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Search results for: density functional calculations
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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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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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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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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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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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Direct estimation of functional and density operators by local operations and classical communication.
PublicationWykazano, że można dokonywać detekcji splątania w paradygmacie odległych laboratoriów. Pokazano, jak można fizycznie zaimplementować strukturalne przybliżenie fizyczne niefizycznego odwzorowania w tym paradygmacie.
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Structure and elastic properties of Mg(OH)2from density functional theory
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Novel Tools for Comprehensive Functional Analysis of LDLR (Low-Density Lipoprotein Receptor) Variants
PublicationFamilial hypercholesterolemia (FH) is an autosomal-dominant disorder caused mainly by substitutions in the low-density lipoprotein receptor (LDLR) gene, leading to an increased risk of premature cardiovascular diseases. Tremendous advances in sequencing techniques have resulted in the discovery of more than 3000 variants of the LDLR gene, but not all of them are clinically relevant. Therefore, functional studies of selected variants...
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The potential of imogolite nanotubes as (co-)photocatalysts: a linear-scaling density functional theory study
PublicationWe report a linear-scaling density functional theory (DFT) study of the structure, wall-polarization absolute band-alignment and optical absorption of several, recently synthesized, open-ended imogolite (Imo) nanotubes (NTs), namely single-walled (SW) aluminosilicate (AlSi), SW aluminogermanate (AlGe), SW methylated aluminosilicate (AlSi-Me), and double-walled (DW) AlGe NTs. Simulations with three different semi-local and dispersion-corrected...
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Excited state properties of a series of molecular photocatalysts investigated by time dependent density functional theory.
PublicationTime dependent density functional theory calculations are applied on a series of molecular photocatalysts of the type [(tbbpy)2M1(tpphz)M2X2]2+ (M1 = Ru, Os; M2 = Pd, Pt; X = Cl, I) in order to provide information concerning the photochemistry occurring upon excitation of the compounds in the visible region. To this aim, the energies, oscillator strengths and orbital characters of the singlet and triplet excited states are investigated....
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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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Adsorption of a metalorganic complex at a metal surface: A density functional theory study vs. model description
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Ground lemon and stevia leaves as renewable functional fillers with antioxidant activity for high-density polyethylene composites
PublicationThe development of new sustainable material solutions in the processing of thermoplastic polymers concerns both the application of biopolymers and the use of valorized plant derivatives as fillers and modifiers of petrochemical polymers. Herein, the possibility of using unprocessed raw parts of two commonly used in the food industry leaves, i.e., lemon (LL) and stevia (ST), as active and functional fillers for high-density polyethylene...
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Electrostatic interactions in finite systems treated with periodic boundary conditions: Application to linear-scaling density functional theory
PublicationWe 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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Performance of extended Lagrangian schemes for molecular dynamics simulations with classical polarizable force fields and density functional theory
PublicationIterative 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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Density Functional Theory Studies on Ir Spectra of the Triphenylene Derivatives. A Scaled Quantum Mechanical Force Field Approach
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The role of Herzberg-Teller effects on the resonance Raman spectrum of trans-porphycene investigated by time dependent density functional theory.
PublicationThe S1 excited state properties as well as the associated absorption and resonance Raman (RR) spectra of trans-porphycene are investigated by means of time dependent density functional theory calculations. The relative magnitude of the Franck-Condon (FC) contribution and of the Herzberg-Teller (HT) effects is evaluated for both the absorption and RR intensities. The accuracy of the calculated spectra is assessed by employing different...
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IR–Raman, NMR and density functional methods in the examination of tautomerism and features of N-methyl substituted 9-acridinamine derivatives
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Hydrogen Production Mechanism in Low-Temperature Methanol Decomposition Catalyzed by Ni3Sn4 Intermetallic Compound: A Combined Operando and Density Functional Theory Investigation
PublicationHydrogen production from methanol decomposition to syngas (H2 + CO) is a promising alternative route for clean energy transition. One major challenge is related to the quest for stable, cost-effective, and selective catalysts operating below 400 °C. We illustrate an investigation of the surface reactivity of a Ni3Sn4 catalyst working at 250 °C, by combining density functional theory, operando X-ray absorption spectroscopy, and high-resolution...
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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
PublicationThis 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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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
PublicationThe 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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Density functional approaches to the many-body problem
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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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Structural properties of hypothetical CeBa2Cu3O7 compound from LSDA+DMFT calculations
PublicationThe 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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Molecular geometry of phenylboronic acid
Open Research DataData presents molecular geometry of the ground singlet state of phenylboronic acid. The geometry was obtained via DFT calculations using Becke–Lee–Yang–Parr density functional (B3LYP) with the balanced polarized triple-zeta def2-TZVP basis set. Geometry is provided in the XYZ file format.
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Effect of the Catalytic Center on the Electron Transfer Dynamics in Hydrogen-Evolving Ruthenium-Based Photocatalysts Investigated by Theoretical Calculations
PublicationThe light-induced relaxation pathways in the molecular photocatalyst [(tbbpy)2Ru(tpphz)PtCl2]2+ are investigated with time-dependent density functional theory calculations together with the Marcus theory of electron transfer (ET). The calculations show that metal (Ru) to ligand (tpphz) charge transfer (MLCT) triplet states are populated following an excitation in the longer wavelength range of the absorption spectrum, but that an...
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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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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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Calculating the Partition Coefficients of Organic Solvents in Octanol/Water and Octanol/Air
PublicationPartition 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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A Novel Ru(II) Polypyridine Black Dye Investigated by Resonance Raman Spectroscopy and TDDFT Calculations
PublicationThe optical properties of a new(bipyridine)2Ru(4H-imidazole) complex presenting a remarkablebroad absorption in the visible range are investigated. Thestrong overlap of the absorption with the solar radiationspectrum renders the studied complex promising as a blackabsorber and hence as a starting structure for applications inthe field of dye-sensitized solar cells. The correlations betweenstructural and electronic features for...
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Ligand-Modified Boron-Doped Diamond Surface: DFT Insights into the Electronic Properties of Biofunctionalization
PublicationWith the increasing power of computation systems, theoretical calculations provide a means for quick determination of material properties, laying out a research plan, and lowering material development costs. One of the most common is Density Functional Theory (DFT), which allows us to simulate the structure of chemical molecules or crystals and their interaction. In developing a new generation of biosensors, understanding the nature...
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A spectroscopic study of the cis/trans-isomers of penta-2,4-dienoic acid attached to gold nanoclusters
PublicationIn this theoretical work, we present a spectroscopic analysis of the cis/trans-isomers of a molecular switch, penta-2,4-dienoic acid, attached to gold clusters of different size (1, 2 and 20 gold atoms). We have simulated 4 different spectroscopic techniques: Infrared spectroscopy, normal Raman scattering, absorption spectra and resonance Raman scattering. We discuss how the position and the conformation of the molecule determine...
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Application of nonmetallic frustrated cations in the activation of small molecules
PublicationThe concept of nonmetallic frustrated cations has been used in small molecule activation. The in situ generated ambiphilic phosphinoborinium cation activated phenyl isocyanate, diisopropylcarbodiimide, and acetonitrile under very mild conditions without any catalyst, yielding single-, double-, or mixed-activation products. Furthermore, the mechanisms of the reactions of the phosphinoborinium cation with small molecules were elucidated...
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Properties of Oxygen Vacancy and Hydrogen Interstitial Defects in Strontium Titanate: DFT + Ud,p Calculations
PublicationThis work presents extensive theoretical studies focused on the mixed ion-electron transport in cubic strontium titanate (STO). A new approach to the description of this difficult system was developed within the framework of linear-scaling Kohn–Sham density functional theory, as realized in the ONETEP program. The description we present is free of any empirical parameters and relies on the Hubbard U and Hund’s J corrections applied...
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Electronic structure calculations in electrolyte solutions: Methods for neutralization of extended charged interfaces
PublicationDensity 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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Antiferromagnetic Order in the Rare-Earth Halide Perovskites CsEuBr3 and CsEuCl3
PublicationBulk CsEuBr3 and CsEuCl3 are experimentally shown to be magnetic semiconductors that order antiferromagnetically at Néel temperatures of 2.0 K and 1.0 K, respectively. Given that nanoparticles and thin films of CsEuCl3 have been reported to order ferromagnetically at a similar temperature, our observation of antiferromagnetic ordering in CsEuBr3 and CsEuCl3 expands the possible applications of halide perovskites to now include...
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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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Crystal structure and electronic structure of CePt2In7
PublicationWe report a corrected crystal structure for the CePt2In7 superconductor, refined from single crystal x-ray diffraction data. The corrected crystal structure shows a different Pt–In stacking along the c-direction in this layered material than was previously reported. In addition, all of the atomic sites are fully occupied with no evidence of atom site mixing, resolving a discrepancy between the observed high resistivity ratio of...
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DFT study of low-energy electron interaction with pyridine, pyrazine and their halo derivatives
PublicationIn this work, the density functional theory with B3LYP hybrid functional was employed to calculate quantities useful for estimating the behavior of pyridine, pyrazine and their derivatives monosubstituted with Cl or Br atom, when exposed to low-energy electron impact. Vertical electron affinities obtained in several Pople basis sets and in aug-cc-pVTZ basis set are reported. Although some of the investigated molecules do not form...
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Sum-over-state expressions including second-order Herzberg–Teller effects for the calculation of absorption and resonance Raman intensities
PublicationThe sum-over-state expressions are derived to calculate the second-order Herzberg–Teller (HT) effects in absorption and resonance Raman spectroscopies. These effects depend on the second derivatives of the transition dipole moment with respect to the vibrational coordinates. The method is applied to the molecule of 1,3-butadiene using density functional theory calculations. It is found that the second-order HT effects are significant...
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Unraveling Energy Transfer and Fluorescence Quenching Dynamics in Biomolecular Complexes: A Comprehensive Study of Imiquimod-Rifampicin Interaction.
PublicationIn 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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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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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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Phosphinoborenium cations stabilized by N-heterocyclic carbenes: synthesis, structure, and reactivity
PublicationPhosphinoborenium cations stabilized by N-heterocyclic carbenes (NHCs) were synthesized via the reaction of bromo(phosphino)boranes with NHCs. Their structures were investigated by heteronuclear magnetic resonance spectroscopy, X-ray diffraction, and density functional theory calculations. They possess a planar trigonal boron center directly bonded with the pyramidal phosphanyl group (PR2) and can be treated as cationic phosphinoboranes....
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Dissociative electron attachment to benzoic acid (C7H6O2)
PublicationThe dissociative electron attachment (DEA) to benzoic acid (C6H5COOH) has been studied using an experimental crossed beam setup of a quadrupole mass spectrometer and a trochoidal electron monochromator. Relative partial cross sections for the DEA to produce negative ion fragments show the main channels for dissociation. The comparison of the present results with the ultraviolet photoelectron spectrum of benzoic acid [J. Meeks,...
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Influence of Protonation State on the Excited State Dynamics of a Photobiologically Active Ru(II) Dyad
PublicationThe influence of ligand protonation on the photophysics of a ruthenium (Ru) dyad bearing the 2-(1-pyrenyl)-1H-imidazo[4,5-f][1,10]-phenanthroline (ippy) ligand was investigated by time-resolved transient absorption spectroscopy. It was found that changes in the protonation state of the imidazole group led to changes in the electronic configuration of the lowest lying excited state. Formation of the fully deprotonated imidazole...
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Weakly Hydrated Solute of Mixed Hydrophobic–Hydrophilic Nature
PublicationInfrared (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...
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Stripe order and magnetic anisotropy in the S=1 antiferromagnet BaMoP2O8
PublicationMagnetic behavior of yavapaiite-type BaMoP2O8 with the spatially anisotropic triangular arrangement of the S=1Mo4+ ions is explored using thermodynamic measurements, neutron diffraction, and density-functional band-structure calculations. A broad maximum in the magnetic susceptibility around 46 K is followed by the stripe antiferromagnetic order with the propagation vector k=(12,12,12) formed below TN≃21 K. This stripe phase is...
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Do positrons measure atomic and molecular diameters?
PublicationWe report on density functional calculations (DFT) of elastic integral scattering cross-sections for positron collisions with argon, krypton, nitrogen and methane. The long-range asymptotic polarization potential is described using higher-order terms going much beyond an induced dipole potential (−α / r 4) while the short-range interaction is modeled by two different forms of electron – positron correlation potential (Boroński-Nieminen...
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Effects of Bromine Doping on the Structural Properties and Band Gap of CH3NH3Pb(I1–xBrx)3 Perovskite
PublicationAn experimental and theoretical study is reported to investigate the influence of bromine doping on CH3NH3Pb(I1−xBrx)3 perovskite for Br compositions ranging from x = 0 to x = 0.1, in which the material remains in the tetragonal phase. The experimental band gap is deduced from UV−vis absorption spectroscopy and displays a linear behavior as a function of bromine concentration. Density functional theory calculations are performed...