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Search results for: DFT CALCULATION
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Synthesis and Spectroscopic Characterization of Selected Phenothiazines and Phenazines Rationalized Based on DFT Calculation
PublicationTwo unique structures were isolated from the phosphorylation reaction of 10H-phenothiazine.The 5,5-dimethyl-2-(10H-phenothiazin-10-yl)-1,3,2-dioxaphosphinane 2-oxide (2a) illustrates theproduct of N-phosphorylation of phenothiazine. Moreover, a potential product of 2a instability,a thiophosphoric acid 2b, was successfully isolated and structurally characterized. Molecule 2a,similarly to sulfoxide derivative...
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Coupled cluster and DFT calculations of 14N nuclear quadrupole coupling constants
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Large-scale DFT calculations in implicit solvent-A case study on the T4 lysozyme L99A/M102Q protein
PublicationW ostatnich latach zaproponowano szereg modeli typu implicit solvent, ktore bazują na bezpośrednim rozwiązaniu niejednorodnego równania Poissona w przestrzeni rzeczywistej. Modele te charakteryzują się elegancją, ponieważ wnęka, w której umieszczona jest molekuła substancji rozpuszczanej zdefiniowana jest bezpośrednio w funkcji gęstości elektronowej, a rozkład ładunku jest w sposób samouzgodniony polaryzowany dzięki reakcji dielektryka,...
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Syntheses, spectroscopic and structural properties of phenoxysilyl compounds: X-ray structures, FT-IR and DFT calculations
PublicationThe reaction of silicon disulfide with alkylphenols leads to tetraphenoxysilane, cyclodisilthiane and silanethiol. The products of the reaction of silicon disulfide with phenols are characterized by FT-IR, NMR, X-ray diffraction and DFT calculations. The intramolecular interactions in the compounds are mainly XH---π (X = C, S) whereas the intermolecular interactions are either very weak CH---π/CH---O contacts found in aryloxysilane...
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Weak hydrogen bonding interaction S-H···O=C studied by FT-IR spectroscopy and DFT calculations
PublicationInteractions between the thiolate group of tri-tert-butoxysilanethiol (TBST) and carbonyl group of acetone are studied with the use of FT-IR spectroscopy and DFT calculations.
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Singlet oxygen in the removal of organic pollutants: An updated review on the degradation pathways based on mass spectrometry and DFT calculations
PublicationThe degradation of pollutants by a non-radical pathway involving singlet oxygen (1O2) is highly relevant in advanced oxidation processes. Photosensitizers, modified photocatalysts, and activated persulfates can generate highly selective 1O2 in the medium. The selective reaction of 1O2 with organic pollutants results in the evolution of different intermediate products. While these products can be identified using mass spectrometry...
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Theoretical estimation of acid–base properties of Lewis and Brønsted centres at the V-W-O catalyst surface: water molecule as the probe in DFT calculations
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Linear-scaling calculation of Hartree-Fock exchange energy with Non-orthogonal Generalised Wannier Functions
PublicationWe 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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Using A Particular Sampling Method for Impedance Measurement
PublicationThe 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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Density functional theory calculations on entire proteins for free energies of binding: Application to a model polar binding site
PublicationIn 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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The voltage across and current through the RC model object tested using pulse excitation in impedance spectroscopy measurement method
Open Research DataThe 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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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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The ONETEP linear-scaling density functional theory program
PublicationWe 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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DFT studies of the refractive index of boron-doped diamond
PublicationThe density functional theory is one of the optimal solutions in calculation of optical properties of materials on the quantum scale. In this paper, we have investigated the refractive index of a boron-doped diamond structure with the usage of Atomistic Toolkit software from Synopsys. During this study, various methods and pseudopotentials were checked to obtain an optimal performanceaccuracy method for calculation of such materials....
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Practical Approach to Large-Scale Electronic Structure Calculations in Electrolyte Solutions via Continuum-Embedded Linear-Scaling Density Functional Theory
PublicationWe 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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Density functional LCAO calculations of vibrational modes and phonon density of states in the strained single-layer phosphorene
PublicationThe paper presents an investigation of phosphorene under axial strain on the phonon density of states and vibrational modes. The studies were performed by means of density functional theory (DFT) within the linear combination of atomic orbitals (LCAO). The strained models were constructed using optimised supercell techniques. The vibrational mode spectra were estimated for strains applied for both the zigzag and armchair directions...
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Theoretical studies of fragmentation processes of neutral and ionized furan molecule
PublicationThis PhD thesis focuses on the fragmentation mechanism of the furan molecule in the gas phase. The approach taken in this work comprised of three theoretical methodologies considering the dynamical, energetical and entropic aspects of the studied process. First, molecular dynamics simulations were performed. Next, the potential energy surfaces were explored at the DFT/B3LYP level of theory. Finally, a new statistical Microcanonical...
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Removal of diphenols using pine biochar. Kinetics, equilibrium, thermodynamics, and mechanism of uptake
PublicationThermal pyrolysis synthesized activated biochar from the Pinus elliottii sawdust (PS) at 600° C. The obtained activated biochar (PB600) was used for the removal of three diphenols, catechol (CAT), resorcinol (RES), and hydroquinone (HYD), which are utilized mainly in different industries. The PB600 was characterized by several analytical techniques. The BET surface area of 1473 m2.g−1 and a total pore volume of 0.707 cm3 g−1 was...