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Matrix Isolation Studies of Structure and UV-Induced Transformations of Selected N-Heterocyclic Molecules

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Matrix Isolation Studies of Structure and UV-Induced Transformations of Selected N-Heterocyclic Molecules Institute of Physics Polish Academy of Sciences Matrix isolation studies of structure and UV-induced transformations of selected N-heterocyclic molecules Ganna Gerega Dissertation submitted to the Institute of Physics of the Polish Academy of Sciences in partial fulfillment of the requirements for the degree of Doctor in Physics Thesis adviser: Doc. dr hab. Maciej J. Nowak Warsaw 2008 Abstract The results of photochemical transformations occurring in isolated molecules exposed to the UV radiation are presented for the range of heterocyclic compounds. This work contains examples of unimolecular photochemical processes leading to the change of a structure of irradiated molecule. Several cases of phototautomeric oxo → hydroxy reaction were described and one example of formation of a new chemical compound, which formally is an isomer of the substrate molecule. Particular emphasis is placed on the estimation of tautomeric equilibrium for the studied compounds. The change of a relative amount of tautomers in a matrix after irradiation, allowed experimental determination of a ratio of tautomers frozen during formation of a matrix. These tautomeric ratios measured for the bicyclic compounds which consist of a benzene ring fused with the heterocyclic ring in different positions (2-quinoxalinone, 2-quinolinone, 1-isoquinoline, 4-quinazolinone) strongly suggest that direct attachment of the benzene ring at one of the double bonds in the structure of the parent compounds (2-pyridinone, 2-pyrazinone and 4-pyrimidinone) leads to a significant increase of stability of the oxo tautomers, with respect to the corresponding hydroxy forms. In this work, it was demonstrated that upon UV irradiation the reaction of intramolecular proton transfer occurred in all studied compounds (with except of 3-hydroxyisoquinoline). This photoreaction underwent in compounds with N-H and C=O groups in α-position attached to heterocyclic ring. The proton was transferred from nitrogen to oxygen atom. In the case of allopurinol, 9-methylhypoxanthine and hypoxanthine, along with oxo → hydroxy photoreaction, the accompanying process was observed leading to formation of open-ring species (conjugated ketenes). The studies of photochemical transformations of N-hydroxypyridine-2(1H)-thione described in the last part of this work allowed a conclusion that the product of the photoreaction is thioperoxy derivative of pyridine. The photochemical formation of this new compound – 2-hydroxysulfanyl-pyridine - occurred in the matrix environment. Isolation of a substrate molecule in a matrix cage prevented fast detachment of photochemically formed ·OH radical, and allowed formation of the product. In this work, the assignment of obtained IR spectra of almost all tautomeric forms of the studied compounds was carried out. This was performed as for tautomers initially present in low-temperature matrices, as for the spectra of photoproducts populated in the matrix upon UV irradiation. In this purpose, the experimental spectra were compared with the spectra simulated by DFT(B3LYP) quantum-mechanical calculations. The good agreement allowed assignment of experimentally observed absorption bands to the normal modes calculated for theoretically predicted spectra. Theoretical analysis of the normal modes was carried out for each compound. The forms of vibrations corresponding to absorption bands were described with calculated elements of PED (potential energy distribution) matrix. The results of theoretical calculations with QCISD method showed that this method predicts well not only the shifts of tautomeric equilibria for the studied compounds, but provides also reliable values for calculated energy differences (ΔE) between tautomers of a given compound. This was demonstrated by comparing theoretically and experimentally estimated values of ΔE. iii I would like to express my deepest respect and most sincere gratitude to my supervisor, doc. dr. hab. Maciej J. Nowak, to thank for valuable help in accomplishing this thesis as well as for all kinds of support provided during my studentship in Warsaw. I want to thank also my colleges from the research group: dr. hab. Leszek Łapiński and dr. Hanna Rostkowska for the science discussions and for valuable remarks and advice. My thanks and gratitude addressed to all my friends and colleagues who helped and supported me at the all stages of the realization of this project. Ganna Gerega v List of publication List of publications containing the results of the dissertation 1. A. Gerega, L. Lapinski, I. Reva, H. Rostkowska, and M. J. Nowak “UV induced generation of rare tautomers of allopurinol and 9-methylhypoxanthine – a matrix isolation FTIR study”, Biophysical Chemistry, 122 (2006) 123. 2. A. Gerega, L. Lapinski, M. J. Nowak and H. Rostkowska “UV-induced oxo → hydroxy unimolecular proton-transfer reactions in hypoxanthine”, Journal of Physical Chemistry A, 110 (2006) 10236. 3. A. Gerega, L. Lapinski, M. J. Nowak, A. Furmanchuk, and J. Leszczynski “Systematic Effect of Benzo-Annelation on Oxo-Hydroxy Tautomerism of Heterocyclic Compounds. Experimental Matrix-Isolation and Theoretical Study” Journal of Physical Chemistry A, 111 (2007) 4934. 4. L. Lapinski, A. Gerega, A.L. Sobolewski and M.J. Nowak „Thioperoxy derivative generated by UV-induced transformation of N-hydroxypyridine-2(1H)-thione isolated in low-temperature matrixes” Journal of Physical Chemistry A, 112 (2008) 238. vii Contents 1. Introduction…………………………………………………………………………………1 1.1. Biological importance of pyrimidines and purines……………………………………1 1.2. Biological function of the studied compounds………………………………….......... 4 1.3. The aim of the thesis………………………………………………………………......8 2. Matrix isolation and matrix-isolation photochemistry…………………………………...10 2.1. Matrix isolation……………………………………………………………………......10 2.2. Infrared spectroscopy and matrix isolation……………………………………………12 2.3. Tautomerism and phototautomerism……………………………………………......... 13 3. Experimental……………………………………………………………………………...... 18 3.1. Experimental setup…………………………………………………………………… 18 3.2. The studied compounds…………………………………………………………......... 22 4. Theoretical background…………………………………………………………………… 24 4.1. Ab initio methods of quantum chemistry…………………………………………...... 24 4.1.1. Møller-Plesset theory MP2……………………………………………………...25 4.1.2. Configuration interaction (CI), Quadratic configuration interaction with single and double excitation (QCISD) and Quadratic configuration interaction with single, double excitation and perturbative corrections for triple excitations QCISD(T)) ……………………………………………...... ………. 27 4.1.3. Density Functional Theory (DFT)………………………………………………29 4.2. Basis sets………………………………………………………………………………33 4.3. Potential Energy Distribution (PED)……………………………………………......... 36 4.4. Technical aspects……………………………………………………………………... 38 5. Results and discussion……………………………………………………………………... 41 5.1. Thermodynamic parameters of tautomeric interconversions………………………… 41 5.2. Systems with single heterocyclic ring………………………………………………... 45 5.3. Systems with fused heterocyclic and benzene rings………………………………......64 5.4. Systems with fused heterocyclic six- and five-membered rings……………………... 91 5.5. N-hydroxypyridine-2(1H)-thione…………………………………………………...... 121 5.6. Reversibility of the phototautomeric reaction………………………………………... 141 5.7. Aromaticity and tautomerism………………………………………………………… 144 6. Concluding discussion……………………………………………………………………... 146 References………………………………………………………………………………………153 Appendices……………………………………………………………………………………...160 ix biological importance of pyrimidines and purines 1 1. Introduction Investigation of isolated molecules is the first step in understanding of the properties of molecular systems. Recently much attention has been paid to experimental and theoretical studies [1-11] of isolated nucleic acid bases and their derivatives. The majority of these studies concerned determination of the structure of non-interacting molecules and photochemical effects occuring after exposure of this class of molecules to UV radiation. The low-temperature matrix isolation technique is one of the most effective methods used for such investigations. The current work presents new results in this area of research. Since it is known that exposure to solar light, among a number of biological effects, may cause mutations, the investigations of the photochemical transformations occurring in molecules present in DNA (or their derivatives) are of crucial importance. UV light generates DNA damage by several different mechanisms [12]. Most commonnly known damages are cyclobutane pyrimidine dimers and 6-4 lesions [13]. The photoprocesses occuring in single molecules which may affect biological material are still almost neglected in research. 1.1. Biological importance of pyrimidines and purines The nucleic acids play a central role in the storage and expression of genetic information. They are divided into two major classes: (i) deoxyribonucleic acids (DNAs) - their function is storage of information, and (ii) ribonucleic acids (RNAs) which are involved in most steps of gene expression and protein biosynthesis. DNA is a long polymer of simple units called nucleotides, with a backbone made of sugar and phosphate moieties joined by ester bounds. One of four types of molecules, called bases, is attached to each sugar. The sequence of these four bases along the backbone encodes genetic information. The bases that occur in nucleic acids are heterocyclic compounds - the derivatives of pyrimidine or purine. Pyrimidines consist of six-membered ring, purines have
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