scholarly journals Polydopamine and eumelanin molecular structures investigated with ab initio calculations

2017 ◽  
Vol 8 (2) ◽  
pp. 1631-1641 ◽  
Author(s):  
Chun-Teh Chen ◽  
Francisco J. Martin-Martinez ◽  
Gang Seob Jung ◽  
Markus J. Buehler
Keyword(s):  
Molecular Dynamics ◽  
Density Functional Theory ◽  
Dft Calculations ◽  
Ab Initio Calculations ◽  
Ab Initio ◽  
Density Functional ◽  
Md Simulations ◽  
Molecular Structures ◽  
Brute Force ◽  
Functional Theory

A set of computational methods that contains a brute-force algorithmic generation of chemical isomers, molecular dynamics (MD) simulations, and density functional theory (DFT) calculations is reported and applied to investigate nearly 3000 probable molecular structures of polydopamine (PDA) and eumelanin.

Density Functional Theory and Ab Initio Molecular Dynamics Study of the Effect of Ti and Zr Transition Metals in D03 Fe3Al

2012 ◽  
Vol 706-709 ◽  
pp. 1095-1099
Author(s):  
Sara Chentouf ◽  
Jean Marc Raulot ◽  
Hafid Aourag ◽  
Thierry Grosdidier
Keyword(s):  
Molecular Dynamics ◽  
Density Functional Theory ◽  
Dft Calculations ◽  
Ab Initio ◽  
Density Functional ◽  
Md Simulations ◽  
Functional Theory ◽  
Ab Initio Md ◽  
Increasing Temperature ◽  
Formation Energies

The formation energies of the T.M impurities Ti and Zr were calculated using DFT calculations at absolute zero and ab initio MD simulations at 300 K. We found that, with increasing temperature, Zr impurities become more stable and prefer to segregate at the interface of ∑5 (310)[001] grain boundary. In the case of Ti, the results show that it remains a stable defect when temperature increases.

Simulating Surfactant-Iron Oxide Interfaces: From Density Functional Theory to Molecular Dynamics

2019 ◽  
Author(s):  
Carlos Ayestaran Latorre ◽  
James Ewen ◽  
Chiara Gattinoni ◽  
Daniele Dini
Keyword(s):  
Molecular Dynamics ◽  
Density Functional Theory ◽  
Iron Oxide ◽  
Dft Calculations ◽  
Density Functional ◽  
Md Simulations ◽  
Oxide Surfaces ◽  
Interaction Energies ◽  
Functional Theory ◽  
Oxide Interfaces

<div>Understanding the behaviour of surfactant molecules on iron oxide surfaces is important for many industrial applications. Molecular dynamics (MD) simulations of such systems have been limited by the absence of a force-feild (FF) which accurately describes the molecule-surface interactions. In this study, interaction energies from density functional theory (DFT) + U calculations with a van der Waals functional are used to parameterize a classical FF for MD simulations of amide surfactants on iron oxide surfaces. The Original FF, which was derived using mixing rules and surface Lennard-Jones (LJ) parameters developed for nonpolar molecules, were shown to signi cantly underestimate the adsorption energy and overestimate the equilibrium adsorption distance compared to DFT. Conversely, the Optimized FF showed excellent agreement with the interaction energies obtained from DFT calculations for a wide range of surface coverages and molecular conformations near to and adsorbed on a-Fe2O3(0001). This was facilitated through the use of a Morse potential for strong chemisorption interactions, modi fied LJ parameters for weaker physisorption interactions, and adjusted partial charges for the electrostatic interactions. The Original FF and Optimized FF were compared in classical nonequilibrium molecular dynamics (NEMD) simulations of amide molecules con fined between iron oxide surfaces. When the Optimized FF was employed, the amide molecules were pulled closer to the surface and the orientation of the headgroups was more similar to that observed in the DFT calculations compared to the Original FF. The Optimized FF proposed here facilitates classical MD simulations of amide-iron oxide interfaces in which the interactions are representative of accurate DFT calculations.</div>

scholarly journals Simulating Surfactant-Iron Oxide Interfaces: From Density Functional Theory to Molecular Dynamics

2019 ◽  
Author(s):  
Carlos Ayestaran Latorre ◽  
James Ewen ◽  
Chiara Gattinoni ◽  
Daniele Dini
Keyword(s):  
Molecular Dynamics ◽  
Density Functional Theory ◽  
Iron Oxide ◽  
Dft Calculations ◽  
Density Functional ◽  
Md Simulations ◽  
Oxide Surfaces ◽  
Interaction Energies ◽  
Functional Theory ◽  
Oxide Interfaces

<div>Understanding the behaviour of surfactant molecules on iron oxide surfaces is important for many industrial applications. Molecular dynamics (MD) simulations of such systems have been limited by the absence of a force-feild (FF) which accurately describes the molecule-surface interactions. In this study, interaction energies from density functional theory (DFT) + U calculations with a van der Waals functional are used to parameterize a classical FF for MD simulations of amide surfactants on iron oxide surfaces. The Original FF, which was derived using mixing rules and surface Lennard-Jones (LJ) parameters developed for nonpolar molecules, were shown to signi cantly underestimate the adsorption energy and overestimate the equilibrium adsorption distance compared to DFT. Conversely, the Optimized FF showed excellent agreement with the interaction energies obtained from DFT calculations for a wide range of surface coverages and molecular conformations near to and adsorbed on a-Fe2O3(0001). This was facilitated through the use of a Morse potential for strong chemisorption interactions, modi fied LJ parameters for weaker physisorption interactions, and adjusted partial charges for the electrostatic interactions. The Original FF and Optimized FF were compared in classical nonequilibrium molecular dynamics (NEMD) simulations of amide molecules con fined between iron oxide surfaces. When the Optimized FF was employed, the amide molecules were pulled closer to the surface and the orientation of the headgroups was more similar to that observed in the DFT calculations compared to the Original FF. The Optimized FF proposed here facilitates classical MD simulations of amide-iron oxide interfaces in which the interactions are representative of accurate DFT calculations.</div>

scholarly journals The excess electron in polymer nanocomposites

2018 ◽  
Vol 20 (43) ◽  
pp. 27528-27538 ◽  
Author(s):  
Fernan Saiz ◽  
Nick Quirke
Keyword(s):  
Molecular Dynamics ◽  
Density Functional Theory ◽  
Dft Calculations ◽  
Ab Initio ◽  
Polymer Nanocomposites ◽  
Density Functional ◽  
Excess Electron ◽  
Functional Theory ◽  
Excess Electrons

We have used ab initio molecular dynamics and density-functional theory (DFT) calculations at the B3LYP/6-31G** level of theory to evaluate the energy and localisation of excess electrons at a number of representative interfaces of polymer nanocomposites.

scholarly journals Ab initio molecular dynamics of hydrogen on tungsten surfaces

2021 ◽  
Author(s):  
Alberto Rodríguez-Fernández ◽  
Laurent Bonnet ◽  
Pascal Larrégaray ◽  
Ricardo Díez Muiño
Keyword(s):  
Molecular Dynamics ◽  
Density Functional Theory ◽  
Ab Initio ◽  
Density Functional ◽  
Ab Initio Molecular Dynamics ◽  
Dissociation Process ◽  
Functional Theory ◽  
Classical Molecular Dynamics ◽  
Hydrogen Molecules

The dissociation process of hydrogen molecules on W(110) was studied using density functional theory and classical molecular dynamics.

scholarly journals Unexpectedly Large Couplings Between Orthogonal Units in Anthraquinone Polymers

2019 ◽  
Author(s):  
Rocco Peter Fornari ◽  
Piotr de Silva
Keyword(s):  
Molecular Dynamics ◽  
Density Functional Theory ◽  
Ab Initio ◽  
Density Functional ◽  
Lone Pair ◽  
Localized States ◽  
Ab Initio Molecular Dynamics ◽  
Coupling Mechanism ◽  
Functional Theory ◽  
Pi Interactions

Directly linked polyanthraquinones have relatively large electronic couplings between charge-localized states despite near-orthogonality of the monomer units. By using density functional theory (DFT) and ab initio molecular dynamics (AIMD) simulations, we investigate this unusual coupling mechanism and show that this is due to strong lone pair-pi interactions, which are maximized around orthogonal conformations. We find that such materials are largely resilient to dynamic disorder and are promising for organic electronics applications.

scholarly journals Tipping the balance: theoretical interrogation of divergent extended heterolytic fragmentations

2020 ◽  
Vol 11 (8) ◽  
pp. 2231-2242 ◽  
Author(s):  
Croix J. Laconsay ◽  
Ka Yi Tsui ◽  
Dean J. Tantillo
Keyword(s):  
Molecular Dynamics ◽  
Density Functional Theory ◽  
Electric Field ◽  
Ab Initio ◽  
External Electric Field ◽  
Density Functional ◽  
Natural Bond Orbital ◽  
Nbo Analysis ◽  
Functional Theory

We interrogate a type of heterolytic fragmentation called a ‘divergent fragmentation’ using density functional theory (DFT), natural bond orbital (NBO) analysis, ab initio molecular dynamics (AIMD), and external electric field (EEF) calculations.

Catalytic polymerization of naphthalene by HF/BF3 super acid: an ab initio density functional theory study

2018 ◽  
Vol 20 (36) ◽  
pp. 23311-23319 ◽  
Author(s):  
Po-Yu Yang ◽  
Hsing-Yin Chen ◽  
Shin-Pon Ju ◽  
Chia-Lin Chang ◽  
Gao-Shee Leu ◽  
...  
Keyword(s):  
Density Functional Theory ◽  
Reaction Mechanism ◽  
Dft Calculations ◽  
Ab Initio ◽  
Density Functional ◽  
Catalytic Polymerization ◽  
Density Functional Theory Study ◽  
Functional Theory ◽  
Detailed Reaction Mechanism ◽  
Super Acid

The detailed reaction mechanism of naphthalene catalytic polymerization by HF/BF3 has been investigated by DFT calculations and the directionality of the naphthalene-derived mesophase molecule has been explained.

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