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Large-scale DFT calculations in implicit solvent-A case study on the T4 lysozyme L99A/M102Q protein
PublikacjaW ostatnich latach zaproponowano szereg modeli typu implicit solvent, ktore bazują na bezpośrednim rozwiązaniu niejednorodnego równania Poissona w przestrzeni rzeczywistej. Modele te charakteryzują się elegancją, ponieważ wnęka, w której umieszczona jest molekuła substancji rozpuszczanej zdefiniowana jest bezpośrednio w funkcji gęstości elektronowej, a rozkład ładunku jest w sposób samouzgodniony polaryzowany dzięki reakcji dielektryka,...
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Calculations of fracture process zones on meso-scale in notched concrete beams subjected to three-point bending.
PublikacjaW artykule przedstawiono wyniki numeryczne MES modelowanie belek betonowych z nacięciem na poziomie skali mezo. Beton został opisany na poziomie skali mezo jako stochastyczny materiał 3-składnikowy złożony z kruszywa, zaczynu cementowego oraz stref kontaktu. Obliczenia wykonano przy wykorzystaniu modelu degradacji sztywności z nielokalnym osłabieniem. Zbadano wpływ stochastycznego rozkładu kruszywa, średnicy, kształtu oraz zagęszczenia...
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Matrix effects and recovery calculations in analyses of pharmaceuticals based on the determination of β-blockers and β-agonists in environmental samples
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Weak hydrogen bonding interaction S-H···O=C studied by FT-IR spectroscopy and DFT calculations
PublikacjaInteractions between the thiolate group of tri-tert-butoxysilanethiol (TBST) and carbonyl group of acetone are studied with the use of FT-IR spectroscopy and DFT calculations.
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Aluminate Red Phosphor in Light-Emitting Diodes: Theoretical Calculations, Charge Varieties, and High-Pressure Luminescence Analysis
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Calculations of notch stress factor of a thin-walled spreader bracket fillet weld with the use of a local stress approach
PublikacjaPresence of geometric notches in welded joints causes concentration of strains and stresses, therefore reducing fatigue strength of such joints. This article presents an analysis of stress concentrations in a fillet weld of a spreader mounting bracket on a small sailing yacht. The aim of this article is to direct the attention of designers, manufacturers and regulatory bodies to issues of fatigue cracks that form in brackets fastening...
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Density functional theory calculations on entire proteins for free energies of binding: Application to a model polar binding site
PublikacjaIn drug optimization calculations, the molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) method can be used to compute free energies of binding of ligands to proteins. The method involves the evaluation of the energy of configurations in an implicit solvent model. One source of errors is the force field used, which can potentially lead to large errors due to the restrictions in accuracy imposed by its empirical nature....
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APPLICATION OF BINARY-ENCOUNTER-BETHE METHOD TO ELECTRON-IMPACT IONIZATION CROSS SECTION CALCULATIONS FOR BIOLOGICALLY RELEVANT MOLECULES
PublikacjaElectron-impact cross sections for platinum chemotherapeutic compounds, purine and pyrimidine molecules calculated using binary-encounterBethe model are presented as examples of possible applications of that method.
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ENERGY EFFICIENT SMALL INLAND PASSENGER SHUTTLE FERRY WITH HYBRID PROPULSION - CONCEPT DESIGN, CALCULATIONS AND MODEL TESTS
PublikacjaIn recent years, there has been a significant development in “green” and energy efficient propulsion systems, which fits into the general trend of environmentally friendly “green shipping”. The pursued goal is to construct a safe passenger ship that is low in energy demand and equipped with a highly energy efficient, emission-free propulsion system. The paper presents main problems encountered by designers of a small, hybrid-powered...
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Effect of the Catalytic Center on the Electron Transfer Dynamics in Hydrogen-Evolving Ruthenium-Based Photocatalysts Investigated by Theoretical Calculations
PublikacjaThe light-induced relaxation pathways in the molecular photocatalyst [(tbbpy)2Ru(tpphz)PtCl2]2+ are investigated with time-dependent density functional theory calculations together with the Marcus theory of electron transfer (ET). The calculations show that metal (Ru) to ligand (tpphz) charge transfer (MLCT) triplet states are populated following an excitation in the longer wavelength range of the absorption spectrum, but that an...
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Singlet oxygen in the removal of organic pollutants: An updated review on the degradation pathways based on mass spectrometry and DFT calculations
PublikacjaThe degradation of pollutants by a non-radical pathway involving singlet oxygen (1O2) is highly relevant in advanced oxidation processes. Photosensitizers, modified photocatalysts, and activated persulfates can generate highly selective 1O2 in the medium. The selective reaction of 1O2 with organic pollutants results in the evolution of different intermediate products. While these products can be identified using mass spectrometry...
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Concrete beams under bending - calculations of size effects within stochastic elasto-plasticity with non-local softening
PublikacjaW artykule przedstawiono wyniki numerycznej analizy efektów skali (efektu deterministycznego i stochastycznego) w belkach betonowych nacięciem poddanych zginaniu z uwzględnieniem lokalizacji odkształceń. Obliczenia wykonano przy zastosowaniu metody elementów skończonych i sprężysto-plastycznego modelu z nielokalnym osłabieniem. Pokazano wpływ wielkości belek betonowych na nośność.
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3D calculations of aerodynamic forces causing self-excited vibrations of turbine rotor systems. Part II: Pressure forces
PublikacjaPrzedstawiono wyniki badań numerycznych sił generowanych w uszczelnieniu nadbandażowym stopnia turbinowego przeprowadzone metodą Fluent. Uwzględniono niecentryczne położenie osi wirnika względem osi korpusu. Rozpatrzono bandaże o różnej geometrii. Niektóre wyniki zweryfikowano doświadczalnie.
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Comparison of two approaches to potential of mean force calculations of hydrophobic association: particle insertion and weighted histogram analysis methods
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Vibrational inelastic electron-H2 scattering revisited: numerically converged coupled channels space frame calculations with model interaction
PublikacjaZderzeniowe wzbudzenie niższych oscylacyjnych poziomów molekuły H2 (^1Σ^+,g) przez elektrony o niskiej energii. Obliczenia wykonano przy użyciu empirycznego modelowego potencjału oraz przez rozwiązanie równania rozpraszania dwukanałowego w układzie współrzędnych, związanych z molekułą.
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Modeling and Strength Calculations of Parts Made Using 3D Printing Technology and Mounted in a Custom-Made Lower Limb Exoskeleton
PublikacjaThis study is focused on the application of 3D-printed elements and conventional elements to create a prototype of a custom-made exoskeleton for lower limb rehabilitation. The 3D-printed elements were produced by using Fused Deposition Modeling technology and acrylonitrile butadiene styrene (ABS) material. The scope of this work involved the design and construction of an exoskeleton, experimental testing of the ABS material and...
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Evaluation of Chemotherapeutic Activity of the Selected Bases’ Analogues of Nucleic Acids Supported by ab initio Various Quantum Chemical Calculations
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Notched concrete beams under bending - calculations of size effects within stochastic elasto-plasticity with non-local softening
PublikacjaW artykule przedstawiono wyniki numerycznej analizy efektów skali (efektu deterministycznego i stochastycznego) w belkach betonowych nacięciem poddanych zginaniu z uwzględnieniem lokalizacji odkształceń. Obliczenia wykonano przy zastosowaniu metody elementów skończonych i sprężysto-plastycznego modelu z nielokalnym osłabieniem. Pokazano wpływ wielkości belek na nośność z uwzględnieniem stochastycznego rozkładu wytrzymałości na...
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FE calculations of a deterministic and statistical size effect in concrete under bending within stochastic elasto-plasticity and non-local softening
PublikacjaW artykule przedstawiony wyniki obliczeń MES deterministycznego i statystycznego efektu skali w belkach betonowych podczas zginania. Zastosowano model w ramach stochastycznej sprężysto-plastyczności i nielokalnego osłabienia. Belki były geometrycznie podobne. Wyniki porównano z modelem efektu skali Bazanta.
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Elastic cross-section calculations for electron collisions with XY4 (X=Si,Ge; Y=H, F, Cl, Br, I) molecules
PublikacjaObliczano elastyczne przekroje czynne dla tetraedrycznych związków krzemu i germanu. Otrzymane wyniki porównano z innymi dostępnymi wynikami obliczeń oraz z danymi doświadczalnymi; dla energii powyżej 100 eV uzyskano zadowalającą zgodność.
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3D calculations of aerodynamic forces causing self-excited vibrations of turbine rotor systems. Part I: Shroud seal flow inwestigations
PublikacjaOpisano numeryczną i doświadczalną metodę badania przepływu w uszczelnieniu nadbandażowym stopnia turbinowego. Badania numeryczne przeprowadzono programem Fluent, a badania doświadczalne wykonano na powietrznej turbinie modelowej. Uwzględniono niesymetryczny rozkład szczeliny nadbandażowej na skuteknie centrycznego położenia osi wirnika względem osi cylindra. Zamieszczono przykładowe wyniki.
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Electron collisions with methyl-substituted ethylenes: Cross section measurements and calculations for 2-methyl–2-butene and 2,3-dimethyl–2-butene
PublikacjaWe report electron-scattering cross sections determined for 2-methyl–2-butene [(H3C)HC==C(CH3)2] and 2,3-dimethyl–2-butene [(H3C)2C=C(CH3)2] molecules. Absolute grand-total cross sections (TCSs) were measured for incident electron energies in the 0.5–300 eV range, using a linear electron-transmission technique. The experimental TCS energy dependences for the both targets appear to be very similar with respect to the shape. In each...
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Probing the binding selected metal ions and biologically active substances to the antimicrobial peptide LL-37 using DSC, ITC measurements and calculations
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Isobutyl acetate: electronic state spectroscopy by high-resolution vacuum ultraviolet photoabsorption, He(I) photoelectron spectroscopy and ab initio calculations
PublikacjaThe 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
PublikacjaThe 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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Practical Approach to Large-Scale Electronic Structure Calculations in Electrolyte Solutions via Continuum-Embedded Linear-Scaling Density Functional Theory
PublikacjaWe present the implementation of a hybrid continuum-atomistic model for including the effects of a surrounding electrolyte in large-scale density functional theory (DFT) calculations within the Order-N Electronic Total Energy Package (ONETEP) linear-scaling DFT code, which allows the simulation of large complex systems such as electrochemical interfaces. The model represents the electrolyte ions as a scalar field and the solvent...
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Influence of Protonation State on the Excited State Dynamics of a Photobiologically Active Ru(II) Dyad
PublikacjaThe influence of ligand protonation on the photophysics of a ruthenium (Ru) dyad bearing the 2-(1-pyrenyl)-1H-imidazo[4,5-f][1,10]-phenanthroline (ippy) ligand was investigated by time-resolved transient absorption spectroscopy. It was found that changes in the protonation state of the imidazole group led to changes in the electronic configuration of the lowest lying excited state. Formation of the fully deprotonated imidazole...
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Theoretical estimation of acid–base properties of Lewis and Brønsted centres at the V-W-O catalyst surface: water molecule as the probe in DFT calculations
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An effective method for studying intermolecular interactions in binary liquids with hydrogen bonds: FTIR spectra and ab initio calculations in the N-methylformamide - methanol system
PublikacjaMolecular complexes in methanol (MeOH)−N-methylformamide (NMF) mixtures were studied based on their FTIR-ATR spectra, to which two methods of analysis were applied: factor analysis and a quantitative version of the difference-spectra method. The mean composition of a complex between NMF and MeOH molecules over the whole range of mixture compositions was determined. Absorbing species differentiated with regard to the interaction...
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Limonene: electronic state spectroscopy by high-resolution vacuum ultraviolet photoabsorption, electron scattering, He(I) photoelectron spectroscopy and ab initio calculations
PublikacjaZbadano limonen metodami spektroskopii absorpcyjnej, elektronowej, fotojonizacyjnej. Wyniki porównano z obliczeniami ab initio. Otrzymano strukturę wibracyjną molekuły.
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Capacity and pressure calculations in hip joint for periodic stochastic effects. Obliczanie ciśnienia i nośności w stawie biodrowym dla periodycznych stochastycznych efektów.
PublikacjaPraca przedstawia konkretne wyniki numeryczne wartości ciśnienia i sił nośnych dla hydrodynamicznego smarowania stawu biodrowego człowieka w okresowym ruchu nieustalonym z uwzględnieniem stochastycznie zmiennej wysokości szczeliny stawu przy założeniu, że współpracujące powierzchnie głowy kostnej i panewki są całkowiecie oddzielone od siebie warstwą synowialnej cieczy smarującej. Smarowanie powierzchni stawowych odbywa się tu na...
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A small-signal sound speed and parameter of non-linearity B/Ain a ternary mixture. Examples of calculations of mixture consisting of air, water and water vapor
PublikacjaZostało wyliczone zaburzenie entropii z dokładnością do członów nieliniowych rzędu drugiego. Jedyne założenie ograniczające, toże para wodna i powietrze są gazami doskonałymi. Ostatecznie,parametr nieliniowości i prędkość fali akustycznej przedstawione jako rodzinę krzywych, zależnych od trzech parametrów. Przedstawiono ilustrację tych zależności.
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Valence and Ionic Lowest-Lying Electronic States of Isobutyl Formate Studied by High-Resolution Vacuum Ultraviolet Photoabsorption, Photoelectron Spectroscopy, and Ab Initio Calculations
PublikacjaThe highest resolution vacuum ultraviolet photoabsorption spectrum of isobutyl formate, C5H10O2, yet reported is presented over the energy range 4.5−10.7 eV (275.5−118.0 nm) 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 and oscillator...
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Valence and ionic lowest-lying electronic states of small esters studied by high resolution vacuum ultraviolet photoabsorption, photoelectron spectroscopy and ab initio calculations
PublikacjaEsters are an important class of oxygenated volatile organic compounds used in food flavorings, perfumes and other cosmetic products. They are present in fruits and pheromones and are emitted to the atmosphere naturally. Esters are also formed in the atmosphere as a product of the oxidation of ethers. Some of them form poly-molecule chains and are used in plastics. Phosphoesters form DNA backbone, while nitroesters are known for...
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Preferential solvation in (amide+alcohol) binary mixtures. Part 2. The N-methylpyrrolidinone+methanol mixture at T = 313.15 K: thermodynamic resultsand molecular dynamics calculations.
PublikacjaBadano zjawisko preferencyjnej solwatacji amidu (N-metylopyrrolidonu) przez metanol wykorzystując dwie uzupełniające się metody: bezpośrednich pomiarów własności termodynamicznych roztworu oraz symulacji komputerowych. W metodzie pierwszej dokonano pomiarów wielkości termodynamicznych takich jak: nadmiarowa energia swobodna mieszania, nadmiarowa objętość mieszania oraz współczynnika ściśliwości izotermicznej mieszaniny,...
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Preferential solvation in (amide+alcohol) binary mixtures. Part 1. The N- methylpyrrolidinone+ethanol mixture at T = 313.15 K: thermodynamic resultsand molecular dynamics calculations.
PublikacjaBadano zjawisko preferencyjnej solwatacji amidu (N-metylopyrrolidonu) przez etanol wykorzystując dwie uzupełniające się metody: bezpośrednich pomiarów własności termodynamicznych roztworu oraz symulacji komputerowych. W metodzie pierwszej dokonano pomiarów wielkości termodynamicznych takich jak: nadmiarowa energia swobodna mieszania, nadmiarowa objętość mieszania oraz współczynnika ściśliwości izotermicznej mieszaniny,...
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Ultrafast Intramolecular Relaxation and Wave-Packet Motion in a Ruthenium-Based Supramolecular Photocatalyst
PublikacjaThe hydrogen-evolving photocatalyst [(tbbpy)2 Ru(tpphz)Pd(Cl)2 ](2+) (tbbpy=4,4'-di-tert-butyl-2,2'-bipyridine, tpphz=tetrapyrido[3,2-a:2',3'-c:3'',2''-h:2''',3'''-j]phenazine) shows excitation-wavelength-dependent catalytic activity, which has been correlated to the localization of the initial excitation within the coordination sphere. In this contribution the excitation-wavelength dependence of the early excited-state relaxation...
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Photophysics of Ru(II) Dyads Derived from Pyrenyl-Substitued Imidazo[4,5-f][1,10]phenanthroline Ligands.
PublikacjaThe photophysics of a series of Ru(II) dyads based on the 2-(1-pyrenyl)-1H-imidazo[4,5-f][1,10]-phenanthroline ligand was investigated. The ability of these metal complexes to intercalate DNA and induce cell death upon photoactivation makes them attractive photosensitizers for a range of photobiological applications, including photodynamic therapy. In the present study, time-resolved transient absorption and emission spectroscopy...
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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
PublikacjaThe 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...
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Cooperativity of Halogen- and Chalcogen-Bonding Interactions in the Self-Assembly of 4‑Iodoethynyl- and 4,7-Bis(iodoethynyl)benzo-2,1,3-chalcogenadiazoles: Crystal Structures, Hirshfeld Surface Analyses, and Crystal Lattice Energy Calculations
PublikacjaSeveral new 4-iodoethynyl- and 4,7-bis- (iodoethynyl)benzo-2,1,3-chalcogenadiazoles were prepared, and a comprehensive analysis of the most prominent secondary bonding interactions responsible for the crystal self-assembly was performed using X-ray diffraction. The presence of both the iodoethynyl and chalcogenadiazole moieties allows an evaluation of the preference of these molecules to aggregate through either chalcogen- or halogen-bonding...
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Theoretical Assessment of Excited State Gradients and Resonance Raman Intensities for the Azobenzene Molecule
PublikacjaThe ground state geometries and vibrational frequencies as well as the excitation energies and excited state gradients of the S 1(nπ*) and S 2(ππ * ) states of trans - and cis -azobenzene are investigated by several DFT methods, namely B3LYP, PBE, M06-2X, CAM-B3LYP, and ω B97X. Excited state properties and in particular gradients are also assessed using the wave function based methods EOM-CCSD and RASPT2/RASSCF. Comparison with...
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Arbutin: Isolation, X-ray structure and computional studies
PublikacjaArbutin, an active component originated from Serratula quinquefolia for skin-whitening use and treating skin related allergic inflammation, was characterized by microanalysis, FTIR, UV-Vis, multinuclear NMR spectroscopy, and single crystal X-ray diffraction method. The geometries of the studied compound were optimized in singlet states using the density functional theory (DFT) method with B3LYP functional. Electronic spectra were...
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Design of Structure of Tension Leg Platform for 6 MW Offshore Wind Turbine Based On Fem Analysis
PublikacjaThe article presents the calculation and design stages of the TLP platform serving as a supporting construction of a 6 MW offshore wind turbine. This platform is designed to anchor at sea at a depth of 60 m. The authors presented the method of parameterization and optimization of the hull geometry. For the two selected geometry variants, the load and motion calculations of the platform subjected to wind, wave and current under...
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Synthesis, spectroscopy and computational studies of some biologically important hydroxyhaloquinolines and their novel derivatives
PublikacjaA series crystalline compounds of methyl and phosphinyl derivatives of 2-methylquinolin-8-ol (1a) and related 5,7-dichloro-2-methylquinolin-8-ol (1b) were quantitatively prepared and characterized by microanalysis, IR, UV-vis and multinuclear NMR spectroscopy. Five of them have been characterized by single crystal X-ray diffraction method. The known compounds, 8-methoxy-2-methylquinoline (2a) and 8-methoxyquinoline (2d), were synthesised...
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Electronic States of Tris(bipyridine) Ruthenium(II) Complexes in Neat Solid Films Investigated by Electroabsorption Spectroscopy
PublikacjaWe present the electric field-induced absorption (electroabsorption, EA) spectra of the solid neat films of tris(bipyridine) Ru(II) complexes, which were recently functionalized in our group as photosensitizers in dye-sensitized solar cells, and we compare them with the results obtained for an archetypal [Ru(bpy)3]2+ ion (RBY). We argue that it is difficult to establish a unique set of molecular parameter values by discrete parametrization...
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Synthetic, Structural, and Spectroscopic Characterization of a Novel Family of High-Spin Iron(II) [(β-Diketiminate)(phosphanylphosphido)] Complexes
PublikacjaThis work describes a series of iron(II) phosphanylphosphido complexes. These compounds were obtained by reacting lithiated diphosphanes R2PP(SiMe3)Li (R = t-Bu, i-Pr) with an iron(II) β-diketiminate complex, [LFe(μ2-Cl)2Li(DME)2] (1), where DME = 1,2-dimethoxyethane and L = Dippnacnac (β-diketiminate). While the reaction of 1 with t-Bu2PP(SiMe3)Li yields [LFe(η1-Me3SiPPt- Bu2)] (2), that of 1 with equimolar amounts of i-Pr2PP(SiMe3)Li,...
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Waves in a short cable at low frequencies, or just hand-waving? What does physics say? (Invited paper)
PublikacjaWe address the question of low-frequency signals in a short cable, which are often considered as waves in engineering calculations. Such an assumption violates several laws of physics, but exact calculations can be carried out via linear network theory.
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In situ spectroelectrochemical and theoretical study on the oxidation of a 4H-imidazole-ruthenium dye adsorbed on nanocrystalline TiO2thin film electrodes
PublikacjaTerpyridine 4H-imidazole-ruthenium(ii) complexes are considered promising candidates for use as sensitizers in dye sensitized solar cells (DSSCs) by displaying broad absorption in the visible range, where the dominant absorption features are due to metal-to-ligand charge transfer (MLCT) transitions. The ruthenium(iii) intermediates resulting from photoinduced MLCT transitions are essential intermediates in the photoredox-cycle...
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Modelling of the Heat Flux Density Distribution for Laser Beam Welding
PublikacjaGreat interest of the laser beam welding in industry is a new theoretical task, making planning the welding procedure specification and the quality control of welded joints easier. Estimating and calculating the dimensions of a weld pool and temperature distribution near weld mainly concern heat source modelling. In the presented work calculations of welding pool shape and thermal field for cylindrical-powered-normally model of...
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Influence of windsurfing fin stiffness distribution on the lift-drag characteristics
PublikacjaThis article addresses the problem of determining the hydromechanical loads generated by flexible hydrofoils. The research was done on the example of the composite windsurfing fin for the RS:X monotype class. Despite the assumption of fins identity, everyday practice showed that variations of mechanical properties occur and strongly affect their performance. Therefore, we decided to study the differences between the windsurfing...