Agnieszka Dybala-Defratyka

email: agnieszka.dybala-defratyka(at)p.lodz.pl
phone: +48 42 631 3198
office: Room 125, Faculty of Chemistry,
Zeromskiego 116

Research Interests:

  • theoretical modeling of reactions mechanisms
  • dehalogenation reactions
  • theory of isotope effects
  • application of isotope effects to studies of mechanisms of biochemical reactions and their chemical models

Education:

2014 D. Sc. (habilitation): Chemistry, Faculty of Chemistry, Lodz University of Technology, Poland: Dehalogenation: from model reactions to real environmental systems

2003 Ph. D.: Chemistry, Department of Chemistry, Technical University of Lodz, Poland Hydrogen kinetic isotope effects in reaction catalyzed by methylmalonyl-CoA mutase; supervisor: prof. P. Paneth

Professional Experience:

2016-present Associate Professor, Lodz University of Technology, Faculty of Chemistry, Poland

2011-2012 Visiting Scholar, University of Minnesota, Department of Chemistry, Minneapolis, MN, USA (Fulbright Senior Advanced Research Grant), host: prof. Christopher J. Cramer

2011-2019 Vice-director of the Institute of Applied Radiation Chemistry

2009-2016 Assistant Professor, Lodz University of Technology, Faculty of Chemistry, Poland

2003-2009 Chemist, Technical University of Lodz, Department of Chemistry, Poland

2008-2009 Publishing Manager, Versita

2003-2008 Managing Editor, Central European Journal of Chemistry, Versita

2002 Visiting Collaboratoe, University of Minnesota, Department of Chemistry, Minneapolis, MN, USA, host: prof. Donald G. Truhlar

2000 Universitat Jaume I, Castellon, Spain (short-term training), host: prof. Vicente Moliner

1998-1999 Visiting Research Associate, University of Nebraska-Lincoln, Department of Biochemistry, Lincoln, NE, USA, host: prof. Ruma Banerjee

Research grants/fellowships:

  • National Science Center (NCN) Poland, SONATA-BIS (2015-2020), Revisiting the approaches for isotope effects prediction in condensed phase, Principal Investigator
  • COST TN1301: Next Generation of Young Scientist: towards a contemporary spirit of R&I, Sci-Generation (2013-2017), Representant for Poland, member of the MC
  • Fulbright Senior Advanced Research Grant (2011-2012), University of Minnesota, Department of Chemistry, Minneapolis, MN, USA, A theoretical model for chlorination process of organic compounds as a probe for tackling transformations important to human health and life at the molecular level
  • FP7-ITN, CSI: Environment (2010-2015), Theoretical modeling of environmentally important biotic and abiotic dehalogenation processes. In particular modelling of dehalogenations catalyzed by LinA, Project Responsible, PhD programme 10
  • FP7 THEME 6 Environment, isoSoil (2009-2012), http://isosoil.eu/, Contaminant-specific isotope analyses as sharp environmental-forensics tools for site characterization, monitoring and source apportionment of pollutants in soil, Participant
  • State Committee for Scientific Research, Poland 3 T09B 007 29 (2005-2009), Study on enzymatic degradation of halogenated phenols with the use of chlorine isotope effects and molecular modeling, Principal Investigator

Selected publications:

  1. S. Kannath, P. Adamczyk, D. Ferro-Costas, D.T. Major, A. Fernandez-Ramos, A. Dybala-Defratyka, Role of Microsolvation and Quantum Effects in the Accurate Prediction of Kinetic Isotope Effects: the Case of Hydrogen Atom Abstraction in Ethanol by Atomic Hydrogen in Aqueous Solution, J. Chem. Theory Comput. 16 (2020) 847, DOI: 10.1021/acs.jctc.9b00774
  2. F. Gelman and A. Dybala-Defratyka, Bromine Isotope Effects: Predictions and Measurements, Chemosphere, 246 (2020) 125746, DOI: 10.1016/j.chemosphere.2019.125746
  3. S. Żaczek, J. Kowalska, A. Dybala-Defratyka, Ligand-Driven Conformational Dynamics Influences Selectvity of UbiX, ChemBioChem, 2018, DOI: 10.1002/cbic.201800389
  4. L. Vasquez, M. Rostkowski, F. Gelman, A. Dybala-Defratyka, Can PIMD Make a Good Approximation for Vapor Pressure Isotope Effects Prediction for Organic Solvents? A Comparison to ONIOM QM/MM and QM Cluster Calculation, J. Phys. Chem. B, 122 (2018) 7353, DOI: 10.1021/acs.jpcb.8b03444
  5. R.N. Manna, A. Grzybkowska, F. Gelman, A. Dybala-Defratyka, Carbon-bromine bond cleavage – A perspective from bromine and carbon kinetic isotope effects on model debromination reactions, Chemosphere 193 (2018) 17-23, DOI: 10.1016/j.chemosphere.2017.10.153
  6. A. Grzybkowska, D.J. Jedrzejczyk, M. Rostkowski, A. Chworos, A. Dybala-Defratyka, RNA Model Evaluation Based on MD Simulation of Four tRNA Analogs, RSC Adv. 6 (2016) 101788, DOI: 10.1039/C6RA14933B
  7. L. Simon-Carballido, T. Vinicius Alves, A. Dybala-Defratyka, and A. Fernandez-Ramos, Kinetic Isotope Effects in Multipath VTST. Application to a Hydrogen Abstraction Reaction, J. Phys. Chem. B, 120 (2016) 1911, DOI: 10.1021/acs.jpcb.5b09671
  8. R.N. Manna, K. Zinovjev, I. Tunon, and A. Dybala-Defratyka, Dehydrochlorination of Hexachlorocyclohexanes Catalyzed by the LinA Dehydrohalogenase. A QM/MM Study, J. Phys. Chem. B, 119 (2015) 15100, DOI: 10.1021/acs.jpcb.5b07538
  9. H.K.V. Schürner, J.L. Seffernick, A. Grzybkowska, A. Dybala-Defratyka, L.P. Wackett, and M. Elsner, Characteristic Isotope Fractionation Patterns in s Triazine Degradation Have Their Origin in Multiple Protonation Options in the s Triazine Hydrolase TrzN, Environ. Sci. Technol., 49 (2015) 3490, DOI: 10.1021/es5055385
  10. R.N. Manna and A. Dybala-Defratyka, A computational study of the dechlorination of β-hexachlorocyclohexane (β-HCH) catalyzed by the haloalkane dehalogenase LinB, Arch. Biochem. Biophys. 562 (2014) 43, DOI: 10.1016/j.abb.2014.07.028
  11. A.H. Meyer, A. Dybala-Defratyka, P.J. Alaimo, I. Geronimo, A.D. Sanchez, C.J. Cramer and M. Elsner, Cytochrome P450-Catalyzed Dealkylation of Atrazine by Rhodococcus sp. strain NI86/21 Involves Hydrogen Atom Transfer rather than Single Electron Transfer, Dalton Trans., 43 (2014) 12175 DOI: 10.1039/C4DT00891J
  12. L. Szatkowski, A. Dybala-Defratyka, C. Batarseh, J. Blum, L. Halicz and F. Gelman, Bromine kinetic isotope effects: insight into Grignard reagent formation, New J. Chem., 37 (2013) 2241
  13. L. Szatkowski, M.K. Thompson, R. Kaminski, S. Franzen, A. Dybala-Defratyka, Oxidative dechlorination of halogenated phenols catalyzed by two distinct enzymes: horseradish peroxidase and dehaloperoxidase, Arch. Biochem. Biophys. 505 (2011) 22, DOI: 10.1016/j.abb.2010.09.018
  14. A. Dybala-Defratyka, L. Szatkowski, R. Kaminski, M. Wujec, A. Siwek, P. Paneth, Kinetic Isotope Effects on Dehalogenations at an Aromatic Carbon, Environ. Sci. Technol. 42 (2008) 7744
  15. A. Dybala-Defratyka, P. Paneth, R. Banerjee, D.G. Truhlar, Coupling of Hydrogenic Tunneling to Active-Site Motion in the Hydrogen Radical Transfer Catalyzed by a Coenzyme B12-Dependent Mutase, Proc. Natl. Acad. Sci. U.S.A.104 (2007) 10774
  16. A. Dybala-Defratyka, M. Rostkowski, O. Matsson, K.C. Westaway, P. Paneth, A New Interpretation of Chlorine Leaving Group Kinetic Isotope Effects; A Theoretical Approach, J. Org. Chem. 69 (2004) 4900