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Wyniki wyszukiwania dla: atom-molecule interaction
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Hydrogen migration in formation of NH(A3Π) radicals in photodissociations of isoxazole and pyridine molecules
PublikacjaIn the present study, the H atom migration was observed in the photodissociation processes of the isoxazole and pyridine molecules in the gas-phase, applying the photon-induced fluorescence spectroscopy (PIFS).
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(μ2-4,4'-Bipyridyl-κ2N:N')bis[bis(tri-tert-butoxysilanothiolato- κ2S,O)cadmium(II)] tetrahydrofuran disolvate
PublikacjaW strukturze tytułowego kompleksu znajdują się oddzielne cząsteczki, w których każdy atom kadmu jest koordynowany przez dwa atomy siarki, dwa atomy tlenu i jeden atom azotu. Geometria każdego z atomów kadmu jest pośrednia pomiędzy piramidą o podstawie kwadratu a bipiramidą trygonalną. Dwie jednostki tri-tert-butoksysilanotiolanu kadmu są połączone cząsteczką 4,4'-bipirydylu. Dodaktowo w strukturze kompleksu znajdują się dwie cząsteczki...
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(2-Ethylimidazole-κN)bis(tri-tert-butoxysilanethiolato-κ2O,S)zinc(II) propan-2-ol solvate
PublikacjaW publikowanym związku [Zn(C12H27O3SSi)2(C5H8N2)]*C3H8O, atom Zn(II) jest koordynowany przez atom azotu 2-etyloimidazolu, dwa atomy siarki i dwa atomy tlenu pochodzące od reszt tri-tert-butoksysilanotiolanowych, a geometria na atomie cynku(II) jest typu trygonalnej bipiramidy. Grupa hydroksylowa cząsteczki rozpuszczalnika 2-propanolu tworzy dwa wiązania wodorowe typu N-H - O i O-H - S z sąsiednią czasteczkĄ kompleksu, przez co...
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Synchrotron radiation photoemission spectroscopy of the oxygen modified CrCl3 surface
PublikacjaWe investigate the experimentally challenging CrCl3 surface by photon energy dependent photoemission (PE). The core and valence electrons after cleavage of a single crystal, either in a ultrahigh vacuum (UHV) or in air, are studied by keeping the samples at 150 1C, aiming at confirming the atomic composition with respect to the expected bulk atomic structure. A common spectroscopic denominator revealed by data is the presence of...
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An insight into the mixed quantum mechanical-molecular dynamics simulation of a ZnII-Curcumin complex with a chosen DNA sequence that supports experimental DNA binding investigations
PublikacjaAn important aspect of research pertaining to Curcumin (HCur) is the need to arrest its degradation in aqueous solution and in biological milieu. This may be achieved through complex formation with metal ions. For this reason, a complex of HCur was prepared with ZnII, that is not likely to be active in redox pathways, minimizing further complications. The complex is monomeric, tetrahedral, with one HCur, an acetate and a molecule...
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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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Monosaccharides as Potential Chiral Probes for the Determination of the Absolute Configuration of Secondary Alcohols
PublikacjaHerein, a new method for the elucidation of the absolute configuration of chiral secondary alcohols is proposed. This method is an alternative for a widely used approach reported by Mosher and Dale and similar methods that are based on the 1H NMR shift (δ) changes of protons that are attached to the substituents of the oxymethine carbon atom. The presented method is not based on tracking the chemical shift changes and utilizes...
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Bromidotetrakis(2-isopropyl-1Himidazole-kN3)copper(II) bromide
PublikacjaAtom Cu(II) w tytułowym kompleksie jest skoordynowany przez cztery atomy N obojętnych cząsteczek imidazolu oraz jon bromkowy. Jon kompleksowy ma geometrię piramidy kwadratowej.
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Why do G-quadruplexes dimerize through the 5’-ends? Driving forces for G4 DNA dimerization examined in atomic detail
PublikacjaG-quadruplexes (G4) are secondary structures formed by guanine-rich nucleic acid sequences and shown to exist in living cells where they participate in regulation of gene expression and chromosome maintenance. G-quadruplexes with solvent-exposed guanine tetrads show the tendency to associate together through cofacial stacking, which may be important for packaging of G4-forming sequences and allows for the design of higher-order...
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Interactions of protons with furan molecules studied by collision-induced emission spectroscopy at the incident energy range of 50–1000 eV
PublikacjaInvestigations of the ion-molecule reactions provide insight into many fields ranging from the stellar wind interaction with interstellar media, up to medicine and industrial applications. Besides the applications, the understanding of these processes is itself a problem of fundamental importance. Thus, interactions of protons with the gas-phase furan molecules have been investigated for the first time in the energy range of 50–1000...
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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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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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Force-deformation spectroscopy in contact mode
Dane BadawczeThe deformation-distance spectroscopic curve is obtained by registering the value of the probe cantilever deflection as a function of the elongation of the piezoelectric scanner. It assumes a simple relationship in the form of Hooke’s law, linking the deformation of the lever with the amount of its deflection caused by the proximity of the probe and...
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2-Methylphenyl 2-methoxyacridine-9-carboxylate
PublikacjaThe title compound, C22H17NO3, crystallizes in the monoclinic space group P21/c with four molecules per unit cell. The molecules are arranged in centrosymmetric pairs, joined via the C and attached H atoms in the meta position relative to the methoxy group. These pairs are bonded in the crystalline phase as a result of non-specific dispersive interactions, and through a network of C—H⋯O interactions involving the non-bonded O...
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Hydration of Oxometallate Ions in Aqueous Solution
PublikacjaThe strength of hydrogen bonding to and structure of hydrated oxometallate ions in aqueous solution have been studied by double difference infrared (DDIR) spectroscopy and large-angle X-ray scattering (LAXS), respectively. Anions are hydrated by accepting hydrogen bonds from the hydrating water molecules. The oxygen atom of the permanganate and perrhenate ions form weaker and longer hydrogen bonds to water than the hydrogen bonds...
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Electronic states of tetrahydrofuran molecules studied by electron collisions
PublikacjaElectronic states of tetrahydrofuran molecules were studied in the excitation energy range 5.5-10 eV using the technique of electron energy loss spectroscopy in the gas phase. Excitation from the two conformations, C2 and Cs, of the ground state of the molecule are observed in the measured energy loss spectra. The vertical excitation energies of the 3(no3s) triplet state from the C2 and Cs conformations of the ground state of the...
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Changes of Conformation in Albumin with Temperature by Molecular Dynamics Simulations
PublikacjaThis work presents the analysis of the conformation of albumin in the temperature range of 300K – 312K, i.e., in the physiological range. Using molecular dynamics simulations, we calculate values of the backbone and dihedral angles for this molecule. We analyze the global dynamic properties of albumin treated as a chain. In this range of temperature, we study parameters of the molecule and the conformational entropy derived from...
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Collision-induced luminescence spectra of pyridine bombarded by 1000 eV He+ cations
PublikacjaHere we show collision-induced luminescence spectra measured for collisions of the He+cations with thearomatic six-membered ring of the pyridine molecule (C5H5N). Distinct emission bands due to the CH(A2Δ→X2Πr;B2Σ+→X2Πr;C2Σ+→X2Πr), CN(B2Σ+→X2Σ+), C2(d3Πg→a3Πu), and NH(A3Π→X3Σ−) transitions, aswell as atomic H, He, and C lines have been observed. Apart from the He atoms, all the emitters arise from thefragmentation of the pyridine...
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International Conference on Relations, Orders and Graphs: Interaction with Computer Science
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International Conference on Multimodal Interaction (International Conference on Multimodal Interfaces)
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CHI PLAY: The Annual Symposium on Computer-Human Interaction in Play
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International Conference on Human-Computer Interaction with Mobile Devices and Services
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International Conference on Interaction Sciences: Information Technology, Culture and Human
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Visual Information Communication and Interaction (Visual Information Communications International)
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Low to intermediate energy elastic electron scattering from dichloromethane (CH2Cl2)
PublikacjaWe report a theoretical-experimental investigation of electron scattering by dichloromethane (CH2Cl2) in the low- and intermediate energy ranges. Experimental elastic differential cross sections (DCS), in the incident electron energy range of 0.5-800 eV and scattering angle range of 10°–130°, were measured using a crossed beam relative flow technique. Integral and momentum- transfer cross sections were determined from the experimental...
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TINKTEP: A fully self-consistent, mutually polarizable QM/MM approach based on the AMOEBA force field
PublikacjaWe present a novel quantum mechanical/molecular mechanics (QM/MM) approach in which a quantum subsystem is coupled to a classical subsystem described by the AMOEBA polarizable force field. Our approach permits mutual polarization between the QM and MM subsystems, effected through multipolar electrostatics. Self-consistency is achieved for both the QM and MM subsystems through a total energy minimization scheme. We provide an expression...
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Computational analysis of substituent effects on proton affinity and gas-phase basicity of TEMPO derivatives and their hydrogen bonding interactions with water molecules
PublikacjaThe study investigates the molecular structure of 2,2,6,6-tetramethylpiperidine-1-oxyl (TEMPO) and its derivatives in the gas phase using B3LYP and M06-2X functional methods. Intermolecular interactions are analyzed using natural bond orbital (NBO) and atoms in molecules (AIM) techniques. NO2-substituted TEMPO displays high reactivity, less stability, and softer properties. The study reveals that the stability of TEMPO derivatives...
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Unraveling the Interplay between DNA and Proteins: A Computational Exploration of Sequence and Structure-Specific Recognition Mechanisms
PublikacjaMy PhD dissertation focused on DNA-protein interactions and the recognition of specific DNA sequences and structures. I discovered that acidic amino acid residues (Asp/Glu) play a crucial role by exhibiting a preference for cytosine. Their contribution to binding affinity depends on nearby cytosines, balancing electrostatic repulsion with specific interactions. Acidic residues act as negative selectors, discouraging non-cytosine...
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Nonlinear increase in bubbles radii caused by sound in a bubbly liquid
PublikacjaThe nonlinear interaction of acoustic and entropy modes in a bubbly liquid is considered. The reasons for interaction are both nonlinearity and dispersion. In the field of intense sound, a decrease in the mixture density is predicted. That corresponds to the well-established growth of bubbles volumes due to rectified diffusion. The nonlinear interaction of modes as a reason for a bubble to grow due to sound, is discovered. The...
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Muramyl dipeptide-based analogs as potential anticancer compounds: Strategies to improve selectivity, biocompatibility, and efficiency
PublikacjaAccording to the WHO, cancer is the second leading cause of death in the world. This is an important global problem and a major challenge for researchers who have been trying to find an effective anticancer therapy. A large number of newly discovered compounds do not exert selective cytotoxic activity against tumorigenic cells and have too many side effects. Therefore, research on muramyl dipeptide (MDP) analogs has attracted interest...
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Geometry optimization of steroid sulfatase inhibitors - the influence on the free binding energy with STS
PublikacjaIn the paper we review the application of two techniques (molecular mechanics and quantum mechanics) to study the influence of geometry optimization of the steroid sulfatase inhibitors on the values of descriptors coded their chemical structure and their free binding energy with the STS protein. We selected 22 STS-inhibitors and compared their structures optimized with MM+, PM7 and DFT B3LYP/6–31++G* approaches considering separately...
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Amides as models to study the hydration of proteins and peptides — spectroscopic and theoretical approach on hydration in various temperatures
PublikacjaInteractions with water are one of the key factors which determine protein stability and activity in aqueous solutions. However, the protein hydration is still insufficiently understood. N-methylacetamide (NMA) is regarded as a minimal part of the peptide backbone and the relative simplicity of its structure makes it a good model for studies on protein–water interactions. In this paper, the influence of NMA and N,N-dimethylacetamide...
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Swapping Space for Time: An Alternative to Time-Domain Interferometry
PublikacjaYoung's double-slit experiment [1] requires two waves produced simultaneously at two different points in space. In quantum mechanics the waves correspond to a single quantum object, even as complex as a big molecule. An interference is present as long as one cannot tell for sure which slit is chosen by the object. The more we know about the path, the worse the interference. In the paper we show that quantum mechanics allows for...
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Modelowanie współpracy odbieraka prądu z siecią trakcyjną
PublikacjaW artykule przedstawiono aspekty oceny współpracy odbieraka prądu z górną siecią trakcyjną na podstawie porównania modeli matematycznych. Zaprezentowano modele odbieraków prądu i sieci jezdnej wskazując na ich użyteczność do oceny siły stykowej i uniesienia przewodów jezdnych. Wykonano szereg symulacji stanów dynamicznych interakcji górnej sieci trakcyjnej i odbieraka prądu dla różnych parametrów. W szczególności zwrócono uwagę...
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Marek Czachor prof. dr hab.
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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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(3,5-Dimethylpyridine)bis(tri-tert-butoxysilanethiolato)zinc(II)
PublikacjaMetodą rentgenowskiej analizy strukturalnej oznaczono strukturę kompleksu 3,5-dimetylopirydyny z Bis(tri-tert-butoksysilanotiolanem)cynku. Atom cynku wykazuje koordynację zniekształconej bipiramidy trygonalnej. Sieć krystaliczna jest stabilizwana tylko poprzez oddziaływania van der Waalsa.
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Structural and dynamic changes adopted by EmrE, multidrug transporter protein—Studies by molecular dynamics simulation
PublikacjaEmrE protein transports positively charged aromatic drugs (xenobiotics) in exchange for two protons and thus provides bacteria resistance to variety of drugs. In order to understand how this protein may recognize ligands, the monomer and asymmetric apo-form of the EmrE dimer embedded in a heterogeneous phospholipid (POPE + POPG) membrane were studied by molecular dynamics simulations. Dimer is regarded as a functional form of the...
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Structural factors affecting affinity of cytotoxic oxathiole-fused chalcones toward tubulin
PublikacjaSynthesis, in vitro cytotoxic activity, and interaction with tubulin of (E)-1-(6-alkoxybenzo[d][1,3]oxathiol- 5-yl)-3-phenylprop-2-en-1-one derivatives (2) are described. Some of the compounds demonstrated cytotoxic activity at submicromolar concentrations, and the activity could be related to interaction with tubulin at the colchicine binding site. Interaction of selected derivatives with tubulinwas evaluated using molecular modeling,...
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MIC/MBC values of the investigated extracts of propolis. Interactions of selected extracts with azoles and echinocandins.
Dane BadawczeThis dataset contains results of our investigation aiming in determination of antimicrobial potential of the propolis extracts produced in our laboratory. The propolis samples were delivered by Polish beekeepers. Moreover in this dataset we presented results of our investigation aiming in assessment of interaction of the selected extracts of propolis...
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A structural study of the hydrated and the dimethylsulfoxide, N, N´-dimet-hylpropyleneurea, acetonitryle, pyridine and N,N-dimethylthioformamide solvated nickel(II) ion in solution and solid state.
PublikacjaOznaczono strukturę w stanie stałym i ciekłym solwatowanego jonu niklu(II) w rozpuszczalnikach o różnych właściwościach donorowych: w wodzie, dimetylo-sulfotlenku, N,N`-dimetylopropylomoczniku, acetonitrylu, pirydynie i N,N-di-metylotioformamidzie. Stwierdzono, że nikiel(II) tworzy przede wszystkim sześciokoordynacyjne solwaty (woda, acetonitryl, DMTF). Jako solwat pięciokoordynacyjny istnieje tylko w dimetylopropylomoczniku....
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Eye tracking within near-to-eye display
PublikacjaIn this paper we investigate the effectiveness of the gaze interaction within near-to-eye display. The practical aspect of the paper is about combining an eye tracker with smart glasses. Presented research is related with the eGlasses project, which is focused on the development of an open platform in the form of multisensory electronic glasses and related interaction methods. One of the implemented interaction methods is the one...
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Janusz Rachoń prof. dr hab. inż.
OsobySprawował urząd rektora w latach 2002-2008 Urodził się 11 sierpnia 1946 r. w Nowym Sączu. Studia wyższe ukończył w 1969 r. na Wydziale Chemicznym Politechniki Gdańskiej, uzyskując tytuł magistra inżyniera chemika. W 1969 r. rozpoczął pracę na Wydziale Chemicznym Politechniki Gdańskiej, na którym uzyskał w 1975 r. doktorat, a w 1985 r. habilitację. Na stanowisko docenta został powołany w 1989 r., na stanowisko profesora nadzwyczajnego...
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Emotion Monitoring – Verification of Physiological Characteristics Measurement Procedures
PublikacjaThis paper concerns measurement procedures on an emotion monitoring stand designed for tracking human emotions in the Human-Computer Interaction with physiological characteristics. The paper addresses the key problem of physiological measurements being disturbed by a motion typical for human-computer interaction such as keyboard typing or mouse movements. An original experiment...
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Activation of N2O and SO2 by the P–B Bond System. Reversible Binding of SO2 by the P–O–B Geminal Frustrated Lewis Pair
PublikacjaHerein, we present the first transformation of borylphosphine into borylphosphinite using nitrous oxide. Borylphosphine reacts with N2O via insertion of a single oxygen atom into the P−B bond and formation of a P−O−B bond system. Borylphosphine and borylphosphinite capture SO2 and activate it in an irreversible and reversible manner, respectively.
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The crystal structure of (1RS,4RS,5RS,6SR)-5-cyano-5-nitro-6-phenyl-bicyclo[2.2.1]hept-2-ene
PublikacjaStructure of nitronorbornene derivative C14H12N2O2 synthesized in the reaction of cyclopentadiene with E-2-phenyl-1-cyano-1-nitroethene was determined by single crystal X-ray diffraction analysis. It was found that in analyzed molecule the nitro group is in endo-position whereas phenyl group have exo-ori-entation.
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Patryk Jasik dr inż.
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Metal ion directed template synthesis using 2-acetyl-1,3-indandione and ethylenediamine: steric and electronic restrictions
PublikacjaA template synthesis using 2-acetyl-1,3-indandione and ethylenediamine results in formation of octahedral Ni complex, whose crystal structure has been resolved using single crystal X-ray diffraction. The structure indicates that only exocyclic enolic oxygen atom of the triketone takes part in the condensation with ethylenediamine.
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Coarse-grained simulation - an efficient approach for studying motions of large proteins
PublikacjaOne of the most important challenges in performing Molecular Dynamics (MD) simulations of large protein complexes is to accommodate the model accuracy and the simulation timescale. Hitherto, for the most relevant dynamics of protein aggregates in an explicit aqueous environment, the timescale reachable for the all-atoms simulations is of hundreds of nanoseconds. This range is four to six orders of magnitude smaller than processes...
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Local structural and chemical ordering of nanosized Pt(3±δ)Co probed by multiple-scattering x-ray absorption spectroscopy
PublikacjaThis work reports a detailed investigation of the local structure and chemical disorder of a Pt(3±δ)Co thin film and Pt(3±δ)Co nanoparticles. We have used a combination of techniques including x-ray absorption spectroscopy (XAS), x-ray diffraction (XRD), and high-resolution transmission electron microscopy (TEM). The important effect of chemical ordering on pair and three-atom configurations has been studied using computer simulations...