Revisiting the approaches for isotope effects prediction in condensed phase
Research project objectives
The objective of the proposed project is to develop the best theoretical framework to predict thermal rate constants in the condensed phase (e.g. in homogenous solution). In particular, it is focused on the calculations of kinetic isotope effects (KIEs), which being ratios of rate constants arisen from isotopic substitution at a particular position in molecules (for instance 12C versus 13C or 1H versus 2H) have already turned out to be one of the most powerful experimental techniques for probing the nature of transition states. Detailed information on the transition state is obligatory for the elucidation of a reaction mechanism. And as such, can only be provided when measurements are accompanied by theoretical predictions.
Research methodology
KIEs on selected model reactions will be measured and calculated. For precise heavy-atom isotope analysis (carbon, chlorine, and bromine), a recently developed method based on gas chromatography – isotope ratio mass spectrometry (GC-IRMS) will be used. It will be combined with modern electronic structure calculations together with dynamical methods used to reliably describe and interpret the experimental findings. A thorough test of available computational methods and tools at different stages of generating necessary input data to calculate isotope effects will be carried out.
Team:
PI: Agnieszka Dybala-Defratyka
Senior Co-Investigators: Faina Gelman (Israel), Michał Rostkowski, Paweł Adamczyk, Agata Sowińska
Junior Co-Invesitgators: Luis Vasquez, Suraj Kannath, Yevgeni Zakon (Israel)
Students: Szymon Żaczek, Martyna Czapnik
Publications:
- M. Rostkowski, H. Schurner, A. Sowińska, L. Vasquez, M. Przydacz, M. Elsner, A. Dybala-Defratyka, Isotope Effects on the Vaporization of Organic Compounds from an Aqueous Solution – Insight from Experiment and Computations, J. Phys. Chem. B, 125 (2021) 13868, DOI: 10.1021/acs.jpcb.1c05574
- P. Paneth and A. Dybala-Defratyka, Isotope Effects as Analytical Probes: Applications of Computational Theory in Theoretical and Computational Chemistry Series No. 20, Computational Techniques for Analytical Chemistry and Bioanalysis, Eds: P. B. Wilson and M. Grootveld, Royal Society of Chemistry 2021, DOI: 10.1039/9781788015882
- K. Klajman, A. Dybala-Defratyka, P. Paneth, Computational investigations of position-specific vapor pressure isotope effects in ethanol toward more powerful isotope models for food forensics, ACS Omega 5 (2020) 18499, DOI: 10.1021/acsomega.0c02446
- C. Lihl, B. Heckel, A. Grzybkowska, A. Dybala-Defratyka, V. Ponsin, C. Torrento, D. Hunkeler, and M. Elsner, Compound-Specific Chlorine Isotope Fractionation in Biodegradation of Atrazine, Environ. Sci.: Processes Impacts, 22 (2020) 792, DOI: 10.1039/C9EM00503J
- S. Kannath, P. Adamczyk, D. Ferro-Costas, D.T. Major, A. Fernandez-Ramos, A. Dybala-Defratyka, The 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. 2020, DOI: 10.1021/acs.jctc.9b00774
- F. Gelman and A. Dybala-Defratyka, Bromine Isotope Effects: Predictions and Measurements, Chemosphere, 246 (2020) 125746, DOI: 10.1016/j.chemosphere.2019.125746
- S. Kannath, P. Adamczyk, L. Wu, H.H. Richnow, A. Dybala-Defratyka, Can Alkaline Hydrolysis of γ-HCH Serve as a Model Reaction to Study Its Aerobic Enzymatic Dehydrochlorination by LinA?, Int. J. Mol. Sci. 20 (2019) 5955, DOI: 10.3390/ijms20235955
- 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
- 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
- S. Zaczek, F. Gelman, A. Dybala-Defratyka, A Benchmark Study of Kinetic Isotope Effects and Barrier Heights for the Finkelstein Reaction, J. Phys. Chem. A 121 (2017) 2311, DOI: 10.1021/acs.jpca.7b00230
- 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
Presentations:
2019:
Name of Conference/Meeting/Workshop: 3rd Workshop on current and future applications of CSIA in chemical and biological processes
Place: Helmholtz Centre for Environmental Research – UFZ, Leipzig, Germany
Date: November 11
Form of presentation: Keynote lecture
Title of presentation: When Measurements and Predictions of Isotope Effects Combine – A Word From A Computational Chemist
Names of all coauthors: A. Dybala-Defratyka
Name of Conference/Meeting/Workshop: 10th Triennial Congress of the International Society for Theoretical Chemical Physics
Place: Tromso, Norway
Date:July 11-17
Form of presentation: Poster
Title of presentation: EFFECT OF SOLVATION ON KINETIC ISOTOPE EFFECTS ON HYDROGEN ABSTRACTION FROM ETHANOL IN AQUEOUS SOLUTION
Names of all coauthors: Suraj Kannath, Pawel Adamczyk, David Ferro-Costas, Antonio Fernandez-Ramos, Agnieszka Dybala-Defratyka
Name of Conference/Meeting/Workshop: Isotopes 2019
Place: Raimeslash, Germany
Date:July 7-11
Form of presentation: Contributed Oral Presentation
Title of presentation: VAPOR PRESSURE ISOTOPE EFFECTS ON EVAPORATION FROM PURE ORGANIC AND AQUEOUS PHASES – A THEORETICAL STUDY
Names of all coauthors: Luis Vasquez, Michal Rostkowski, Agnieszka Dybala-Defratyka
Name of Conference/Meeting/Workshop: XIX International Workshop on Quantum Atomic and Molecular Tunneling Systems
Place: Borovets, Bulgaria
Date: June 17-21
Form of presentation: Invited Talk
Title of presentation: Effect of solvation on kinetic isotope effects on Hydrogen abstraction from ethanol in aqueous solution
Names of all coauthors: Suraj Kannath, Pawel Adamczyk, David Ferro-Costas, Antonio Fernandez-Ramos, Agnieszka Dybala-Defratyka
Name of Conference/Meeting/Workshop: scientific visit at the Geology Survey of Israel and the Hebrew University
Place: Jerusalem, Israel
Date: June 4-7
Form of presentation: Talk
Title of presentation: Isotope Effects as Analytical Probes – A Computational Perspective
Names of all coauthors: Agnieszka Dybala-Defratyka
Name of Conference/Meeting/Workshop: Annual 3rd Year PhD Students of the Faculty of Chemistry, TUL Seminar
Place: Łódź, Poland
Date: January
Form of presentation: Talk
Title of presentation: EFFECT OF SOLVATION ON HYDROGEN KINETIC ISOTOPE EFFECTS ON Hydrogen abstraction from ethanol IN aqueous SOLUTION
Names of all coauthors: Suraj Kannath
Title of presentation: REACHING THE LIMITS OF VAPOUR PRESSURE ISOTOPE EFFECT CALCULATION BY PATH INTEGRAL PRINCIPLE
Names of all coauthors: Luis Vasquez
2018:
1. Name of Conference/Meeting/Workshop: 9th PULS Conference on Pulse Investigations in Chemistry, Physics, and Biology & 4th RKCM Conference on Reaction Kinetics in Condensed Matter
Place: Łódź, Poland
Date: September
Form of presentation: Poster
Title of presentation: Hydrogen atom abstraction from ethanol by atomic hydrogen in an aqueous solution
Names of all coauthors: Pawel Adamczyk, Suraj Kannath, Agnieszka Dybala-Defratyka
2. Name of Conference/Meeting/Workshop: 54th Symposium on Theoretical Chemistry
Place: Germany
Date: September
Form of presentation: Poster
Title of presentation: Isotope effects by the infinite improbability drive
Names of all coauthors: Luis Vasquez, Agnieszka Dybala-Defratyka
3. Name of Conference/Meeting/Workshop: 4th ORCA User Meeting
Place: Germany
Date: September
Form of presentation: Poster
Title of presentation: Isotope effects by the infinite improbability drive
Names of all coauthors: Luis Vasquez, Agnieszka Dybala-Defratyka
4. Name of Conference/Meeting/Workshop: Path Integral Quantum Mechanics: From the Basics to the Latest Developments (School)
Place: Lausanne, Switzerland
Date: June 25-29
Form of presentation: Poster and Flash-talk
Title of presentation: Path-integral approach to hydrogen atom abstraction from ethanol by atomic hydrogen in aqueous solution.
Names of all coauthors:Suraj Kannath, Pawel Adamczyk and Agnieszka Dybala-Defratyka
2017:
1. Name of Conference/Meeting/Workshop: 11th Triennial Congress of the World Association of Theoretical and Computational Chemists (WATOC-2017)
Place: Munich, Germany
Date: August 27-September 1
Form of presentation: Poster and Flash Talk
Title of presentation: Hydrogen atom abstraction from ethanol by atomic hydrogen in aqueous solution.
Names of all coauthors:Suraj Kannath, Pawel Adamczyk, Antonio Fernandez-Ramos and Agnieszka Dybala-Defratyka
2. Name of Conference/Meeting/Workshop: Workshop on understanding quantum phenomena with path integrals : From chemical systems to quantum fluids and solids
Place: ICTP, Trieste, Italy
Date: July 3-7
Form of presentation: Poster and Flash-talk
Title of presentation: Hydrogen atom abstraction from ethanol by atomic hydrogen in aqueous solution.
Names of all coauthors: Suraj Kannath, Pawel Adamczyk, Antonio Fernandez-Ramos and Agnieszka Dybala-Defratyka
3. Name of Conference/Meeting/Workshop: 5 Workshop on Understanding Quantum Phenomena with Path Integrals: From Chemical Systems to Quantum fluids and Solids
Place: Italy
Date: June
Form of presentation: Poster
Title of presentation: The beauty of PIMD
Names of all coauthors: Luis Vasquez, Agnieszka Dybala-Defratyka
2016:
1. Name of Conference/Meeting/Workshop: Gordon Research Conference: Computational Chemistry
Place: Girona, Spain
Date: July 24-29
Form of presentation: Poster
Title of presentation: Influence of solvent treatment on calculations of equilibrium properties of solvated organic compounds, Michał Rostkowski, Agnieszka Dybala-Defratyka
Title of presentation: Effect of Solvent on Elimination Reaction Revisited, Rabindra Nath Manna, Anna Grzybkowska, Faina Gelman, and Agnieszka Dybala-Defratyka
2. Name of Conference/Meeting/Workshop: Current Trends in Theoretical Chemistry VI
Place: Krakow, Poland
Date: September 4-8
Form of presentation: Poster
Title of presentation: Hydrogen atom abstraction from ethanol by atomic hydrogen in aqueous solution.
Names of all coauthors: Suraj Kannath, Pawel Adamczyk, Antonio Fernandez-Ramos, and Agnieszka Dybala-Defratyka
Scientific visits:
2018:
Dan. T. Major, Department of Chemistry, Bar-Ilan University, Ramat-Gan, Israel
Seminar 1: Multiscale Modeling: From Enzymes to Renewable Energy
Seminar 2: Classical and Quantum Multiscale Simulations – Approaches
2016:
Antonio Fernandez-Ramos, Department of Physical Chemistry and CIQUS, Universidade de Santiago de Compostela, Spain
Seminar: Practical theoretical methods to study hydrogen transfer reactions in polyatomic systems
Faina Gelman, Geological Survey of Israel
Collaborators:
Antonio Fernandez-Ramos, Department of Physical Chemistry and CIQUS, Universidade de Santiago de Compostela, Spain
Iñaki Tuñón, Departamento de Química Fisica, Universidad de Valencia, Spain