scholarly journals Do Better Quality Embedding Potentials Accelerate the Convergence of QM/MM Models? The Case of Solvated Acid Clusters

Molecules ◽  
2018 ◽  
Vol 23 (10) ◽  
pp. 2466 ◽  
Author(s):  
Junming Ho ◽  
Yihan Shao ◽  
Jin Kato
Keyword(s):  
Density Functional ◽  
Density Functional Theory Calculations ◽  
Water Model ◽  
Reaction Centre ◽  
Empirical Methods ◽  
Functional Theory ◽  
Highly Sensitive ◽  
Solvent Molecules ◽  
Dynamics Simulations ◽  
Semi Empirical

This study examines whether the use of more accurate embedding potentials improves the convergence of quantum mechanics/molecular mechanics (QM/MM) models with respect to the size of the QM region. In conjunction with density functional theory calculations using the ωB97X-D functional, various embedding potentials including the TIP3P water model, the effective fragment potential (EFP), and semi-empirical methods (PM6, PM7, and DFTB) were used to simulate the deprotonation energies of solvated acid clusters. The calculations were performed on solvated neutral (HA) and cationic (HB+) acids clusters containing 160 and 480 water molecules using configurations sampled from molecular dynamics simulations. Consistently, the ωB97X-D/EFP model performed the best when using a minimal QM region size. The performance for the other potentials appears to be highly sensitive to the charge character of the acid/base pair. Neutral acids display the expected trend that semi-empirical methods generally perform better than TIP3P; however, an opposite trend was observed for the cationic acids. Additionally, electronic embedding provided an improvement over mechanical embedding for the cationic systems, but not the neutral acids. For the best performing ωB97X-D/EFP model, a QM region containing about 6% of the total number of solvent molecules is needed to approach within 10 kJ mol−1 of the pure QM result if the QM region was chosen based on the distance from the reaction centre.

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.

scholarly journals STRUCTURAL AND ELECTRONIC PROPERTIES OF BRIDGED BITHIOPHENE S-OXIDES (BTO) WITH S, S=O, O, SiH2 and BH2 BRIDGE: SEMI-EMPIRICAL AND AB INITIO STUDY

2010 ◽  
Vol 18 (18) ◽  
pp. 1-10
Author(s):  
Banjo Semire ◽  
Isaiah Ajibade Adejoro ◽  
Olusegun Ayobami Odunola
Keyword(s):  
Density Functional Theory ◽  
Thermodynamic Properties ◽  
Ab Initio ◽  
Density Functional ◽  
Ab Initio Study ◽  
Empirical Methods ◽  
Functional Theory ◽  
Structural And Electronic Properties ◽  
Semi Empirical ◽  
Good Agreement

In this paper, we theoretically studied the geometries, stabilities, electronic and thermodynamic properties of bridged bithiophene S-oxide (BTO-X) derivates (with X = BH2, SiH2, S, S=O, and O) by using semi-empirical methods, ab-initio, and Density functional theory. The geometries and thermodynamic parameters calculated by PM3 were in good agreement with that of B3LYP/6-31G(d). The bandgap calculated by B3LYP/6-31G(d) ranged from 3.94eV (BTO-O)-3.16eV (BTO-BH2). The absorption λmax calculated suing B3LYP/6-31G(d) shifted to longer wavelength with X=BH2, SiH2, and S=O due to enhancement of π-conjugated system whereas, BTO-S and BTO-O shifted to shorter wavelengths as compared to dimmer thiophene S-oxide (2TO).

scholarly journals Density functional tight binding: values of semi-empirical methods in an ab initio era

2014 ◽  
Vol 16 (28) ◽  
pp. 14368-14377 ◽  
Author(s):  
Qiang Cui ◽  
Marcus Elstner
Keyword(s):  
Density Functional Theory ◽  
Ab Initio ◽  
Density Functional ◽  
Tight Binding ◽  
Empirical Methods ◽  
Functional Theory ◽  
Hartree Fock ◽  
Semi Empirical

Semi-empirical (SE) methods are derived from Hartree–Fock (HF) or Density Functional Theory (DFT) by neglect and approximation of electronic integrals.

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.

Insights into structural and dynamical features of water at halloysite interfaces probed by DFT and classical molecular dynamics simulations

2016 ◽  
Vol 18 (3) ◽  
pp. 2164-2174 ◽  
Author(s):  
Davide Presti ◽  
Alfonso Pedone ◽  
Giordano Mancini ◽  
Celia Duce ◽  
Maria Rosaria Tiné ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Density Functional ◽  
Density Functional Theory Calculations ◽  
Water Molecules ◽  
Functional Theory ◽  
Structure And Dynamics ◽  
Classical Molecular Dynamics ◽  
Dynamical Features ◽  
Dynamics Simulations

Density functional theory calculations and classical molecular dynamics simulations have been used to investigate the structure and dynamics of water molecules on kaolinite surfaces and confined in the interlayer of a halloysite model of nanometric dimension.

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 DFT-D study of the interaction of methane, carbon monoxide, and nitrogen with cation-exchanged SAPO-34

2015 ◽  
Vol 230 (5) ◽  
Author(s):  
Michael Fischer ◽  
Robert G. Bell
Keyword(s):  
Density Functional Theory ◽  
Carbon Monoxide ◽  
Density Functional ◽  
Density Functional Theory Calculations ◽  
Dispersion Correction ◽  
Functional Theory ◽  
Guest Molecules ◽  
Semi Empirical ◽  
Methane Carbon

AbstractDensity-functional theory calculations including a semi-empirical dispersion correction (DFT-D) are employed to study the interaction of small guest molecules (CH

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