.
    T. Kubař, K. Welke, and G. Groenhof. J Comput Chem 36(26):19781989, 2015. link
  • Solvent driving force ensures fast formation of a persistent and well-separated radical pair in plant cryptochrome.
    G. Lüdemann, I.A. Solov'yov, T. Kubař, and M. Elstner. J Am Chem Soc 137(3):1147–1156, 2015. link
  • Parameterization of the DFTB3 method for Br, Ca, Cl, F, I, K and Na in organic and biological systems.
    M. Kubillus, T. Kubař, M. Gaus, J. ؐezáč, and M. Elstner. J Chem Theory Comput 11(1):332342, 2015. link
  • Size-consistent multipartitioning QM/MM: A stable and efficient adaptive QM/MM method.
    H.C. Watanabe, T. Kubař, and M. Elstner. J Chem Theory Comput 10(10):42424252, 2014. link
  • Fragment orbital based description of charge transfer in peptides including backbone orbitals.
    A. Heck, P.B. Woiczikowski, T. Kubař, K. Welke, T. Niehaus, B. Giese, S. Skourtis, M. Elstner, and T.B. Steinbrecher. 
    J Phys Chem B 118(16):42614272, 2014. link
  • Modeling charge transport in DNA using multi-scale methods.
    T. Kubař, R. Gutiérrez, U. Kleinekathöfer, G. Cuniberti, and M. Elstner.
     Phys Stat Sol B 250(11):22772287, 2013. link
  • Charge transport in desolvated DNA.
    M. Wolter, M. Elstner, and T. Kubař. J Chem Phys 139(12):125102, 
    2013. link
  • A hybrid approach to simulation of electron transfer in complex molecular systems.
    T. Kubař and M. Elstner. J
     Royal Soc Interface, 10(87):20130415, 2013. link
  • Charge transfer in E. coli DNA photolyase: Understanding polarization and stabilization effects via QM/MM simulations.
    G. Lüdemann, P.B. Woiczikowski, T. Kubař, M. Elstner, and T.B. Steinbrecher.
    J Phys Chem B 117(37):1076910778, 2013. link
  • Force distribution analysis of mechanochemically reactive dimethylcyclobutene.
    W. Li, S.A. Edwards, L. Lu, T. Kubař, S.P. Patil, H. Grubmüller, G. Groenhof, and F. Gräter.
    ChemPhysChem, 14(12):26872697, 2013. link
  • Parametrization of the SCC-DFTB method for halogens.
    T. Kubař, Z. Bodrog, M. Gaus, C. Köhler, B. Aradi, T. Frauenheim, and M. Elstner.
    J Chem Theory Comput 9(7):29392949, 2013. link
  • Efficient algorithms for the simulation of non-adiabatic electron transfer in complex molecular systems: Application to DNA.
    T. Kubař and M. Elstner.
    Phys Chem Chem Phys 15(16):57945813, 2013. link
  • Charge transfer in model peptides: Obtaining Marcus parameters from molecular simulation.
    A. Heck, P.B. Woiczikowski, T. Kubař, B. Giese, M. Elstner, and T.B. Steinbrecher.
    J Phys Chem B 16(7):22842293, 2012. link

2007 – 2011 (Braunschweig)

  • Response of the electric conductivity of double-stranded DNA on moderate mechanical stretching stresses.
    M. Wolter, P.B. Woiczikowski, M. Elstner, and T. Kubař.
    Phys Rev B 85(7):075101, 2012. link
  • On the structure and stretching of microhydrated DNA.
    M. Wolter, M. Elstner, and T. Kubař. J Phys Chem 
    A 115(41):1123811247, 2011. link
  • Nonadiabatic QM/MM simulations of fast charge transfer in Escherichia coli DNA photolyase.
    P.B. Woiczikowski, T. Steinbrecher, T. Kubař, and M. Elstner.
    J Phys Chem B 115(32):98469863, 2011. link
  • On the role of London dispersion forces in biomolecular structure determination.
    M. Kolář, T. Kubař, and P. Hobza.
    J Phys Chem B 115(24):80388046, 2011. link
  • Effect of nitrogen adsorption on the mid-infrared spectrum of water clusters.
    W. Hujo, M. Gaus, M. Schultze, T. Kubař, J. Grunenberg, M. Elstner, and S. Bauerecker.
    J Phys Chem A 115(23):62186225, 2011. link
  • Structural stability versus conformational sampling in biomolecular systems: Why is the charge transfer efficiency in G4-DNA better than in double-stranded DNA?
    P.B. Woiczikowski, T. Kubař, R. Gutiérrez, G. Cuniberti, and M. Elstner. J Chem Phys 133(3):035103, 2010. link
  • Sequence-dependent congurational entropy change of DNA upon intercalation.
    M. Kolář, T. Kubař, and P. Hobza. J Phys Chem B 114(42):1344613454, 2010. link
  • Coarse-grained time-dependent density functional simulation of charge transfer in complex systems: Application to hole transfer in DNA.
    T. Kubař and M. Elstner.
    J Phys Chem B 114(34):1122111240, 2010. link
  • Structural fluctuations and quantum transport through DNA molecular wires: A combined molecular dynamics and model Hamiltonian approach.
    R. Gutiérrez, R. Caetano, P.B. Woiczikowski, T. Kubař, M. Elstner, and G. Cuniberti.
    New J Phys, 12:023022, 2010. link
  • Simulation of charge transfer in DNA.
    T. Kubař, and M. Elstner. Challenges and Advances in Computational Chemistry and Physics 12:213–245, 2010. link
  • Solvent fluctuations drive the hole transfer in DNA: A mixed quantum-classical study.
    T. Kubař, U. Kleinekathöfer, and M. Elstner.
     J Phys Chem B 113(39):1310713117, 2009. link
  • Combined density functional theory and Landauer approach for hole transfer in DNA along classical molecular dynamics trajectories.
    P.B. Woiczikowski, T. Kubař, R. Gutiérrez, R.A. Caetano, G. Cuniberti, and M. Elstner. J Chem Phys 130(21):215104, 2009. link
  • Charge transport through biomolecular wires in a solvent: Bridging molecular dynamics and model Hamiltonian approaches.
    R. Gutiérrez, R.A. Caetano, P.B. Woiczikowski, T. Kubař, M. Elstner, and G. Cuniberti.
    Phys Rev Lett 102(20):208102, 2009. link
  • Solvent reorganization energy of hole transfer in DNA.
    T. Kubař and M. Elstner. J Phys Chem B 
    113(16):56535656, 2009. link
  • What governs the charge transfer in DNA? The role of DNA conformation and environment.
    T. Kubař and M. Elstner.
    J Phys Chem B 112(29):87888798, 2008. link
  • Efficient calculation of charge-transfer matrix elements for hole transfer in DNA.
    T. Kubař, P.B. Woiczikowski, G. Cuniberti, and M. Elstner.
    J Phys Chem B 112(26):79377947, 2008. link

< 2007 (Prague)

  • Dispersion interactions govern the strong thermal stability of a protein.
    J. Vondrášek, T. Kubař, F.E. Jenney Jr., M.W.W. Adams, M. Kožíšek, J. ȃerný, V. Sklenář, and P. Hobza.
    Chem Eur J 13(32):90229027, 2007. link
  • Density-functional, density-functional tight-binding, and wave function calculations on biomolecular systems.
    T. Kubař, P. Jurečka, J. ȃerný, J. ؐezáč, M. Otyepka, H. Valdés, and P. Hobza.
    J Phys Chem A 111(26):56425647, 2007. link
  • How the stabilization of INK4 tumor suppressor 3D structure evaluated by quantum chemical and molecular mechanics calculations corresponds well with experimental results: Interplay of association enthalpy, entropy, and solvation effects.
    M. Otyepka, P. Sklenovský, D. Horinek, T. Kubař, and P. Hobza.
    J Phys Chem B 110(9):44234429, 2006. link
  • Binding of cationic and neutral phenanthridine intercalators to a DNA oligomer is controlled by dispersion energy: Quantum chemical calculations and molecular mechanics simulations.
    T. Kubař, M. Hanus, F. Ryjáček, and P. Hobza.
    Chem Eur J 12(1):280290, 2005. link
  • New parameterization of the Cornell et al. empirical force field covering amino group nonplanarity in nucleic acid bases.
    F. Ryjáček, T. Kubař, and P. Hobza.
    J Comput Chem 24(15):18911901, 2003. link
  • Correlated ab initio study of nucleic acid bases and their tautomers in the gas phase, in a microhydrated environment and in aqueous solution. Guanine: Surprising stabilization of rare tautomers in aqueous solution.
    M. Hanus, F. Ryjáček, M. Kabeláč, T. Kubař, T.V. Bogdan, S.A. Trygubenko, and P. Hobza. J Am Chem Soc 125(25):76787688, 2003. link