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Wyniki wyszukiwania dla: DFT STUDIES
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Raw data for the paper "Mutually polarizable QM/MM model with in situ optimized localized basis functions"
Dane BadawczeThis dataset contains raw data used to generate plots in the paper Mutually polarizable QM/MM model with in situ optimized localized basis functions. The paper is devoted to a second generation of the TINKTEP model -- an QM/MM approach combining linear-scaling DFT (ONETEP) and a polarizable force field (AMOEBA).
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5-Thiocyanato-2′-deoxyuridine as a possible radiosensitizer: electron-induced formation of uracil-C5-thiyl radical and its dimerization
PublikacjaIn this work, we have synthesized 5-thiocyanato-2′-deoxyuridine (SCNdU) along with the C6-deuterated nucleobase 5-thiocyanatouracil (6-D-SCNU) and studied their reactions with radiation-produced electrons. ESR spectra in γ-irradiated nitrogen-saturated frozen homogeneous solutions (7.5 M LiCl in H2O or D2O) of these compounds show that electron-induced S–CN bond cleavage occurs to form a thiyl radical (dU-5-S˙ or 6-D-U-5-S˙) and...
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Anharmonic Infrared Spectroscopy through the Fourier Transform of Time Correlation Function Formalism in ONETEP
PublikacjaDensity functional theory molecular dynamics (DFT-MD) provides an efficient framework for accurately computing several types of spectra. The major benefit of DFTMD approaches lies in the ability to naturally take into account the effects of temperature and anharmonicity, without having to introduce any ad hoc or a posteriori corrections. Consequently, computational spectroscopy based on DFT-MD approaches plays a pivotal role in...
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Accuracy improvement of short signal frequency estimation with the use of digital filtration
PublikacjaW pracy przedstawiono metodę estymacji częstotliwości krótkiej obserwacji zaszumionego sygnału sinusoidalnego. Podstawowy pomiar uzyskuje się za pomocą DFT. Jednak taki pomiar dla krótkich obserwacji cechuje bardzo mała dokładność. W omawianej metodzie pomiar ten jest poprawiany z użyciem specjalnie dobranego filtru cyfrowego. Jakość przedstawianej metody porównano z kilkoma innymi metodami również bazującymi na DFT.
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Density functional theory-based simulations of sum frequency generation spectra involving methyl stretching vibrations: effect of the molecular model on the deduced molecular orientation and comparison with an analytical approach
PublikacjaThe knowledge of the first hyperpolarizability tensor elements of molecular groups is crucial for a quantitative interpretation of the sum frequency generation (SFG) activity of thin organic films at interfaces. Here, the SFG response of the terminal methyl group of a dodecanethiol (DDT) monolayer has been interpreted on the basis of calculations performed at the density functional theory (DFT) level of approximation. In particular,...
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Comparative analysis of various transformation techniques for voiceless consonants modeling
PublikacjaIn this paper, a comparison of various transformation techniques, namely Discrete Fourier Transform (DFT), Discrete Cosine Transform (DCT) and Discrete Walsh Hadamard Transform (DWHT) are performed in the context of their application to voiceless consonant modeling. Speech features based on these transformation techniques are extracted. These features are mean and derivative values of cepstrum coefficients, derived from each transformation....
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Structure of Small Platinum Clusters Revised
PublikacjaW pracy opisano wyniki obliczeń metodą DFT struktury 2-15 atomowych klastrów platyny.
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Electrostatic interactions in finite systems treated with periodic boundary conditions: Application to linear-scaling density functional theory
PublikacjaWe present a comparison of methods for treating the electrostatic interactions of finite, isolated systems within periodic boundary conditions (PBCs), within density functional theory (DFT), with particular emphasis on linear-scaling (LS) DFT. Often, PBCs are not physically realistic but are an unavoidable consequence of the choice of basis set and the efficacy of using Fourier transforms to compute the Hartree potential. In such...
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The voltage across and current through the RC model object tested using pulse excitation in impedance spectroscopy measurement method
Dane BadawczeThe raw data (voltage across and current through RC model object ) obtained using pulse excitation EIS impedance spectroscopy measurement method. The data was acquired using 12-bit ADC (LTC1420) with sampling frequency changed in time segments. The 1V voltage pulse excitation duration was set to 0.1s and the total acqusition time was set to 1000s. For...
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Calculating the Partition Coefficients of Organic Solvents in Octanol/Water and Octanol/Air
PublikacjaPartition coefficients define how a solute is distributed between two immiscible phases at equilibrium. The experimental estimation of partition coefficients in a complex system can be an expensive, difficult, and time-consuming process. Here a computational strategy to predict the distributions of a set of solutes in two relevant phase equilibria is presented. The octanol/water and octanol/air partition coefficients are predicted...
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Variable-temperature X-ray diffraction study of structural parameters of NH---S hydrogen bonds in triethylammonium and pyridinium silanethiolates
PublikacjaHydrogen bonds in triethylammonium and pyridinium silanethiolate salts have been characterized by X-ray, FT–IR and NMR spectroscopies. DFT calculations reveal strongly asymmetric double-well minima at the potential energy curves of the studied compounds
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Udokładnianie pomiaru częstotliwości krótkich obserwacji sinusoidy przy użyciu filtracji cyfrowej
PublikacjaW pracy pogłębiono i przebadano koncepcję metody pomiaru częstotliwości krótkiego fragmentu zaszumionego sygnału sinusoidalnego wykorzystującą filtrację cyfrową do zwiększania dokładności pomiaru. Podstawowy pomiar realizowany jest z użyciem transformaty DFT. Pomiar ten w przypadku krótkich sygnałów nie oferuje jednak wystarczającej dokładności. Dlatego w omawianej metodzie wprowadzono dodatkowy etap udokładniania częstotliwości....
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Spectroscopic and cytotoxic characteristics of (p-cymene)Ru(II) complexes with bidentate coumarins and density functional theory comparison with selected Pd(II) complexes
PublikacjaThis paper presents the synthesis of two new (p-cymene)-ruthenium(II) complexes with the bidentate coumarin ligands. Both complexes were characterized by FTIR spectroscopy, 1H NMR, 13C NMR, MS, elemental analysis and DFT calculations. The X-ray structure of complex 3a was also solved. The cytotoxic properties of both complexes were examined on human leukemia NALM-6 and HL-60 cells and melanoma WM-115 cells. The complexes possess...
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Electrochemistry from first-principles in the grand canonical ensemble
PublikacjaProgress in electrochemical technologies, such as automotive batteries, supercapacitors, and fuel cells, depends greatly on developing improved charged interfaces between electrodes and electrolytes. The rational development of such interfaces can benefit from the atomistic understanding of the materials involved by first-principles quantum mechanical simulations with Density Functional Theory (DFT). However, such simulations are...
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Influence of substituents in vinyl groups on reactivity of parylene during polymerization process
PublikacjaPraca zawiera wyniki obliczeń kwantowych wielokonfiguracyjnych i DFT mechanizmów reakcji parylenu i cząsteczek z wiązaniami podwójnymi w fazie gazowej. Zbadany został i zanalizowany wpływ podstawników w strukturach alkenów na reaktywność parylenu i alkenów.
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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...
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Metoda szczególnego próbkowania a FFT w pomiarach elektroenergetycznych
PublikacjaW referacie przedstawiono podstawowe różnice pomiędzy metodami wykorzystującymi próbkowanie równomierne, a więc DFT i FFT a metodą szczególnego próbkowania, opracowaną specjalnie do pomiarów elektroenergetycznych, które wymagają dużej dokładności amplitudowej i fazowej ale ograniczonej liczby wyznaczanych harmonicznych.
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Density functional theory calculations on entire proteins for free energies of binding: Application to a model polar binding site
PublikacjaIn drug optimization calculations, the molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) method can be used to compute free energies of binding of ligands to proteins. The method involves the evaluation of the energy of configurations in an implicit solvent model. One source of errors is the force field used, which can potentially lead to large errors due to the restrictions in accuracy imposed by its empirical nature....
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Theoretical study of the photoelectron spectrum of ethyl formate: Ab initio and density functional theory investigation
PublikacjaThe 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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Designing efficient A-D-A1-D-A type fullerene free acceptor molecules with enhanced power conversion efficiency for solar cell applications
PublikacjaThe achievement of highly efficient power conversion efficiency (PCE) is a big concern for non-fullerene organic solar cells (NF-OSCs) because PCE can depend on numerous variables. Here, new five novel acceptor molecules without fullerenes were developed and investigated using DFT (density functional theory) and TD-DFT (time dependent-density functional theory). Compared to the recently synthesized molecule (PZ-dIDTC6), the developed...
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DMSO and TMAO—Differences in Interactions in Aqueous Solutions of the K-Peptide
PublikacjaInteractions between a solvent and their co-solute molecules in solutions of peptides are crucial for their stability and structure. The K-peptide is a synthetic fragment of a larger hen egg white lysozyme protein that is believed to be able to aggregate into amyloid structures. In this study, a complex experimental and theoretical approach is applied to study systems comprising the peptide, water, and two co-solutes: trimethylamide...
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The ONETEP linear-scaling density functional theory program
PublikacjaWe present an overview of the ONETEP program for linear-scaling density functional theory (DFT) calculations with large basis set (planewave) accuracy on parallel computers. The DFT energy is computed from the density matrix, which is constructed from spatially localized orbitals we call Non-orthogonal Generalized Wannier Functions (NGWFs), expressed in terms of periodic sinc (psinc) functions. During the calculation, both the...
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Diaminophosphinoboranes: effective reagents for phosphinoboration of CO2
PublikacjaThe monomeric diaminophosphinoboranes readily react with CO2 under mild conditions to cleanly form products of the general formula R2P-C(=O)-O-B(NR2)2 in the absence of a catalyst. The isolated products from the CO2-phosphinoboration were fully characterized by NMR spectroscopy, IR spectroscopy, and X-ray diffraction. The mechanism of CO2 phosphinoboration with diaminophosphinoboranes was elucidated by DFT calculations.
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Color prediction from first principle quantum chemistry computations: a case of alizarin dissolved in methanol
PublikacjaThe electronic spectrum of alizarin (AZ) in methanol solution was measured and used as reference data for color prediction. The visible part of the spectrum was modelled by different DFT functionals within the TD-DFT framework. The results of a broad range of functionals applied for theoretical spectrum prediction were compared against experimental data by a direct color comparison. The tristimulus model of color expressed in terms...
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Comments on “Closed Form Variable Fractional Time Delay Using FFT”
PublikacjaIn this letter drawbacks of the aforementioned paper are pointed out. The proposed approach is improved with minor modifications of the discrete frequency response. This allows for design of fractional delay filters which are close to optimal and can be efficiently implemented in the frequency domain using the sliding DFT based structure. Alternatively, the derived equivalent closed form formulae for offset windows can be used...
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The synthesis and structure of a potential immunosuppressant: N-mycophenoyl malonic acid dimethyl ester
PublikacjaThe synthesis of a potential immunosuppressant, i.e. dimethyl ester of N-mycophenoyl malonic acid was optimized in the reaction of mycophenolic acid (MPA) with amino malonic dimethyl ester in the presence of propanephosphonic anhydride (T3P) as a coupling reagent. The structural properties of the obtained MPA derivative were investigated by NMR, MS and single crystal X-ray diffraction methods. Theoretical considerations of conformational...
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Correlation–polarization effects in electron/positron scattering from acetylene: A comparison of computational models
PublikacjaDifferent computational methods are employed to evaluate elastic (rotationally summed) integral and differential cross sections for low energy (below about 10 eV) positron scattering off gas-phase C2H2 molecules. The computations are carried out at the static and static-plus-polarization levels for describing the interaction forces and the correlation–polarization contributions are found to be an essential component for the correct...
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Practical Approach to Large-Scale Electronic Structure Calculations in Electrolyte Solutions via Continuum-Embedded Linear-Scaling Density Functional Theory
PublikacjaWe present the implementation of a hybrid continuum-atomistic model for including the effects of a surrounding electrolyte in large-scale density functional theory (DFT) calculations within the Order-N Electronic Total Energy Package (ONETEP) linear-scaling DFT code, which allows the simulation of large complex systems such as electrochemical interfaces. The model represents the electrolyte ions as a scalar field and the solvent...
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Lead(II) coordination polymers with imidazole-4- and pyrazole-3-carboxylate isomeric linkers: Structural diversity and luminescence properties
PublikacjaUsing 1H-imidazole-4-carboxylic acid (4imCOOH) and 1H-pyrazole-3-carboxylic acid (3pyrCOOH) coordination polymers [Pb(4imCOO)2(H2O)]n (1) and [Pb2(3pyrCOO)4]n (2) were constructed. Obtained polymers were characterized via FT-IR, X-ray, PL and TG methods. The coordination polyhedron around Pb(II) in 1 is described as distorted pentagonal pyramid with hemidirected coordination sphere (based on DFT calculations). Compound 2 consists...
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Performance of extended Lagrangian schemes for molecular dynamics simulations with classical polarizable force fields and density functional theory
PublikacjaIterative energy minimization with the aim of achieving self-consistency is a common feature of Born-Oppenheimer molecular dynamics (BOMD) and classical molecular dynamics with polarizable force fields. In the former, the electronic degrees of freedom are optimized, while the latter often involves an iterative determination of induced point dipoles. The computational effort of the self-consistency procedure can be reduced by re-using...
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The reactivity of 1,1-dichloro-2,2-di-tert-butyldiphosphane towards lithiated metal carbonyls: a new entry to phosphanylphosphinidene dimers
PublikacjaReactions of [Cp*(OC)3M]Li (Cp* = C5Me5, M = Mo, W) towards t-Bu2P–PCl2 lead to the formation of phosphanylphosphinidene dimers [Cp*(OC)3M(η2-t-Bu2P–P)]2 in fairly good yields. The formation of a tetraphosphorus ligand proceeds via reductive dimerization of t-Bu2P–P units. NMR, X-ray investigations and DFT calculations show that the resulting tetraphosphorus ligand has a structure of dication t-Bu2P+=P–P=P+t-Bu2.
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Fast Real-Time RDFT- and GDFT-Based Direct Fault Diagnosis of Induction Motor Drive
PublikacjaThis paper presents the theoretical analysis and experimental verification of a direct fault harmonic identification approach in a converter-fed electric drive for automated diagnosis purposes. On the basis of the analytical model of the proposed real-time direct fault diagnosis, the fault-related harmonic component is calculated using recursive DFT (RDFT) and Goertzel DFT (GDFT), applied instead of the full spectrum calculations...
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Ab-initio study of electrical and optical properties of allylamine
PublikacjaThe 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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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...
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Ab-initio study of electrical and optical properties of allylamine
PublikacjaThe 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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Sulfurization of phosphanylphosphinidene ligand: Access to phosphinothioyltrithiophosphonato platinum(II) complexes
PublikacjaThe reactivity of phosphanylphosphinidene Pt(0) complexes [DppePt(η2-P–PtBu2)] (1) and [(pTol3P)2Pt(η2-P–PtBu2)] (2) toward sulfur was studied. Reactions of 1 and 2 with an excess of sulfur led to the formation of the first transition metal complexes 3 and 4 with phosphinothioyltrithiophosphonato ligands with the formula [tBu2P(=S)–P(=S)S2]2-. In contrast to previous reports on the phosphanylphosphinidene moiety sulfurization,...
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The Reactivity of the Imine Bond within Polynuclear Nickel(II) Complexes
PublikacjaThree novel Ni complexes with the Schiff base ligand 2-methoxy-6-(E-2-pyridyliminomethyl)-phenol (L1) are described. In comparison with the similar 2-(pyridine-2-ylimino-methyl)phenol (pymp), the mode of coordination of L1 is altered due to the presence of methoxy substituent introducing the sterical hindrance. During the synthesis of the complexes, partial hydrolysis of the ligand was observed. Since such immediate hydrolysis...
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Metody projektowania ułatwiającego testowanie dla układów cyfrowych
PublikacjaPrzedstawiono przegląd metod ułatwiających testowanie DFT (Design for Testability) dla układów cyfrowych. Zaprezentowano metody stosowane na poziomie układów scalonych, pakietów oraz systemów elektronicznych. Pokazano heurystyczne metody projektowania pozwalające na zwiększenie sterowalności i obserwowalności układów oraz metody strukturalne, a wśród nich układy BILBO (Built-In Logic Block Observer), BIST (Built-In Self Test),...
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Using A Particular Sampling Method for Impedance Measurement
PublikacjaThe paper presents an impedance measurement method using a particular sampling method which is an alternative to DFT calculation. The method uses a sine excitation signal and sampling response signals proportional to current flowing through and voltage across the measured impedance. The object impedance is calculated without using Fourier transform. The method was first evaluated in MATLAB by means of simulation. The method was...
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Inrush and short circuit current identification based on real-time spectral analysis with the use of the FPGA FFT processor
PublikacjaW artykule przedstawiono krótkookresową analize widmową prądu załączeniowego i prądu zwarciowego transformatora w czasie rzeczywistym z zastosowaniem procesora FFT zrealizowanego w FPGA. Otrzymane widmo ułatwia rozróżnienie rodzaju prądu, co może być zastosowanei do lepszego sterowania zabezpieczneiem różnicowo-prądowym. Określono tez teoretyczne przebiegi prądów dla przyjetego modelu transformatora. Przeprowadzono ponadto analizę...
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Emerging oxidized and defective phases in low-dimensional CrCl3
PublikacjaTwo-dimensional (2D) magnets such as chromium trihalides CrX3 (X ¼ I, Br, Cl) represent a frontier for spintronics applications and, in particular, CrCl3 has attracted research interest due its relative stability under ambient conditions without rapid degradation, as opposed to CrI3. Herein, mechanically exfoliated CrCl3 flakes are characterized at the atomic scale and the electronic structures of pristine, oxidized, and defective...
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Electronic structure calculations in electrolyte solutions: Methods for neutralization of extended charged interfaces
PublikacjaDensity functional theory (DFT) is often used for simulating extended materials such as infinite crystals or surfaces, under periodic boundary conditions (PBCs). In such calculations, when the simulation cell has non-zero charge, electrical neutrality has to be imposed, and this is often done via a uniform background charge of opposite sign (“jellium”). This artificial neutralization does not occur in reality, where a different...
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Exploring thiophene-2-acetate and thiophene-3-acetate binding modes towards the molecular and supramolecular structures and photoluminescence properties of Pb(ii) polymers
PublikacjaTo evaluate the impact of the flexible positional isomeric ligands thiophene-2-acetate (2tpacCOO) andthiophene-3-acetate (3tpacCOO) on the construction and self-assembly process of Pb(II) polymers, twonovel compounds, [Pb(2tpacCOO)2(H2O)]n(1) and [Pb(3tpacCOO)2]n(2), were preparedviaanonhydro-thermal method with respect to green chemistry rules. The obtained polymers were fully characterized byelemental analysis, TG/DTG and PXRD,...
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Linear-scaling calculation of Hartree-Fock exchange energy with Non-orthogonal Generalised Wannier Functions
PublikacjaWe present a method for the calculation of four-centre two-electron repulsion integrals in terms of localised non-orthogonal generalised Wannier functions (NGWFs). Our method has been imple- mented in the ONETEP program and is used to compute the Hartree-Fock exchange energy component of Hartree-Fock and Density Functional Theory (DFT) calculations with hybrid exchange-correlation functionals. As the NGWFs are optimised in situ...
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A comparison of structural and luminescence properties of lead(II) coordination polymers with isomeric thiophenecarboxylate ligands
PublikacjaTwo new lead(II) coordination polymers with isomeric thiophenecarboxylates, namely [Pb(2tpCOO)2]n (1) and [Pb(3tpCOO)2(H2O)]n (2) (2tpCOO− = thiophene-2-carboxylate, 3tpCOO− = thiophene-3-carboxylate), were synthesized and characterized. Single crystal X-ray crystallography revealed a distorted pentagonal pyramidal geometry {PbO6} around Pb in 1 and a distorted dodecahedral geometry {PbO8} in 2. The distortion derived from the...
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In situ transformation boosts the pseudocapacitance of CuNi-MOF via cooperative orientational and electronic governing
PublikacjaThe disordered arrangement and thereof inferior conductivity of 2D MOF sheets seriously hinder their practical application. Herein, we propose in situ transformation strategy to architect vertically oriented bimetallic CuNi-MOF as a self-supporting electrode, leading to a decuple high specific capacitance of 1262 C g-1 in comparison with the pristine Ni-MOF powder of 114 C g-1 at 2 A g-1. DFT calculations reveal that introduction...
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Unraveling Energy Transfer and Fluorescence Quenching Dynamics in Biomolecular Complexes: A Comprehensive Study of Imiquimod-Rifampicin Interaction.
PublikacjaIn nature, numerous biomolecules are implicated in charge transfer (CT) and energy transfer (ET) mechanisms crucial for fundamental processes such as photosynthesis. Unveiling these mechanisms is pertinent to multiple disciplines including chemistry, engineering and biochemistry. This letter presents a study involving two molecules forming a model system with efficient ET properties. Specifically, their complex exhibits dark quenching...
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Structural properties of hypothetical CeBa2Cu3O7 compound from LSDA+DMFT calculations
PublikacjaThe hypothetical stoichiometric CeBa2Cu3O7 (Ce123) compound, which has not been synthesized as a single phase yet, was studied by the density functional theory (DFT). We utilized a method which merges the local spin density approximation (LSDA) with the dynamical mean-field theory (DMFT) to account for the electronic correlations. The LSDA+DMFT calculations were performed in the high-temperature range. The particular emphasis was...
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Compressible gas density measurement by means of Fourier analysis of interferograms
PublikacjaThis paper describes a method for nonintrusive compressible gas density measurement by means of automated analysis of interferograms using FFT (Fast Fourier Transform), and its implementation using DFT (Discrete Fourier Transform), that does make this measurement technique a fairly valuable and accessible experimental method. The presented approach makes it possible to use the finite fringe setting of the interferometer, thus reducing...
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Self-testing of analog parts of mixed-signal electronic microsystems based on multiple sampling of time responses
PublikacjaW artykule przedstawiono nowe podejście samo-testowania toru analogowego zakończonego przetwornikiem A/C w mieszanych sygnałowo elektronicznych systemach wbudowanych sterowanych mikrokontrolerami. Bazuje ono na nowej metodzie diagnostycznej opartej na przekształceniu transformującym zbiór próbek odpowiedzi czasowej układu badanego na pobudzenie impulsem prostokątnym na rodzinę krzywych identyfikacyjnych umieszczonych w przestrzeni...