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Równowagi asocjacyjne alkilopochodnych mocznika i tiomocznika

Rospenk M., Koll A., Obrzud M.

Wiadomości Chemiczne

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2017

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[Z] 71, 7-8

559--608

EN

The studies and comparison of a series of molecular mono- and di-substituted derivatives of urea and thiourea in solvents of increasing polarity are presented [1–4]. These substances are characterized by a high tendency to self-associate through the formation of intermolecular hydrogen bonds due to the presence in their structure both groups as donors (NH) as well as proton acceptors (C=O) or (C=S). Studies were performed by using IR spectroscopy, method of measuring the average molecular weight and the dipole moments. The experimental data were verified by DFT quantum chemical calculations with B3PW91 correlation functional. Simultaneous use of these techniques alowed establishing not only the efficiency of aggregation, but also the structure and polarity of formed aggregates. It was shown, that in solvents with weak acidic C-H groups the aggregation was strongly limited because of molecular interactions between solute and solvent. The theoretical DFT calculations which included the impact of the environment on the nature of interactions in the complex were carried out [e.g. Scheme 4.1.4]. A combination of geometry optimization in polarizable continuum model (PCM) with the connection of chloroform molecules (1,2-dichloroethane) with urea dimers enabled to obtain the expected theoretical simulation compliance with the experiment. The equilibrium constants were calculated on the basis of data obtained in two independent methods of measurement: IR spectroscopy and measurements of average molecular weights. Good agreement of experimental data of both research techniques were found up to concentration of 0.03 mol/dm3 [Fig. 2.5]. The type of associates have been assessed following the dipole moments measured as a function of concentration, and on the results of density-functional theory (DFT) calculations on the structure and energy of particular species. All of the urea derivatives demonstrated an increase in dipole moment with increased concentration, suggesting linear-type aggregation [Fig. 4.1.3]. Contrastingly, the dipole moments of the N,N-dimethylthiourea and mono-N-alkyl-substituted thioureas decreased with concentration and suggest that cyclic dimers or trimers are formed by C=S…(HR)2N-C=S interactions [Fig. 4.2.2]. The efficiency of self-aggregation was described by use of two equilibrium constants. The first constant, K1, was describing dimer formation and the second constant, K2, the subsequent multimer formation. In N,N’-thioureas aggregation was lower than for the related urea compounds [Table 4.1.1 and Table 4.2.1]. Differences between urea and thiourea derivatives result from the fact that the ureas are stronger bases and, therefore, more active in aggregation.

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Characterization of the Structure of PDP-DPPC Bilayers by DFT and PM3 Calculations

Cieślik-Boczula K., Koll A.

Polish Journal of Chemistry

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2007

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Vol. 81, nr 5-6

1081-1093

EN

The character of 3-pentadecylphenol (PDP)-dipalmitoylophosphatidylcholine (DPPC) interactions in a bilayer system was investigated using DFT and semi-empirical calculations. The obtained results were supported by ATR-IR spectra. The strongest intermolecular hydrogen bond was found between the phenolic OH and the PO2 groups of the DPPC molecule. The presence of water and hydrocarbon chains slightly weakens the strength of this PDP-DPPC interaction. In contrast to a pureDPPC bilayer, thewater molecules do not destroy the H-bonds formed by PO2 moieties and even enhance the total energy of the interaction. Both the van derWaals’interactions in the hydrophobic core of the PDP-DPPC aggregate and the intermolecular H-bond in the hydrophilic part make this complex more rigid, which influences its physical and chemical properties.

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Synthesis, X-ray Crystallography and Computer-Aided Design of 5-Amino-3-methylisoxazole-4-carboxylic Acid N-(2,4,6-Trimethylpyridinium)amide Chlorate(VII) Salt and Its Analogues

Jezierska A., Zygmunt J., Głowiak T., Koll A., Ryng S.

Polish Journal of Chemistry

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2003

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Vol. 77 / nr 11

1461-1471

EN

Experimental and theoretical investigations were performed for 5-amino-3-methylisoxazole- 4-carboxylic acid N-(2,4,6-trimethylpyridinium)amide chlorate(VII) salt, which belongs to the group of isoxazole derivatives, potential antibacterial or antifungal agents. The results related to its synthesis and X-ray diffraction are presented. Quantum- chemical DFT calculations were carried out for the title molecule and its analogues. Atomic charges were calculated according to Bader's Atoms In Molecules Theory in order to find the quantum similarities of the molecules. The Polarizable Continuum Model (SCRF/PCM) with water (_ = 78.39) as a solvent was used to determine the environment effects on molecular properties. The solid-state geometry optimization with Geodecker's pseudopotentials and plane-wave basis set was used to compare experimental and calculated geometrical parameters for the title compound.

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The Proton Localization in solid 2-(N-Diethylamino-N-oxomethyl)-4,6-dichlorophenol by Quantum Mechanical Calculations

Koll A., Janski J., Mavri J.

Polish Journal of Chemistry

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2002

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Vol. 76 / nr 2-3

471-481

EN

One-dimensional proton potentials for O-H stretching are calculated for 2-(N-diethylamino- N-oxomethyl)-4,6-dichlorophenol, forming very short (2.400(5) A) intramolecular O...H…O hydrogen bond. The calculated O-H bond length at different level of theory are compared with neutron diffraction data. The comparison of experimental IR spectra with calculated anharmonic (OH) band positions is performed. The problems of the basis set and appropriate structure selection as well as the role of surroundings are discussed.

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Spectroscopic Studies and VFF Model calculations on Dynamic and Electrooptic Characteristics of N-H Bonds in Amides

Borisenko V., Morev A. V., Bidulya Y. V., Koll A.

Polish Journal of Chemistry

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2002

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Vol. 76 / nr 10

1481-1494

EN

IR spectroscopic studies of propionamide, n-butyramide, benzamide and 2-(F, Cl, Br)- benzamides within the _(NH) and (HNH) absorption range of -NH2 group for the "free" (in CCl4 solutions) molecules and forming complexes with proton acceptor solvents (benzene, toluene, acetonitrile, dimethylformamide, dimethylsulphoxide and hexamethylphosphoramide) have been performed. Modifying the strength of the intermolecular interactions one can achieve the canceling of the primary non-equivalency of the N-H bonds in the -NH2 group of amides. It allows establishing, for the first time, quantitative measures of dynamic (K(NH)) and electrooptic (_/q) characteristics of N-H bonds in amides in framework of the R-NH2 valence force field model. Dynamic and electrooptic non-equivalencies enhance with the increase of the hydrogen bonding strength. For the hydrogen-bonded complexes with acetonitrile, dimethylformamide, dimethylsulfoxide and hexamethylphosphoramide, the dynamic non-equivalency of NH bonds is increased 10-20%, while the electrooptic parameters _1/q1 and _2/q2 grow two or even three times. The electrooptic coupling of the N-H bonds (the parameter _i/qj, where i, j = 1, 2; i _ j) increases with the strength of the hydrogen bonding.

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Quantum-Chemical study with Application of the PCM Model on Correlation Between Biological Activity and Molecular Structure of 5-Amino-3-methylisoxazole-4-carboxylic Acid Hydrazide Schiff Base Derivatives

Jezierska A., J. Panek J., Ryng S., Zimecki M., Fedorowicz A., Koll A.

Polish Journal of Chemistry

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2002

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Vol. 76 / nr 9

1255-1262

EN

Theoretical calculations on 5-amino-3-methylisoxazole-4-carboxylic acid hydrazide Schiff base derivatives using Polarizable Continuum Model in order to account for water solvation effects are presented. The compounds studied exhibit biological (immunosuppressing or immunostimulating) activity, measured experimentally in various assays. The quantum chemical DFT calculations are used to obtain electronic descriptors of molecular structure. These descriptors, together with other physicochemical parameters, are used to derive quantitative relationships between the structure and the biological activity.

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FT-IR Studies of CH...B Interactions in Fluoroform Containing Cryosolutions

Melikova S., Rutkowski K. S., Rodziewicz P., Koll A.

Polish Journal of Chemistry

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2002

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Vol. 76 / nr 9

1271-1285

EN

A transition from a blue shifted frequency of the _(CH) vibrations of CF3H to a conventional red frequency shift, accompanied by unusually varying integrated intensity of the corresponding _1 band, have been studied in CF3H/B systems, where B = Ar, N2, CO, CO2, O(CD3)2, NH3, and N(CD3)3. DFT/B3LYP and ab initio MP2 calculations, utilizing the 6-311++G(3df,3pd) basis set, predict a weakly H-bond-like linear F3CH…B complex formation in the series studied and reproduce experimentally observed variations of spectroscopic parameters. The results obtained are treated in the framework of induced dipole moment, taking into account opposite directions of the CH bond dipole moment and the dipole moment of the whole molecule. In the range of overtone and combination bands of fluoroform, new weak bands have been detected. They were attributed to simultaneous excitations of vibrations of interacting CF3HandB(=CO,CO2) molecular pairs.