Research projects

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Revisiting the approaches for isotope effects prediction in condensed phase

The objective of the project is to develop the best theoretical framework to predict thermal rate constants in condensed phase (e.g. in homogenous solution). KIEs on selected model reactions are 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) is used in the collaboration with dr. Faina Gelman from the Geological Survey of Israel.  It is combined with modern electronic structure calculations together with dynamical methods used to reliably describe and interpret the experimental findings. Thorough test of available computational methods and tools at different stages of generating necessary input data to calculate isotope effects is carried out.

Degradation of Nitroaromatics

Within the studies of environmental pollutants we work on isotopic fractionation of nitroaromatic compounds. These studies are carried out with a group at Eawag, Zurich which delivers experimental measurements of deuterium, carbon and nitrogen signatures which are predicted theoretically in our laboratory for the relevant chemical and enzyme-catalyzed processes.

Polish-Swiss Research Programme

CSI ITN project

Dehalogenations

Chlorine atoms present in a proportionally big amount in polychlorinated hydrocarbons are suspected to be a source of toxicity, carcinogenicity and other negative properties of these compounds. Taking into account the vast number of different sources of halogenated compounds, Nature has developed several mechanisms in order to reduce the levels of these toxic molecules. Many groups of enzymes are capable of degrading the halogenated compounds. For example, hydrolytic dehalogenases replace the halogen with a hydroxyl group, reductive dehalogenases replace the halogen with a hydrogen, and oxidative dehalogenases exchange the halogen for oxygen with concomitant substrate oxidation.

Our group has been exploring different aspects and faces of dehalogenation process since late 90s. The earlier studies comprise a number of hydrolytic dehalogenases and some model systems. The most important contributions have been collected and presented in the following publications: P. Paneth, Acc. Chem. Res. 2003; Y. Fang et al. Chem. Eur. J. 2003; A. Dybala-Defratyka et al., J. Org. Chem. 2004; P. Paneth in Isotope Effects in Chemistry and Biology, Chapter 35; A. Kohen, H.H. Limbach, Eds.; CRC Press, 2006. Most recently we have turned our attention to other mechanisms of halogen substituents removal.

Oxidative dehalogenation catalyzed by selected peroxidases

Two dehalogenating oxidoreductases and their activity toward chlorinated phenols are being explored with a use of experimentally and theoretically predicted chlorine kinetic isotope effects. The obtained results so far allowed us to make a working hypothesis that the peroxidase activity of the studied enzymes is mostly focused on a transformation of the toxic halogenated substrate into a cationic intermediate form which can easily expel a halogen substitutent to form a lesser toxic compound. For both HRP and DHP, the dehalogenation reaction takes place at an external site, and the QM/MM calculations suggest that the HRP- and DHP- catalyzed dehalogenation reactions happen in a very similar fashion as the same reaction in solution without the enzyme (MSHE, Poland).

Abiotic and biotic hydrolysis of s-triazines

s-Triazine anthropogenic compounds were introduced into the environment more than half century ago as dyes, resins and herbicides. Especially herbicides based on s-triazine ring have been used worldwide by direct application either to soils or plants. Their widespread presence and environmental accumulation leading to certain dysfunctions in vertebrate species or toxic conditions to other species present in the shared contaminated area have emerged many laboratory studies aiming at their biodegradation. In a collaboration with prof. Larry Wackett from University of Minnesota we are planning to provide a detailed description of transformation taking place in the polluted environment during herbicides biodegradation. The proposed investigation of TrzN and AtzA enzymes, their mutants and their catalytic activities with both terbutylazine and atrazine using an interdisciplinary approach should help us to elucidate underlying mechanism of reaction catalyzed by these enzymes and understand in depth transformation processes occurring at the contaminated sites (NCN, Poland 2011-2014).

Hexachlorocyclohexanes dehydrochlorination catalyzed by Lin enzymes

Within CSI-ITN project we attempt to theoretically predict isotopic fractionation on dehalogenation of HCH isomers catalyzed by LinA and LinB enzymes. Apart from providing detailed mechanistic insights we hope to explore whether chlorine isotope effects can be used as a mechanistic indicator for these systems and how the predicted values would fit to the existing data on chlorine fractionation accompanying elimination reaction.


Reductive dehalogenation of chloroethylenes

One of approaches used for removing chlorine substituents is reductive dehalogenation. Among metal-mediated reductive dehalogenation cobalt species have gathered special attention due to its wide presence in reductive dehalogenases - enzymes responsible for catalyzing degradation of chlorinated organic compounds during in situ biodegradation. Such systems contain cobalt complexes in a form of corrinoid-like molecule.

Due to their widespread use and top position among the most common groundwater contaminants worldwide chlorinated ethenes (CEs) such as tetrachloroethene (PCE) and trichloroethene (TCE) and the studies regarding their assessment and attenuation have received a great interest. Despite extensive efforts and numerous attempts directed to detailed description of possible degradation pathways of CEs a mechanism that would satisfactorily explain all experimental observations collected so far has not been proposed yet.

In order to shed some additional light onto this ongoing mechanistic debate theoretical investigation of carbon and chlorine isotope fractionation has been undertaken. Different operative pathways for reductive degradation of PCE in the presence of cobalt species have been explored with the use of quantum mechanical calculations (isoSoil).



Isotopic Food Authentification

Isotopic signature of materials can be employed in studies of their age, geographic origin, manufacturer etc. One of a very promising applications of isotopic analysis is food authentication. In collaboration with University of Nantes, France we are developing new methods of authentication of foodstuff and plan to extend it to drugs and pharmaceuticals. We have pending Polish patent application for isotopic authentication of coffee beans by carbon isotopic analysis.

Rational Drug Design

The emergence of multi-drug resistant strains is one of the most challenging problems of modern pharmacology that prompts interdisciplinary studies in quest for new antibiotics. We participate in such studies in collaboration with the Medical University of Lublin. Within these studies a few families of heterocyclic molecules are evaluated for their biological activity, and their physico-chemical properties evaluated experimentally and theoretically are used to guide future rational synthesis of effective antibacterials. Quantum-chemical calculations are used to find a reasonably robust and inexpensive theory level that allows SAR-like descriptors such as geometries, partial atomic charges, ionization potentials, electron affinities, HOMO, LUMO, HOMO-LUMO gaps, logP, hydration energy, refractivity, and polarizability to be calculated for large number of compounds. Furthermore, in order to understand interactions of the synthesized inhibitors with the active site of target enzymes (such as for example topoisomerase and HIV reverse transcriptase) docking, MD, and QM/MM calculations are carried out. We also try to employ isotope effects, and in particular binding isotope effects in these studies.



Theoretical Calculations of Isotope Effects


Isoeff, one of the most popular programs for recalculation of isotope effects from results of quantum-calculation has been developed in our laboratory. It can also be used for analysis of the influence of small changes in force constants on isotope effects. The original program has been described in
„ISOEFF98. A Program for Studies of Isotope Effects Using Hessian Modifications” V.Anisimov, P.Paneth J. Mathem. Chem. 26, 75-86 (1999)
and is distributed upon request to authors. It can also be used interactively at app.isosoil.eu

Isotopic fractionation data base


An exhaustive data base of isotopic fractionations has been compiled in our laboratory and is being constantly updated. Selected entries are available at app.isosoil.eu