Search results for: PHYSICAL AND CHEMICAL
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The HAlF4 superacid fragmentation induced by an excess electron attachment
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Dissociative electron attachment to gas phase thiothymine: experimental and theoretical approaches
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Adaptive resolution simulation of liquid para-hydrogen: testing the robustness of the quantum-classical adaptive coupling
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Oxidizing CO2 with superhalogens
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The quantum free energy barrier for hydrogen vacancy diffusion in Na3AlH6
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Dissociative electron attachment to HGaF4 Lewis–Brønsted superacid
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Mechanisms of carbon monoxide hydrogenation yielding formaldehyde catalyzed by the representative strong mineral acid, H2SO4, and Lewis–Brønsted superacid, HF/AlF3
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Elastic moduli of biological fibers in a coarse-grained model: crystalline cellulose and β-amyloids
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Creation of mesopores in carbon nanotubes with improved capacities for lithium ion batteries
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Dynamics and stability of icosahedral Fe–Pt nanoparticles
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Defect engineering, microstructural examination and improvement of ultrafast third harmonic generation in GaZnO nanostructures: a study of e-beam irradiation
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Application of the tetraphenylphosphonium tetraphenylborate (TPTB) assumption to the thermodynamic properties of solvated ions in dimethylsulfoxide
PublicationW niniejszej pracy za pomocą spektroskopii ATR FTIR sprawdzano możliwość zastosowania tetrafenyloboranu tetrafenylofosfoniowego w metodzie elektrolitu wzorcowego, służącej do podziału wielkości termodynamicznych elektrolitów w dimetylosulfotlenku na udziały jonowe. Jednoznacznie stwierdzono, że poza termodynamiczne założenie o identycznych oddziaływaniach jonów w elektrolicie wzorcowym z cząsteczkami DMSO jest nieprawdziwe. Uzyskane...
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Hydrophobic hydration and pairwise hydrophobic interaction of Lennard-Jones and Mie particles in different water models
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Radiative lifetime of a BODIPY dye as calculated by TDDFT and EOM-CCSD methods: solvent and vibronic effects
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Raman spectroscopic study of Ni2+-DNA interactions in aqueous systems
PublicationMetodą ramanowskich widm różnicowych określono sposób oddziaływania jonu Ni2+ z DNA(CT) w układach wodnych. Kation Ni(II) koordynuje w pozycjach N7 guaniny (G) i adeniny (A) w powtarzających się sekwencjach GG, AA i GA cząsteczki DNA. Jednocześnie Ni2+ oddziałuje zewnątrz sferowo poprzez cząsteczki wody z grupami fosforanowymi DNA.
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Reactivity induced at 25 K by low-energy electron irradiation of condensed NH3-CH3COOD (1:1) mixture
PublicationW wyniku bombardowania niskoenergetycznymi elektronami skondensowanej mieszaniny kwasu octowego (CH3COOD) i amoniaku (NH3) następuje synteza najprostszego aminokwasu - glicyny - bez potrzeby dodatkowej aktywacji termicznej. Filmy molekularne przed i po bombardowaniu elektronami były badane techniką HREELS.
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Energy levels in CaWO4:Tb3+ at high pressure
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Comparison of quenching mechanisms in Gd3Al5−xGaxO12:Ce3+ (x = 3 and 5) garnet phosphors by photocurrent excitation spectroscopy
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Temperature effect on the emission spectra of narrow band Mn4+phosphors for application in LEDs
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Spectroscopic properties and location of the Tb3+ and Eu3+ energy levels in Y2O2S under high hydrostatic pressure
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Spectroscopic properties and location of the Ce3+ energy levels in Y3Al2Ga3O12 and Y3Ga5O12 at ambient and high hydrostatic pressure
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Reply to the ‘Comment on “Spectroscopic properties and location of the Ce3+ energy levels in Y3Al2Ga3O12 and Y3Ga5O12 at ambient and high hydrostatic pressure”’ by Y. Wang, M. Głowacki, M. Berkowski, A. Kamińska and A. Suchocki, Phys. Chem. Chem. Phys., 2019, 21, DOI: 10.1039/C8CP06154H
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Study of persistent luminescence and thermoluminescence in SrSi2N2O2:Eu2+,M3+(M = Ce, Dy, and Nd)
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Spectroscopic properties of high-temperature sintered SrS:0.05%Ce3+ under high hydrostatic pressure
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Spectroscopic properties and location of the Tb3+ and Eu3+ energy levels in Y2O2S under high hydrostatic pressure
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Peculiar hydrogen bonding behaviour of water molecules inside the aqueous nanochannels of lyotropic liquid crystals
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Unusual cis-diprotonated forms and fluorescent aggregates of non-peripherally alkoxy-substituted metallophthalocyanines
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Water-mediated long-range interactions between the internal vibrations of remote proteins
PublicationIt is generally acknowledged that the mobility of protein atoms and the mobility of water molecules in the solvation layer are connected. In this article, we answer the question whether a similar interdependence exists between the motions of atoms of proteins separated by the hydration layers of variable thickness. The system consisted of a kinesin catalytic domain and a tubulin dimer. It was studied using molecular dynamics simulations....
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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
PublicationTerpyridine 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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Interaction of cisplatin and two potential antitumoral platinum(ii) complexes with a model lipid membrane: a combined NMR and MD study
PublicationIn this study, the interaction of cisplatin (1) and two potential antitumoral Pt(II) complexes (2 and 3) with a model DMPC bilayer was investigated by multinuclear NMR spectroscopy and MD simulations in order to understand its implication for the different antitumoral properties shown by the three complexes. In particular, 31P, 13C and 2H solid state NMR experiments were performed to obtain information on the phase structure, phase...
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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.
PublicationBadano 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.
PublicationBadano 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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Properties of water in the region between a tubulin dimer and a single motor head of kinesin
PublicationA kinesin is a molecular motor that can perform movement on a microtubule track in a stepping-like manner. This motion is connected with processes of association and dissociation of kinesin and tubulin. Water is an important participant in these kinds of molecular interactions. This is why we have decided to investigate the dynamical and structural properties of water in the region between the kinesin catalytic domain and the tubulin...
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The importance of the shape of the protein–water interface of a kinesin motor domain for dynamics of the surface atoms of the protein
PublicationA single kinesin motor domain immersed in water has been investigated using molecular dynamics. It has been found that local properties of water in the solvation shell change along with the nature of the neighboring protein surface. However, a detailed analysis leads to the conclusion that the geometrical features of hydrogen bonds and overall structure of kinesin hydration water are not very different from bulk water. The local...
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Core–shell excitation of isoxazole at the C, N, and O K-edges – an experimental NEXAFS and theoretical TD-DFT study
PublicationThe near-edge X-ray absorption fine structure (NEXAFS) spectra of the gas-phase isoxazole molecule have been measured by collecting total ion yields at the C, N, and O K-edges. The spectral structures have been interpreted using time-dependent density functional theory (TD-DFT) with the short-range corrected SRC2-BLYP exchange–correlation functional. Experimental and calculated energies of core excitations are generally in good...
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Characteristics of hydration water around hen egg lysozyme as the protein model in aqueous solution. FTIR spectroscopy and molecular dynamics simulation
PublicationW niniejszej pracy przedstawiono wyniki badań dotyczące hydratacji białka modelowego - lizozymu z jaja kurzego w roztworze wodnym. Wiodącą techniką stosowaną w badaniach była spektroskopia oscylacyjna FTIR z zastosowaniem techniki rozcieńczenia izotopowego wody półciężkiej HDO w roztworze wody zwykłej. Analiza widma HDO przy pomocy "metody widm zaburzonych" pozwoliła na wyizolowanie widma wody zaburzonej przez lizozym, a tym samym...
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The importance of the shape of the protein-water interface of a kinesin motor domain for dynamics of the surface atoms of the protein
PublicationSingle kinesin motor domain immersed in water has been investigated using molecular dynamics. It has been found that local properties of water in solvation shell change along with the nature of neighboring protein surface. However, a detailed analysis leads to the conclusion that the geometrical features of hydrogen bonds and overall structure of kinesin hydration water is not very different from bulk water. The local values of...
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Limonene: electronic state spectroscopy by high-resolution vacuum ultraviolet photoabsorption, electron scattering, He(I) photoelectron spectroscopy and ab initio calculations
PublicationZbadano limonen metodami spektroskopii absorpcyjnej, elektronowej, fotojonizacyjnej. Wyniki porównano z obliczeniami ab initio. Otrzymano strukturę wibracyjną molekuły.
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Influence of temperature and interactions with ligands on dissociation of dsDNA and ligand-dsDNA complexes of various types of binding : an electrochemical study.
PublicationSeveral medicinally important compounds that bind to dsDNA strands via intercalation (C-1311, C-1305, EtBr), major groove binding (Hoechst 33258) and covalent binding (cis-Pt) were examined. The obtained results suggest that both the transfer of conformation B to C and the denaturation process, for the ligand-dsDNA complexes, except for covalently bound cis-Pt, took place at higher temperatures compared to the unbound helix. Furthermore,...
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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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Are stabilizing osmolytes preferentially excluded from the protein surface? FTIR and MD studies
PublicationInteractions between osmolytes and hen egg white lysozyme in aqueous solutions were studied by means of FTIR spectroscopy and molecular dynamics. A combination of difference spectra method and chemometric analysis of spectroscopic data was used to determine the number of osmolyte molecules interacting with the protein, and the preferential interaction coefficient in presented systems. Both osmolytes – L-proline and trimethylamine-N-oxide...
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A spectroscopic study of the cis/trans-isomers of penta-2,4-dienoic acid attached to gold nanoclusters
PublicationIn this theoretical work, we present a spectroscopic analysis of the cis/trans-isomers of a molecular switch, penta-2,4-dienoic acid, attached to gold clusters of different size (1, 2 and 20 gold atoms). We have simulated 4 different spectroscopic techniques: Infrared spectroscopy, normal Raman scattering, absorption spectra and resonance Raman scattering. We discuss how the position and the conformation of the molecule determine...
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Photoinduced electron transfer in 5-bromouracil labeled DNA. A contrathermodynamic mechanism revisited by electron transfer theories
PublicationThe understanding of the 5-bromouracil (BrU) based photosensitization mechanism of DNA damage is of large interest due to the potential applications in photodynamic therapy. Photoinduced electron transfer (ET) in BrU labeled duplexes comprising the 50 -GBrU or 50 -ABrU sequence showed that a much lower reactivity was found for the 50 -GBrU pattern. Since the ionization potential of G is lower than that of A, this sequence selectivity...
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Unique agreement of experimental and computational infrared spectroscopy: a case study of lithium bromide solvation in an important electrochemical solvent
PublicationInfrared (IR) spectroscopy is a widely used and invaluable tool in the studies of solvation phenomena in electrolyte solutions. Using state-of-the-art chemometric analysis of a spectral series measured in a concentration-dependent manner, the spectrum of the solute-affected solvent can be extracted, providing a detailed view of the structural and energetic states of the solvent molecules influenced by the solute. Concurrently,...
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How water mediates the long-range interactions between remote protein molecules
PublicationThe high crowding of macromolecules in the cytoplasm affects the processes that occur inside a living cell. It can, for example, promote the forming of various loosely connected structures of proteins. It also means that bulk water is, essentially, not present there. The relatively thin layer of solvent that separates macromolecules may be able to participate in the long-range interactions between them and make them respond to...
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Modelling charge transfer processes in C2+ -tetrahydrofuran collision for ion-induced radiation damage in DNA building blocks
PublicationInvestigations of collision-induced processes involving carbon ions and molecules of biological interest in particular DNA building blocks, are crucial to model the effect of radiation on cells in order to improve medical treatments for cancer therapy. Using carbon ions appears to be one of the most efficient ways to increase biological effectiveness to damage cancerous cells by irradiating deep-seated tumors. Therefore, interest...
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Water-mediated influence of a crowded environment on internal vibrations of a protein molecule
PublicationThe influence of crowding on the protein inner dynamics is examined by putting a single protein molecule close to one or two neighboring protein molecules. The presence of additional molecules influences the amplitudes of protein fluctuations. Also, a weak dynamical coupling of collective velocities of surface atoms of proteins separated by a layer of water is detected. The possible mechanisms of these phenomena are described....
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Superconductivity in CaBi2
PublicationSuperconductivity is observed with critical temperature Tc = 2.0 K in self-flux-grown single crystals of CaBi2. This material adopts the ZrSi2 structure type with lattice parameters a = 4.696(1) Å, b = 17.081(2) Å and c = 4.611(1) Å. The crystals of CaBi2 were studied by means of magnetic susceptibility, specific heat and electrical resistivity measurements. The heat capacity jump at Tc is DC/gTc = 1.41, confirming bulk superconductivity;...
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On the relationship between the structural and volumetric properties of solvated metal ions in O-donor solvents using new structural data in amide solvents
PublicationThe structures of the N,N-dimethylformamide (dmf), N,N-dimethylacetamide (dma), and N,N-dimethylpropionamide (dmp) solvated strontium and barium ions have been determined in solution using large angle X-ray scattering and EXAFS spectroscopy. The strontium ion has a mean coordination number (CN) between 6.2 and 6.8, and the barium ion has a mean CN between 7.1 and 7.8 in these amide solvents. The non-integer numbers indicates that...
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Electronic structure and rovibrational predissociation of the 2^1Π state in KLi
PublicationAdiabatic potential energy curves of the 3^1Σ^+, 3^3Σ^+, 2^1Π and 2^3Π states correlating for large internuclear distance with the K(4s) + Li(2p) atomic asymptote were calculated. Very good agreement between the calculated and the experimental curve of the 2^1Π state allowed for a reliable description of the dissociation process through a small (∼20 cm−1 for J = 0) potential energy barrier. The barrier supports several rovibrational...