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Wyniki wyszukiwania dla: physical organic chemistry
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Modification of Titanium (IV) Dioxide with Small Silver Nanoparticles: Application in Photocatalysis
PublikacjaThe 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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Multicomponent ionic liquid CMC prediction
PublikacjaWe 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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Diamond-Phase (Sp3-C) Rich Boron-Doped Carbon Nanowalls (Sp2-C): A Physico-Chemical And Electrochemical Properties
PublikacjaThe 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
PublikacjaThe 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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Self-Association of Amphotericin B: Spontaneous Formation of Molecular Structures Responsible for the Toxic Side Effects of the Antibiotic
PublikacjaAmphotericin 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
PublikacjaIn 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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Specific Binding of Cholesterol to the Amyloid Precursor Protein: Structure of the Complex and Driving Forces Characterized in Molecular Detail
PublikacjaC99 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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Local Structure and Stability of SEI in Graphite and ZFO Electrodes Probed by As K-edge Absorption Spectroscopy
PublikacjaThe 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
PublikacjaSuperconductivity 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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General Mechanism of Osmolytes’ Influence on Protein Stability Irrespective of the Type of Osmolyte Cosolvent
PublikacjaThe 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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Hydroperoxyl radical and formic acid formation from common DNA stabilizers upon low energy electron attachment
Publikacja2-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
PublikacjaWe 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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Unusual Influence of Fluorinated Anions on the Stretching Vibrations of Liquid Water
PublikacjaInfrared (IR) spectroscopy is a commonly used and invaluable tool in the studies of solvation phenomena in aqueous solutions. Concurrently, ab initio molecular dynamics (AIMD) simulations deliver the solvation shell picture at a molecular detail level and allow for a consistent decomposition of the theoretical IR spectrum into underlying spatial correlations. Here, we demonstrate how the novel spectral decomposition techniques...
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Effect of osmolytes on the thermal stability of proteins: replica exchange simulations of Trp-cage in urea and betaine solutions
PublikacjaAlthough osmolytes are known to modulate the folding equilibrium, the molecular mechanism of their effect on thermal denaturation of proteins is still poorly understood. Here, we simulated the thermal denaturation of a small model protein (Trp-cage) in the presence of denaturing (urea) and stabilizing (betaine) osmolytes, using the all-atom replica exchange molecular dynamics simulations. We found that urea destabilizes Trp-cage...
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Why the Solvation Water around Proteins Is More Dense than Bulk Water
PublikacjaThe 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
PublikacjaA 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
PublikacjaSeveral 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
PublikacjaA 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)
PublikacjaThe 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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Unique agreement of experimental and computational infrared spectroscopy: a case study of lithium bromide solvation in an important electrochemical solvent
PublikacjaInfrared (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
PublikacjaThe 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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U-Turn Compression to a New Isostructural Ferrocene Phase
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Unwinding Au+···Au+ Bonded Filaments in Ligand-Supported Gold(I) Polymer under Pressure
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Pressure-Enhanced Environment Effects in Ferrocene Phases
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Theoretical study of the energetics of the reactions of triplet dioxygen with hydroquinone, semiquinone, and their protonated forms: relation to the mechanism of superoxide generation in the respiratory chain = Badanie teoretyczne energii z energii reakcji dioksygenu potrójnego z wodorem, półkiną i ich formami protony: relacja z mechanizmem wytwarzania supertlenku w łańcuchu oddechowym
PublikacjaW pracy prezentujemy wyniki obliczeń kwantowych ab initio i półempirycznych energetyki reakcji redukcji jednoelektronowej tlenu trypletowego. Zaproponowaliśmy cztery możliwe mechanizmy redukcji i przeprowadziliśmy obliczenia kwantowe. Z obliczeń wynika, że najprawdopodobniejszy mechanizm reakcji wiedzie poprzez przeniesienie elektronu z anionu hydrochinonu po deprotonacji lub też z rodnika semichinonowego na tlen cząsteczkowy,...
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A low-band gap, nitrogen-modified titania visible-light photocatalyst
PublikacjaFotokatalizatory tlenku tytanu(IV) zmodyfikowanego azotem zostały zsyntetyzowane poprzez ogrzewanie wodorotlenku tytanu i mocznika w temperaturze 400ºC. Otrzymane fotokatalizatory charakteryzują się silną absorpcją w zakresie promieniowania widzialnego (400-500 nm) odznaczając się niskimi wartościami energii pasma wzbronionego (2,20 i 2,46 eV). Aktywność fotokatalityczną w świetle widzialnym potwierdzono przeprowadzając reakcję...
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Two-particle entropy and structural ordering in liquid water
PublikacjaEntropies of simple point charge (SPC) water were calculated over the temperature range 278-363 K using the two-particle correlation function approximation. Then, the total two-particle contribution to the entropy of the system was divided into three parts, which we call translational, configurational, and orientational. The configurational term describes the contribution to entropy, which originates from spatial distribution of...
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Modification of titanium dioxide with platinum ions and clusters: application in photocatalysis
PublikacjaW celu polepszenia właściwości fotokatalitycznych, TiO2 (komercyjny-P25 oraz syntezowany metoda zol-żel) był domieszkowany za pomocą jonów lub klasterów [Pt3(CO)6]62- platyny. Własności fizyczne fotokatalizatorów były badane za pomocą elektronowego mikroskopu transmisyjnego (TEM), dyfraktometru rentgenowskiego (XRD) oraz analizatora powierzchni właściwej (BET). Dyfuzyjna spektrometria odbiciowa (DRS) została zastosowana w celu...
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Hydration of simple amides. FTIR spectra of HDO and theoretical studies
PublikacjaZastosowano metodę ważonych widm różnicowych do opisu hydratacji amidów w roztworach wodnych: formamidu, N-metyloformamidu, N,N-dimetyloformaidu, acetamidu, N-metyloacetamidu, N,N-dimetyloacetamidu. Narzędziem wspomagającym interpretację wyników eksperymentalnych są struktury agregatów solwatacyjnych wokół cząsteczki substancji rozpuszczonej uzyskane na podstawie obliczeń teoretycznych metodą ab initio z korelacją elektronową...
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Molar volumes and heat capacities of electrolytes and iIons in N,N-dimethylformamide
PublikacjaZmierzono gęstości i molowe pojemności elektrolitów typu 1:1 oraz o soli o wyższych liczbach ładunkowych jonów w roztworach w N,N-dimetyloformamidzie w temperaturze 25 stopni Celsjusza. W oparciu o te pomiary wyznaczono standardowe objętości molowe oraz standardowe wartości izobarycznych ciepeł molowych. Uzyskane wartości podzielono na udziały jonowe wykorzystując tetrafenyloboran tetrafenylofosfoniowy (TPTB) jako elektrolit odniesienia....
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Structural and dynamic properties of water within the solvation layer around various conformations of the glycine-based polypeptide
PublikacjaSeveral conformations of the solvated glycine-based polypeptides were investigated using molecular dynamics simulations. Some properties of water in the neighbouring 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 it equals to approximately 0.28 nm....
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Effects of acceptor doping on a metalorganic switch: DFT vs. model analysis
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Efficient sampling of high-energy states by machine learning force fields
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Optimization of Parameters in Macromolecular Potential Energy Functions by Conformational Space Annealing
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Molecular Origin of Anticooperativity in Hydrophobic Association
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Optimization of the UNRES Force Field by Hierarchical Design of the Potential-Energy Landscape. 1. Tests of the Approach Using Simple Lattice Protein Models
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Modification and Optimization of the United-Residue (UNRES) Potential Energy Function for Canonical Simulations. I. Temperature Dependence of the Effective Energy Function and Tests of the Optimization Method with Single Training Proteins
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Potential of Mean Force of Association of Large Hydrophobic Particles: Toward the Nanoscale Limit
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Hydrophobic hydration and pairwise hydrophobic interaction of Lennard-Jones and Mie particles in different water models
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Development of Physics-Based Energy Functions that Predict Medium-Resolution Structures for Proteins of the α, β, and α/β Structural Classes
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Molecular Simulation Study of the Potentials of Mean Force for the Interactions between Models of Like-Charged and between Charged and Nonpolar Amino Acid Side Chains in Water
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Comment on “Molecular Origin of Anticooperativity in Hydrophobic Association”
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Optimization of the UNRES Force Field by Hierarchical Design of the Potential-Energy Landscape. 3. Use of Many Proteins in Optimization
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Global Optimization-Based Method for Deriving Intermolecular Potential Parameters for Crystals
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Reply to “Comment on ‘Crystal Structure Prediction by Global Optimization as a Tool for Evaluating Potentials: Role of the Dipole Moment Correction Term in Successful Predictions'” by B. P. van Eijck and J. Kroon
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Chemical Vapor Transport Route toward Black Phosphorus Nanobelts and Nanoribbons
PublikacjaChemical 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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Potential of Mean Force of Hydrophobic Association: Dependence on Solute Size
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Parametrization of Backbone−Electrostatic and Multibody Contributions to the UNRES Force Field for Protein-Structure Prediction from Ab Initio Energy Surfaces of Model Systems
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Optimization of the UNRES Force Field by Hierarchical Design of the Potential-Energy Landscape. 2. Off-Lattice Tests of the Method with Single Proteins
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Extension of the UNRES Coarse-Grained Force Field to Membrane Proteins in the Lipid Bilayer
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