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Pozycja Propedeutyka kierunkowych oddziaływań międzycząsteczkowych. Wiązania wodorowe, oddziaływania asocjacji warstwowej i wiązania halogenowe(Wydawnictwo Politechniki Łódzkiej, 2011) Kruszyński, RafałThe review presents the typical bonding intermolecular interactions: hydrogen bonds, halogen bonds and stacking interactions. The first part describes the specific types of intermolecular interactions, including their definitions, energy and selected properties. The second part deals with the application of quantum-mechanical methods to study of intermolecular interactions, especially the appliance of the natural bond orbitals method, and usage of ab intio calculations for solving of structural problems appearing during the above mentioned studies. All above referred interactions have been presented in orbital terms. The third part describes the novel employment of graph theory to characterise the motifs formed by intermolecular interactions in the solid state.Pozycja Thermal properties of diene elastomers(2014) Rybiński, Przemysław; Kucharska-Jastrząbek, Agnieszka; Janowska, GrażynaThe paper presents the results of investigating the effect of the macromolecule chemical structure and the spatial network structure of butadiene (BR), butadiene-styrene (SBR) and butadiene-acrylonitrile (NBR) rubbers on their thermal properties. The rubbers were cross-linked by the conventional method by means of dicumyl peroxide or sulfur as well as by the non-conventional way using iodoform (CH3I). The rubber and their vulcanizates were assessed by the derivatographic method (under air) and by means of differential scanning calorimetry (DSC) under inert gas. The thermal cross-linking degree of the polydienes and the efficiency of the cross-linking processes, dependent on both the chemical structure of elastomer macromolecules and their spatial network structure were determined. The cross-linking of elastomers with iodoform changes the thermal properties of polymers, significantly increasing their glass transition temperature during both sample heating and cooling, which results from the increase in mutual interaction of macromolecules connected with their modification with iodine compounds.Pozycja Indanthrone dye revisited after sixty years(2014) Kotwica, Kamil; Bujak, Piotr; Wamil, Damian; Materna, Mariusz; Skórka, Łukasz; Gunka, Piotr A.; Nowakowski, Robert; Golec, Barbara; Łuszczyńska, Beata; Zagórska, Małgorzata; Pron, AdamIndanthrone, an old, insoluble dye can be converted into a solution processable, self-assembling and electroluminescent organic semiconductor, namely tetraoctyloxydinaptho[2,3-a:20,30-h]phenazine (P-C8), in a simple one-pot process consisting of the reduction of the carbonyl group by sodium dithionite followed by the substitution with solubility inducing groups under phase transfer catalysis conditionsPozycja Decomposition of Azo Dye C.I. Direct Yellow 86 by the Fenton Process in the Presence of Nanoparticles of Iron Oxides(Instytut Biopolimerów i Włókien Chemicznych (IBWCh) , Łódź, Polska, 2014) Kos, Lech; Sójka-Ledakowicz, Jadwiga; Michalska, Karina; Perkowski, JanThe aim of the study was to determine the efficiency of decomposition of azo dye C.I. Direct Yellow 86 by the Fenton method in the presence of nanoparticles of iron oxides and to compare it with the classical Fenton method. Water solutions of the dye were subjected to the classical purification method with the application of ferrous sulfate and – for comparison – to a process in which iron (II,III) oxide nanopowder was added to the ferrous sulfate. Analysis of the effect of the ferrous sulfate, iron (II,III) oxide nanopowder, hydrogen peroxide and the pH of the solution on the treatment efficiency showed that the process was optimised. The use of iron oxide nanopowder increased the efficiency of dye decomposition.Pozycja A Convenient Approach to a Novel Group of Quaternary Amino Acids Containing a Geminal Bisphosphonate Moiety(2014) Dzięgielewski, Marek; Hejmanowska, Joanna; Albrecht, ŁukaszQuaternary amino acids containing a geminal bisphosphonate moiety have been synthesized for the first time. The developed two-step reaction sequence utilizes the Michael addition of α-substituted azlactones to a vinylidene bisphosphonate as the key step. The reaction proceeds under catalytic conditions with excellent regioselectivity. Subsequent, acid-mediated azlactone ring opening affords the target quaternary amino acids with good overall yields. Attempts to develop an enantioselective version of the synthetic strategy are described.Pozycja How accurate is the strongly orthogonal geminal theory in predicting excitation energies? Comparison of the extended random phase approximation and the linear response theory approaches(American Institute of Physics, 2014) Pernal, Katarzyna; Chatterjee, Koushik; Kowalski, Piotr H.Performance of the antisymmetrized product of strongly orthogonal geminal (APSG) ansatz in describing ground states of molecules has been extensively explored in the recent years. Not much is known, however, about possibilities of obtaining excitation energies from methods that would rely on the APSG ansatz. In the paper we investigate the recently proposed extended random phase approximations, ERPA and ERPA2, that employ APSG reduced density matrices. We also propose a time-dependent linear response APSG method (TD-APSG). Its relation to the recently proposed phase including natural orbital theory is elucidated. The methods are applied to Li2, BH, H2O, and CH2O molecules at equilibrium geometries and in the dissociating limits. It is shown that ERPA2 and TD-APSG perform better in describing double excitations than ERPA due to inclusion of the so-called diagonal double elements. Analysis of the potential energy curves of Li2, BH, and H2O reveals that ERPA2 and TD-APSG describe correctly excitation energies of dissociating molecules if orbitals involved in breaking bonds are involved. For single excitations of molecules at equilibrium geometries the accuracy of the APSG-based methods approaches that of the time-dependent Hartree-Fock method with the increase of the system size. A possibility of improving the accuracy of the TD-APSG method for single excitations by splitting the electron-electron interaction operator into the long- and short-range terms and employing density functionals to treat the latter is presented.Pozycja Role of water in metal catalyst performance for ketone hydrogenation: a joint experimental and theoretical study on levulinic acid conversion into gamma-valerolactone(2014) Carine, Michel; Jérémie, Zaffran; Ruppert, Agnieszka M.; Matras-Michalska, Joanna; Jędrzejczyk, Marcin; Grams, Jacek; Sautet, PhilippeWhile Ru is a poor hydrogenation catalyst compared to Pt or Pd in the gas phase, it is efficient under aqueous phase conditions in the hydrogenation of ketones such as the conversion of levulinic acid into gamma-valerolactone. Combining DFT calculations and experiments, we demonstrate that water is responsible for the enhanced reactivity of Ru under those conditions.Pozycja Erratum: “How accurate is the strongly orthogonal geminal theory in predicting excitation energies? Comparison of the extended random phase approximation and the linear response theory approaches” [J. Chem. Phys.140, 014101 (2014)](American Institute of Physics, 2014) Pernal, Katarzyna; Chatterjee, Koushik; Kowalski, Piotr H.Pozycja Theoretical predictions of isotope effects versus their experimental values for an example of uncatalyzed hydrolysis of atrazine(Royal Society of Chemistry, 2014) Grzybkowska, Anna; Kamiński, Rafał; Dybała-Defratyka, AgnieszkaKinetic isotope effects are one of the most powerful experimental techniques for establishing the nature of a chemical process. However their interpretation very often seeks support from electronic structure calculations in order to get detailed information regarding the transition state which is not experimentally available. For an example of atrazine hydrolysis we have shown how the match between experimentally and theoretically determined magnitudes of carbon, nitrogen and chlorine kinetic isotope effects can be used to discuss the mechanism under different reaction conditions. Two different density functionals combined with the explicit presence of solvent molecules and a continuum solvation model revealed that although the reaction proceeds via the same concerted mechanism regardless of the reaction conditions the transition state structure for an acid and base-catalyzed pathway is different.Pozycja Effect of Formic Acid on Pollutant Decomposition in Textile Wastewater Subjected to Treatment by the Fenton Method(Instytut Biopolimerów i Włókien Chemicznych (IBWCh) , Łódź, Polska, 2014) Kos, Lech; Michalska, Karina; Żyłła, Renata; Perkowski, JanThe aim of this research was to determine the effect of formic acid on pollutant decomposition in textile wastewater subjected to treatment by the Fenton method. To estimate the effect of formic acid on treatment efficiency for different types of textile wastewater tested, COD reduction in mixtures of wastewater and formic acid was calculated. The values of COD calculated were then compared with COD values obtained experimentally during the oxidation of samples of wastewater-formic acid mixtures in the Fenton process. It was found that the presence of formic acid did not deteriorate the conditions of wastewater treatment in the Fenton process. Thus the presence of formic acid in textile wastewater is more advantageous than that of acetic acid.Pozycja New Eco-friendly Method for Paper Dyeing(Institute of Biopolymers and Chemical Fibres, 2014) Blus, Kazimierz; Czechowski, Jacek; Koziróg, AnnaFor economical and environmental reasons, the paper industry has shifted the production of paper products towards dyed products made from pulp grades with a high content of recovered paper. The basic method for dyeing paper products is pulp colouring with direct and basic dyes. Disadvantages of this method include coloured white water and so-called „bleeding” processes when using those products. „Bleeding” processes are undesired when using tissue products. A new eco-friendly method for dyeing pulp with adducts of reactive dyes and selected cationic aliphatic polyamine compouds was developed. A reactive dye is added to refined pulp and then a cationic polyamine compound. The dyeing substance is adsorbed on the entire surface of refined cellulose based semi finished products in a water medium with a pH near to neutral. After web consolidation, an uniform dye penetrated paper product is obtained, with high colour life and strength. Reactive dyes contain 3’-carboxypyridine-1,3,5-triazine systems that react with cellulose in a medium near to neutral and at a temperature similar to web drying. As polyamine compounds, polycondensates of guanidine with hexamethylene-1.6-diamine and octamethylene-1,8-diamine were used. As was proved by a test done on coloured paper, these compounds are characterised by bactericidal and fungicidal properties, which are advised for tissue paper. The polyamine compounds mentioned cause the quantitative adsorption of dyes on cellulose based pulp, increasing the retention of cellulose fibre fines, and the white water is practically colourless. In principle, this dyeing method does not change the strength, optical, structural and dimensional properties of selected paper products.Pozycja Opracowanie innowacyjnej i efektywnej kosztowo technologii redukcji emisji rtęci do atmosfery z procesów spalania węgla(2014) Szynkowska, Małgorzata Iwona; Góralski, Jacek; Maćkiewicz, Elżbieta; Kula, Piotr; Niedzielski, Piotr; Pietrasik, Robert; Jóźwik, KrzysztofPozycja Site-selected incorporation of 5-carboxymethylaminomethyl(- 2-thio)uridine into RNA sequences by phosphoramidite chemistry(2014) Leszczyńska, Grażyna; Pięta, Jakub; Woźniak, Karolina; Małkiewicz, Andrzej5-Carboxymethylaminomethyluridine (cmnm5U) and 5-carboxymethylaminomethyl-2-thiouridine (cmnm5s2U) are located at the wobble position in several cytosolic and mitochondrial tRNA sequences. In this paper, we report the first site-selected incorporation of cmnm5U and cmnm5s2U into RNA sequences by phosphoramidite chemistry on a CPG solid support. Trifluoroacetyl and 2-(trimethylsilyl)ethyl were selected for the protection of the amine and carboxyl functions, respectively.Pozycja The impact of nanosilver addition on element ions release form light-cured dental composite and compomer into 0.9% NaCl(2014) Sokołowski, Krzysztof; Szynkowska, Małgorzata Iwona; Pawlaczyk, Aleksandra; Łukomska-Szymańska, Monika; Sokołowski, JerzyThe aim of this paper was to identify and to assess in semi-quantified way the release of different ions from composite and compomer restorative materials subjected to 0.9% NaCl solution, which simulates the environment of the human body. In the present study, the number of ions (Al, Ag, Ba, Sr, Ti) released from dental fillings over time (one week, one month and 3 months), in different temperatures (23°C, 37°C) and depending on the materials applied (unmodified/modified with nanosilver) was investigated. The results suggest that nanosilver addition influences directly on the process of metal ion releasing into 0.9% NaCl solution. The increase in the number of counts of metal ions was observed in the solutions in which samples modified with nanosilver were kept. Higher amount of metal ion release was observed for composite samples rather than for compomer materials. The study revealed that in general the number of released metal ions increases with the time of storage (for metal ions: Ti, Ba, Sr) and at higher temperature (Ag, Ti, Ba). Reverse tendency observed for silver ion release versus incubation time may be caused by the process of silver adsorption, which takes place on the surface of analyzed material and test-tube walls, where samples were incubated.Pozycja Triazole-Based Compound as a Candidate To Develop Novel Medicines To Treat Toxoplasmosis(2014) Dzitko, Katarzyna; Paneth, Agata; Plech, Tomasz; Pawełczyk, Jakub; Węglińska, Lidia; Paneth, PiotrThis article reports anti-Toxoplasma gondii activity of 3-(thiophen-2-yl)-1,2,4-triazole-5-thione. The compound displayed significant and reproducible antiparasitic effects at nontoxic concentrations for the host cells, with an experimentally determined 50% inhibitory concentration (IC50) at least 30 times better than that of the known chemotherapeutic agent sulfadiazine. Purine nucleoside phosphorylase was defined as the probable target for anti-Toxoplasma activity of the tested compound. These results provide the foundation for future work to develop a new class of medicines to better treat toxoplasmosis.Pozycja Effect of N-donor ancillary ligands on structural and magnetic properties of oxalate copper(II) complexes(Royal Society of Chemistry, 2014) Świtlicka-Olszewska, Anna; Machura, Barbara; Mroziński, Jerzy; Kalińska, Bożena; Kruszyński, Rafał; Penkala, MateuszThrough varying the auxiliary N-donor ligands under similar synthetic conditions nine new compounds: [Cu(C2O4)(pz)]n (1), [Cu(C2O4)(apz)2]n·(3H2O)n (2), [Cu2(μ-C2O4)2(H2O)2(ampz)4] (3), [Cu(C2O4)(mpz)2]n (4), [Cu(C2O4)(aind)2]n (5), [Cu2(C2O4)2(bpzm)2]n·(3.5H2O)n (6), [Cu(C2O4)(ampy)(H2O)]n (7) {[Cu2(μ-C2O4)(aepy)2][Cu(C2O4)2(H2O)2]}n·(2H2O)n (8) and [Cu4(μ-C2O4)3(aepy)4(H2O)2]Cl2 (9) (pz = pyrazole, apz = 3(5)-aminopyrazole, mpz = 3(5)-methylpyrazole, ampz = 3(5)-amino-5(3)-methylpyrazole, aind = 7-azaindole, bpzm = bis(pyrazol-1-yl)methane, ampy = 2-aminomethylpyridine and aepy = 2-(2-pyridyl)ethylamine) have been synthesized and characterised structurally (by single crystal X-ray analysis) and spectroscopically. On the basis of structural data, the influence of neutral N-donor ligands on the control of the final complex structures and the role of weak intermolecular interactions in the creation of molecular architectures have been discussed in detail. The two independent oxalate anions in 1, adopting μ3-oxalato-1κ2O1,O2:2κO1:3κO2a and a relatively rare μ4-oxalato-1κ2O1,O2:2κO1:3κO1a,O2a:4κO2a coordination mode, connect the Cu centers into a two-dimensional net extending along the crystallographic plane (100). Simultaneous existence of both amino and methyl groups in the ampz ligand results in the formation of a 0D dimeric structure of 3. Compounds 2 and 4–8 display one-dimensional coordination structures, and the most significant differences between these structures concern the geometry around the copper(II) center and the coordination mode of the oxalate bridge. The structures of 2–9 are stabilized by the extensive hydrogen-bonding interactions that give rise to the supramolecular architectures. Additionally, the magnetic properties of the complexes 1–9 have been investigated and discussed in the context of their structures.Pozycja A DFT and ONIOM study of C–H hydroxylation catalyzed by nitrobenzene 1,2-dioxygenase(Royal Society of Chemistry, 2014) Geronimo, Inacrist; Paneth, PiotrA detailed description of the mechanism of C–H hydroxylation by Rieske non-heme iron dioxygenases remains elusive, as the nature of the oxidizing species is not definitively known. DFT calculations on cluster models of nitrobenzene 1,2-dioxygenase were done to explore possible mechanisms arising from oxidation by either the experimentally observed FeIII–OOH complex or the putative high-valent HO–FeVQO intermediate formed through a heterolytic O–O bond cleavage. Hydrogen abstraction by HO–FeVQO, followed by oxygen rebound, was found to be consistent with experimental studies. The findings from the quantum mechanical cluster approach were verified by accounting for the effect of the protein environment on transition state geometries and reaction barriers through ONIOM calculations.Pozycja Cytochrome P450-catalyzed dealkylation of atrazine by Rhodococcus sp. strain NI86/21 involves hydrogen atom transfer rather than single electron transfer(Royal Society of Chemistry, 2014) Meyer, Armin H.; Dybała-Defratyka, Agnieszka; Alaimo, Peter J.; Geronimo, Inacrist; Sanchez, Ariana D.; Cramer, Christopher J.; Elsner, MartinCytochrome P450 enzymes are responsible for a multitude of natural transformation reactions. For oxidative N-dealkylation, single electron (SET) and hydrogen atom abstraction (HAT) have been debated as underlying mechanisms. Combined evidence from (i) product distribution and (ii) isotope effects indicate that HAT, rather than SET, initiates N-dealkylation of atrazine to desethyl- and desisopropylatrazine by the microorganism Rhodococcus sp. strain NI86/21. (i) Product analysis revealed a non-selective oxidation at both the αC and βC-atom of the alkyl chain, which is expected for a radical reaction, but not SET. (ii) Normal 13C and 15N as well as pronounced 2H isotope effects (εcarbon: −4.0‰ ± 0.2‰; εnitrogen: −1.4‰ ± 0.3‰, KIEH: 3.6 ± 0.8) agree qualitatively with calculated values for HAT, whereas inverse 13C and 15N isotope effects are predicted for SET. Analogous results are observed with the Fe(IV)[double bond, length as m-dash]O model system [5,10,15,20-tetrakis(pentafluorophenyl)porphyrin-iron(III)-chloride + NaIO4], but not with permanganate. These results emphasize the relevance of the HAT mechanism for N-dealkylation by P450.Pozycja 1,4-disubstituted thiosemicarbazide derivatives are potent inhibitors of toxoplasma gondii proliferation.(2014) Dzitko, Katarzyna; Paneth, Agata; Plech, Tomasz; Pawełczyk, Jakub; Stączek, Paweł; Stefańska, Joanna; Paneth, PiotrA series of 4-arylthiosemicarbazides substituted at the N1 position with a 5-membered heteroaryl ring was synthesized and evaluated in vitro for T. gondii inhibition proliferation and host cell cytotoxicity. At non-toxic concentrations for the host cells all studied compounds displayed excellent anti-parasitic effects when compared to sulfadiazine, indicating a high selectivity of their anti-T. gondii activity. The differences in bioactivity investigated by DFT calculations suggest that the inhibitory activity of 4-arylthiosemicarbazides towards T. gondii proliferation is connected with the electronic structure of the molecule. Further, these compounds were tested as potential antibacterial agents. No growth-inhibiting effect on any of the test microorganisms was observed for all the compounds, even at high concentrations.Pozycja Ensemble density variational methods with selfand ghost-interaction-corrected functionals(American Institute of Physics, 2014) Pastorczak, Ewa; Pernal, KatarzynaEnsemble density functional theory (DFT) offers a way of predicting excited-states energies of atomic and molecular systems without referring to a density response function. Despite a significant theoretical work, practical applications of the proposed approximations have been scarce and they do not allow for a fair judgement of the potential usefulness of ensemble DFT with available functionals. In the paper, we investigate two forms of ensemble density functionals formulated within ensemble DFT framework: the Gross, Oliveira, and Kohn (GOK) functional proposed by Gross et al. [Phys. Rev. A37, 2809 (1988)] alongside the orbital-dependent eDFT form of the functional introduced by Nagy [J. Phys. B34, 2363 (2001)] (the acronym eDFT proposed in analogy to eHF – ensemble Hartree-Fock method). Local and semi-local ground-state density functionals are employed in both approaches. Approximate ensemble density functionals contain not only spurious self-interaction but also the so-called ghost-interaction which has no counterpart in the ground-state DFT. We propose how to correct the GOK functional for both kinds of interactions in approximations that go beyond the exact-exchange functional. Numerical applications lead to a conclusion that functionals free of the ghost-interaction by construction, i.e., eDFT, yield much more reliable results than approximate self- and ghost-interaction-corrected GOK functional. Additionally, local density functional corrected for self-interaction employed in the eDFT framework yields excitations energies of the accuracy comparable to that of the uncorrected semi-local eDFT functional.