Selected Publications:

·       L. Martini, A. Kells, R. Covino, G. Hummer, N.V. Buchete, E. Rosta, Variational identification of markovian transition states, Physical Review X, Vol. 7, 10.1103/PhysRevX.7.031060, 2017

·       V. Sharma, P.G. Jambrina, M. Kaukonen, E. Rosta, P.R. Rich, Insights into functions of the H channel of cytochrome c oxidase from atomistic molecular dynamics simulations, Proc. Natl. Acad. Sci. U.S.A., In press, 2017

·       A. Palma, M. Artelsmair, G. Wu, X. Lu, S.J. Barrow, N. Uddin, E. Rosta, E. Masson, O.A. Scherman, Cucurbit[7]uril as a Supramolecular Artificial Enzyme for Diels-Alder Reactions, Angewandte Chemie, In press, 10.1002/anie.201706487, 2017

·       L.S. Stelzl, A. Kells, E. Rosta, G. Hummer, Dynamic Histogram Analysis to Determine Free Energies and Rates from Biased Simulations, J Chem Theory Comput, Vol., 10.1021/acs.jctc.7b00373, 2017

·       P. Saura, R. Suardíaz, L. Masgrau, À. González-Lafont, E. Rosta, J.M. Lluch, Understanding the Molecular Mechanism of the Ala-versus-Gly Concept Controlling the Product Specificity in Reactions Catalyzed by Lipoxygenases: A Combined Molecular Dynamics and QM/MM Study of Coral 8R-Lipoxygenase, ACS Catalysis, Vol. 7, 4854-4866, 10.1021/acscatal.7b00842, 2017

·       J.A. McCune, E. Rosta, O.A. Scherman, Modulating the oxidation of cucurbit[n]urils, Organic and Biomolecular Chemistry, Vol. 15, 998-1005, 10.1039/C6OB02594C, 2017

·       C.T. Leahy, A. Kells, G. Hummer, N.-V. Buchete, E. Rosta, Peptide dimerization-dissociation rates from replica exchange molecular dynamics, The Journal of Chemical Physics, Vol. 147, 152725, 10.1063/1.5004774, 2017

·       G. Di Martino, V.A. Turek, A. Lombardi, I. Szabó, B. De Nijs, A. Kuhn, E. Rosta, J.J. Baumberg, Tracking Nanoelectrochemistry Using Individual Plasmonic Nanocavities, Nano Letters, Vol. 17, 4840-4845, 10.1021/acs.nanolett.7b01676, 2017

·        G.N. Nagy, R. Suardiaz, A. Lopata, O. Ozohanics, K. Vekey, B.R. Brooks, I. Leveles, J. Toth, B.G. Vertessy and E. Rosta, "Structural Characterization of Arginine Fingers: Identification of an Arginine Finger for the Pyrophosphatase dUTPases", J. Am. Chem. Soc., DOI: 10.1021/jacs.6b09012, 2016

·        S.T.J. Ryan, J. del Barrio, R. Suardiaz, D.F. Ryan, E. Rosta, and O.A. Scherman, “A Dynamic and Responsive Host in Action: Light-Controlled Molecular Encapsulation”, Angewandte Chemie, DOI: 10.1002/anie.201607693, 2016

·        G. Sanchez-Sanz, B. Tywoniuk, D. Matallanas, D. Romano, L.K. Nguyen, B. Kholodenko, E. Rosta, W. Kolch, and N-V. Buchete, “Molecular Mechanism of MST2-RASSF protein-protein interactions through SARAH domains”, PLoS Computational Biology, 12 (10), e1005051, 2016

·        C. Leahy, R. Murphy, G. Hummer, E. Rosta, N-V. Buchete, “Coarse Master Equations for Binding Kinetics of Amyloid Peptide Dimers”, J. Phys. Chem. Lett.,  7 (14), 2676-2682, 2016

·         R. Chikkaraddy, B. de Nijs, F. Benz, S. Barrow, O.A. Scherman,  E. Rosta, A. Demetriadou, P. Fox, O. Hess, and J.J. Baumberg, “Single-molecule strong coupling at room temperature in plasmonic nanocavities”, Nature, DOI: 10.1038/nature17974, 2016

·         R. Suardiaz, P.G. Jambrina, L. Masgrau, A. Gonzalez-Lafont*, E. Rosta*, and J.M. Luch, “Understanding the Mechanism of the Hydrogen Abstraction from Arachidonic Acid Catalyzed by the Human Enzyme 15-Lipoxygenase-2. A Quantum Mechanics/Molecular Mechanics Free Energy Simulation”, J. Chem. Theory Comput.,  DOI: 10.1021/acs.jctc.5b01236, 2016

·         J. del Barrio, S.T.J. Ryan, P.G. Jambrina, E. Rosta, and O.A. Scherman, “Light-regulated Molecular Trafficking in a Synthetic Water-soluble Host”, J. Am. Chem. Soc. Commun., DOI: 10.1021/jacs.5b11642, 2016

·         L. Hamdan, K. Abdel-Maksoud, …, A. Andreou, O.A. Scherman, and E. Rosta, “Deviation from the anti-Markovnikov Rule: A Computational Study of the Regio- and Stereoselectivity of Diene Hydroboration Reactions”, Theor. Chemistry Accounts, DOI: 10.1007/s00214-015-1768-6, 2016

·         P. G. Jambrina, N. Rauch, K. Rybakova, L. Nguyen, B. Kholodenko, N.-V. Buchete, W. Kolch, and E. Rosta, “Phosphorylation of RAF Kinase Dimers Drives Conformational Changes Facilitating Transactivation”, Angewandte Chemie, DOI 10.1002/anie.201509272, 2016

·         G. Sanchez-Sanz, D. Matallanas, L.K. Nguyen, B.N. Kholodenko, E. Rosta, W. Kolch, and N-V. Buchete, “Mst2-RASSF Protein-protein Interactions through SARAH Domains”, Briefings in Bioinformatics, DOI: 10.1093/bib/bbv070, 2015

·         A. Lopata, P.G. Jambrina, P.K. Sharma, B. Brooks, J. Toth, B.G. Vertessy and E. Rosta; “Mutations decouple proton transfer from phosphate cleavage in the dUTPase catalytic reaction”, ACS catalysis, Vol. 5, 3225, 2015 

·         L. Zheng, S. Sonzini, M. Ambarwati, E. Rosta, O.A. Scherman and A. Herrmann, “Turning cucurbit[8]uril into a supramolecular nanoreactor for asymmetric catalysis”, Angewandte Chemie, DOI : 10.1002/anie.201505628, 2015

·         A. Andreou, M. Leskes, P.G. Jambrina, G.J. Tustin, C.P. Grey, E. Rosta and O.A. Scherman, “Divergence from the classical hydroboration reactivity; boron containing materials through a hydroboration cascade of small cyclic dienes”, Chemical Science, DOI: 10.1039/C4SC02729A, 2015

·         Y. Shao, “Advances in molecular quantum chemistry contained in the Q-Chem 4 program package”, Molecular Physics, Vol. 113, 184, 2015

·         H. Wu, A.S.J.S. Mey, E. Rosta and F. Noé, “Statistically optimal analysis of state-discretized trajectory data from multiple thermodynamic states”, J. Chem. Phys., Vol. 141, 214106, 2014

·         E. Rosta and G. Hummer, “Free energies from dynamic weighted histogram analysis using unbiased Markov state model”, J. Chem. Theory Comput., 2015 (DOI: 10.1021/ct500719p)

·         S. Bui, D. Stetten, P.G. Jambrina, T. Prangé, N. Colloc’h, D.D. Sanctis, A. Royant, E. Rosta and R.A. Steiner, “Direct evidence for a peroxide intermediate and reactive enzyme-substrate-O2 configuration in a cofactor-free oxidase”, Angewandte Chemie, Vol. 53, 13710, 2014

·         P.G. Jambrina, O. Bohuszewicz, N-V. Buchete, W. Kolch and E. Rosta, “Molecular mechanisms of asymmetric RAF dimer activation”, Biochem. Soc. Trans., Vol. 42, 784, 2014

·         E. Rosta, W. Yang and G. Hummer, "Calcium inhibition of Ribonuclease H1 two-metal ion catalysis", J. Am. Chem. Soc., Vol. 136, 3137, 2014

·         A. Ganguy, P. Thaplyal, E. Rosta, P. Bevilaqua and S. Hammes-Schiffer, “Quantum Mechanical/Molecular Mechanical Free Energy Simulations of the Self-Cleavage Reaction in the Hepatitis Delta Virus Ribozyme", J. Am. Chem. Soc., Vol. 136, 1483, 2014

·         T. Pesnot, L. M. Tedaldi, P. G. Jambrina, E. Rosta and G. K. Wagner, “Exploring the role of the 5-substituent for the intrinsic fluorescence of 5-aryl and 5-heteroaryl uracil nucleotides: a systematic study”, Organic & Biomolecular Chemistry, Vol. 11, 6357, 2013

·         O. Barabas, V. Nemeth-Pongracz, A. Bodor, A. Perczel, E. Rosta, Z. Kele, I. Zagyva, Z. Szabadka, V. I. Grolmusz, M. Wilmanns and B. G. Vertessy, “Catalytic mechanism of α-phosphate attack in dUTPase is revealed by X-ray crystallographic snapshots of distinct intermediates, 31P-NMR spectroscopy and reaction path modelling”, Nucleic Acids Research, Vol. 41, 10542, 2013

·         I. Lans, M. Medina, E. Rosta, G. Hummer, M. Garcia-Viloca, À. González-Lafont and J. M. Lluch. “Theoretical study of the mechanism of the hydride transfer between ferredoxin NADP+ reductase and NADP+. The role of Tyr303.”, J. Am. Chem. Soc., Vol. 134, 20544, 2012 

·         E. Rosta and A. Warshel, “Origin of Linear Free Energy Relationships: Exploring the Nature of the Off-Diagonal Coupling Elements in SN2 Reactions”, J. Chem. Theory Comput., Vol. 8, 3574, 2012  

·         E. Rosta, M. Nowotny, W. Yang and G. Hummer, “Catalytic Mechanism of RNA Backbone Cleavage by Ribonuclease H from QM/MM Simulations”, J. Am. Chem. Soc., Vol. 133, 8934, 2011 

·         E. Rosta and G. Hummer, “Error and Efficiency of Simulated Tempering Simulations”, J. Chem. Phys.,Vol. 131, 034102, 2010 

·         E. Rosta and G. Hummer, “Error and Efficiency of Replica Exchange Molecular Dynamics Simulations”, J. Chem. Phys., Vol. 131, 165102, 2009 

·         E. Rosta, N-V. Buchete and G. Hummer, “Thermostat Artifacts in Replica Exchange Molecular Dynamics Simulations”, J. Chem. Theory Comput., Vol. 5, 1393, 2009 

·         E. Rosta, H. L. Woodcock, B. Brooks and G. Hummer, “Artificial Reaction Coordinate “Tunneling” in Free Energy Calculations: the Catalytic Reaction of Ribonuclease H”, J. Comp. Chem., Vol. 96, 573a, 2009 

·         E. Rosta, S. L. Kamerlin and A. Warshel, “On the Interpretation of the Observed Linear Free Energy Relationship in Phosphate Hydrolysis: A Thorough Computational Study of Phospate Diester Hydrolysis in Solution”, Biochemistry, Vol. 47, 3725, 2008 

·         E. Rosta, M. Klähn and A. Warshel, “Towards Accurate ab initio QM/MM Calculations of Free Energy Profiles of Enzymatic Reactions”, J. Phys. Chem. B, Vol. 110, 2934, 2006

·         M. Klähn, E. Rosta and A. Warshel, “On the Mechanism of Hydrolysis of Phosphate Monoesters Dianions in Solutions and Proteins”, J.  Am. Chem. Soc., Vol. 128, 15310, 2006 

·         G. Hong, E. Rosta and A. Warshel, “Using the Constrained Density Functional Theory Approach in Generating Diabatic Surfaces and Off-diagonal Terms for Modeling Reactions in Condensed Phases”, J. Phys. Chem. B,  Vol. 110, 19570, 2006 

·         Y. Shao, et al., “Advances in methods and algorithms in a modern quantum chemistry program package”, Phys. Chem. Chem. Phys., Vol. 8, 3172, 2006 

·         M. Klähn, S. Braun-Sand, E. Rosta and A. Warshel, “On Possible Pitfalls in ab initio QM/MM Minimization Approaches for Studies of Enzymatic Reactions”, J. Phys. Chem. B, Vol. 109, 15645, 2005 

·         E. Rosta and P. R. Surján, “Two-body Zeroth Order Hamiltonians in Multireference Perturbation Theory: the APSG Reference State”, J. Chem. Phys., Vol. 116, 878-890, 2002