scholarly journals Extended Hückel Semi-Empirical Approach as an Efficient Method for Structural Defects Analysis in 4H-SiC

Materials ◽  
2021 ◽  
Vol 14 (5) ◽  
pp. 1247
Author(s):  
Janusz Wozny ◽  
Andrii Kovalchuk ◽  
Jacek Podgorski ◽  
Zbigniew Lisik
Keyword(s):  
Efficient Method ◽  
Density Functional ◽  
Energy Levels ◽  
Computing Time ◽  
Structural Defects ◽  
Dft Methods ◽  
Atomic Structures ◽  
Extended Hückel ◽  
Defects Analysis ◽  
Semi Empirical

This paper presents an efficient method to calculate the influence of structural defects on the energy levels and energy band-gap for the 4H-SiC semiconductor. The semi-empirical extended Hückel method was applied to both ideal 4H-SiC crystal and different structures with defects like vacancies, stacking faults, and threading edge dislocations. The Synopsys QuatumATK package was used to perform the simulations. The results are in good agreement with standard density functional theory (DFT) methods and the computing time is much lower. This means that a structure with ca. 1000 atoms could be easily modeled on typical computing servers within a few hours of computing time, enabling fast and accurate simulation of non-ideal atomic structures.

scholarly journals Analysis of the structural and electronic properties of 1-(5-Hydroxymethyl - 4 –[ 5 – (5-oxo-5-piperidin-1-yl-penta- 1,3dienyl)-benzo[1,3]dioxol-2-yl] -tetrahydro-furan-2-yl)-5- methyl-1H-pyrimidine-2,4dione molecule

2018 ◽  
Vol 33 (1) ◽  
pp. 71
Author(s):  
Ali Hashem Essa ◽  
A. F. Jalbout
Keyword(s):  
Density Functional Theory ◽  
Electronic Properties ◽  
Ground State ◽  
Density Functional ◽  
Molecular Orbital Calculations ◽  
Active Molecule ◽  
Dft Methods ◽  
Functional Theory ◽  
Structural And Electronic Properties ◽  
Semi Empirical

The structural and electronic properties of 1-(5-Hydroxymethyl - 4 –[ 5 – (5-oxo-5-piperidin- 1 -yl-penta- 1,3 -dienyl)-benzo [1,3] dioxol- 2 -yl]- tetrahydro -furan-2 -yl)-5-methy l-1Hpyrimidine-2,4dione (AHE) molecule have been investigated theoretically by performing density functional theory (DFT), and semi empirical molecular orbital calculations. The geometry of the molecule is optimized at the level of Austin Model 1 (AM1), and the electronic properties and relative energies of the molecules have been calculated by density functional theory in the ground state. The resultant dipole moment of the AHE molecule is about 2.6 and 2.3 Debyes by AM1 and DFT methods respectively, This property of AHE makes it an active molecule with its environment, that is AHE molecule may interacts with its environment strongly in solution.

scholarly journals Quantum Chemical Methods for Modeling Covalent Modification of Biological Thiols

2019 ◽  
Author(s):  
Ernest Awoonor-Williams ◽  
William Isley ◽  
Stephen Dale ◽  
Erin Johnson ◽  
Haibo Yu ◽  
...  
Keyword(s):  
Density Functional ◽  
Functional Performance ◽  
Low Cost ◽  
Md Simulations ◽  
Potential Of Mean Force ◽  
Covalent Modification ◽  
Dft Methods ◽  
Aqueous Solvent ◽  
Exact Exchange ◽  
Semi Empirical

Targeted covalent inhibitor drugs require computational methods that go beyond simple molecular-mechanical force fields in order to model the chemical reactions that occur when they bind to their targets. Here, several semi-empirical and density-functional theory (DFT) methods are assessed for their ability to describe the potential energy surface and reaction energies of the covalent modification of a thiol by an electrophile. Functionals such as PBE and B3LYP fail to predict a stable enolate intermediate. This is largely due to delocalization error, which spuriously stabilizes the pre-reaction complex, in which excess electron density is transferred from the thiolate to the electrophile. Functionals with a high-exact exchange component, range-separated DFT functionals, and variationally-optimized exact exchange (i.e., the LC-B05minV functional) correct this issue to various degrees. The large gradient behaviour of the exchange enhancement factor is also found to significantly affect the results, leading to the improved performance of PBE0. While ωB97X-D and M06-2X were easonably accurate, no method provided quantitative accuracy for all three electrophiles, making this a very strenuous test of functional performance. Additionally, one drawback of M06-2X was that MD simulations using this functional were only stable if a fine integration grid was used. The low-cost semi-empirical methods, PM3, AM1, and PM7, provide a qualitatively correct description of the reaction mechanism, although the energetics are not quantitatively reliable. As a proof of concept, the potential of mean force for the addition of methylthiolate to MVK was calculated using QM/MM MD in an explicit polarizable aqueous solvent.<br>

scholarly journals Simulation Study of Surface Transfer Doping of Hydrogenated Diamond by MoO3 and V2O5 Metal Oxides

Micromachines ◽  
2020 ◽  
Vol 11 (4) ◽  
pp. 433 ◽  
Author(s):  
Joseph McGhee ◽  
Vihar P. Georgiev
Keyword(s):  
Charge Transfer ◽  
Metal Oxides ◽  
Density Functional ◽  
Energy Levels ◽  
Dft Method ◽  
Functional Theory ◽  
Empirical Density ◽  
P Type ◽  
Semi Empirical ◽  
Enhanced Surface

In this work, we investigate the surface transfer doping process that is induced between hydrogen-terminated (100) diamond and the metal oxides, MoO3 and V2O5, through simulation using a semi-empirical Density Functional Theory (DFT) method. DFT was used to calculate the band structure and charge transfer process between these oxide materials and hydrogen terminated diamond. Analysis of the band structures, density of states, Mulliken charges, adsorption energies and position of the Valence Band Minima (VBM) and Conduction Band Minima (CBM) energy levels shows that both oxides act as electron acceptors and inject holes into the diamond structure. Hence, those metal oxides can be described as p-type doping materials for the diamond. Additionally, our work suggests that by depositing appropriate metal oxides in an oxygen rich atmosphere or using metal oxides with high stochiometric ration between oxygen and metal atoms could lead to an increase of the charge transfer between the diamond and oxide, leading to enhanced surface transfer doping.

scholarly journals Quantum Chemical Methods for Modeling Covalent Modification of Biological Thiols

2019 ◽  
Author(s):  
Ernest Awoonor-Williams ◽  
William Isley ◽  
Stephen Dale ◽  
Erin Johnson ◽  
Haibo Yu ◽  
...  
Keyword(s):  
Density Functional ◽  
Functional Performance ◽  
Low Cost ◽  
Md Simulations ◽  
Potential Of Mean Force ◽  
Covalent Modification ◽  
Dft Methods ◽  
Aqueous Solvent ◽  
Exact Exchange ◽  
Semi Empirical

Targeted covalent inhibitor drugs require computational methods that go beyond simple molecular-mechanical force fields in order to model the chemical reactions that occur when they bind to their targets. Here, several semi-empirical and density-functional theory (DFT) methods are assessed for their ability to describe the potential energy surface and reaction energies of the covalent modification of a thiol by an electrophile. Functionals such as PBE and B3LYP fail to predict a stable enolate intermediate. This is largely due to delocalization error, which spuriously stabilizes the pre-reaction complex, in which excess electron density is transferred from the thiolate to the electrophile. Functionals with a high-exact exchange component, range-separated DFT functionals, and variationally-optimized exact exchange (i.e., the LC-B05minV functional) correct this issue to various degrees. The large gradient behaviour of the exchange enhancement factor is also found to significantly affect the results, leading to the improved performance of PBE0. While ωB97X-D and M06-2X were easonably accurate, no method provided quantitative accuracy for all three electrophiles, making this a very strenuous test of functional performance. Additionally, one drawback of M06-2X was that MD simulations using this functional were only stable if a fine integration grid was used. The low-cost semi-empirical methods, PM3, AM1, and PM7, provide a qualitatively correct description of the reaction mechanism, although the energetics are not quantitatively reliable. As a proof of concept, the potential of mean force for the addition of methylthiolate to MVK was calculated using QM/MM MD in an explicit polarizable aqueous solvent.<br>

scholarly journals Quantum Chemical Methods for Modeling Covalent Modification of Biological Thiols

2019 ◽  
Author(s):  
Ernest Awoonor-Williams ◽  
William Isley ◽  
Stephen Dale ◽  
Erin Johnson ◽  
Haibo Yu ◽  
...  
Keyword(s):  
Density Functional ◽  
Functional Performance ◽  
Low Cost ◽  
Md Simulations ◽  
Potential Of Mean Force ◽  
Covalent Modification ◽  
Dft Methods ◽  
Aqueous Solvent ◽  
Exact Exchange ◽  
Semi Empirical

Targeted covalent inhibitor drugs require computational methods that go beyond simple molecular-mechanical force fields in order to model the chemical reactions that occur when they bind to their targets. Here, several semi-empirical and density-functional theory (DFT) methods are assessed for their ability to describe the potential energy surface and reaction energies of the covalent modification of a thiol by an electrophile. Functionals such as PBE and B3LYP fail to predict a stable enolate intermediate. This is largely due to delocalization error, which spuriously stabilizes the pre-reaction complex, in which excess electron density is transferred from the thiolate to the electrophile. Functionals with a high-exact exchange component, range-separated DFT functionals, and variationally-optimized exact exchange (i.e., the LC-B05minV functional) correct this issue to various degrees. The large gradient behaviour of the exchange enhancement factor is also found to significantly affect the results, leading to the improved performance of PBE0. While ωB97X-D and M06-2X were easonably accurate, no method provided quantitative accuracy for all three electrophiles, making this a very strenuous test of functional performance. Additionally, one drawback of M06-2X was that MD simulations using this functional were only stable if a fine integration grid was used. The low-cost semi-empirical methods, PM3, AM1, and PM7, provide a qualitatively correct description of the reaction mechanism, although the energetics are not quantitatively reliable. As a proof of concept, the potential of mean force for the addition of methylthiolate to MVK was calculated using QM/MM MD in an explicit polarizable aqueous solvent.<br>

BAND NN: A Deep Learning Framework For Energy Prediction and Geometry Optimization of Organic Small Molecules

2019 ◽  
Author(s):  
Siddhartha Laghuvarapu ◽  
Yashaswi Pathak ◽  
U. Deva Priyakumar
Keyword(s):  
Machine Learning ◽  
Density Functional ◽  
Computational Cost ◽  
Geometry Optimization ◽  
Dft Methods ◽  
Energy Prediction ◽  
Machine Learning Model ◽  
Equilibrium Structures ◽  
High Level ◽  
Non Equilibrium

Recent advances in artificial intelligence along with development of large datasets of energies calculated using quantum mechanical (QM)/density functional theory (DFT) methods have enabled prediction of accurate molecular energies at reasonably low computational cost. However, machine learning models that have been reported so far requires the atomic positions obtained from geometry optimizations using high level QM/DFT methods as input in order to predict the energies, and do not allow for geometry optimization. In this paper, a transferable and molecule-size independent machine learning model (BAND NN) based on a chemically intuitive representation inspired by molecular mechanics force fields is presented. The model predicts the atomization energies of equilibrium and non-equilibrium structures as sum of energy contributions from bonds (B), angles (A), nonbonds (N) and dihedrals (D) at remarkable accuracy. The robustness of the proposed model is further validated by calculations that span over the conformational, configurational and reaction space. The transferability of this model on systems larger than the ones in the dataset is demonstrated by performing calculations on select large molecules. Importantly, employing the BAND NN model, it is possible to perform geometry optimizations starting from non-equilibrium structures along with predicting their energies.

Quantum Mechanical Investigation of Geometrical Structure and Dynamic Behavior of h-BNNT (9,9-5) and h-AlNNT (9,9-5)Single-Walled Nanotubes: NBO Analysis

2019 ◽  
Vol 16 (9) ◽  
pp. 705-717
Author(s):  
Mehrnoosh Khaleghian ◽  
Fatemeh Azarakhshi
Keyword(s):  
Carbon Nanotubes ◽  
Density Functional ◽  
Structural Parameters ◽  
Energy Levels ◽  
Nbo Analysis ◽  
Electronic Energy ◽  
Boron Nitride Nanotubes ◽  
Basis Set ◽  
B3lyp Method ◽  
Mechanical Investigation

In the present research, B45H36N45 Born Nitride (9,9) nanotube (BNNT) and Al45H36N45 Aluminum nitride (9,9) nanotube (AlNNT) have been studied, both having the same length of 5 angstroms. The main reason for choosing boron nitride nanotubes is their interesting properties compared with carbon nanotubes. For example, resistance to oxidation at high temperatures, chemical and thermal stability higher rather than carbon nanotubes and conductivity in these nanotubes, unlike carbon nanotubes, does not depend on the type of nanotube chirality. The method used in this study is the density functional theory (DFT) at Becke3, Lee-Yang-Parr (B3LYP) method and 6-31G* basis set for all the calculations. At first, the samples were simulated and then the optimized structure was obtained using Gaussian 09 software. The structural parameters of each nanotube were determined in 5 layers. Frequency calculations in order to extract the thermodynamic parameters and natural bond orbital (NBO) calculations have been performed to evaluate the electron density and electrostatic environment of different layers, energy levels and related parameters, such as ionization energy and electronic energy, bond gap energy and the share of hybrid orbitals of different layers.

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.

scholarly journals Unraveling the electrochemical and spectroscopic properties of neutral and negatively charged perylene tetraethylesters

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Christian Wiebeler ◽  
Joachim Vollbrecht ◽  
Adam Neuba ◽  
Heinz-Siegfried Kitzerow ◽  
Stefan Schumacher
Keyword(s):  
Absorption Spectra ◽  
Density Functional ◽  
Energy Levels ◽  
Spectroscopic Properties ◽  
Absorption Bands ◽  
Functional Theory ◽  
Vertical Excitation ◽  
Hartree Fock ◽  
Tauc Plot ◽  
Electrochemical Approach

AbstractA detailed investigation of the energy levels of perylene-3,4,9,10-tetracarboxylic tetraethylester as a representative compound for the whole family of perylene esters was performed. It was revealed via electrochemical measurements that one oxidation and two reductions take place. The bandgaps determined via the electrochemical approach are in good agreement with the optical bandgap obtained from the absorption spectra via a Tauc plot. In addition, absorption spectra in dependence of the electrochemical potential were the basis for extensive quantum-chemical calculations of the neutral, monoanionic, and dianionic molecules. For this purpose, calculations based on density functional theory were compared with post-Hartree–Fock methods and the CAM-B3LYP functional proved to be the most reliable choice for the calculation of absorption spectra. Furthermore, spectral features found experimentally could be reproduced with vibronic calculations and allowed to understand their origins. In particular, the two lowest energy absorption bands of the anion are not caused by absorption of two distinct electronic states, which might have been expected from vertical excitation calculations, but both states exhibit a strong vibronic progression resulting in contributions to both bands.

scholarly journals A quantitative evaluation of computational methods to accelerate the study of alloxazine-derived electroactive compounds for energy storage

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Qi Zhang ◽  
Abhishek Khetan ◽  
Süleyman Er
Keyword(s):  
Energy Storage ◽  
Density Functional ◽  
Tight Binding ◽  
Computational Cost ◽  
Redox Potentials ◽  
Storage Compounds ◽  
Computational Screening ◽  
Chemical Descriptor ◽  
Lowest Unoccupied Molecular Orbital ◽  
Semi Empirical

AbstractAlloxazines are a promising class of organic electroactive compounds for application in aqueous redox flow batteries (ARFBs), whose redox properties need to be tuned further for higher performance. High-throughput computational screening (HTCS) enables rational and time-efficient study of energy storage compounds. We compared the performance of computational chemistry methods, including the force field based molecular mechanics, semi-empirical quantum mechanics, density functional tight binding, and density functional theory, on the basis of their accuracy and computational cost in predicting the redox potentials of alloxazines. Various energy-based descriptors, including the redox reaction energies and the frontier orbital energies of the reactant and product molecules, were considered. We found that the lowest unoccupied molecular orbital (LUMO) energy of the reactant molecules is the best performing chemical descriptor for alloxazines, which is in contrast to other classes of energy storage compounds, such as quinones that we reported earlier. Notably, we present a flexible in silico approach to accelerate both the singly and the HTCS studies, therewithal considering the level of accuracy versus measured electrochemical data, which is readily applicable for the discovery of alloxazine-derived organic compounds for energy storage in ARFBs.

Sign in / Sign up

Export Citation Format

Share Document