scholarly journals Classical Polarizable Force Field to Study Hydrated Hectorite: Optimization on DFT Calculations and Validation against XRD Data

Minerals ◽  
2018 ◽  
Vol 8 (5) ◽  
pp. 205 ◽  
Author(s):  
Ragnhild Hånde ◽  
Vivien Ramothe ◽  
Stéphane Tesson ◽  
Baptiste Dazas ◽  
Eric Ferrage ◽  
...  
Keyword(s):  
Force Field ◽  
Density Functional ◽  
Density Functional Theory Calculations ◽  
X Ray Diffraction ◽  
Electronic Density ◽  
Functional Theory ◽  
Polarizable Force Field ◽  
Xrd Patterns ◽  
The One ◽  
Dynamics Simulations

Following our previous works on dioctahedral clays, we extend the classical Polarizable Ion Model (PIM) to trioctahedral clays, by considering dry Na-, Cs-, Ca- and Sr-hectorites as well as hydrated Na-hectorite. The parameters of the force field are determined by optimizing the atomic forces and dipoles on density functional theory calculations. The simulation results are validated by comparison with experimental X-ray diffraction (XRD) data. The XRD patterns calculated from classical molecular dynamics simulations performed with the PIM force field are in very good agreement with experimental results. In the bihydrated state, the less structured electronic density profile obtained with PIM compared to the one from the state-of-the-art non-polarizable force field clayFF explains the slightly better agreement between the PIM results and experiments.

A novel ternary bismuthide, NaMgBi: crystal and electronic structure and electrical properties

2021 ◽  
Vol 0 (0) ◽  
Author(s):  
Takahiro Yamada ◽  
Naoki Matsuo ◽  
Masanori Enoki ◽  
Hisanori Yamane
Keyword(s):  
Electronic Structure ◽  
Density Functional ◽  
Density Functional Theory Calculations ◽  
Polycrystalline Sample ◽  
X Ray Diffraction ◽  
Functional Theory ◽  
Sodium Magnesium ◽  
Small Band ◽  
The One ◽  
Structure Calculations

Abstract A new ternary sodium magnesium bismuthide, NaMgBi, has been synthesized from the constituent metals, and its crystal structure was determined by single-crystal X-ray diffraction. NaMgBi crystallizes in a tetragonal PbFCl-type structure corresponding to the space group P4/nmm, where Z = 2, a = 4.7123(4) and c = 7.8158(7) Å. The structure is composed of layers formed by edge-sharing Bi tetrahedra centered with Mg stacked in the c-axis direction, and these layers sandwich the Na atoms. First-principles computations based on density functional theory calculations have verified that the most stable atomic configuration is the one in which the Na and Mg atoms occupy the 2a and 2c sites, respectively. The electrical resistivity measured for a sintered polycrystalline sample of NaMgBi with a relative density of 70% was found to gradually decrease from 868 to 26.4 mΩ cm upon increasing the temperature from 297 to 506 K, and the Seebeck coefficient decreased from 273 to 180 μV K−1 upon increasing the temperature from 298 to 496 K. Electronic structure calculations have revealed that NaMgBi must be a semiconductor with a small band gap of ∼0.1 eV.

X-ray diffraction and density functional theory studies of R(Fe0.5Co0.5)O3 (R = Pr, Nd, Sm, Eu, Gd)

2016 ◽  
Vol 31 (4) ◽  
pp. 259-266 ◽  
Author(s):  
W. Wong-Ng ◽  
G. Liu ◽  
I. Levin ◽  
I. Williamson ◽  
P. Ackerman ◽  
...  
Keyword(s):  
Density Functional Theory ◽  
Density Functional ◽  
Density Functional Theory Calculations ◽  
Lattice Parameter ◽  
X Ray Diffraction ◽  
Functional Theory ◽  
X Ray ◽  
Transmission Electron ◽  
Bond Strain ◽  
Xrd Patterns

The structure of a series of lanthanide iron cobalt perovskite oxides, R(Fe0.5Co0.5)O3 (R = Pr, Nd, Sm, Eu, and Gd), have been investigated. The space group of these compounds was confirmed to be orthorhombic Pnma (No. 62), Z = 4. From Pr to Gd, the lattice parameter a varies from 5.466 35(13) Å to 5.507 10(13) Å, b from 7.7018(2) to 7.561 75(13) Å, c from 5.443 38(10) to 5.292 00(8) Å, and unit-cell volume V from 229.170(9) Å3 to 220.376(9) Å3, respectively. While the trend of V follows the trend of the lanthanide contraction, the lattice parameter “a” increases as the ionic radius r(R3+) decreases. X-ray diffraction (XRD) and transmission electron microscopy confirm that Fe and Co are disordered over the octahedral sites. The structure distortion of these compounds is evidenced in the tilt angles θ, ϕ, and ω, which represent rotations of an octahedron about the pseudocubic perovskite [110]p, [001]p, and [111]p axes. All three tilt angles increase across the lanthanide series (for R = Pr to R = Gd: θ increases from 12.3° to 15.2°, ϕ from 7.5° to 15.8°, and ω from 14.4° to 21.7°), indicating a greater octahedral distortion as r(R3+) decreases. The bond valence sum for the sixfold (Fe/Co) site and the eightfold R site of R(Fe0.5Co0.5)O3 reveal no significant bond strain. Density Functional Theory calculations for Pr(Fe0.5Co0.5)O3 support the disorder of Fe and Co and suggest that this compound to be a narrow band gap semiconductor. XRD patterns of the R(Fe0.5Co0.5)O3 samples were submitted to the Powder Diffraction File.

Graphene adlayer growth between nonepitaxial graphene and Ni(111) substrate: a promising theoretical scheme

2020 ◽  
Author(s):  
Lijuan Meng ◽  
Jinlian Lu ◽  
Yujie Bai ◽  
Lili Liu ◽  
Tang Jingyi ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Density Functional Theory ◽  
Chemical Vapor Deposition ◽  
Molecular Dynamics Simulations ◽  
Vapor Deposition ◽  
Density Functional ◽  
Chemical Vapor ◽  
Density Functional Theory Calculations ◽  
Functional Theory ◽  
Dynamics Simulations

Understanding the fundamentals of chemical vapor deposition bilayer graphene growth is crucial for its synthesis. By employing density functional theory calculations and classical molecular dynamics simulations, we have investigated the...

scholarly journals Assessment of Amyloid Forming Tendency of Peptide Sequences from Amyloid Beta and Tau Proteins Using Force-Field, Semi-Empirical, and Density Functional Theory Calculations

2021 ◽  
Vol 22 (6) ◽  
pp. 3244
Author(s):  
Charuvaka Muvva ◽  
Natarajan Arul Murugan ◽  
Venkatesan Subramanian
Keyword(s):  
Force Field ◽  
Density Functional ◽  
Amyloid Β ◽  
Density Functional Theory Calculations ◽  
Tau Proteins ◽  
Functional Theory ◽  
Energy Profiles ◽  
Α Helix ◽  
Semi Empirical ◽  
Β Sheet

A wide variety of neurodegenerative diseases are characterized by the accumulation of protein aggregates in intraneuronal or extraneuronal brain regions. In Alzheimer’s disease (AD), the extracellular aggregates originate from amyloid-β proteins, while the intracellular aggregates are formed from microtubule-binding tau proteins. The amyloid forming peptide sequences in the amyloid-β peptides and tau proteins are responsible for aggregate formation. Experimental studies have until the date reported many of such amyloid forming peptide sequences in different proteins, however, there is still limited molecular level understanding about their tendency to form aggregates. In this study, we employed umbrella sampling simulations and subsequent electronic structure theory calculations in order to estimate the energy profiles for interconversion of the helix to β-sheet like secondary structures of sequences from amyloid-β protein (KLVFFA) and tau protein (QVEVKSEKLD and VQIVYKPVD). The study also included a poly-alanine sequence as a reference system. The calculated force-field based free energy profiles predicted a flat minimum for monomers of sequences from amyloid and tau proteins corresponding to an α-helix like secondary structure. For the parallel and anti-parallel dimer of KLVFFA, double well potentials were obtained with the minima corresponding to α-helix and β-sheet like secondary structures. A similar double well-like potential has been found for dimeric forms for the sequences from tau fibril. Complementary semi-empirical and density functional theory calculations displayed similar trends, validating the force-field based free energy profiles obtained for these systems.

The Role of SiH3 Diffusion in Determining the Surface Smoothness of Plasma-Deposited Amorphous Si Thin Films: An Atomic-Scale Analysis

2005 ◽  
Vol 862 ◽  
Author(s):  
Mayur S. Valipa ◽  
Tamas Bakos ◽  
Eray S. Aydil ◽  
Dimitrios Maroudas
Keyword(s):  
Thin Films ◽  
Density Functional ◽  
Activation Barrier ◽  
Density Functional Theory Calculations ◽  
Atomic Scale ◽  
Functional Theory ◽  
Weak Adsorption ◽  
Dynamics Simulations ◽  
Hydrogenated Amorphous

AbstractDevice-quality hydrogenated amorphous silicon (a-Si:H) thin films grown under conditions where the SiH3 radical is the dominant deposition precursor are remarkably smooth, as the SiH3 radical is very mobile and fills surface valleys during its diffusion on the a-Si:H surface. In this paper, we analyze atomic-scale mechanisms of SiH3 diffusion on a-Si:H surfaces based on molecular-dynamics simulations of SiH3 radical impingement on surfaces of a-Si:H films. The computed average activation barrier for radical diffusion on a-Si:H is 0.16 eV. This low barrier is due to the weak adsorption of the radical onto the a-Si:H surface and its migration predominantly through overcoordination defects; this is consistent with our density functional theory calculations on crystalline Si surfaces. The diffusing SiH3 radical incorporates preferentially into valleys on the a-Si:H surface when it transfers an H atom and forms a Si-Si backbond, even in the absence of dangling bonds.

A high-pressure study of HfC and nano-crystalline TiC by X-ray diffraction and density functional theory calculations

2020 ◽  
Vol 34 (34) ◽  
pp. 2050393
Author(s):  
Lun Xiong ◽  
Bin Li ◽  
Bi Liang ◽  
Jinxia Zhu ◽  
Hong Yi ◽  
...  
Keyword(s):  
Density Functional Theory ◽  
High Pressure ◽  
Bulk Modulus ◽  
Density Functional ◽  
Density Functional Theory Calculations ◽  
Xrd Analysis ◽  
X Ray Diffraction ◽  
Functional Theory ◽  
X Ray ◽  
Nano Crystalline

The equation of state (EOS) of HfC and nanosized TiC at high pressure has been studied by means of synchrotron radiation X-ray diffraction (XRD) in a diamond anvil cell (DAC) at ambient temperature, and density functional theory (DFT) calculations. XRD analysis showed that the cubic structure of HfC and nanosized TiC maintained to the maximum pressures. The XRD data yield a bulk modulus [Formula: see text] GPa with [Formula: see text] of HfC. In addition, the bulk modulus of nanosized TiC derived from XRD data is [Formula: see text] GPa with [Formula: see text].

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