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Wyniki wyszukiwania dla: physical organic chemistry
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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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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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Photoinduced electron transfer in 5-bromouracil labeled DNA. A contrathermodynamic mechanism revisited by electron transfer theories
PublikacjaThe 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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3D Hierarchical Boron-Doped Diamond-Multilayered Graphene Nanowalls as an Efficient Supercapacitor Electrode
PublikacjaSynthesis of stable hybrid carbon nanostructure for high-performance supercapacitor electrode with long life-cycle for electronic and energy storage devices is a real challenge. Here, we present a one-step synthesis method to produce conductive boron-doped hybrid carbon nanowalls (HCNWs), where sp2-bonded graphene has been integrated with and over a three-dimensional curved wall-like network of sp3-bonded diamond. The spectroscopic...
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Molecular dynamics study on the role of solvation water in the adsorption of hyperactive AFP to the ice surface
PublikacjaUsing computer simulations, the early stages of the adsorption of the CfAFP molecule to the ice surface were analyzed. We found that the ice and the protein interact at least as early as when the protein is about 1 nm away from the ice surface. These interactions are mediated by interfacial solvation water and are possible thanks to the structural ordering of the solvent. This ordering leads to positional preference of the protein...
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5-Thiocyanato-2′-deoxyuridine as a possible radiosensitizer: electron-induced formation of uracil-C5-thiyl radical and its dimerization
PublikacjaIn this work, we have synthesized 5-thiocyanato-2′-deoxyuridine (SCNdU) along with the C6-deuterated nucleobase 5-thiocyanatouracil (6-D-SCNU) and studied their reactions with radiation-produced electrons. ESR spectra in γ-irradiated nitrogen-saturated frozen homogeneous solutions (7.5 M LiCl in H2O or D2O) of these compounds show that electron-induced S–CN bond cleavage occurs to form a thiyl radical (dU-5-S˙ or 6-D-U-5-S˙) and...
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Mechanisms of Damage to DNA Labeled with Electrophilic Nucleobases Induced by Ionizing or UV Radiation
PublikacjaHypoxia—a hallmark of solid tumors—makes hypoxic cells radioresistant. On the other hand, DNA, the main target of anticancer therapy, is not sensitive to the near UV photons and hydrated electrons, one of the major products of water radiolysis under hypoxic conditions. A possible way to overcome these obstacles to the efficient radio- and photodynamic therapy of cancer is to sensitize the cellular DNA to electrons and/or ultraviolet...
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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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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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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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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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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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MgPdSb─An Electron-Deficient Half-Heusler Phase
PublikacjaThe 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
PublikacjaMechanisms 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
PublikacjaPrion 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
PublikacjaThis 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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Atomic-Scale Finite-Element Modeling of Elastic Mechanical Anisotropy in Finite-Sized Strained Phosphorene Nanoribbons
PublikacjaNanoribbons are crucial nanostructures due to their superior mechanical and electrical properties. This paper is devoted to hybrid studies of the elastic mechanical anisotropy of phosphorene nanoribbons whose edges connect the terminals of devices such as bridges. Fundamental mechanical properties, including Young’s modulus, Poisson’s ratio, and density, were estimated from first-principles calculations for 1-layer, 3-layer, and...
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Integrated Experimental and Theoretical Approach for Efficient Design and Synthesis of Gold-Based Double Halide Perovskites
PublikacjaApplied cutting-edge electronic structure and phonon simulations provide a reliable knowledge about the stability of perovskite structures and their electronic properties, which are crucial for design of effective nanomaterials. Gold is one of the exceptional elements, which can exist both as a monovalent and a trivalent ion in the B site of a double perovskite such as A2BI BIIIX6. However, until now, electronic properties of Cs2AuI AuIIIX6...
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Non-ergodic fragmentation upon collision-induced activation of cysteine–water cluster cations
PublikacjaCysteine–water cluster cations Cys(H2O)3,6 + and Cys(H2O)3,6H+ are assembled in He droplets and probed by tandem mass spectrometry with collision-induced activation. Benchmark experimental data for this biologically important system are complemented with theory to elucidate the details of the collisioninduced activation process. Experimental energy thresholds for successive release of water are compared to water dissociation energies...
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A general approach to study molecular fragmentation and energy redistribution after an ionizing event
PublikacjaWe 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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Practical Approach to Large-Scale Electronic Structure Calculations in Electrolyte Solutions via Continuum-Embedded Linear-Scaling Density Functional Theory
PublikacjaWe present the implementation of a hybrid continuum-atomistic model for including the effects of a surrounding electrolyte in large-scale density functional theory (DFT) calculations within the Order-N Electronic Total Energy Package (ONETEP) linear-scaling DFT code, which allows the simulation of large complex systems such as electrochemical interfaces. The model represents the electrolyte ions as a scalar field and the solvent...
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Mechanism of Osmolyte Stabilization–Destabilization of Proteins: Experimental Evidence
PublikacjaIn 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
PublikacjaThe 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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Linear and Nonlinear Optical Properties of Azobenzene Derivatives Modified with an (Amino)naphthalene Moiety
PublikacjaThe 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
PublikacjaIn 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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Superconductivity in the Endohedral Ga Cluster Compound PdGa5
PublikacjaSuperconductivity 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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Revealing the Frank–Evans “Iceberg” Structures within the Solvation Layer around Hydrophobic Solutes
PublikacjaUsing 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
PublikacjaThe 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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Radiative lifetime of a BODIPY dye as calculated by TDDFT and EOM-CCSD methods: solvent and vibronic effects
PublikacjaThe 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
PublikacjaFo 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
PublikacjaIntermolecular 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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Role of the Solvation Water in Remote Interactions of Hyperactive Antifreeze Proteins with the Surface of Ice
PublikacjaMost 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...
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Dissociative ionization dynamics of dielectric gas C3F7CN
PublikacjaFluoronitrile 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.
PublikacjaTime 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?
PublikacjaMolecular 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
PublikacjaTwo-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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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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On the relationship between the structural and volumetric properties of solvated metal ions in O-donor solvents using new structural data in amide solvents
PublikacjaThe 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
PublikacjaAdiabatic 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...
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Enhanced Charge Storage Mechanism And Long-Term Cycling Stability In Diamondized Titania Nanocomposite Supercapacitors Operating In Aqueous Electrolytes
PublikacjaThe 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...