Wyszukiwarka
Filtry
wszystkich: 1037
wybranych: 907
-
Katalog
- Publikacje 907 wyników po odfiltrowaniu
- Czasopisma 1 wyników po odfiltrowaniu
- Osoby 12 wyników po odfiltrowaniu
- Projekty 24 wyników po odfiltrowaniu
- Laboratoria 4 wyników po odfiltrowaniu
- Zespoły Badawcze 2 wyników po odfiltrowaniu
- Kursy Online 62 wyników po odfiltrowaniu
- Wydarzenia 1 wyników po odfiltrowaniu
- Dane Badawcze 24 wyników po odfiltrowaniu
Filtry wybranego katalogu
Wyniki wyszukiwania dla: obliczenia ab initio
-
Dimeric structure of the N-terminal domain of PriB protein from Thermoanaerobacter tengcongensis solved ab initio
PublikacjaPriB 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...
-
Ab initio study of phenyl benzoate: structure, conformational analysis, dipole moment, IR and Raman vibrational spectra
Publikacja -
Ab initio studies of the structure, physicochemical properties and behavior of lead chlorides and chloroplumbate anions in gaseous and aqueous phases
Publikacja -
Ab initio electronic structure of HCN− and HNC− dipole-bound anions and a description of electron loss upon tautomerization
Publikacja -
Tailoring optical constants of few-layer black phosphorus coatings: Spectroscopic ellipsometry approach supported by ab-initio simulation
Publikacja2D 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...
-
Evaluation of Chemotherapeutic Activity of the Selected Bases’ Analogues of Nucleic Acids Supported by ab initio Various Quantum Chemical Calculations
Publikacja -
Pharmacological Classification and Activity Evaluation of Furan and Thiophene Amide Derivatives Applying Semi-Empirical ab initio Molecular Modeling Methods
Publikacja -
Isobutyl acetate: electronic state spectroscopy by high-resolution vacuum ultraviolet photoabsorption, He(I) photoelectron spectroscopy and ab initio calculations
PublikacjaThe 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...
-
Electronic state spectroscopy by high-resolution vacuum ultraviolet photoabsorption, He(I) photoelectron spectroscopy and ab initio calculations of ethyl acetate
PublikacjaThe 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...
-
Limonene: electronic state spectroscopy by high-resolution vacuum ultraviolet photoabsorption, electron scattering, He(I) photoelectron spectroscopy and ab initio calculations
PublikacjaZbadano limonen metodami spektroskopii absorpcyjnej, elektronowej, fotojonizacyjnej. Wyniki porównano z obliczeniami ab initio. Otrzymano strukturę wibracyjną molekuły.
-
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
PublikacjaMolecular 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...
-
Parametrization of Backbone−Electrostatic and Multibody Contributions to the UNRES Force Field for Protein-Structure Prediction from Ab Initio Energy Surfaces of Model Systems
Publikacja -
Valence and Ionic Lowest-Lying Electronic States of Isobutyl Formate Studied by High-Resolution Vacuum Ultraviolet Photoabsorption, Photoelectron Spectroscopy, and Ab Initio Calculations
PublikacjaThe 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...
-
Valence and ionic lowest-lying electronic states of small esters studied by high resolution vacuum ultraviolet photoabsorption, photoelectron spectroscopy and ab initio calculations
PublikacjaEsters are an important class of oxygenated volatile organic compounds used in food flavorings, perfumes and other cosmetic products. They are present in fruits and pheromones and are emitted to the atmosphere naturally. Esters are also formed in the atmosphere as a product of the oxidation of ethers. Some of them form poly-molecule chains and are used in plastics. Phosphoesters form DNA backbone, while nitroesters are known for...
-
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
PublikacjaThe 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...
-
Electronic structure of CeBa2Cu3O7.
PublikacjaPrzeprowadzono 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.
-
Theoretical study of the energetics of the reactions of triplet dioxygen with hydroquinone, semiquinone, and their protonated forms: relation to the mechanism of superoxide generation in the respiratory chain = Badanie teoretyczne energii z energii reakcji dioksygenu potrójnego z wodorem, półkiną i ich formami protony: relacja z mechanizmem wytwarzania supertlenku w łańcuchu oddechowym
PublikacjaW pracy prezentujemy wyniki obliczeń kwantowych ab initio i półempirycznych energetyki reakcji redukcji jednoelektronowej tlenu trypletowego. Zaproponowaliśmy cztery możliwe mechanizmy redukcji i przeprowadziliśmy obliczenia kwantowe. Z obliczeń wynika, że najprawdopodobniejszy mechanizm reakcji wiedzie poprzez przeniesienie elektronu z anionu hydrochinonu po deprotonacji lub też z rodnika semichinonowego na tlen cząsteczkowy,...
-
Hydration of simple amides. FTIR spectra of HDO and theoretical studies
PublikacjaZastosowano metodę ważonych widm różnicowych do opisu hydratacji amidów w roztworach wodnych: formamidu, N-metyloformamidu, N,N-dimetyloformaidu, acetamidu, N-metyloacetamidu, N,N-dimetyloacetamidu. Narzędziem wspomagającym interpretację wyników eksperymentalnych są struktury agregatów solwatacyjnych wokół cząsteczki substancji rozpuszczonej uzyskane na podstawie obliczeń teoretycznych metodą ab initio z korelacją elektronową...
-
Minimal parameter implicit solvent model for ab initioelectronic-structure calculations
PublikacjaAbstract - 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...
-
Conformational analysis of N-isopropylbenzohydroxamic acids:Crystal structure, DFT and NMR studies
PublikacjaCelem pracy było znalezienie różnic strukturalnych dwóch wybranych kwasów N-izopropylobenzhydroksamowych, które rzutują na ich zaobserwowaną wcześniej zróżnicowaną reaktywność wobec odczynników elektrofilowych i porównanie ich budowy z budową znanych kwasów N-metylobenzhydroksamowych. Na podstawie analizy rentgenostrukturalnej monokryształu, obliczeń kwantowo-mechanicznych metodami ab initio oraz DFT w fazie gazowej oraz wyników...
-
Zero-range potentials in multi-channel diatomic molecule scattering
PublikacjaZagadnienie o rozpraszaniu elektronów na molekułach rozwiązuje się w sposób jawny w modelu potencjałów o zerowym promieniu. Uwzględniając stany wzbudzone wprowadzamy potencjał macierzowy. Dla przykładu e+H_2 porównujemy wyniki obliczeń przekrojów czynnych z innymi (ab initio) oraz z doświadczeniem.
-
Generalized Zero Range Potentials and Multichannel Electron Molecule Scattering.
PublikacjaZagadnienie o rozpraszaniu elektronów na molekułach rozwiązuje się w sposób jawny w modelu potencjałów o zerowym promieniu. Uwzględniając stany wzbudzone wprowadzamy potencjał macierzowy. Dla przykładu stanów wibracyjnych e+H_2 porównujemy wyniki obliczeń przekrojów czynnych z innymi (ab initio) oraz z doświadczeniem.
-
Low-energy positron scattering from gas-phase pyrimidine: A quantum treatment of the dynamics and a comparison with experiments
PublikacjaWe are reporting detailed quantum scattering calculations that describe the diffusion of a beam of low-energy positrons interacting with the pyrimidine target as a gas-phase partner. The calculations have employed an essentially ab initio model for the short-range correlation interaction and for the electrostatic interaction of an impinging positron and the electron+nuclear structure of the target molecule at its equilibrium geometry.
-
Imidazolium silanethiolates relevant to the active site of cysteineproteases. A cooperative effect in a chain of NH(+)...S(-) hydrogenbonds
PublikacjaThree 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...
-
Potential Energy Curves of Diatomic Alkali Molecules Datasets
PublikacjaThe datasets described in this article contain potential energy curves for several diatomic systems. The data was obtained via high-performance computing using MOLPRO, a system of ab initio programs for advanced molecular electronic structure calculations. The datasets allow to model bond lengths, energy levels, spectra and time-evolution of molecular dimers for which the data are presented.
-
Interatomic potential suitable for the modeling of penta-graphene: Molecular statics/molecular dynamics studies
PublikacjaWe test the potentials available for elemental carbon, with the scope to choose the potential suitable for the modeling of penta-graphene, the latest two dimensional carbon allotrope. By using molecular statics and molecular dynamics simulations we show that there is only one potential e namely the Tersoff-type potential proposed by Erhart and Albe in 2005 e which is able to correctly describe all the important features of penta-graphene....
-
Structural and electronic properties of some intriguing (rare-earth)Ba2Cu3O7 compounds.
PublikacjaW 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....
-
Superconductivity in Bismuth Pyrochlore Lattice Compounds RbBi2 and CsBi2: The Role of Relativistic Effects
PublikacjaSuperconducting 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...
-
A first-principles study of electron attachment to the fully hydrated bromonucleobases
PublikacjaDegradation mechanism of four brominated nucleobases (BrX), potential DNA radiosensitizers, is studied in explicit water solution, using ab initio molecular dynamics. Several fs long dynamics is needed to localize an electron on the nucleobase. Produced by electron attachment BrX anion radical degrades through the bromide anion abstraction, barrier-free (purines) or with low barrier (pyrimidines), to a reactive nucleobase radical....
-
Potential energy surfaces of the low-lying electronic states of the Li+LiCs system
PublikacjaAb 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...
-
Polarisation effects in low-energy positron–molecule scattering
PublikacjaThe UK molecular R-matrix method has been adapted to treat positron collisions from polyatomic targets. A simple empirical enhancement factor which corrects for the underestimation of electron–positron polarisation and correlation effects in the calculations performed with the static-plus-polarization model at low scattering energies is presented. Application of this model to positron scattering from carbon dioxide at energies...
-
Proton transfer reactions for ionized water clusters
PublikacjaCalculations 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...
-
Modeling protein structures with the coarse-grained UNRES force field in the CASP14 experiment
PublikacjaThe 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...
-
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
PublikacjaX-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...
-
Hydrogen migration in formation of NH(A3Π) radicals via superexcited states in photodissociation of isoxazole molecules
PublikacjaFormation 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...
-
Visualizing spatially decomposed intermolecular correlations in the infrared spectra of aprotic liquids
PublikacjaInfrared (IR) spectroscopy is commonly used to study intermolecular interactions in the liquid phase, including solvation phenomena. On the other hand, ab initio molecular dynamics (AIMD) simulations offer the possibility to obtain IR spectra from first principles. Surpassing the experiment, AIMD simulations can deliver additional information on the spatial intermolecular correlations underlying the IR spectrum of the liquid. Although...
-
Elimination and migration of hydrogen in the vacuum-ultraviolet photodissociation of pyridine molecules
PublikacjaElimination 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...
-
Born–Oppenheimer potential energy curves of NaK from the optimised atomic basis sets
PublikacjaThe 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...
-
Positron collisions with molecular hydrogen: cross sections and annihilation parameters calculated using theR-matrix with pseudo-states method
PublikacjaThe molecular R-matrix with pseudo-states (MRMPS) method is employed to study positron collisions with H2. The calculations employ pseudo-continuum orbital sets containing up to h (l = 5) functions. Use of these high l functions is found to give converged eigenphase sums. Below the positronium formation threshold, the calculated cross sections agree with other high-accuracy theories and generally with the measurements. Calculation...
-
The role of low-energy electrons in the charging process of LISA test masses
PublikacjaThe 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...
-
Weakly Hydrated Solute of Mixed Hydrophobic–Hydrophilic Nature
PublikacjaInfrared (IR) spectroscopy is a commonly used and invaluable tool in studies of solvation phenomena in aqueous solutions. Concurrently, density functional theory calculations and ab initio molecular dynamics simulations deliver the solvation shell picture at the molecular detail level. The mentioned techniques allowed us to gain insights into the structure and energy of the hydrogen bonding network of water molecules around methylsulfonylmethane...
-
1,3-alternate calix[4]arene-bonded silica stationary phases. Effect of calixarene skeleton substituents on the retention mechanism and column selectivity
PublikacjaFour 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....
-
Low-energy positron scattering from DNA nucleobases: the effects from permanent dipoles
PublikacjaAb initio quantum calculations for low-energy positron scattering from gas-phase isolated molecular nucleobases which are part of the DNA structure are presented and discussed over the range of 1 eV to 25 eV. The calculations report the integral cross sections (ICSs) and the momentum-transfer cross sections (MTCSs) for Adenine, Guanine, Thymine and Cytosine. The calculations show very clearly the important role of the dominant...
-
Modeling the Structure, Dynamics, and Transformations of Proteins with the UNRES Force Field
PublikacjaThe physics-based united-residue (UNRES) model of proteins ( www.unres.pl ) has been designed to carry out large-scale simulations of protein folding. The force field has been derived and parameterized based on the principles of statistical-mechanics, which makes it independent of structural databases and applicable to treat nonstandard situations such as, proteins that contain D-amino-acid residues. Powered by Langevin dynamics...
-
Computational methods for calculation of binding free energy for ligand-receptor complexes
PublikacjaAccurate description of the molecular complexes energetic influence is required for understanding of many biological functions carried out by proteins. Therefore, estimation of binding free energy for ligand-receptor complexes is of highest importance for structure-based ligand design and drug discovery approaches.Experimental methods of determination of difference in Gibbs'es free energy have many limitations. Thus, computational...
-
A non-adiabatic wavepacket dynamical study of the low energy chargetransfer process in the S3+ + H collision
PublikacjaThe collisional system S3+ + H?S2+ + H+ has been studied using a time-dependent wavepacket methodologyin two-dimensions. Using available potential energy surfaces and coupling matrix elementsobtained from multireference ab initio calculations, five non-adiabatically coupled electronic states of1P symmetry have been included in the dynamical simulations. The collision has been studied in thelow energy regime of 1-10 eV. The wavepacket...
-
Rotational state-changing collisions of C2H− and C2N− anions with He under interstellar and cold ion trap conditions: A computational comparison
PublikacjaWe present an extensive range of quantum calculations for the state-changing rotational dynamics involving two simple molecular anions that are expected to play some role in the evolutionary analysis of chemical networks in the interstellar environments, C2H− (X1Σ+) and C2N− (X3Σ−), but for which inelastic rates are only known for C2H−. The same systems are also of direct interest in modeling selective photo-detachment experiments...
-
On the electronic structure of methyl butyrate and methyl valerate
PublikacjaWe 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...
-
Multi-state vibronic interactions in the fluorobenzene radical cation: The importance of quadratic coupling terms
PublikacjaThe multi-mode multi-state vibronic interactions in the set of X^2B_1 - D^2A_1 electronic states of the monofluoro benzene radical cation are investigated theoretically, based on a quadratic vibronic coupling approach. The underlying ionization potentials and coupling constants are obtained from ab initio coupled-cluster calculations. Previous investigations (relying on the linear coupling approach) are extended by including all...
-
A semiempirical model for low energy electron–atom transport cross sections: The case of noble gases
PublikacjaA 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...