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Search results for: DYNAMIKA MOLEKULARNA AB INITIO
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An ab initio study of the excited states of the vinoxy radical
PublicationMetodą ab initio obliczone zostały powierzchnie energii potencjalnej oraz radialne sprzężenia nieadiabatyczne. Rozpatrzono podprzestrzeń dwóch aktywnych kątów zaangażowanych w proces fotodysocjacji. Opracowany został schemat kwaziadiabatyczny w sąsiedztwie przecięcia stożkowego. Przedyskutowano niektóre konsekwencje możliwego mechanizmu fotodysocjacji winoksylu z różnych ścieżek formacji.
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Electronic structure and charge distribution in DyBa2Cu3O7: The ab initio approach
PublicationW pracy wykonano obliczenia kwantowomechaniczne struktury elektronowej nadprzewodzącego materiału DyBa2Cu3O7 (Dy123) metodą FP-LAPW (full potential - linearized augmented plane wave) w ramach formalizmu DFT (density functional theory) stosując przybliżenie GGA (generalized gradient approximation). Ze względu na silne oddziaływania korelacyjne elektronów 4f w atomie Dy zastosowano dodatkowo poprawkę kulombowską U w ramach modelu...
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Solvent Exchange around Aqueous Zn(II) from Ab Initio Molecular Dynamics Simulations
PublicationHydrated zinc(II) cations, due to their importance in biological systems, are the subject of ongoing research concerning their hydration shell structure and dynamics. Here, ab initio molecular dynamics (AIMD) simulations are used to study solvent exchange events around aqueous Zn2+, for which observation in detail is possible owing to the considerable length of the generated trajectory. While the hexacoordinated Zn(H2O)62+ is the...
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The ab initio calculations of single nitrogen-vacancy defect center in diamond.
PublicationW artykule zaprezentowano rezultaty kwantowomechanicznych obliczeń ''ab initio'' struktury elektronowej defektu azot-wakans w diamencie. Do obliczeń wykorzystano model złożony z 63 atomów. Otrzymane wyniki zostały porównane z wcześniejszymi pracami teoretycznymi i doświadczalnymi.
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Ab Initio Study of the Electronic Spectrum of 7-Hydroxyquinoline
PublicationThe electronic spectrum of 7-hydroxyquinoline has been studied by using ab initio Multi-State Multi-Reference Møller-Plesset Second-Order Perturbation Theory (MSMRMP2). The energy range up to 6.5 eV is taken into consideration. The lowest π–π* transition is calculated to have an energy of 3.65 eV in good agreement with experimental data. Several other π–π* transitions are predicted to have excitation energies of 4.93, 5.20, 5.47,...
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Ab initio elasticity of chalcopyrites
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Theoretical study of the photoelectron spectrum of ethyl formate: Ab initio and density functional theory investigation
PublicationThe first ionization energy and associated photoelectron spectrum of ethyl formate are investigated with quantum chemistry calculations. The geometries, harmonic vibrational frequencies and first ionization energy are computed at the Hartree-Fock (HF) and at the second order Moller-Plesset perturbation theory (MP2). Moreover, accurate ionization energies are obtained with the Coupled-Cluster theory including singles and doubles...
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Hydration of N-Hydroxyurea from Ab Initio Molecular Dynamics Simulations
PublicationN-Hydroxyurea (HU) is an important chemotherapeutic agent used as a first-line treatment in conditions such as sickle cell disease and β-thalassemia, among others. To date, its properties as a hydrated molecule in the blood plasma or cytoplasm are dramatically understudied, although they may be crucial to the binding of HU to the radical catalytic site of ribonucleotide reductase, its molecular target. The purpose of this work...
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Charge distribution and magnetic interactions in PrBa2Cu3O7 with substitutional defects and oxygen disorder: the ab initio approach
PublicationW artykule zaprezentowano rezultaty kwantowomechanicznych obliczeń ''ab initio: struktury elektronowej układu PrBa2Cu3O7 zawierającego defekty substytucyjne (Pr_Ba) w podsieci barowo-tlenowej oraz wykazującego zaburzoną stechiometrię tlenową (O5). Badane defekty są odpowiedzialne za redystrybucję ładunku w układzie. Defekty Pr_Ba generują silnie zlokalizowane momenty magnetyczne, które oddziałują głównie na płaszczyzny miedziowo-tlenowe.
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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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Ab initio Structure Determination of Mg10Ir19B16
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The ab initio and experimental study of the spectroscopic and magnetic properties of Ho(III)-EDTA
Open Research DataIn this dataset, the ab initio calculations of the electronic structure and the magnetic properties are discussed in the context of the experimental data for the Ho–EDTA complex. In the calculations different models of the cluster have been applied to examine the influence of various parts of the environment of the Ho(III)-EDTA complex on its properties....
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Limonene: electronic state spectroscopy by high-resolution vacuum ultraviolet photoabsorption, electron scattering, He(I) photoelectron spectroscopy and ab initio calculations
PublicationZbadano limonen metodami spektroskopii absorpcyjnej, elektronowej, fotojonizacyjnej. Wyniki porównano z obliczeniami ab initio. Otrzymano strukturę wibracyjną molekuły.
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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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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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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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Catalytic Mechanism of Non-Target DNA Cleavage in CRISPR-Cas9 Revealed by Ab Initio Molecular Dynamics
PublicationCRISPR-Cas9 is a cutting-edge genome editing technology, which uses the endonuclease Cas9 to introduce mutations at desired sites of the genome. This revolutionary tool is promising to treat a myriad of human genetic diseases. Nevertheless, the molecular basis of DNA cleavage, which is a fundamental step for genome editing, has not been established. Here, quantum–classical molecular dynamics (MD) and free energy methods are used...
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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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Isobutyl acetate: electronic state spectroscopy by high-resolution vacuum ultraviolet photoabsorption, He(I) photoelectron spectroscopy and ab initio calculations
PublicationThe high-resolution vacuum ultraviolet photoabsorption spectrum of isobutyl acetate, C6H12O2, is presented here and was measured over the energy range 4.3–10.8 eV (290–115 nm). Valence and Rydberg transitions with their associated vibronic series have been observed in the photoabsorption spectrum and are assigned in accordance with new ab initio calculations of the vertical excitation energies and oscillator strengths. The measured...
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Electronic state spectroscopy by high-resolution vacuum ultraviolet photoabsorption, He(I) photoelectron spectroscopy and ab initio calculations of ethyl acetate
PublicationThe high-resolution vacuum ultraviolet photoabsorption spectrum of ethyl acetate, C4H8O2, is presented over the energy range 4.5−10.7 eV (275.5−116.0 nm). Valence and Rydberg transitions and their associated vibronic series observed in the photoabsorption spectrum, have been assigned in accordance with new ab initio calculations of the vertical excitation energies and oscillator strengths. Also, the photoabsorption cross sections...
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Non-ionic and zwitterionic forms of neutral arginine – an ab initio study
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Negative Ion Formation in Sodium Chloride TrimerAn ab Initio Study
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Ab initio and nuclear inelastic scattering studies of Fe3Si/GaAs heterostructures
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Ab initio molecular treatment for charge transfer by S3+ ion on hydrogen.
PublicationPoliczono adiabatyczne potencjały oddziaływania między jonem siarki i wodoru. Dokonano obliczeń nieadiabatycznych sprzężeń pomiędzy tymi potencjałami. Obliczenia wykazały, że należy wziąć pod uwagę niezbadany wcześniej poziom energetyczny jonu siarki aby dokładnie wyjaśnić mechanizm przechwytu ładunku.
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Ab initio chemical kinetics of Isopropyl acetate oxidation with OH radicals
PublicationGlobal reactivity descriptors of isopropyl acetate (IPA) and thermo-kinetic aspects of its oxidation via OH radicals have been studied. Transition state theory (TST) was utilized to estimate the bimolecular rate constants. Ten oxidation pathways have been investigated, and all of them are exothermic. The potential energy diagram has been sketched using different pre- and post-reactive complexes for all reaction pathways. Rate coefficient...
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An ab initio study on BeX3− superhalogen anions (X = F, Cl, Br)
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Ab initio studies of phonons in MgO by the direct method including LO mode
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Lattice dynamics and elasticity of silver thiogallate (AgGaS2) from ab initio calculations
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Valence and Ionic Lowest-Lying Electronic States of Isobutyl Formate Studied by High-Resolution Vacuum Ultraviolet Photoabsorption, Photoelectron Spectroscopy, and Ab Initio Calculations
PublicationThe highest resolution vacuum ultraviolet photoabsorption spectrum of isobutyl formate, C5H10O2, yet reported is presented over the energy range 4.5−10.7 eV (275.5−118.0 nm) revealing several new spectral features. Valence and Rydberg transitions and their associated vibronic series observed in the photoabsorption spectrum have been assigned in accordance with new ab initio calculations of the vertical excitation energies and oscillator...
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Dynamika molekularna oddziaływań przeciwgrzybowych heptaenów aromatycznych i ich izomerów all-trans ze sterolami w błonach lipidowych
PublicationAromatyczne heptaeny (AH) należą do grupy makrolidów polienowych o działaniu przeciwgrzybowym. Antybiotyki z tej grupy były pierwszymi, które zostały wykorzystane w terapii układowych infekcji grzybiczych. Amfoterycyna B (AmB) oraz nystatyna, czyli niearomatyczni przedstawiciele makrolidów heptaenowych, mają istotne znaczenie kliniczne w leczeniu, odpowiednio, grzybic wewnętrznych i zewnętrznych. Molekularne podstawy mechanizmu...
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Valence and ionic lowest-lying electronic states of ethyl formate as studied by high-resolution vacuum ultraviolet photoabsorption, He(I) photoelectron spectroscopy, and ab initio calculations
PublicationThe highest resolution vacuum ultraviolet photoabsorption spectrum of ethyl formate, C2H5OCHO, yet reported is presented over the wavelength range 115.0–275.5 nm (10.75–4.5 eV) revealing several new spectral features. Valence and Rydberg transitions and their associated vibronic series, observed in the photoabsorption spectrum, have been assigned in accordance with new ab initio calculations of the vertical excitation energies...
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An effective method for studying intermolecular interactions in binary liquids with hydrogen bonds: FTIR spectra and ab initio calculations in the N-methylformamide - methanol system
PublicationMolecular complexes in methanol (MeOH)−N-methylformamide (NMF) mixtures were studied based on their FTIR-ATR spectra, to which two methods of analysis were applied: factor analysis and a quantitative version of the difference-spectra method. The mean composition of a complex between NMF and MeOH molecules over the whole range of mixture compositions was determined. Absorbing species differentiated with regard to the interaction...
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Ab initio and experimental studies of polarization and polarization related fields in nitrides and nitride structures
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Excess Electron Attachment to Disulfide-Bridged l,l-Cystine. An ab Initio Study
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An ab initio study on MgX3− and CaX3− superhalogen anions (X=F, Cl, Br)
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THE PERFORMANCE OF SELECTED AB INITIO METHODS IN ESTIMATING ELECTRON BINDING ENERGIES OF SUPERHALOGEN ANIONS
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BX4− and AlX4− Superhalogen Anions (X = F, Cl, Br): An ab Initio Study
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Ab initio and density functional theory calculations of proton affinities for volatile organic compounds
PublicationThe Hatree-Fock method with 6-311G** split-valence molecular orbitals basis sets and the density function theory-B3LYP have been applied to geometrical optimizations and calculations of total electronic, zero point vibrational energies and proton affinities at 298 K for volatile organic compounds. Calculated values of proton affinities are compared with experimental data.
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Ab Initio Analysis of a Quantum Dot Induced by a Local External Potential in a Semiconducting Carbon Nanotube
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First Evidence of Rhombic (NaCl)2-. Ab Initio Reexamination of the Sodium Chloride Dimer Anion
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Band structure, Born effective charges, and lattice dynamics of CuInS2 from ab initio calculations
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Dimeric structure of the N-terminal domain of PriB protein from Thermoanaerobacter tengcongensis solved ab initio
PublicationPriB is one of the components of the bacterial primosome, which catalyzes the reactivation of stalled replication forks at sites of DNA damage. The N-terminal domain of the PriB protein from the thermophilic bacterium Thermoanaerobacter tengcongensis (TtePriB) was expressed and its crystal structure was solved at the atomic resolution of 1.09 Å by direct methods. The protein chain, which encompasses the first 104 residues of the...
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Ab-initio investigations for structural, mechanical, optoelectronic, and thermoelectric properties of Ba2SbXO6 (X Nb, Ta) compounds
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Ab initio studies of the structure, physicochemical properties and behavior of lead chlorides and chloroplumbate anions in gaseous and aqueous phases
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Ab initio electronic structure of HCN− and HNC− dipole-bound anions and a description of electron loss upon tautomerization
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Ab initio study of phenyl benzoate: structure, conformational analysis, dipole moment, IR and Raman vibrational spectra
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Tailoring optical constants of few-layer black phosphorus coatings: Spectroscopic ellipsometry approach supported by ab-initio simulation
Publication2D black phosphorus (BP) has attracted extensive attention as an anisotropic platform for novel optoelectronic and polarizing optics applications. Insight into the factors that tune the optical and polarizing properties of 2D BP reveals their essential influence on BP-based photonic and optoelectronic devices. In this work, studies of the optical constants of few-layer black phosphorus coatings are studied and discussed, with particular...
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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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