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Calculating the Partition Coefficients of Organic Solvents in Octanol/Water and Octanol/Air
PublicationPartition coefficients define how a solute is distributed between two immiscible phases at equilibrium. The experimental estimation of partition coefficients in a complex system can be an expensive, difficult, and time-consuming process. Here a computational strategy to predict the distributions of a set of solutes in two relevant phase equilibria is presented. The octanol/water and octanol/air partition coefficients are predicted...
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Electron energy-loss spectroscopy of excited states of the diazine molecules: Pyridazine
PublicationExcitation of the valence electronic states of the pyridazine molecules in the gas phase have been studied using the technique of electron energy-loss spectroscopy. Varying the electron scattering conditions, the residual electron energy and scattering angle, enabled the optically-allowed and -forbidden excitations to be differentiated. The measured energy-loss spectra enabled the vertical excitation energies of the observed states...
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Binary-Encounter Model for Direct Ionization of Molecules by Positron-Impact
PublicationWe introduce two models for the computation of direct ionization cross sections by positron impact over a wide range of collision energies. The models are based on the binary-encounter-Bethe model and take into account an extension of the Wannier theory. The cross sections computed with these models show good agreement with experimental data. The extensions improve the agreement between theory and experiment for collision energies...
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Cold recycled mixtures for binder courses - laboratory evaluation of mechanical properties
PublicationCold recycled mixtures composed with cement and bituminous emulsion are nowadays commonly used material for base layer. Typical pavement with cold recycled mixtures usually consists of two asphalt courses (wearing and binding course) constructed over cold recycled base. Therefore the next step in cold recycling is possibility of design of binding courses with recycled materials, but with potential to obtain high quality mixtures...
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Quantitative fluorescent determination of DNA – Ochratoxin a interactions supported by nitrogen-vacancy rich nanodiamonds
PublicationOchratoxin A (OTA) is a hazardous contaminant of a large variety of plant and animal originated food. Herein, we report an interaction of OTA with calf thymus DNA (ct DNA) on the nanodiamond surface. We employed multispectroscopic techniques to elucidate the binding mechanism of OTA with ct DNA. The fluorescence and UV–Vis spectroscopy results show that OTA binds to ds ct DNA and forms complexes. We obtained the binding constants...
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Simultaneous voltammetric determination of Cd2+, Pb2+, and Cu2+ ions captured by Fe3O4@SiO2 core-shell nanostructures of various outer amino chain length
PublicationIn the present study, we examined a novel functionalised magnetic nanoparticles Fe3O4@SiO2-Nn as a nano adsorbent for binding of Cd2+, Pb2+, Cu2+ ions in an aqueous solution. First, we obtained the nanoparticles functionalised with various carbon chains containing different number of amino groups: (3-amino)propyltriethoxysilane (Fe3O4@SiO2-N1), N-(2-aminoethyl)-3-aminopropyltrimethoxysilane (Fe3O4@SiO2-N2) and N1-(3-trimethoxysilylpropyl)diethylenetriamine...
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Polarisation effects in low-energy positron–molecule scattering
PublicationThe UK molecular R-matrix method has been adapted to treat positron collisions from polyatomic targets. A simple empirical enhancement factor which corrects for the underestimation of electron–positron polarisation and correlation effects in the calculations performed with the static-plus-polarization model at low scattering energies is presented. Application of this model to positron scattering from carbon dioxide at energies...
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Proton transfer reactions for ionized water clusters
PublicationCalculations of formation energies of the ionized water clusters and energies of reactions between small (including less than eight water molecules) neutral and positively ionized water clusters are presented. Moreover, we discuss some reaction paths between neutral and positively charged dimers, trimers and tetramers and proton transfer reactions (PTR) between cyclic clusters and H3O+ ions which can appear in beam experiments...
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Molecular dynamics simulations of the affinity of chitin and chitosan for collagen: the effect of pH and the presence of sodium and calcium cations
PublicationChitosan and chitin are promising biopolymers used in many areas including biomedical applications, such as tissue engineering and viscosupplementation. Chitosan shares similar properties with hyaluronan, a natural component of synovial fluid, making it a good candidate for joint disease treatment. The structural and energetic consequences of intermolecular interactions are crucial for understanding the biolubrication phenomenon...
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Interaction of human serum albumin with volatiles and polyphenols from some berries
PublicationHeadspace solid-phase microextraction coupled with comprehensive two-dimensional gas chromatography with time-of-flight mass spectrometry (HS-SPME/GC GCeTOFMS) identified 19 and quantified 6 monoterpenes in gooseberries, blueberries and cranberries. As a protein model human serum albumin (HSA) was used in interaction with terpenes. Specific binding of terpenes to HSA under the physiological conditions was a result of the formation...
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Joanna Czerska dr inż.
PeopleI am a woman whose mission and passion is the development of people and organizations. My motto is: "There is no such fantasy that human will and reason cannot transform into reality." William Shakespeare In my life I am guided by the values of respect, teamwork and a positive attitude. They define me and decide what kind of person I am. My adventure with Lean began when I was writing my diploma thesis during my studies at WZiE...
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Production of singlet oxygen atoms by photodissociation of oxywater
PublicationQuantum chemical calculations are reported for the energies of the few lowest electronic singlet states of oxywater along dissociation of the oxygen-oxygen bond into water and singlet oxygen using multistate multireference second-order Møller–Plesset perturbation theory. We compute an energy of 21 kcal/mol to remove one oxygen atom in the lowest singlet state. The two lowest excited singlet states have vertical excitation energies...
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Structural factors affecting affinity of cytotoxic oxathiole-fused chalcones toward tubulin
PublicationSynthesis, in vitro cytotoxic activity, and interaction with tubulin of (E)-1-(6-alkoxybenzo[d][1,3]oxathiol- 5-yl)-3-phenylprop-2-en-1-one derivatives (2) are described. Some of the compounds demonstrated cytotoxic activity at submicromolar concentrations, and the activity could be related to interaction with tubulin at the colchicine binding site. Interaction of selected derivatives with tubulinwas evaluated using molecular modeling,...
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Born-Oppenheimer potential energy curves of the NaK molecule
Open Research DataAdiabatic potential energy curves (APEC) of the singlet (s) and triplet (t) Sigma+, Pi, and Delta electronic states have been calculated for the NaK molecule. All results of the presented molecular states have been obtained by the nonrelativistic multireference configuration interaction (MRCI) method used with pseudopotentials describing the interaction...
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Receptor for advanced glycation end‐products: Biological significance and imaging applications
PublicationThe receptor for advanced glycation end-products (RAGE or AGER) is a transmembrane, immunoglobulin-like receptor that, due to its multiple isoform structures, binds to a diverse range of endo- and exogenous ligands. RAGE activation caused by the ligand binding initiates a cascade of complex pathways associated with producing free radicals, such as reactive nitric oxide and oxygen species, cell proliferation, and immunoinflammatory...
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Self-healing mechanism of metallopolymers investigated by QM/MM simulations and Raman spectroscopy
PublicationThe thermally induced self-healing mechanisms in metallopolymers based on bisterpyridine complexes of iron(II) sulfate and cadmium(II) bromide, respectively, were studied by means of combined quantum mechanical/molecular mechanical (QM/MM) simulations and Raman spectroscopy. Two possible healing schemes, one based on a decomplexation of the cross-linking complexes and a second one relying on the dissociation of ionic clusters,...
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Electron-impact ionization cross section calculations for selected ribonucleosides
PublicationTotal cross sections for the single electron-impact ionization of selected ribonuclosides (guanosine, adenosine, cytidine and uridine) have been calculated for electron energies ranging from the ionization threshold up to 5 keV.
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Molecular basis and quantitative assessment of TRF1 and TRF2 protein interactions with TIN2 and Apollo peptides
PublicationShelterin is a six-protein complex (TRF1, TRF2, POT1, RAP1, TIN2, and TPP1) that also functions in smaller subsets in regulation and protection of human telomeres. Two closely related proteins, TRF1 and TRF2, make high-affinity contact directly with double-stranded telomeric DNA and serve as a molecular platform. Protein TIN2 binds to TRF1 and TRF2 dimer-forming domains, whereas Apollo makes interaction only with TRF2. To elucidate...
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Optimization of Chemical Functionalities of Indole-2-carboxamides To Improve Allosteric Parameters for the Cannabinoid Receptor 1 (CB1)
Publication5-Chloro-3-ethyl-N-(4-(piperidin-1-yl)phenethyl)-1H-indole-2-carboxamide (1; ORG27569) is a prototypical allosteric modulator for the cannabinoid type 1 receptor (CB1). Here, we reveal key structural requirements of indole-2-carboxamides for allosteric modulation of CB1: a critical chain length at the C3-position, an electron withdrawing group at the C5-position, the length of the linker between the amide bond and the phenyl ring...
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In vitro affinity of Deinococcus radiodurans MutS towards mismatched DNA exceeds that of its orthologues from Escherichia coli and Thermus thermophilus
PublicationThe mismatch binding protein MutS is responsible for the recognition of mispaired and unpaired bases, which is the initial step in DNA repair. Among the MutS proteins most extensively studied in vitro are those derived from Thermus thermophilus, Thermus aquaticus and Escherichia coli. Here, we present the first report on the in vitro examination of DNA mismatch binding activity of MutS protein from Deinococcus radiodurans and confront...
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Full CI ground state potential energy curves and one-electron relativistic corrections for hydrogen molecule in various basis sets
Open Research DataThis dataset consists of Full CI ground state Born-Oppenheimer potential energy curves and one-electron relativistic corrections for hydrogen dimer. Nonrelativistic energies, as well as one electron relativistic corrections (treated perturbatively with help of the Cowan-Griffin Hamiltonian) are presented for internuclear distances between 0.8 and 10...
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Excited state properties of a series of molecular photocatalysts investigated by time dependent density functional theory.
PublicationTime dependent density functional theory calculations are applied on a series of molecular photocatalysts of the type [(tbbpy)2M1(tpphz)M2X2]2+ (M1 = Ru, Os; M2 = Pd, Pt; X = Cl, I) in order to provide information concerning the photochemistry occurring upon excitation of the compounds in the visible region. To this aim, the energies, oscillator strengths and orbital characters of the singlet and triplet excited states are investigated....
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Justification of quasi-stationary approximation in models of gene expression of a self-regulating protein
PublicationWe analyse a model of Hes1 gene transcription and protein synthesis with a negative feedback loop. The effect of multiple binding sites in the Hes1 promoter as well as the dimer formation process are taken into account. We consider three, possibly different, time scales connected with: (i) the process of binding to/dissolving from a binding site, (ii) formation and dissociation of dimers, (iii) production and degradation of Hes1...
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Towards β-selectivity in functional estrogen receptor antagonists
PublicationBased on the benzo[b]naphtho[1,2-d]furan and benzo[b]naphtho[1,2-d]thiophene frameworks, a series of ligands with different basic side chains (BSCs) has been synthesized and pharmacologically evaluated. Also, their binding modes have been modelled using docking techniques. It was found that the introduction of a BSC in these systems brings about a decrease of affinity for both estrogen receptors α and β in an in vitro competitive...
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The Role of Electron Transfer in the Fragmentation of Phenyl and Cyclohexyl Boronic Acids
PublicationIn this study, novel measurements of negative ion formation in neutral potassium-neutral boronic acid collisions are reported in electron transfer experiments. The fragmentation pattern of phenylboronic acid is comprehensively investigated for a wide range of collision energies, i.e., from 10 to 1000 eV in the laboratory frame, allowing some of the most relevant dissociation channels to be probed. These studies were performed in...
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Determination of long-chain aldehydes using a novel quartz crystal microbalance sensor based on a biomimetic peptide
PublicationThere is an increasingly popular trend aimed at improvement of fundamental metrological parameters of sensors via implementation of materials mimicking biological olfactory systems. This study presents investigation on usefulness of the peptide mimicking HarmOBP7 region as a receptor element of the piezoelectric sensor for selective analysis of long-chain aldehydes. Identification of odorant binding proteins creates new possibilities...
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DNA restriction analysis as a supportive tool in mechanistic studies carried out by 32P-postlabelling
PublicationNumerous antitumor and carcinogenic compounds are able to modify DNA by forming covalent bonds with its constituents, while some anticarcinogenic compounds are known to prevent such a modification. All these processes are of vital biological import_ance, though deeper inside into factors influencing formation of DNA adducts is difficult due to the low level of their occurrence. 32P-Postlabelling approach ensures very sensitive...
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Isobutyl acetate: electronic state spectroscopy by high-resolution vacuum ultraviolet photoabsorption, He(I) photoelectron spectroscopy and ab initio calculations
PublicationThe high-resolution vacuum ultraviolet photoabsorption spectrum of isobutyl acetate, C6H12O2, is presented here and was measured over the energy range 4.3–10.8 eV (290–115 nm). Valence and Rydberg transitions with their associated vibronic series have been observed in the photoabsorption spectrum and are assigned in accordance with new ab initio calculations of the vertical excitation energies and oscillator strengths. The measured...
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Electronic state spectroscopy by high-resolution vacuum ultraviolet photoabsorption, He(I) photoelectron spectroscopy and ab initio calculations of ethyl acetate
PublicationThe high-resolution vacuum ultraviolet photoabsorption spectrum of ethyl acetate, C4H8O2, is presented over the energy range 4.5−10.7 eV (275.5−116.0 nm). Valence and Rydberg transitions and their associated vibronic series observed in the photoabsorption spectrum, have been assigned in accordance with new ab initio calculations of the vertical excitation energies and oscillator strengths. Also, the photoabsorption cross sections...
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Janusz Smulko prof. dr hab. inż.
PeopleHe was born on April 25, 1964 in Kolno. He graduated in 1989 with honors from the Faculty of Electronics at Gdańsk University of Technology, specialising in measuring instruments. In 1989 he took second place in the Red Rose competition for the best student in the Pomerania Region. Since the beginning of his career ha has been associated with Gdańsk University of Technology: research assistant (1989-1996), Assistant Professor (1996-2012),...
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Proton affinity and proton transfer energy for selected organic molecules
PublicationThe Hartree-Fock method in 6-311G** molecular orbitals basis set has been applied to calculations of proton affinities and proton transfer reaction energies for water, methanol, acetaldehyde, ethanol, acetone, acetic acid, methyl acetate and ethyl acetate.
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Thermodynamics and Intermolecular Interactions of Nicotinamide in Neat and Binary Solutions: Experimental Measurements and COSMO-RS Concentration Dependent Reactions Investigations
PublicationIn this study, the temperature-dependent solubility of nicotinamide (niacin) was measured in six neat solvents and five aqueous-organic binary mixtures (methanol, 1,4-dioxane, acetonitrile, DMSO and DMF). It was discovered that the selected set of organic solvents offer all sorts of solvent effects, including co-solvent, synergistic, and anti-solvent features, enabling flexible tuning of niacin solubility. In addition, differential...
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An inter-laboratory validation of methods of lipid peroxidation measurement in UVA-treated human plasma samples
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Natural and synthetic antioxidants: An updated overview
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The onset of lipid peroxidation in rheumatoid arthritis: consequences and monitoring
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Personalized nutrition in ageing society: redox control of major-age related diseases through the NutRedOx Network (COST Action CA16112)
PublicationA healthy ageing process is important when it is considered that one-third of the population of Europe is already over 50 years old, although there are regional variations. This proportion is likely to increase in the future, and maintenance of vitality at an older age is not only an important measure of the quality of life but also key to participation and productivity. So, the binomial “nutrition and ageing” has different aspects...
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Diet is Not Responsible for the Presence of Several Oxidatively Damaged DNA Lesions in Mouse Urine
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Urinary excretion rates of 8-oxoGua and 8-oxodG and antioxidant vitamins level as a measure of oxidative status in healthy, full-term newborns
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8-Oxo-7,8-dihydroguanine and 8-oxo-7,8-dihydro-2′-deoxyguanosine levels in human urine do not depend on diet
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The plasma concentration of advanced oxidation protein products and arterial stiffness in apparently healthy adults
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The spontaneous electron emission and rotational predissociation lifetimes of the diatomic silver anion
Open Research DataThe process of a two-channel decay of the diatomic silver anion (Ag2-), namely the spontaneous electron ejection giving Ag2 + e- and the dissociation leading to Ag- + Ag is theoretically studied. The ground state potential energy curves (PECs) of the neutral silver dimer and anionic silver diatomic molecule are calculated using the single reference...
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The estrogenicity of wastewater samples.
Open Research DataThe principle of operation of the kit is based on the fact that the tested sample with endocrine activity (containing compounds capable of binding to the human estrogen receptor α, hERα) releases the fluorescently labeled ligand (FluormoneTM ES2) from the receptor-ligand complex, which results in a reduction of the polarization value fluorescence. The...
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Complex modulus of Cement Bitumen Treated Material Mixture (28 days of curing at 20C)
Open Research DataDataset presents data of complex modulus determined for cold recycled mixture – cement bitumen treated material mixture with 3 combinations of binding agents: 2% cement, 6% emulsion (C2E6), 6% cement, 6% emulsion (C6E6), 6% cement, 2% emulsion (C6E2). Mixture was designed according to Polish requirements for the base course of pavement. Mixture contains...
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Karaś P., Kochanowicz K., Pitek M., Domański P., Obuchowski I., Tomiczek B., Liberek K.: Evolution towards simplicity in bacterial small heat shock protein system// eLife -, (2023), s.1-21
PublicationEvolution can tinker with multi-protein machines and replace them with simpler single-protein systems performing equivalent functions in an equally efficient manner. It is unclear how, on a molecular level, such simplification can arise. With ancestral reconstruction and biochemical analysis, we have traced the evolution of bacterial small heat shock proteins (sHsp), which help to refold proteins from aggregates using either...
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Evolution towards simplicity in bacterial small heat shock protein system
PublicationEvolution can tinker with multi-protein machines and replace them with simpler single-protein systems performing equivalent functions in an equally efficient manner. It is unclear how, on a molecular level, such simplification can arise. With ancestral reconstruction and biochemical analysis, we have traced the evolution of bacterial small heat shock proteins (sHsp), which help to refold proteins from aggregates using either two...
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Characterization of Bioactivity of Selective Molecules in Fruit Wines by FTIR and NMR Spectroscopies, Fluorescence and Docking Calculations
PublicationFourier transform infrared (FTIR) and proton nuclear magnetic resonance (1H NMR) spectroscopies were applied to characterize and compare the chemical shifts in the polyphenols’ regions of some fruit wines. The obtained results showed that FTIR spectra (1800–900 cm−1) and 1H NMR (δ 6.5–9.3 ppm) of different fruit wines can be used as main indices of the year of vintage and quality of fruit wines. In addition to the classical determination...
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Electron-impact ionization cross section calculations for 5-chloropyridine and 5-bromopyridine molecules
PublicationThe total cross sections for the single electron-impact ionization of 5-chloropyridine (5-C5H4ClN) and 5-bromopyridine (5-C5H4BrN) molecules have been calculated using binary-encounter-Bethe method for electron energies ranging from the ionization threshold up to 5 keV.
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Variational principles for bound states of Schrödinger and Dirac equations allowing the use of discontinuous trial functions
PublicationWe present systematic constructions of variational principles for energies of bound states of the Schroedinger and Dirac equations. The principles allow the use of discontinuous trial functions. The method employed is based on a generalized Lagrange procedure. Relationships between our variational principles and those available in the literature are established.
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Carboxylation Enhances Fragmentation of Furan upon Resonant Electron Attachment
PublicationWe report a dissociative electron attachment study to 2-furoic acid (C5H4O3) isolated in a gas phase, which is a model molecule consisting of a carboxylic group and a furan ring. Dissociation of furan by low energy electrons is accessible only via electronic excited Feshbach resonances at energies of incident electrons above 5 eV. On the other hand, carboxylic acids are well- known to dissociate via attachment of electrons at subexcitation energies....
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Valence and ionic lowest-lying electronic states of ethyl formate as studied by high-resolution vacuum ultraviolet photoabsorption, He(I) photoelectron spectroscopy, and ab initio calculations
PublicationThe highest resolution vacuum ultraviolet photoabsorption spectrum of ethyl formate, C2H5OCHO, yet reported is presented over the wavelength range 115.0–275.5 nm (10.75–4.5 eV) revealing several new spectral features. Valence and Rydberg transitions and their associated vibronic series, observed in the photoabsorption spectrum, have been assigned in accordance with new ab initio calculations of the vertical excitation energies...