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Właściwości wewnątrzcząsteczkowych wiązań wodorowych w wybranych N-tlenkach pochodnych chinoliny

Jezierska Aneta, Panek Jarosław J., Błaziak Kacper

Wiadomości Chemiczne

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2019

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[Z] 73, 1-2

75--95

EN

In the current article we would like to summarize our research shedding light onto properties of intramolecular hydrogen bonds present in N-oxide quinoline derivatives. The compounds for the current study were chosen to contain diverse types of hydrogen bonds. Therefore, in the current study we analyze three kinds of hydrogen bonding and their properties. It is well known, that the presence of intramolecular hydrogen bonds stabilizes conformations of molecules. Substituent effects (inductive and steric) influence the strength of the H-bonding as well as its features. Moreover, the intramolecular hydrogen bond in the studied N-oxides belongs to the family of resonance assisted hydrogen bonds (RAHB). Our short overview presents the summary of results obtained for twelve N-oxides of quinoline derivatives. Quantum-chemical simulations were performed on the basis of static models (classical DFT and MP2 approaches) as well as ab initio molecular dynamics (Car-Parrinello MD). The metadynamics method was applied to reproduce the maps of free energy for the motion of the bridged proton. The computations were performed in the gas and in the crystalline phases. Electronic ground state is a natural framework in which chemical compounds exist most of the time. However, in many chemical species we observe a spontaneous internal reorganization of their chemical bonds and atoms e.g. proton transfer phenomenon and the appearance of tautomeric forms already in the ground state. Therefore, it was interesting to investigate some N-oxides in the excited electron state knowing that they exhibit excited- state-induced proton transfer (ESIPT effect). At the end of the article we draw some conclusions related to the intramolecular H-bond properties present in the discussed N-oxides of quinoline derivatives.

2

Numerical methods in understanding reaction pathways NOx oxidation

Jaroszyńska-Wolińska J., Malinowski S.

Budownictwo i Architektura

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2016

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Vol. 15, nr 3

75--81

EN

Different quantum chemical models were applied in energetic analysis of the process of oxidation of NO and NO2 through reaction with ozone generated by non-thermal equilibrium (low temperature), atmospheric pressure plasma. The potential energy surfaces of systems comprising NO and NO2 with ozone were characterized. The NOx oxidation processes well known, at the molecular level, were modelled by ab initio quantum chemistry methods to calculate the total reaction energy, Et, of each step in the reaction chain. Quantum chemistry was further applied in an attempt to detect the presence of any transition states and to calculate the activation energy, Ea, of reactions (1) NO + O3 and (2) NO2 + O3 using the MP2 level of theory with three different basis sets and fine potential energy scan resolution.

3

Diazene, a Potential New Hydrogen Bond Donor and Acceptor with Blue-Shifted N-H Stretching Modes: A Theoretical Study

Karpfen A., Liedl E., Wolschann P.

Polish Journal of Chemistry

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2009

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Vol. 83, nr 5

933-942

EN

The structure and vibrational spectra of hydrogen-bonded complexes formed between trans-HNNH (diazene or diimide) and the fluoromethanes CH3F, CH2F2, and CHF3 are stud ied at the MP2/6-311++G(2d,2p) level. For each fluoromethane, complex structures were detected in which diazene plays either the role of a hydrogen bond do nor or a hydrogen bond acceptor. In addition to the well-known blue shifts of the fluoromethane C–H stretch ing frequencies, blue-shifted N–H stretching frequencies are predicted for the diazene molecule, irrespective of whether HNNH acts as do nor or acceptor. It is shown that this finding can be interpreted as a consequence of the negative intramolecular coupling (NIC) between N–N and N–H stretching degrees of free domin the isolated HNNH molecule which, upon complex formation, leads to a negative intramolecular response (NIR)

4

A Theoretical Study of the cis-syn Cytosine-containing Pyrimidine Dimers in the Gase Phase and a Water Cluster and a Tautomer-Bypass Mechanism for the Origin of UV-induced Mutations

Danilov V., Leś A., Alderfer J. L.

Polish Journal of Chemistry

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2001

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Vol. 75, nr 7

1039-1049

EN

A quantum mechanical study of cis-syn cyclobutane cytosine-containing photodimers including the normal and rare tautomeric forms of bases has been performed using the ab initio method at HF/6-31G(d,p), MP2(fc)//HF/6-31G(d,p) and MP2(fc)/6-31G(d,p) levels. It is predicted that in the gas phase all photodimers containing the rare imino form of cytosine are more stable than those containing its normal form. The Monte Carlo study of the hydration for cytosine-consisting dimers showed that the dimer containing the imino form of cytosine is stabilized by water cluster more than that containing its amino forms. As a result, the imino form of cytosine in the cytosine-containing dimer directs the incorporation of adenine in the complementary strand during replicative bypass. Data obtained point to the cytosine tautomerism as a possible mechanism for the origin of UV-induced mutation.

5

H-bridges gas phase clusters of methanol (dimers to hexamers): ab initio calculations of their structure and vibrational spectra

Sauer J., Bleiber A.

Polish Journal of Chemistry

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1998

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Vol. 72, nr 7S

1524-1539

EN

Hartree-Fock calculations using a polarized basis set are performed on methanol clusters of two to six molecules. Electron is included by second order Moller-Plesset perturbation theory for the trimer and structure of the hexamer only. Starting from trimers, among several optimized structure the cyclic ones are found most stable. Harmonic vibrational frequencies and infrared intensities are calculated and comparison is made with observed spectra in the CO and OH stretch region.