Employee profile

Professor Tomasz Borowski

Employee since 2006

Head of the Group

Room: 239

Phone: +48 12 6395 218

E-mail: ncborows(at)cyf-kr.edu.pl

Research topics:

- Reaction mechanisms – theoretical studies
- Metalloenzymes with transition metal ions
- Reactions of dioxygen
- Protein crystallography


- Calculations of structure, energy and electronic properties with quantum chemistry (DFT) and hybrid (QM/MM) methods
- Molecular dynamics simulations with classical force fields
- Modelling enzyme-substrate complexes – molecular docking simulations
- Macromolecular crystallography


(2018) Professor of chemistry
(2009) Habilitated Doctor, Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Krakow
(2003) PhD Thesis, Jagiellonian University, Krakow
(1998) MSc Thesis, Jagiellonian University, Krakow

- 1998/1999 - 4-months TEMPUS fellowship, Italy, Bolonia University
- 2003-2006 - post-doc fellowship, Sweden, Stockholm University
- 2007 - 2-months DAAD fellowship, Germany, Free University in Berlin


  • Caleb R. Schlachter, Leily Daneshian, Jose Amaya, Vincent Klapper, Nicky Wybouw, Tomasz Borowski, Thomas Van Leeuwen, Vojislava Grbic, Miodrag Grbic, Thomas M. Makris, Maksymilian Chruszcz, "Structural and functional characterization of an intradiol ring-cleavage dioxygenase from the polyphagous spider mite herbivore Tetranychus urticae Koch", Insect Biochemistry and Molecular Biology, 107 (2019) 19-30
  • Roberta Aina, Pawel Dubiela, Sabine Geiselhart, Merima Bublin, Maurizio Bruschi, Christian Radauer, Christoph Nagl, Piotr Humeniuk, Riccardo Asero, Charlotte Gotthard Mortz, Christine Hafner, Karin Hoffmann-Sommergruber, Tomasz Borowski, "Distinct nsLTPs display different IgE-binding capacities which are affected by fatty acids binding", Allergy, European Journal of Allergy and Clinical Immunology, 74 (2019) 827-831
  • Pawel Dubiela, Rebecca del Conte, Francesca Cantini, Tomasz Borowski, Roberta Aina, Christian Radauer, Merima Bublin, Karin Hoffmann-Sommergruber, and Stefano Alessandri, "Impact of lipid binding on the tertiary structure and allergenic potential of Jug r 3, the non-specific lipid transfer protein from walnut", Scientific Reports, 9 (2019) 2007
  • Agnieszka Stańczak, Anna Miłaczewska, Tomasz Borowski, "Reaction mechanism between Cu(II)-enolate complex and O2 as a test case for methodology used in DFT computational studies", Journal of Molecular Modeling, 25 (2019) 122
  • A. Wójcik-Augustyn, A.J. Johansson, T. Borowski, "Mechanism of Sulfate Activation Catalyzed by ATP Sulfurylase - Magnesium Inhibits the Activity", Computational and Structural Biotechnology Journal, 17 (2019) 770-784
  • A. Miłaczewska, T. Borowski, "On the reaction mechanism of an endoperoxide ring formation by fumitremorgin B endoperoxidase. The right arrangement makes a difference", Dalton Transactions, (2019) 16211-16221
  • T. Borowski, M. Szaleniec, "Challenges in Modelling Metalloenzymes", Transition Metals in Coordination Environments. Challenges and Advances in Computational Chemistry and Physics, 29 (2019) 503-525


  • A.M. Miłaczewska, E. Kot, J.A. Amaya, T.M. Makris, M. Zając, J. Korecki, A. Chumakov, B. Trzewik, S. Kędracka-Krok, W. Minor, M. Chruszcz, T. Borowski, "On structure and reaction mechanism of human acireductone dioxygenase", CHEM-EUR J, (2018) 5225-5237
  • T. Hunter, R. Bonetta, A. Sacco, M. Vella, P-M. Sultana, C.H. Trinh, H.B.R. Fadia, T. Borowski. R. Garcia-Fandino, T. Stockner, G.J. Hunter, "A Single Mutation is Sufficient to Modify the Metal Selectivity and Specificity of a Eukaryotic Manganese Superoxide Dismutase to Encompass Iron", Chem Eur J, (2018) 5303-5308
  • A. Kluza, E. Niedzialkowska, K. Kurpiewska, Z. Wojdyla, M. Quesne, E. Kot, P.J. Porebski, T. Borowski, "Crystal structure of thebaine 6-O-demethylase from the morphine biosynthesis pathway", Journal of Structural Biology, (2018) 229-235
  • Z. Wojdyla, T. Borowski, "On how the binding cavity of AsqJ dioxygenase controls the desaturation reaction regioselectivity: a QM/MM study.", J Biol Inorg Chem, 23 (2018) 795-808
  • M. Szaleniec, A. M. Wojtkiewicz, R. Bernhardt, T. Borowski, M. Donova, "Bacterial steroid hydroxylases: enzyme classes, their functions and comparison of their catalytic mechanisms", Appl. Microbiol. Biotechnol., 102(19) (2018) 8153-8171
  • A. Timmins, M. Quesne, T. Borowski, S. de Visser, "Group transfer to an aliphatic bond: A biomimetic study inspired by nonheme iron halogenases.", ACS Catalysis, 8 (2018) 8685-8698


  • P. Dubiela, R. Aina, D. Polak, S. Geiselhart, P. Humeniuk, B. Bohle, S. Alessandri, R. Del Conte, F. Cantini, T. Borowski, M. Bublin, K. Hoffmann-Sommergruber, "Enhanced Pru p 3 IgE-binding activity by selective free fatty acid interaction", J Allergy Clin Immunol, (2017) 1728-1731


  • Matthew G. Quesne, Tomasz Borowski, Sam P. de Visser, "Quantum Mechanics/Molecular Mechanics Modeling of Enzymatic Processes: Caveats and Breakthroughs", Chemistry - A European Journal, 22 (2016) 2562 – 2581
  • A. Wójcik, M. Radoń, T. Borowski, "Mechanism of O2 Activation by alpha-Ketoglutarate Dependent Oxygenases Revisited. A Quantum Chemical Study", J Phys Chem A, 120 (2016) 1261-1274
  • Z. Wojdyła, T. Borowski, "DFT study of the mechanism of manganese quercetin 2,3-dioxygenase: quest for origins of enzyme unique nitroxygenase activity and regioselectivity", J. Biol. Inorg. Chem., 21 (2016) 475-489
  • S. Saraf, A. Miłaczewska, T. Borowski, C. James, D. Tierney, M. Popova, A. Arif, L. Berreau, "Anion Effects in Oxidative Aliphatic Carbon-carbon Bond Cleavage Reactions of Cu(II) Chlorodiketonate Complexes", Inorg. Chem., 55 (2016) 6916-6928
  • B. Trzewik, K. Chruszcz-Lipska, A. Miłaczewska, J. Opalińska-Piskorz, R. Karcz, R. Gryboś, M. Oszajca, K. Luberda-Durnaś, W. Łasocha, A. N. Fitch, B. Sulikowski and T. Borowski, "Synthesis and crystal structure of dimeric 1-hydroxyhexane-2,3-dione and spectral characteristics of a model acireductone", New J Chem, 40 (2016) 9291-9303


  • K. Hupert-Kocurek, D. Wojcieszyńska, U. Guzik, T. Borowski, "A single amino acid substitution within catalitically nonactive N-terminal domain of catechol 2,3-dioxygenase (C23O) increasees enzyme activity towards 4-chlorocatechol"", J. Mol. Cat. B. Enz., 122 (2015) 64-71
  • L.R. Offermann, M. Bublin, M.L. Perdue, S. Pfeifer, P. Dubiela, T. Borowski, M. Chruszcz, K. Hoffmann-Sommergruber, "Struture and functional characterization of the hazelnut allergen Cor a 8", J. Agric. Food Chem., 63 (2015) 9150-9158
  • T. Borowski, M. Quesne, M. Szaleniec, "QM and QM/MM methods compared: case studies on reaction mechanisms of metalloenzymes", Advances in Protein Chemistry and Structural Biology, 100 (2015) 187-224


  • M. Szaleniec, A. Dudzik, B. Kozik, T. Borowski, J. Heider, M. Witko,, "Mechanistic basis for the Enantioselectivity of the Anaerobic Hydroxylation of Alkylaromatic compounds by Ethylbenzene Dehydrogenase", J. Inorg. Biochem., 139 (2014) 9–20
  • C.J. Allpress, A. Miłaczewska, T. Borowski, J.R. Bennett, D.L. Tierney, A.M. Arif, L.M. Berreau, "Halide-promoted dioxygenolysis of a carbon-carbon bond by a copper(II) diketonate complex.", J. Am. Chem. Soc., 136 (2014) 7821-7824
  • Anna Wójcik, Ewa Broclawik, Per E.M. Siegbahn, Marcus Lundberg, Graham Moran,Tomasz Borowski, "The role of substrate positioning in the catalytic reaction of 4-hydroxyphenylpyruvate dioxygenase – a QM/MM study", J. Am. Chem. Soc., 136 (2014) 14472-14485
  • Tomasz Borowski, Ewa Broclawik, "Bioinorganic Reaction Mechanisms – Quantum Chemistry Approach", (Eds. A. Liwo), Springer-Verlag, Berlin, Heidelberg 2014, , 783–808, [978-3-642-28553-0]
  • Margareta R. A. Blomberg, Tomasz Borowski, Fahmi Himo, Rong-Zhen Liao, Per E. M. Siegbahn, "Quantum Chemical Studies of Mechanisms for Metalloenzymes", Chem. Rev., 114 (2014) 3601-3658


  • M. Lundberg, T. Borowski, "Oxoferryl species in mononuclear non-heme iron enzymes: Biosynthesis, properties and reactivity from a theoretical perspective.", Coordination Chemistry Reviews, 257 (2013) 277-289
  • A. Miłaczewska, E. Broclawik, T. Borowski, "On the catalytic mechanism of (S)-2-hydroxypropylphosphonic acid epoxidase (HppE). A Hybrid DFT Study.", Chemistry - A European Journal, 19 (2013) 771-781
  • A. Dudzik, B. Kozik, M. Tataruch, A. Wójcik, D. Knack, T. Borowski, J. Heider, M. Witko, M. Szaleniec, "The reaction mechanism of chiral hydroxylation of p-OH and p-NH2 substituted compounds by ethylbenzene dehydrogenase", Can. J. Chem., 91 (2013) 775-786


  • M. Szaleniec, A. Salwiński, T. Borowski, J. Heider, M. Witko, "Quantum chemical modeling studies of ethylbenzene dehydrogenase activity", Int. J. Quant. Chem., 112 (2012) 1990–1999
  • T. Borowski, A. Wójcik, A. Miłaczewska, V. Georgiev, M.R.A. Blomberg, P.E.M. Siegbahn, "The alkenyl migration mechanism catalyzed by extradiol dioxygenases: a hybrid DFT study.", Journal of Biological Inorganic Chemistry, 17 (2012) 881-890
  • A. Wójcik, E. Broclawik, P.E.M. Siegbahn, T. Borowski, "Mechanism of benzylic hydroxylation by 4-Hydroxymandelate synthase. A computational study.", Biochemistry, 51 (2012) 9570-9580


  • P.E.M. Siegbahn, T. Borowski, "Comparison of QM-only and QM/MM models for the mechanism of tyrosinase", Faraday Discuss., 148 (2011) 109-117
  • L.M. Berreau, T. Borowski, K. Grubel, C. Allpress, J.P. Wikstrom, M.E. Germain, E.V. Rybak-Akimova, D.L. Tierney, "Mechanistic Studies of the O2-dependent Aliphatic Carbon-carbon bond Cleavage Reaction of a Nickel Enolate Complex", Inorg. Chem., 50 (2011) 1047-1057
  • A. Wójcik, T. Borowski, E. Brocławik, "The mechanism of the reaction of intradiol dioxygenase with hydroperoxy probe. A DFT study", Cat. Today, (2011) 207-216
  • T. Borowski, P.E.M. Siegbahn , "Density Functional Theory Studies on Non-Heme Iron Enzymes", in "Iron-Containing Enzymes" (Eds. S.P. de Visser and D. Kumar), RCS Publishing, 2011, 88-118 [ISBN: 978-1-84973-181-2]


  • M. Szaleniec, T. Borowski, K. Schühle, M. Witko, J. Heider, "Ab inito modeling of ethylbenzene dehydrogenase reaction mechanism", J. Am. Chem. Soc., 132 (2010) 6014-6024
  • V. Georgiev, H. Noack, T. Borowski, M.R.A. Blomberg, P.E.M. Siegbahn, "DFT Study on the Catalytic Reactivity of a Functional Model Complex for Intradiol-Cleaving Dioxygenases", J. Phys. Chem. B, 114 (2010) 5878-5885
  • T. Borowski, H. Noack, M. Radoń, K. Zych, P.E.M. Siegbahn, "Mechanism of Selective Halogenation by SyrB2 - a Computational Study", J. Am. Chem. Soc., 132 (2010) 12887-12898
  • T. Borowski, V. Georgiev, P.E.M. Siegbahn, "On the observation of a gem diol intermediate after O-O bond cleavage by extradiol dioxygenases. A Hybrid DFT Study", J. Mol. Model., 16 (2010) 1673-1677


  • T.Borowski, M.R.A.Blomberg, P.E.M.Siegbahn "Reaction Mechanism of Apocarotenoid Oxygenase (ACO). A DFT Study", Chem. Eur. J., 14(2008) 2264-2276
  • V.Georgiev, T.Borowski, M.R.A.Blomberg, P.E.M.Siegbahn "A Comparison of the Reaction Mechanisms of Iron and Manganese-Containing 2,3-HPCD: an Important Spin Transition for Manganese", J. Biol. Inorg. Chem., 13(2008) 929-940


  • S. S. Ng, K. L. Kavanagh, M. A. McDonough, D. Butler, E. S. Pilka, B. M. Lienard, J. E. Bray, P. Savitsky, O. Gileadi, F. von Delft, N. R. Rose, J. Offer, J. C. Scheinost, T. Borowski, M. Sundstrom, C. J. Schofield, U. Oppermann "Crystal Structures of Histone Demethylase JMJD2A Reveal Basis for Substrate Specificity", Nature, 448 (2007) 87-91
  • T. Borowski, S. de Marothy, E. Broclawik, C.J. Schofield, P.E.M. Siegbahn, "Mechanism for Cyclization Reaction by Clavaminic Acid Synthase. Insights from Modeling Studies", Biochemistry, 46 (2007) 3682-3691


  • A. Bassan, T. Borowski, C. J. Schofield, P. E. M. Siegbahn "Ethylene Biosynthesis by 1-Aminocyclopropane-1-Carboxylic Acid Oxidase: A DFT Study", Chem. - Eur. J., 12 (2006) 8835-8846
  • T. Borowski, A. Bassan, P. E. M. Siegbahn "DFT Study of the Uncatalyzed Dioxygenation of Acireductone", J. Mol. Struct. Theochem., 772 (2006) 89-92
  • T. Borowski, E. Brocławik, C. J. Schofield, P. E. M. Siegbahn "Epimerization and Desaturation by Carbapenem Synthase (CarC). A Hybrid DFT Study", J. Comput. Chem., 27 (2006) 740-748
  • T. Borowski, P. E. M. Siegbahn "Mechanism for Catechol Ring-Cleavage by Non-Heme Iron Intradiol Dioxygenases. A Hybrid DFT Study", J. Am. Chem. Soc., 128 (2006) 12941-12953
  • V. Georgiev, T. Borowski, P. E. M. Siegbahn "Theoretical Study of the Catalytic Reaction Mechanism of MndD", J. Biol. Inorg. Chem., 11 (2006) 571-585
  • A. Bassan, M.R.A. Blomberg, T. Borowski, P.E.M. Siegbahn, "Theoretical Studies of Enzyme Mechanisms Involving High-Valent Iron Intermediates", J. Inorg. Bioch., 100 (2006) 727-743
  • P. E. M. Siegbahn, T. Borowski "Modeling Enzymatic Reactions Involving Transition Metals", Account Chem. Res., 39 (2006) 729-738
  • A. Bassan, T. Borowski, M. Lundberg, P.E.M. Siegbahn, "Theoretical Modeling of Redox Processes in Enzymes and Biomimetic Systems", Concepts and Model Systems in Bioinorganic Chemistry, (2006)


  • T. Borowski, V. Georgiev, P.E.M. Siegbahn, "Catalytic Reaction Mechanism of Homogentisate Dioxygenase. A Hybrid DFT Study", J. Am. Chem. Soc., 127 (2005) 17303-17314
  • T. Borowski, A. Bassan, N.G.J. Richards, P.E.M. Siegbahn, "Catalytic Reaction Mechanism of Oxalate Oxidase (Germin). A Hybrid DFT Study", J. Chem. Theory Comput, 1 (2005) 686-693


  • T.Borowski, W.Szczepanik, M.Chruszcz, E.Brocławik "First Principle Calculations for the Active Centres in Vanadium-Containing Chloroperoxidase and its Functional Models: Geometrical and Spectral Properties", Int. J. Quantum Chem., 99 (2004) 864-875
  • A. Bassan, T. Borowski, P.E.M. Siegbahn, "Quantum Chemical Studies of Dioxygen Activation by Mononuclear Non-Heme Iron Enzymes with the 2-His-1-carboxylate Facial Triad", Dalton T., 20 (2004) 3153-3162
  • A. Bassan, M.R.A. Blomberg, T. Borowski, P.E.M. Siegbahn, "Oxygen Activation by Rieske Non-Heme Iron Oxygenases, a Theoretical Insight", J. Phys. Chem. B, 108 (2004) 13031-13041
  • T. Borowski, A. Bassan, P.E.M. Siegbahn, "4-Hydroxyphenylpyruvate Dioxygenase: A Hybrid Density Functional Study of the Catalytic Reaction Mechanism", Biochemistry, 43 (2004) 12331-12342
  • T. Borowski, A. Bassan, P.E.M. Siegbahn, "A Hybrid Density Functional Study of O-O Bond Cleavage and Phenyl Ring Hydroxylation for a Biomimetic Non-Heme Iron Complex", Inorg. Chem., 43 (2004) 3277-3291
  • T. Borowski, A. Bassan, P.E.M. Siegbahn, "Mechanism of Dioxygen Activation in 2-Oxoglutarate-Dependent Enzymes: A Hybrid DFT Study", Chem. Eur. J., 10 (2004) 1031-1041
  • M. Król, T. Borowski, I. Roterman, B. Piekarska, B. Stopa, J. Rybarska, L. Konieczny, "Force-field Parametrization and Molecular Dynamics Simulations of Congo Red", J. Comput. Aid. Mol. Des., 18 (2004) 41-53


  • T. Borowski, E. Brocławik "Catalytic Reaction Mechanism of Lipoxygenase. A Density Functional Theory Study", J. Phys. Chem. B, 107 (2003) 4639-4646