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Search results for: physical chemistry
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Local Ordering Changes in Pt-Co Nanocatalyst Induced by Fuel Cell Working Conditions
PublicationPraca poświęcona jest szczegółowej analizie zmian w lokalnej strukturze atomowej i elektronowej nanocząstek Pt-Co pracujących jako katalizatory w polimerowych ogniwach paliwowych wywołanych cyklicznie zmieniającymi się warunkami pracy ogniwa. Do analizy wykorzystano badania XAS realizowane ex-situ i in-situ, XRD i TEM. Analizując widma XAFS wzięto pod uwagę możliwy wpływ nieporządku chemicznego oraz redukcję liczb koordynacyjnych...
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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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A Novel Ru(II) Polypyridine Black Dye Investigated by Resonance Raman Spectroscopy and TDDFT Calculations
PublicationThe optical properties of a new(bipyridine)2Ru(4H-imidazole) complex presenting a remarkablebroad absorption in the visible range are investigated. Thestrong overlap of the absorption with the solar radiationspectrum renders the studied complex promising as a blackabsorber and hence as a starting structure for applications inthe field of dye-sensitized solar cells. The correlations betweenstructural and electronic features for...
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Theoretical Design of the Molecular Structure of Bent-Core Mesogens with Large Second-Order Nonlinear Optical Properties
PublicationABSTRACT: The first hyperpolarizability of two series of moleculeswith bent-shaped structures has been calculated at the ab initio level.The two series consist of carboxyl derivatives for which somemolecules are known to exhibit banana phases and of their sulfinatehomologues that have not been synthesized yet. The final purpose isto reveal the relevance or not in synthesizing these latter molecules.The strategy is based on reporting...
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Structural Control of Photoinduced Dynamics in 4H-Imidazole- Ruthenium Dyes
PublicationThe photoinduced dynamics of a series ofterpyridine 4H-imidazole-ruthenium complexes, which constitutea new family of panchromatic dyes, is investigated. Thedynamics involves two excited states localized within the 4Himidazolesphere. Upon MLCT excitation, an excited state ispopulated, which is localized on the central part of the 4Himidazoleligand caused by its nonplanar conformation. Thepopulation of the second excited state is...
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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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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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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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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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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 commonly observed phenomenon of increasing water density within solvation shell of proteins. We have observed that geometry of the water-water hydrogen bond network within solvation layer differs from the one in bulk water and it is the effect of interactions of water molecules with protein surface. Altered geometry of the network reflects changes in the structure...
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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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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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Preparation of platinum modified titanium dioxide nanoparticles with the use of laser ablation in water
PublicationWe report on the preparation method of nanocrystalline titanium dioxide modified with platinum by using nanosecond laser ablation in liquid (LAL). Titania in the form of anatase crystals has been prepared in a two-stage process. Initially, irradiation by laser beam of a titanium metal plate fixed in a glass container filled with deionized water was conducted. After that, the ablation process was continued, with the use of a platinum...
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Novel Functionalization of Boron-Doped Diamond by Microwave Pulsed-Plasma Polymerized Allylamine Film
PublicationWe report the novel modification of a hydrogen-terminated polycrystalline boron-doped electrode with a microwave pulsed-plasma polymerized allylamine. Boron-doped diamond (BDD) was coated with a very thin layer of adherent cross-linked, pinhole- and additive-free allylamine plasma polymer (PPAAm) resistant to hydrolysis and delamination and characterized by a high density of positively charged amino groups. The pulsed microwave...
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Specific Binding of Cholesterol to the Amyloid Precursor Protein: Structure of the Complex and Driving Forces Characterized in Molecular Detail
PublicationC99 is the C-terminal membrane-bound fragment of the amyloid precursor protein that is cleaved by γ-secretase to release Aβ peptides, the hallmark of Alzheimer’s disease (AD). Specific interactions of C99 with cholesterol have been proposed to underlie the recognized role of cholesterol in promoting amyloidogenesis. By using molecular dynamics simulations, we studied cholesterol binding to C99 in a lipid bilayer. We determined...
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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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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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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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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...
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Redox State Sensitive Spectroscopy of the Model Compound [(H-dcbpy)(2)Ru-II(NCS)(2)](2-) (dcbpy=2,2 '-Bipyridine-4,4 '-dicarboxylato)
PublicationThe charge transfer reaction mechanism in a ruthenium polypyridine model complex with isothiocyanato ligands, i.e., [(H-dcbpy)(2)Ru(NCS)(2)](2-) 2Bu(4)N(+) (Ru2H) (dcbpy = 2,2'-bipyridine-4,4'-dicarboxylato), has been investigated by combining UV-vis absorption, resonance Raman spectroscopy, and electrochemical methods. Understanding the photophysics of light-harvesting complexes of this class is an indispensable prerequisite to...
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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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Influence of Osmolytes on Protein and Water Structure: A Step To Understanding the Mechanism of Protein Stabilization
PublicationResults concerning the thermostability of hen egg white lysozyme in aqueous solutions with stabilizing osmolytes, trimethylamine-N-oxide (TMAO), glycine (Gly), and its N-methyl derivatives, N-methylglycine (NMG), N,N-dimethylglycine (DMG), and N,N,N-trimethylglycine (betaine, TMG), have been presented. The combination of spectroscopic (IR) and calorimetric (DSC) data allowed us to establish a link between osmolytes’ influence on...
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Determination of Local Dye Concentration in Hybrid Porous Silica Thin Films
PublicationThe idea of determination of local dye concentration in a nanoporous matrix is proposed based on donor − acceptor energy transfer. The method was tested for a Rhodamine 110 − Rhodamine 101 system in silica and methylated silica nanolayers. Evaluation of acceptor (Rhodamine 101) local concentration was carried out by comparing the results of Monte Carlo simulation of energy transfer from donor (Rhodamine 110) to acceptor (Rhodamine...
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Self-assemblies of novel magnesium porphyrins mimicking natural chlorosomal bacteriochlorophylls
PublicationSelf-assembling porphyrins are promising materials to mimic natural bacteriochlorophylls c, d, or e encountered in the chlorosomes of photosynthetic bacteria. We have studied four novel magnesium porphyrins mimicking this chlorosomal antenna system. In contrast to previous articles reporting synthetic Zn-porphyrins, our studies focus on porphyrins with Mg as the central atom, which mimic more closely the natural bacteriochlorophylls....
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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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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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Programmed metalloporphyrins for self-assembly within light-harvesting stacks: 5,15-dicyano-10,20-bis(3,5-di-tert-butylphenyl)-porphyrinato zinc(II) and its push-pull 15-N,N-dialkylamino-5-cyano congeners obtained by a facile direct amination.
PublicationThe title dicyano compound was synthesized via cyanation and it self-assembles in nonpolar solvents giving red-shifted and broad absorption maxima just as the bacteriochlorophylls which are encountered in the light-harvesting organelles of early photosynthetic bacteria. In the crystal, stacks are formed through a hierarchic combination of π-stacking and a CNZn electrostatic interaction. Push−pull 15-N,N-dialkylamino-5-cyano congeners...
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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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Photosensitization of TiO2 and SnO2 by Artificial Self-Assembling Mimics of the Natural Chlorosomal Bacteriochlorophylls
PublicationOf all known photosynthetic organisms, the green sulfur bacteria are able to survive under the lowest illumination conditions due to highly efficient photon management and exciton transport enabled by their special organelles, the chlorosomes, which consist mainly of self-assembled bacteriochlorophyll c, d, or e molecules. A challenging task is to mimic the principle of self-assembling chromophores in artificial light-harvesting...
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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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Local Dye Concentration and Spectroscopic Properties of Monomer−Aggregate Systems in Hybrid Porous Nanolayers
PublicationAnalysis of absorption, fluorescence, and time-resolved emission spectra of rhodamine 6G in hybrid porous nanolayers at high dye concentration allowed identification of two fluorescent species: monomers and fluorescent aggregates. The method of determination of mean local concentration of aggregates in matrices is proposed based on the energy transfer process between monomers and fluorescent aggregates. Evaluation of aggregate...
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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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General Mechanism of Osmolytes’ Influence on Protein Stability Irrespective of the Type of Osmolyte Cosolvent
PublicationThe stability of proteins in an aqueous solution can be modified by the presence of osmolytes. The hydration sphere of stabilizing osmolytes is strikingly similar to the enhanced hydration sphere of a protein. This similarity leads to an increase in the protein stability. Moreover, the hydration sphere of destabilizing osmolytes is significantly different. These solutes generate in their surroundings so-called “structurally different...
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Multicomponent ionic liquid CMC prediction
PublicationWe created a model to predict CMC of ILs based on 704 experimental values published in 43 publications since 2000. Our model was able to predict CMC of variety of ILs in binary or ternary system in a presence of salt or alcohol. The molecular volume of IL (Vm), solvent-accessible surface (Sˆ), solvation enthalpy (DsolvGN), concentration of salt (Cs) or alcohol (Ca) and their molecular volumes (Vms and Vma, respectively) were chosen...
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Highly Visible-Light-Photoactive Heterojunction Based on TiO2 Nanotubes Decorated by Pt Nanoparticles and Bi2S3 Quantum Dots
PublicationA heterojunction with excellent visible light response and stability based on titanium dioxide nanotubes (TiO2 NTs), bismuth sulfide quantum dots (Bi2S3 QDs), and platinum nanoparticles (Pt NPs) is proposed. Both Pt NPs (3.0 ± 0.2 nm) and Bi2S3 QDs (3.50 ± 0.20 nm) are well distributed on the (i) top parts, (ii) inner walls, and (iii) outer walls of the TiO2 NTs. Visible-light-induced photoreaction was initialized by excitation...
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Diamond-Phase (Sp3-C) Rich Boron-Doped Carbon Nanowalls (Sp2-C): A Physico-Chemical And Electrochemical Properties
PublicationThe growth of B-CNW with different boron doping levels controlled by the [B]/[C] ratio in plasma, and the influence of boron on the obtained material’s structure, surface morphology, electrical properties and electrochemical parameters, such as -ΔE and k°, were investigated. The fabricated boron-doped carbon nanowalls exhibit activity towards ferricyanide redox couple, reaching the peak separation value of only 85 mV. The flatband...
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Electronic structure and time-dependent description of rotational predissociation of LiH
PublicationThe adiabatic potential energy curves of the ^1Sigma+ and ^1Pi states of the LiH molecule were calculated. They correlate asymptotically to atomic states, such as 2s + 1s, 2p + 1s, 3s + 1s, 3p + 1s, 3d + 1s, 4s + 1s, 4p + 1s and 4d + 1s. A very good agreement was found between our calculated spectroscopic parameters and the experimental ones. The dynamics of the rotational predissociation process of the 1^1Pi state were studied...
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Hydroperoxyl radical and formic acid formation from common DNA stabilizers upon low energy electron attachment
Publication2-Amino-2-(hydroxymethyl)-1,3-propanediol (TRIS) and ethylenediaminetetraacetic acid (EDTA) are key components of biological buffers and are frequently used as DNA stabilizers in irradiation studies. Such surface or liquid phase studies are done with the aim to understand the fundamental mechanisms of DNA radiation damage and to improve cancer radiotherapy. When ionizing radiation is used, abundant secondary electrons are formed...
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Dissociative electron attachment and anion-induced dimerization in pyruvic acid
PublicationWe report partial cross sections for the dissociative electron attachment to pyruvic acid. A rich fragmentation dynamics is observed. Electronic structure calculations facilitate the identification of complex rearrangement reactions that occur during the dissociation. Furthermore, a number of fragment anions produced at electron energies close to 0 eV are observed, that cannot originate from single electron-molecule collisions....
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Local Structure and Stability of SEI in Graphite and ZFO Electrodes Probed by As K-edge Absorption Spectroscopy
PublicationThe evolution of the solid electrolyte interphase (SEI) during the first Li uptake in advanced Li-ion electrodes is studied by X-ray absorption spectroscopy (XAS). The As atoms present in the electrolyte solution were used as a local probe for monitoring the SEI growth on different electrodes. High-quality As K-edge spectra were collected in fluorescence mode for a set of graphite and carbon-coated ZnFe2O4 electrodes. XAS measurements...
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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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Effect of Polymerization Statistics on the Electronic Properties of Copolymers for Organic Photovoltaics
PublicationStatistical block copolymers, composed of donor (D) and acceptor (A) blocks, are a novel type of material for organic photovoltaics (OPVs) devices. In particular a new series of polymers based on PBTZT-stat-BDTT-8, recently developed by Merck, offers high solubility in different solvents, and a high power conversion efficiency (PCE) in different device architectures. Although it is known that the electronic properties of these...
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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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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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Role of the Solvation Water in Remote Interactions of Hyperactive Antifreeze Proteins with the Surface of Ice
PublicationMost protein molecules do not adsorb onto ice, one of the exceptions being so-called antifreeze proteins. In this paper, we describe that there is a force pushing an antifreeze protein molecule away from the ice surface when it is not oriented with its ice-binding plane toward the ice and that this pushing force may be also present even when the protein is oriented with its ice-binding plane toward the ice. This force is absent...