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Search results for: AB INITIO MOLECULAR DYNAMICS
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Electronic structure of CeBa2Cu3O7.
PublicationPrzeprowadzono obliczenia ab initio struktury elektronowej związku CeBa2Cu3-O7(Ce123) metodą LAPW oraz porównano z analogicznymi strukturami otrzymanymi dla YBa2Cu3O7 (Y123), NdBa2Cu3O7(Nd123) i PrBa2Cu3O7(Pr123). Wszystkie wyliczone struktury pasmowe są zasadniczo podobne. W pracy postawiono hipotezę dotyczącą korelacji pomiędzy silnym rozszczepieniem spinowym w Pr123 i Ce123a niestabilnością strukturalną tych układów.
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Multi-mode vibronic interactions in the five lowest electronic states of the fluorobenzene radical cation
PublicationThe multi-mode vibronic interactions between the five lowest electronic states of the fluorobenzene radical cation are investigated theoretically, based on ab initio electronic structure data, and employing the linear vibronic coupling model. Low-energy conical intersections, and strong vibronic couplings are found to prevail within the set of X-A and B-C-D cationic states, while the interactions between these two sets of states...
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Local Conformation and Cocrystallization Phenomena in Renewable Diaminoisoidide-Based Polyamides Studied by FT-IR, Solid State NMR, and WAXD
PublicationBiobased polyamides synthesized from diaminoisoidide (DAII), 1,4-diaminobutane, and sebacic acid are investigated by FT-IR, 13C{1H} magic-angle spinning/cross-polarization (CP/MAS) NMR spectroscopy, and WAXD. Their molecular conformation and mobility undergo distinct changes as a function of temperature and diaminoisoidide content in the compositions. The presence of randomly distributed diaminoisoidide (DAII) in the polyamides...
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The Role of Electron Transfer in the Fragmentation of Phenyl and Cyclohexyl Boronic Acids
PublicationIn this study, novel measurements of negative ion formation in neutral potassium-neutral boronic acid collisions are reported in electron transfer experiments. The fragmentation pattern of phenylboronic acid is comprehensively investigated for a wide range of collision energies, i.e., from 10 to 1000 eV in the laboratory frame, allowing some of the most relevant dissociation channels to be probed. These studies were performed in...
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Configurations of H 3 + (H2)n clusters and their energies
PublicationThe H-3(+) ion plays an important role in low temperature astrophysical and laboratory plasmas. It is considered as the initiator of many ion-molecule chemistries. Also its clusters with H-2 are quite interesting. We study configurations of the H-3(+)(H-2)(n) clusters for n = 1 up to n = 12 as a simple test system. Total energies for these structures, with zero point vibration corrections have been calculated. Stabilization energies...
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Studies on the solid-liquid equilibria and intermolecular interactions Urea binary mixtures with Sulfanilamide and Sulfacetamide
PublicationThe binary phase diagrams of Sulfanilamide-Urea (SN-U) and Sulfacetamide-Urea (SC-U) were measured using differential scanning calorimetry technique (DSC). Both examined mixtures were found to form simple binary eutectics. The limited miscibility in the solid state observed by DSC, proving inability of co-crystallization in new multi-molecular form, was also confirmed using PXRD and FTIR-ATR measurements of solid dispersions...
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Structural and electronic properties of some intriguing (rare-earth)Ba2Cu3O7 compounds.
PublicationW rozdziale przedstawiono przegląd wyników eksperymentalnych i teoretycznych dotyczących wybranych związków o wzorze (lantanowiec)Ba2Cu3O7 wykazujących całkowicie odmienne właściwości w porównaniu z całą klasą nadprzewodzących związków tlenkowych o stechiometrii 1:2:3. Szczególny nacisk położono na analizę procesu wzrostu kryształów i powstawania defektów punktowych determinujących późniejsze własności fizyczne tych materiałów....
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Superconductivity in Bismuth Pyrochlore Lattice Compounds RbBi2 and CsBi2: The Role of Relativistic Effects
PublicationSuperconducting properties of two bismuthide intermetallic compounds, RbBi2 and CsBi2, were studied by means of experimental measurements and ab initio calculations. We show that in both compounds, the superconductivity emerges from the pyrochlore Bi lattice and its formation is heavily influenced by relativistic effects. Based on our analysis of the effect of spin–orbit coupling on the electron–phonon coupling, we suggest a possible...
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Imidazolium silanethiolates relevant to the active site of cysteineproteases. A cooperative effect in a chain of NH(+)...S(-) hydrogenbonds
PublicationThree imidazolium silanethiolates relevant to the active site of cysteine proteases have been synthesized and investigated by X-ray diffraction, IR spectroscopy and computational methods. As indicated by crystallographic and FT-IR data in the solid state, the transfer of proton from thiol to imidazole takes place and a thiolato-imidazolium ion pair is formed. The FT-IR spectra of crystalline imidazolium silanethiolates exhibit...
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Potential energy surfaces of the low-lying electronic states of the Li+LiCs system
PublicationAb initio quantum chemistry calculations are performed for the mixed alkali triatomic system. Global minima of the ground and first excited doublet states of the trimer are found and Born-Oppenheimer potential energy surfaces of the Li atom interacting with the LiCs molecule were calculated for these states. The lithium atom is placed at various distances and bond angles from the lithium-caesium dimer. Three-body nonadditive forces...
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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
PublicationW 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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Proton transfer reactions for ionized water clusters
PublicationCalculations of formation energies of the ionized water clusters and energies of reactions between small (including less than eight water molecules) neutral and positively ionized water clusters are presented. Moreover, we discuss some reaction paths between neutral and positively charged dimers, trimers and tetramers and proton transfer reactions (PTR) between cyclic clusters and H3O+ ions which can appear in beam experiments...
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Modeling protein structures with the coarse-grained UNRES force field in the CASP14 experiment
PublicationThe UNited RESidue (UNRES) force field was tested in the 14th Community Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction (CASP14), in which larger oligomeric and multimeric targets were present compared to previous editions. Three prediction modes were tested (i) ab initio (the UNRES group), (ii) contact-assisted (the UNRES- contact group), and (iii) template-assisted (the UNRES-template...
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Molecular geometry and optical activity of helically chiral N-nitrosamines derived from 1,2,3,4-tetrahydro- and 1,2,3,4,7,8,9,10-octahydro-1,10-phenanthroline
PublicationX-ray crystallographic analysis of the title N-nitrosamines revealed that they assume helical conformations in the solid state. Nitrosamines 1b and 2b were resolved by inclusion crystallization with optically active diols (TADDOLs). The absolute configuration of the guest molecules in the complexes 1b·3b and 2b·3b was assigned as M. The optical activity of the resolved compounds is manifested by their solid state CD spectra, which...
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Hydrogen migration in formation of NH(A3Π) radicals via superexcited states in photodissociation of isoxazole molecules
PublicationFormation of the excited NH(A 3Π) free radicals in the photodissociation of isoxazole (C3H3NO) molecules has been studied over the 14-22 eV energy range using photon-induced fluorescence spectroscopy. The NH(A 3Π) is produced through excitation of the isoxazole molecules into higher-lying superexcited states. Observation of the NH radical, which is not a structural unit of the isoxazole molecule, corroborates the hydrogen atom...
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Elimination and migration of hydrogen in the vacuum-ultraviolet photodissociation of pyridine molecules
PublicationElimination of the excited hydrogen atoms H(n), n = 4–7, and hydrogen migration in formation of the excited NH(A 3Π) free radicals in the photodissociation of pyridine, C5H5N, molecules have been studied over the 17.5–70 eV photon energy range. In the measurements the photon-induced fluorescence spectroscopy technique has been applied. Both fragments are produced through excitation of pyridine molecules into higher-lying superexcited...
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Application of the neural networks for developing new parametrization of the Tersoff potential for carbon
PublicationPenta-graphene (PG) is a 2D carbon allotrope composed of a layer of pentagons having sp2- and sp3-bonded carbon atoms. A study carried out in 2018 has shown that the parameterization of the Tersoff potential proposed in 2005 by Ehrhart and Able (T05 potential) performs better than other potentials available for carbon, being able to reproduce structural and mechanical properties of the PG. In this work, we tried to improve the...
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Born–Oppenheimer potential energy curves of NaK from the optimised atomic basis sets
PublicationThe article presents adiabatic potential energy curves of the ground and excited electronic states for the diatomic NaK molecule. The calculations were made using the ab initio computational methods to include electron correlation. The studied molecule was calculated as the effective two-electron problem, in which only the valence electrons of the molecule are explicitly taken into account. The remaining electrons with atomic nuclei...
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1,3-alternate calix[4]arene-bonded silica stationary phases. Effect of calixarene skeleton substituents on the retention mechanism and column selectivity
PublicationFour novel 1,3-alternate calix[4]arene-bonded silica gel stationary phases possessing different aromatic and aliphatic substituents at the upper rim (CalixNph, CalixBph, CalixHex and CalixDdc) were prepared and structurally characterized. The comparison and selectivity of these phases was done by using alkylbenzenes, fatty acid p-bromophenacyl esters, aromatic positional isomers and polynuclear aromatic hydrocarbons as analytes....
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The role of low-energy electrons in the charging process of LISA test masses
PublicationThe estimate of the total electron yield is fundamental for our understanding of the test-mass charging associated with cosmic rays in the Laser Interferometer Space Antenna (LISA) Pathfinder mission and in the forthcoming gravitational wave observatory LISA. To unveil the role of low energy electrons in this process owing to galactic and solar energetic particle events, in this work we study the interaction of keV and sub-keV...
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Minimal parameter implicit solvent model for ab initioelectronic-structure calculations
PublicationAbstract - We present an implicit solvent model for ab initio electronic-structure calculations which is fully self-consistent and is based on direct solution of the nonhomogeneous Poisson equation. The solute cavity is naturally defined in terms of an isosurface of the electronic density according to the formula of Fattebert and Gygi (J. Comput. Chem., 23 (2002) 662). While this model depends on only two parameters, we demonstrate...
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On the electronic structure of methyl butyrate and methyl valerate
PublicationWe present novel results of the analysis of the electronic structure of two aliphatic esters: methyl butyrate and methyl valerate. High-resolution photoabsorption spectra were collected and analyzed over the energy range 4.0–10.8 eV and showed for both the molecules not only a clear band of the HOMO to LUMO transition, but also vibronic structure associated with the first Rydberg-valence transition. Photoelectron spectra recorded...
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A semiempirical model for low energy electron–atom transport cross sections: The case of noble gases
PublicationA semiempirical approach to describe low energy electron–atom transport cross sections of easy implementation and reproduction is presented. The heart of the model is an energy independent two-parameter potential that was adjusted to reproduce the accurate total cross sections for He, Ne, Ar and Kr, measured with a threshold photoelectron source technique from meV up to 20 eV. Once the potential was conceived, the model was validated...
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An Investigation of Polyamides Based on Isoidide-2,5-dimethyleneamine as a Green Rigid Building Block with Enhanced Reactivity
PublicationNovel, semicrystalline polyamides and copolyamides were synthesized from a new carbohydrate-based diamine, namely isoidide-2,5-dimethyleneamine (IIDMA). In combination with 1,6-hexamethylene diamine (1,6-HDA) as well as the biobased sebacic acid (SA) or brassylic acid (BrA), the desired copolyamides were obtained via melt polymerization of the nylon salts followed by a solid-state polycondensation (SSPC) process. Depending on the...
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Ab initio elasticity of chalcopyrites
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A facile method for Tauc exponent and corresponding electronic transitions determination in semiconductors directly from UV–Vis spectroscopy data
PublicationIn this work, a facile method allowing for estimation of the exponent in the Tauc equation directly from the UV–vis spectra is presented. It is based on the Taylor expansion of the logarithmic version of the Tauc equation. The Tauc exponent is calculated from the tangent slope of the absorption data. Knowledge of this coefficient provides information about the optical transition types and is used as an input for the calculations...
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Cytocompatibility of stabilized black phosphorus nanosheets tailored by directly conjugated polymeric micelles for human breast cancer therapy
PublicationThe novel procedure of few-layer black phosphorus (FLBP) stabilization and functionalisation was here proposed. The cationic polymer PLL and non-ionic PEG have been involved into encapsulation of FLBP to allow sufficient time for further nanofabrication process and overcome environmental degradation. Two different spacer chemistry was designed to bind polymers to tumor-homing peptides. The efficiency of functionalisation was examined...
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Hydration of simple amides. FTIR spectra of HDO and theoretical studies
PublicationZastosowano 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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Photoelectron spectroscopy of a series of acetate and propionate esters
PublicationThe electronic state and photoionization spectroscopy of a series of acetate esters: methyl acetate, isopropyl acetate, butyl acetate and pentyl acetate as well as two propionates: methyl propionate and ethyl propionate, have been determined using vacuum-ultraviolet photoelectron spectroscopy. These experimental investigations are complemented by ab initio calculations. The measured first adiabatic and vertical ionization energies...
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Ab initio Structure Determination of Mg10Ir19B16
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Ab initio Structure Determination of Mg10Ir19B16
PublicationOkreślono strukturę krystalograficzną nowego, nie-centrosymetrycznego nadprzewodzącego związku chemicznego, mg10ir19b16. Została zastosowana cała gama technik eksperymentalnych: dyfrakcja elektronowa, proszkowa dyfrakcja promieniowania rentgenowskiego, mikroskopia elektronowa wysokiej rozdzielczości, itd. Określenie struktury krystalograficznej było skrajnie trudne ponieważ jest to nowy, nieznany dotąd typ struktury krystalicznej,...
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Mechanisms of Li deposition on graphite anodes: surface coverage and cluster growth
PublicationLi plating on the anode is a side reaction in Li-ion batteries which competes with Li intercalation and leads to loss of capacity. Growth of Li clusters into dendrites is a potential safety hazard for batteries which can lead to internal short-circuit and fires. We consider two possibilities of Li deposition on the surface of graphite anode: deposition of Li+ ions uniformly on the surface and deposition of clusters of metallic...
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Enhanced photocatalytic properties of lanthanide-TiO2 nanotubes: An experimental and theoretical study
PublicationA series of Er-, Yb-, Ho-, Tb-, Gd-, Pr-TiO2 nanotubes (RE-NTs) was prepared via an electrochemical method. The as-prepared photocatalysts were characterized by X-ray diffraction (XRD), X-ray photoelectron spectroscopy (XPS), UV–vis absorption, scanning electron microscopy (SEM) and luminescent spectroscopy. The experiments demonstrated that toluene in the gas phase was successfully degraded under visible light (LEDs λmax = 465...
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Superconductivity and appearance of negative magnetocaloric effect in Ba1–xKxBiO3 perovskites, doped by Y, La and Pr
PublicationRecently, substantial attention is given to the bismuth-based perovskites for variety of electronic applications. The perovskites are used for quantum dots displays (QLED), photovoltaic systems and superconducting (HTS) devices. In this paper comprehensive studies of Ba1–xKxBi1–yREyO3 bismuth perovskites (REBKBO, RE = Y , La or Pr) are reported. Apart from structural anomalous behavior at low temperatures, the electronic properties...
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Linking optical and electronic properties to photoresponse of heterojunctions based on titania nanotubes and chromium, molybdenum, and tungsten oxides
PublicationThe development of photosensitization strategies for titanium dioxide is necessary for the enhancement of its optical and electronic properties towards its application potential in solar photoelectrochemistry. In this work, significant differences in the photosensitizing capability of the 6th group transition metal oxides applied on the surface of titania nanotubes are reported. For the first time, correlations between the experimentally...
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Structure and properties of liquid Al–Cu alloys: Empirical potentials compared
PublicationWe report on the structure and mass transport properties of liquid Al–Cu alloys predicted by two recently-developed empirical many-body potentials: MEAM (Jelinek et al., 2012) and EAM-ADP (Apostol and Mishin, 2011), and by the well-known Gupta potential. Total and partial pair correlation functions, angular distribution functions, densities, coordination numbers and self-diffusion coefficients are compared with published experimental...
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How acidic amino acid residues facilitate DNA target site selection
PublicationDespite the negative charge of the DNA backbone, acidic residues (Asp/Glu) commonly participate in the base readout, with a strong preference for cytosine. In fact, in the solved DNA/protein structures, cytosine is recognized almost exclusively by Asp/Glu through a direct hydrogen bond, while at the same time, adenine, regardless of its amino group, shows no propensity for Asp/Glu. Here, we analyzed the contribution of Asp/Glu...
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Atomic-Scale Finite-Element Modeling of Elastic Mechanical Anisotropy in Finite-Sized Strained Phosphorene Nanoribbons
PublicationNanoribbons 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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Stable Field Electron Emission and Plasma Illumination from Boron and Nitrogen Co‐Doped Edge‐Rich Diamond‐Enhanced Carbon Nanowalls
PublicationSuperior field electron emission (FEE) characteristics are achieved in edge-rich diamond-enhanced carbon nanowalls (D-ECNWs) grown in a single-step chemical vapor deposition process co-doped with boron and nitrogen. The structure consists of sharp, highly conductive graphene edges supplied by a solid, diamond-rich bottom. The Raman and transmission electron microscopy studies reveal a hybrid nature of sp3-diamond and sp2-graphene...
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Ab-initio study of electrical and optical properties of allylamine
PublicationThe Density functional theory is one of most promising methodology in fast and accurate calculations of electrical and optical properties from the atomic basis. In this paper, we calculate electrical and optical properties of allylamine (2-propen 1- amine) in terms of accuracy and speed of calculations obtained by selection of DFT-1/2 method with ultrasoft Vanderbilt pseudopotentials. Comparison of density of states between...
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Reactions of parylenes with double bonds: An ab initio study
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Elastic scattering of electrons by water: An ab initio study
PublicationIn this work we devise a theoretical and computational method to compute the elastic scattering of electrons from a non-spherical potential, such as in the case of molecules and molecular aggregates. Its main feature is represented by the ability of calculating accurate wave functions for continuum states of polycentric systems via the solution of the Lippmann-Schwinger equation, including both the correlation effects and multi-scattering...
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Ab-initio study of electrical and optical properties of allylamine
PublicationThe Density functional theory is one of most promising methodology in fast and accurate calculations of electrical and optical properties from the atomic basis. In this paper, we calculate electrical and optical properties of allylamine (2-propen 1- amine) in terms of accuracy and speed of calculations obtained by selection of DFT-1/2 method with ultrasoft Vanderbilt pseudopotentials. Comparison of density of states between molecule...
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Molecular dynamics studies of polyurethane nanocomposite hydrogels
PublicationPolyurethane PEO-based hydrogels have a broad range of biomedical applicability. They are attractive for drug-controlled delivery systems, surgical implants and wound healing dressings. In this study, a PEO based polyurethane hydrogels containing Cloisite R 30B, an organically modified clay mineral, was synthesized. Structure of nanocomposite hydrogels was determined using XRD technique. Its molecular dynamics was studied by means...
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Cationic and anionic daughters of AlOH and GaOH. An ab initio study
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Dynamical properties of pnictide ZnSnP2 from ab initio calculations
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Electron attachment to representative cations composing ionic liquids
PublicationUsing ab initio electronic structure methods with flexible atomic orbital basis sets, we investigated the electronic structure and stability of reduction products of selected representative cations (C+) constituting ionic liquids. We found that an electron attachment to such cations leads to the neutral radicals, whereas a subsequent attachment of another (i.e., excess) electron leads to adiabatically stable anions only in two...
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Charge Distribution and Hyperfine Interactions in GdBa2Cu3O7 from First Principles
PublicationW rozdziale przedstawiono wyniki obliczeń "z zasad pierwszych" (''ab initio'') struktury elektronowej, rozkładu ładunku i struktury nadsubtelnej, w szczególności gradientu pola elektrycznego (EFG) i składnika kontaktowego pola nadsubtelnego (HFF), nadprzewodnika wysokotemperaturowego o wzorze GdBa2Cu3O7 (Gd123). Do obliczeń wykorzystano metodę FP-LAPW (full-potential linearized augmented plane wave). Efekty związane z oddziaływaniami...
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Charge Transfer, Complexes Formation and Furan Fragmentation Induced by Collisions with Low-Energy Helium Cations
PublicationThe present work focuses on unraveling the collisional processes leading to the fragmentation of the gas-phase furan molecules under the He+ and He2+ cations impact in the energy range 5–2000 eV. The presence of different mechanisms was identified by the analysis of the optical fragmentation spectra measured using the collision-induced emission spectroscopy (CIES) in conjunction with the ab initio calculations. The measurements of...
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Non-ionic and zwitterionic forms of neutral arginine – an ab initio study
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