Publications

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2012

P. Wang, J. Blumberger, "Blocking of gas diffusion in [NiFe]-hydrogenase mutants: A mechanistic picture from multiscale simulation", submitted (2012). P. J. Ballester, M. Mangold, N. I. Howard, R. L. Marchese Robinson, C. Abell, J. Blumberger, J. B. O. Mitchell "Hierarchical virtual screening for the discovery of new molecular scaffolds in antibacterial drug lead identification" , submitted (2012). V. Tipmanee, J. Blumberger, "Kinetics of the terminal electron transfer step in cytochrome c oxidase" J. Phys. Chem. B 116, 1876 (2012). [online link]

2011

R. Seidel, S. Thurmer, J. Moens, P. Geerlings, J. Blumberger, B. Winter, "Valence photoemission spectra of aqueous Fe2+/3+ and [Fe(CN)6]4-/3- and their interpretation by DFT calculations" J. Phys. Chem. B 115, 11671 (2011) [Cover Article]. [online link] J. Blumberger, F. Baletto, A. Shluger, "Editorial: 1st TYC workshop on energy materials", Phys. Chem. Chem. Phys. 13, 7602 (2011). [click here] P. Wang, R. B. Best, J. Blumberger, "A microscopic model for gas diffusion dynamics in a [NiFe]-hydrogenase" Phys. Chem. Chem. Phys. 13, 7708 (2011). [click here] P. Wang, R. B. Best, J. Blumberger, "Multiscale simulation reveals multiple pathways for H2 and O2 transport in a [NiFe]-hydrogenase" J. Am. Chem. Soc. 133, 3548 (2011). [click here] M. Mangold, L. Rolland, F. Costanzo, M. Sprik, M. Sulpizi, J. Blumberger, "Absolute pKa values and solvation structure of amino acids from density functional based molecular dynamics simulation", J. Chem. Theor. Comput. 7, 1951 (2011). [click here] M. Alfonso-Prieto, H. Oberhofer, M. L. Klein, C. Rovira, J. Blumberger, "Proton transfer drives protein radical formation in Helicobacter pylori catalase but not in Penicillium vitale catalase" J. Am. Chem. Soc. 133, 4285 (2011). [click here]

2010

V. Tipmanee, H. Oberhofer, M. Park, K. S. Kim, J. Blumberger, "Prediction of reorganization free energies for biological electron transfer: a comparative study of Ru-modified cytochromes and a 4-helix bundle protein", J. Am. Chem. Soc. 132, 17032 (2010). [online link] H. Oberhofer, J. Blumberger, "Electronic coupling matrix elements from charge constrained density functional theory calculations using a plane wave basis set", J. Chem. Phys. 133, 244105 (2010) [Cover Article]. [online link] J. Moens, R. Seidel, P. Geerlings, M. Faubel, B. Winter, J. Blumberger, "Energy levels and redox properties of aqueous Mn2+/3+ from photoemission spectroscopy and density functional molecular dynamics simulation", J. Phys. Chem. B 114, 9173 (2010) [Cover Article]. [online link] H. Oberhofer, J. Blumberger, "Insight into the mechanism of the Ru2+ - Ru3+ electron self-exchange reaction from quantitative rate calculations" Angew. Chem. Int. Ed. 49, 3631 (2010). [online link]

2009

R. Seidel, M. Faubel, B. Winter, J. Blumberger, "Single-ion reorganization free energy of aqueous Ru(bpy)32+/3+ and Ru(H2O)62+/3+ from photoemission spectroscopy and density functional molecular dynamics simulation" J. Am. Chem. Soc. 131, 16127 (2009). [online link] H. Oberhofer, J. Blumberger, "Charge constrained density functional molecular dynamics for simulation of condensed phase electron transfer reactions" J. Chem. Phys. 131 , 064101 (2009) [Cover Article]. [online link] L. M. Blomberg, M. Mangold, J. B. O. Mitchell, J. Blumberger, "Theoretical Study of the Reaction Mechanism of Streptomyces Coelicolor Type II Dehydroquinase" J. Chem. Theor. Comput. 5 , 1284 (2009). [online link]

2008

J. Blumberger, "Cu+aq/Cu2+aq redox reaction exhibits strong non-linear solvent response due to change in coordination number" J. Am. Chem. Soc. 130 , 16065 (2008). [online link] J. Blumberger, "Free energies for biological electron transfer from QM/MM calculation: Method, application and critical assessment" Phys. Chem. Chem. Phys. 10 , 5651 (2008) [Inside Cover article]. [online link] J. Blumberger, G. Lamoureux, "Reorganization free energies and quantum corrections for a model electron self-exchange reaction: comparison of polarizable and non-polarizable solvent models" Mol. Phys. 106 , 1597 (2008). [online link]

2007

J. Blumberger, G. Lamoureux, M. L. Klein, "Peptide hydrolysis in thermolysin: Ab-initio QM/MM investigation of the Glu143 assisted water addition mechanism" J. Chem. Theor. Comput. 3 , 1837 (2007). [online link] Y. Tateyama, J. Blumberger, T. Ohno, M. Sprik,"Free energy calculation of water addition coupled to reduction of aqueous RuO4-" J. Chem. Phys. 126 , 204506 (2007). [online link]

2006

J. Blumberger, M. L. Klein,"Reorganization free energies for long range electron transfer in a porphyrin binding four-helix bundle protein" J. Am. Chem. Soc. 128, 13854 (2006). [online link] J. Blumberger, B. Ensing, M. L. Klein,"Formamide hydrolysis in alkaline aqueous solution: Insight from ab initio metadynamics calculations" Angew. Chem. Int. Ed. 45, 2893 (2006). [online link] J. Blumberger, M. L. Klein, "Revisiting the free energy profile for the nucleophilic attack of hydroxide on formamide in aqueous solution" Chem. Phys. Lett. 422, 210 (2006). [online link] J. Blumberger, M. Sprik, "Redox free energies from vertical energy gaps: Ab initio molecular dynamics implementation" Lecture notes for the International School of Solid State Physics - 34th course: Computer Simulations in Condensed Matter: from Materials to Chemical Biology, Erice, Sicily, 20 July - 1 August 2005; Springer Lect. Notes Phys. 704, 467-491 (2006). J. Blumberger, I. Tavernelli, M. L. Klein, M. Sprik, "Diabatic free energy curves and coordination fluctuations for the aqueous Ag+/Ag2+ redox couple: A biased Born-Oppenheimer molecular dynamics investigation" J. Chem. Phys. 124, 064507 (2006). [online link] J. Blumberger, M. Sprik,"Quantum versus classical electron transfer energy as reaction coordinate for the aqueous Ru2+ /Ru3+ redox reaction" Theor. Chem. Acc. 115 , 113 (2006). [online link]

2005

J. Blumberger, Y. Tateyama, M. Sprik, "Ab initio molecular dynamics simulation of redox reactions in solution" Comp. Phys. Comm. 169, 256 (2005). [online link] Y. Tateyama, J. Blumberger, M. Sprik, I. Tavernelli, "Density functional molecular dynamics study of the redox reactions of two anionic aqueous transition metal complexes" J. Chem. Phys. 122, 234505 (2005). [online link] J. Blumberger, M. Sprik,"Ab initio molecular dynamics simulation of the aqueous Ru2+/Ru3+ redox reaction: The Marcus perspective"J. Phys. Chem. B 109, 6793 (2005). [online link]

2004

L. Bernasconi, J. Blumberger, M. Sprik, R. Vuilleumier,"Optical response of Cu+ and Ag+ aqua ions:A DFT/TDDFT study"J. Chem. Phys.121, 11885, (2004). [online link] J. Blumberger, L. Bernasconi, I. Tavernelli, R. Vuilleumier, M. Sprik,"Electronic structure and solvation of copper and silver Ions: A theoretical picture of a model aqueous redox reaction" J. Am. Chem. Soc. 126, 3928 (2004). [online link] J. Blumberger, M. Sprik,"Free energy of oxidation of metal aqua ions by an enforced change of Coordination"J. Phys. Chem. B. 108,6529 (2004). [online link]

2000-2003

Z. Bacic, Y. Qiu, J. Blumberger, L. Oeltjen, M. Quack Faraday Disc. Chem. Soc. 118, 431 (2001). J. Blumberger, T.K. Ha, J. Paff, M. Quack, G. Seyfang, "Time resolved FTIR detection of IR-multiphoton initiated dissociation of formic acid dimer: Evidence for a dimer with a single strong hydrogen bond" in D. Bassi, P. Tosi, ed., SASP 2000, XII. Symposium on Atomic and Surface Physics and Related Topics, Folgaria, Trento, 2000, pages PR-11, 1-4.