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Search results for: physical organic chemistry
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Dissociative ionization dynamics of dielectric gas C3F7CN
PublicationFluoronitrile C3F7CN is a promising candidate for the replacement of SF6 dielectric gas in high-voltage insulation. We present a combined experimental and theoretical study on its ionization dynamics probed in the 0-100 eV energy range. We exploited the total ion collection technique to determine the absolute ionization cross section, mass spectrometry to determine the fragment branching ratios and ab initio nonadiabatic molecular...
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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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Why is the cubic structure preferred in newly formed ice?
PublicationMolecular dynamics was employed to explain the preference for the cubic structure in newly formed crystals of ice. The results showed that in supercooled liquid water the molecules connected by hydrogen bonds are more likely to adopt relative orientations similar to the ones characteristic for cubic ice. The observed preference for certain relative orientations of molecules in the hydrogen-bonded pairs results in the higher probability...
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Electrochemical Stability of Few-Layered Phosphorene Flakes on Boron-Doped Diamond: A Wide Potential Range of Studies in Aqueous Solutions
PublicationTwo-dimensional phosphorene has attracted great interest since its discovery as a result of its extraordinary properties. Two-dimensional single crystals of phosphorene can be useful for electrochemical (EC) sensing applications due to their enhanced surface-to-volume ratio. We proposed to investigate the electrochemical performance of phosphorene deposited directly on boron-doped diamond (BDD) electrodes. Noncovalent interaction...
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Mollecular mechanism and chemicl kinetic description of nitrobenzene liquid membrane oscillator containing benzyldimethyltetradecylammonium chloride surfactant
PublicationBadano oscylacje róznicy potencjału między fazami wodnymi oscylatora z nitrobenzenową membraną ciekłą zawierającego chlorek benzylodimetylotetradecyloamoniowy. Opisano chemię fizyczną tego oscylatora oraz omówiono rolę efektów hydrodynamicznych w powstawaniu oscylacji. Zaproponowano nowy mechanizm oparty na transferze masy par jonowych. Oscylacje są generowane na granicy faza akceptowa/ membrana ciekła i są spowodowane autokatalityczną...
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Effects of Urea and Trimethylamine-N-oxide on the Properties of Water and the Secondary Structure of Hen Egg White Lysozyme
PublicationW celu określenia sposobu hydratacji mocznika i N-tlenku trimetyloaminy, wykorzystano spektroskopię oscylacyjną FTIR. Dane eksperymentalne, otrzymane z pomiarów widm oscylacyjnych wody półciężkiej (HDO) rozcieńczonej izotopowo w wodnych roztworach badanych związków, analizowane były za pomocą "metody widm różnicowych". Strukturalno-energetyczna charakterystyka wody zaburzonej przez cząsteczki osmolitów wskazuje, że woda zaburzona...
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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
PublicationMolecular 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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How the “Liquid Drop” Approach Could Be Efficiently Applied for Quantitative Structure–Property Relationship Modeling of Nanofluids
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Study of Phase Transformation Processes Occurring in the Nanocrystalline Iron/Ammonia/Hydrogen System by the Magnetic Permeability Measurement Method
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Promotion of Photocatalytic Hydrogen Evolution under Visible Light with NiO/C Fabricated via a Super Facile and General Strategy
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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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Revealing the Frank–Evans “Iceberg” Structures within the Solvation Layer around Hydrophobic Solutes
PublicationUsing computer simulations, the structural properties of solvation water of three model hydrophobic molecules, methane and two fullerenes (C60 and C80), were studied. Systems were simulated at temperatures in the range of 250−298 K. By analyzing both the local ordering of the molecules of water in the solvation layers and the structure of hydrogen bond network, it is shown that in the solvation layer of hydrophobic molecules, ordered...
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Light-Modulated Sunscreen Mechanism in the Retina of the Human Eye
PublicationThe functioning of the human eye in the extreme range of light intensity requires a combination of the high sensitivity of photoreceptors with their photostability. Here, we identify a regulatory mechanism based on dynamic modulation of light absorption by xanthophylls in the retina, realized by reorientation of pigment molecules induced by trans–cis photoisomerization. We explore this photochemically switchable system using chromatographic...
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Chemical Vapor Transport Route toward Black Phosphorus Nanobelts and Nanoribbons
PublicationChemical vapor transport (CVT) method is widely used for bulk black phosphorus (BP) fabrication. In this work, we demonstrate that CVT provides a route for the fabrication of BP nanoribbons and nanobelts. This method consists of a two-step procedure, including initial BP column growth using the CVT technique, followed by ultrasonic treatment and centrifugation. The obtained nanostructures preserve BP column dimensions, forming...
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Anionic states of C6Cl6 probed in electron transfer experiments
PublicationThis is the first comprehensive investigation on the anionic species formed in collisions of fast neutral potassium (K) atoms with neutral hexachlorobenzene (C6Cl6) molecules in the laboratory frame range from 10 up to 100 eV. In such ion-pair formation experiments, we also report a novel K+ energy loss spectrum obtained in the forward scattering giving evidence of the most accessible electronic states. The vertical electron affinity...
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Linear and Nonlinear Optical Properties of Azobenzene Derivatives Modified with an (Amino)naphthalene Moiety
PublicationThe design of two-photon absorbing azobenzene (AB) derivatives has received much attention; however, the two-photon absorption (2PA) properties of bis-conjugated azobenzene systems are relatively less explored. Here, we present the synthesis of six azobenzene derivatives and three bisazobenzenes substituted (or not) at para position(s) with one or two amino group(s). Their linear and nonlinear absorption properties are studied...
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Solubility of Methane in Water: Some Useful Results for Hydrate Nucleation
PublicationIn this paper, the solubility of methane in water along the 400 bar isobar is determined by computer simulations using the TIP4P/Ice force field for water and a simple LJ model for methane. In particular, the solubility of methane in water when in contact with the gas phase and the solubility of methane in water when in contact with the hydrate has been determined. The solubility of methane in a gas–liquid system decreases as temperature...
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MgPdSb─An Electron-Deficient Half-Heusler Phase
PublicationThe half-Heusler family consists of many semiconducting intermetallic compounds, virtually all of them having a valence electron count (VEC) of 18. We have studied an electron-deficient (VEC = 17) phase MgPdSb and its Pd-stuffed variant MgPd1.25Sb. The cubic F4̅3m crystal structure was confirmed by the Rietveld refinement of powder X-ray diffraction (XRD) data. The lattice parameter is a = 6.284 and 6.335 Å for MgPdSb and MgPd1.25Sb,...
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Hopping or Tunneling? Tailoring the Electron Transport Mechanisms through Hydrogen Bonding Geometry in the Boron-Doped Diamond Molecular Junctions
PublicationMechanisms of charge transport in molecular junctions involving hydrogen bonds are complex and remain mostly unclear. This study is focused on the elucidation of the electron transfer in a molecular device consisting of two boron-doped diamond interfaces bound with an aromatic linker and a hydrogen bonding surrogating molecule. The projected local density of states (PLODS) analysis coupled with transmission spectra and current−voltage...
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Early Stages of RNA-Mediated Conversion of Human Prions
PublicationPrion diseases are characterized by the conversion of prion proteins from a PrPC fold into a disease-causing PrPSC form that is self-replicating. A possible agent to trigger this conversion is polyadenosine RNA, but both mechanism and pathways of the conversion are poorly understood. Using coarse-grained molecular dynamic simulations we study the time evolution of PrPC over 600 μs. We find that both the D178N mutation and interacting...
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Properties of Oxygen Vacancy and Hydrogen Interstitial Defects in Strontium Titanate: DFT + Ud,p Calculations
PublicationThis work presents extensive theoretical studies focused on the mixed ion-electron transport in cubic strontium titanate (STO). A new approach to the description of this difficult system was developed within the framework of linear-scaling Kohn–Sham density functional theory, as realized in the ONETEP program. The description we present is free of any empirical parameters and relies on the Hubbard U and Hund’s J corrections applied...
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Radiative lifetime of a BODIPY dye as calculated by TDDFT and EOM-CCSD methods: solvent and vibronic effects
PublicationThe radiative emission lifetime and associated S1 excited state properties of a BODIPY dye are investigated with TDDFT and EOM-CCSD calculations. The effects of a solvent are described with the polarizable continuum model using the linear response (LR) approach as well as state-specific methods. The Franck–Condon (FC), Herzberg–Teller (HT) and Duschinsky vibronic effects are evaluated for the absorption and emission spectra, and...
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Determinants of Directionality and Efficiency of the ATP Synthase Fo Motor at Atomic Resolution
PublicationFo subcomplex of ATP synthase is a membrane-embedded rotary motor that converts proton motive force into mechanical energy. Despite a rapid increase in the number of high-resolution structures, the mechanism of tight coupling between proton transport and motion of the rotary c-ring remains elusive. Here, using extensive all-atom free energy simulations, we show how the motor’s directionality naturally arises from the interplay...
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Guanosine Dianions Hydrated by One to Four Water Molecules
PublicationIntermolecular interactions such as those present in molecule···water complexes may profoundly influence the physicochemical properties of molecules. Here, we carried out an experimental–computational study on doubly deprotonated guanosine monophosphate···water clusters, [dGMP – 2H]2–·nH2O (n = 1–4), using a combination of negative anion photoelectron spectroscopy (NIPES) with molecular dynamics (MD) and quantum chemical (QM) calculations....
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Mechanism of Osmolyte Stabilization–Destabilization of Proteins: Experimental Evidence
PublicationIn this work, we investigated the influence of stabilizing (N,N,N-trimethylglycine) and destabilizing (urea) osmolytes on the hydration spheres of biomacromolecules in folded forms (trpzip-1 peptide and hen egg white lysozyme─hewl) and unfolded protein models (glycine─GLY and N-methylglycine─NMG) by means of infrared spectroscopy. GLY and NMG were clearly limited as minimal models for unfolded proteins and should be treated with...
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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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Enhanced Charge Storage Mechanism And Long-Term Cycling Stability In Diamondized Titania Nanocomposite Supercapacitors Operating In Aqueous Electrolytes
PublicationThe long cycle life stability jointly with high energy density are limiting broader feasible applications of supercapacitors. The novel diamondized titania nanocomposite supercapacitors deliver high power and energy densities along with high capacitance retention rates. Supercapacitor electrodes were fabricated utilizing a combination of Ti anodization followed by chemical vapor deposition resulting in simultaneous growth of complex...
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Systematic Water Uptake Energetics of Yttrium-Doped Barium Zirconate—A High Resolution Thermochemical Study
PublicationA combination of surface area analyzer and microcalorimetry was employed to investigate the in situ water uptake energetics and the mechanism of proton incorporation in yttrium-doped barium zirconate in the temperature range 200–400 °C. The BaZr1–xYxO3 solid solutions are made with variable yttrium content (x = 10, 20, and 30 mol %) by a controlled oxidant-peroxo synthesis method. The water uptake increases as the partial pressure...
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A general approach to study molecular fragmentation and energy redistribution after an ionizing event
PublicationWe propose to combine quantum chemical calculations, statistical mechanical methods, and photoionization and particle collision experiments to unravel the redistribution of internal energy of the furan cation and its dissociation pathways. This approach successfully reproduces the relative intensity of the different fragments as a function of the internal energy of the system in photoelectron–photoion coincidence experiments and...
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Superconductivity in the Endohedral Ga Cluster Compound PdGa5
PublicationSuperconductivity is observed below Tc = 1.6 K in an endohedral Ga cluster compound PdGa5 using magnetization and heat capacity measurements. Electronic structure calculations show that the density of states (DOS) at the Fermi level is dominated by Ga s and p states and that the overall shape of DOS is similar to what was found in other endohedral Ga cluster superconductors, such as MoxGa5x+1, ReGa5, and T2Ga9 (T = Rh and Ir)....
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Practical Approach to Large-Scale Electronic Structure Calculations in Electrolyte Solutions via Continuum-Embedded Linear-Scaling Density Functional Theory
PublicationWe 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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Effect of the Catalytic Center on the Electron Transfer Dynamics in Hydrogen-Evolving Ruthenium-Based Photocatalysts Investigated by Theoretical Calculations
PublicationThe 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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Hydration of Carboxylate Anions: Infrared Spectroscopy of Aqueous Solutions
PublicationHydratacja anionów karboksylanowych w roztworach wodnych ich soli sodowych została zbadana przy wykorzystaniu spektroskopii FTIR z zastosowaniem cząsteczki HDO jako sondy molekularnej. Do wyznaczenia widm wody zaburzonej przez rozpuszczalnik wykorzystano ilościową wersję metody widm różnicowych. Widma te wykazują dwa pasma składowe przy ok. 2550 i ok. 2420 cm-1. Pasma te przypisano grupie -COO- anionu R-COO- (R = H, CH3, C2H5),...
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Systematic Study of Hydration Patterns of Phosphoric(V) Acid and Its Mono-, Di-, and Tripotassium Salts in Aqueous Solution
PublicationSpektroskopia oscylacyjna FTIR w zakresie drgania OD cząsteczki HDO została zastosowana do zbadania różnych form fosforanów w kolejności malejącego stopnia protonacji: H3PO4, KH2PO4, K2HPO4, K3PO4. HDO rozcieńczona izotopowo w H2O została otrzymana przez dodanie odpowiednich ilości wody ciężkiej (D2O) do roztworów w wodzie zwykłej. Do wyizolowania widm HDO zaburzonej przez substancję rozpuszczoną zastosowano metodę widm różnicowych....
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Ionic liquids: predictions of physicochemical properties with experimental and/or DFT-calculated LFER parameters to understand molecular interactions in solution
PublicationPublikacja zawiera modele pozwalające na przewidywanie współczynnika podziału oktanol-woda (log P), rozpuszczalności w wodzie oraz krytycznego stężenia micelizacji (CMC) cieczy jonowych oraz współczynników aktywności anionowej i hydrofobowości w wodzie i w mieszaninie oktanolu z wodą. Modele oparte są na liniowych zależnościach energii swobodnej (LFER) i wykorzystują parametry zmierzone i/lub wyliczone na podstawie funkcjonalnej...
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Long-Distance FRET Analysis: A Monte Carlo Simulation Study
PublicationZaproponowano nową metodę na rozszerzenie zakresu stosowalności rezonansowego transferu energii (FRET) przetestowaną przy pomocy metody Monte Carlo. Otrzymane rezultaty dowodzą, że wydajność procesu FRET może być znacząco zwiększona w porównaniu z wydajnością pojedynczego akceptora, gdy dla ustalonej od donora umieścimy układ blisko siebie położonych akceptorów na makromolekule. Z drugiej strony metoda ta umożliwia zwiększenie...
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On the Possibility of the Amphotericin B-Sterol Complex Formation in Cholesterol- and Ergosterol-Containing Lipid Bilayers: A Molecular Dynamics Study
PublicationAmphotericin B (AmB) is a well-known membrane-active antibiotic that has been used to treat systemicfungal infections for more than 45 years. Therapeutic application of AmB is based on the fact that it is moreactive against ergosterol-containing membranes of fungal cells than against mammalian membranes withcholesterol. In this paper, we examine the hypothesis according to which the selectivity of the AmB's membraneaction originates...
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Electron attachment and electron iozization of acetic acid clusters embedded in helium nanodroplets
PublicationThe effect of incident electrons on acetic acid clusters is explored for the first time. The acetic acid clusters are formed inside liquid helium nanodroplets and both cationic and anionic productsejected in to the gas phase aredetected by mass spectrometry.
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Visible-light-induced photocatalysis through surface Plasmon excitation of gold on titania surfaces
PublicationPietnascie komercyjnych probek tlenku tytanu(IV) zostalo zmodyfikowanych zlotem za pomoca fotodepozycji oraz scharakteryzowanych. Fotoaktywnosci proszkow Au/TiO2 zostaly przebadane dla fotodegradacji kwasu octowego i 2-propanolu podczas naswietlania promieniowaniem widzialnym oraz ultrafioletowym. Wykazano, ze fotokatalityczne aktywnosci scisle zaleza od wlasciwosci nanoczastek zlota i tlenku tytanu. Analizy spektrum działania...
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A XAS study of a highly diluted Pt electrocatalyst operating in PEM fuel cells
PublicationWe present an X-ray absorption spectroscopy (XAS) study of a low Pt content catalyst layer(Pt loading 0.1 mg c2) operating at the cathode of a proton exchange membrane fuel cell(PEMFC). This catalyst is based on the use of a mesoporous inorganic matrix as a support forthe catalyst Pt nanoparticles. Due to the high Pt dilution, in situ measurements of itsstructural properties by XAS are challenging and suitable experimental strategies...
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Structural properties of hydration shell around various conformations of simple polypeptides
PublicationIn this paper we investigate structural properties of water within the solvation shell around the peptide core created by a well-defined conformation of polypeptide chain. The following secondary structures are investigated: linear (straight chain), and three helices PII (polyproline-like), 310, and α. We propose using the two-particle contribution to entropy as a rational measure of the water structural ordering within the solvation...
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Self-Association of Amphotericin B: Spontaneous Formation of Molecular Structures Responsible for the Toxic Side Effects of the Antibiotic
PublicationAmphotericin B (AmB) is a lifesaving antibiotic used to treat deep-seated mycotic infections. Both the pharmaceutical activity and highly toxic side effects of the drug rely on its interaction with biomembranes, which is governed by the molecular organization of AmB. In the present work we present detailed analysis of self-assembly of AmB molecules in different environments, interesting from the physiological standpoint, based...
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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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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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Modification of Titanium (IV) Dioxide with Small Silver Nanoparticles: Application in Photocatalysis
PublicationThe surface of commercial TiO2 compounds (P25 and ST01) has been modified with Ag nanoparticles induced by radiolysis. On P25, the Ag nanoclusters are very small (1−2 nm) and homogeneous in size while on ST01, two populations of nanoparticles are obtained, small nanoparticles (1−2 nm) and larger ones (mean diameter 7 to 12 nm depending on the silver loading). The photocatalytic properties of Ag-modified TiO2 have been studied for...
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SOLUBILIZATION OF BENZENE, TOLUENE, AND XYLENE (BTX) IN AQUEOUS MICELLAR SOLUTIONS OF AMPHIPHILIC IMIDAZOLIUM IONIC LIQUIDS
PublicationRozpuszczalne w wodzie ciecze jonowe wykazują aktywność powierzchniową oraz zdolność do tworzenia zorganizowanych struktur w roztworach wodnych. W pracy przedstawiono zdolność wodnych układów micelarnych chlorków 1-alkilo-3-metyloimidazoliowych do zwiększania rozpuszczalności węglowodorów aromatycznych – benzenu, toluenu i ksylenu. Zaobserwowano, że po przekroczeniu krytycznego stężenia micelizacji cieczy jonowych w wodzie, następuje...
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Why the Solvation Water around Proteins Is More Dense than Bulk Water
PublicationThe main aim of this work is to propose a rational explanation of the commonly observed phenomenon of increasing water density within solvation shell of proteins. We have observed that the geometry of the water–water hydrogen bond network within solvation layer differs from the one in bulk water, and it is the result of interactions of water molecules with protein surface. Altered geometry of the network reflects changes in the...
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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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Structural and Dynamic Properties of Water within the Solvation Layer around Various Conformations of the Glycine-based Polypeptide
PublicationSeveral conformations of the solvated glycine-based polypeptides were investigated using molecular dynamics simulations. Some properties of water in the neighboring space around these molecules were investigated. It was found that water forms a well-defined layer—the first solvation shell—around the peptide molecule, and thickness of this layer is independent of the peptide structure and is equal to approximately 0.28 nm. Within...
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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...