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Witaminy z grupy B : opis właściwości fizykochemicznych oraz bioaktywności z wykorzystaniem przykładowych narzędzi cheminformatycznych

Banach Sylwia, Jezierska Aneta

Wiadomości Chemiczne

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2023

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[Z] 77, 9-10

873--896

EN

This paper presents a literature review of the biochemistry of vitamins B and the results of in silico physicochemical properties and bioactivity studies. The description was performed by cheminformatics tools closely related to the field of Medicinal Chemistry. It allows us to predict a great number of properties e.g. logP, TPSA, molecular volume or bioactivity associated with the chosen proteins (like kinases, proteases etc.). These investigations were carried out with the use of cheminformatics web tool Molinspiration. Its great advantages are mainly its wide availability, ease of application and quick analysis of small compounds. Thanks to the comparison with literature data of well–known B vitamins, it is possible to confirm that current cheminformatic web tools provide high reliability of the results and can support Drug Design methods.

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Właściwości kwasu salicylowego i jego wybranych pochodnych w świetle metod modelowania molekularnego

Kaczmarek Anna, Kizior Beata, Zierkiewicz Wiktor, Jezierska Aneta

Chemik

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2023

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Nr 1-4

66--70

PL

Salicylany są stosowane od wieków jako leki na różne dolegliwości. Wiele związków z tej grupy powstało w wyniku modyfikacji kwasu salicylowego, np. kwasu acetylosalicylowego (popularnego leku aspiryny) czy salicylanu fenylu (Salolu). Interesującym związkiem jest również kwas salicylurowy, będący głównym metabolitem salicylanów. Dla wspomnianych cząsteczek wykonano symulacje kwantowo-chemiczne w oparciu o Teorię Funkcjonału Gęstości (DFT) w fazie gazowej, a także w obecności rozpuszczalnika. Wpływ wewnątrzcząsteczkowego wiązania wodorowego, obecnego w kwasie salicylowym i salicylanie fenylu, na właściwości cząsteczek został również uwzględniony w badaniach. Analizę topologiczną i struktury elektronowej badanych cząsteczek wykonano według Kwantowej Teorii Atomów w Cząsteczkach (QTAIM) oraz Indeksu Oddziaływań Niekowalencyjnych (NCI).

EN

Salicylates have been used for centuries as medicine for various ailments. Many compounds of this group were obtained as a result of modification of salicylic acid, such as acetylsalicylic acid (a popular aspirin drug) and phenyl salicylate (Salol). Salicyluric acid, which is the main metabolite of salicylates, is also an interesting compound. Quantum-chemical simulations based on Density Functional Theory (DFT) in the gas phase, as well as in the presence of a continuum solvation model, were performed for the mentioned molecules. The effect of intramolecular hydrogen bonding, present in salicylic acid and phenyl salicylate, on the properties of the molecules was taken into account in the study. Topological and electron structure analyses of the molecules were carried out according to the Quantum Theory of Atoms in Molecules (QTAIM) and the Non-Covalent Interactions (NCI) index.

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Charakterystyka oddziaływań międzycząsteczkowych : od dimerów do modeli mikrosolwatacyjnych

Panek Jarosław J., Jezierska Aneta

Wiadomości Chemiczne

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2020

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[Z] 74, 9-10

645--662

EN

Intermodular interactions play an important role in many processes at the molecular level. In the contemporary science, there is a growing interest concerning the characteristics of such interactions. Therefore, the computational chemistry can provide answers to many questions, which could not be answered using experimental methods. The Symmetry-Adapted Perturbation Theory (SAPT) method was applied to characterize the energy partitioning in dimers, trimers and microsolvation models. The investigated complexes belong to various classes of compounds, e.g. • dimers of: NH3 ˑˑˑHX, HF-pyridine, cycloalkanes, hypohalous acids; • trimers of: NH3 ˑˑˑNH3ˑˑˑHF or NH3ˑˑˑHFˑˑˑHF; • microsolvation models (biotin - water molecules). The current study summarizes recent years of our research devoted to the intermolecular interactions.

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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.

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Charakterystyka mocy poszczególnych wiązań wodorowych w parach zasad DNA

Szatyłowicz Halina, Sadlej-Sosnowska Nina, Jezierska Aneta

Wiadomości Chemiczne

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2019

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[Z] 73, 1-2

53--74

EN

The main idea of the current review is to present methods useful to characterize the strength of individual hydrogen bonds in nucleic acids base-pairs. In the paper, the Authors discuss the energy definition of intermolecular interactions taking into account the presence of one intermolecular hydrogen bond (HB) as well as the situation when several intermolecular interactions (namely intermolecular hydrogen bonds) are present. In the Section 2 of the review a general overview of methods developed to estimate the strength of the individual intermolecular hydrogen bond in DNA/RNA base-pairs is presented. Thus, the reader can find detailed information on the methods used so far: the rotational method (2003), compliance constants method (2004), the EML equation application (2006), the atom replacement method (2007), the estimation of hydrogen bond energy on the basis of electron density (calculated by using the AIM theory) at BCP values (2009), the application of NBO method (2010), the comparison of HB strength based on the last two approaches (2015) and the application of coordinates interaction approach (2017). It should be emphasized, that these methods allow to estimate the strength of intermolecular interactions both in the model base-pairs and in other systems with several intermolecular hydrogen bonds. The discussion of the presented methods is supported by Tables 1-10, containing numerical values characteristics of the strength of the particular HB, and Figures 1–2. The section 3 contains a critical comparison of results based on the presented methods. Concluding remarks are given in the last Section.