Stabilization of DPPC lipid bilayers in the presence of co-solutes: molecular mechanisms and interaction patterns

2021 ◽  
Author(s):  
Fabian Keller ◽  
Andreas Heuer ◽  
Hans-Joachim Galla ◽  
Jens Smiatek
Keyword(s):  
Molecular Dynamics ◽  
Density Functional Theory ◽  
Lipid Bilayers ◽  
Density Functional ◽  
Molecular Mechanisms ◽  
Md Simulations ◽  
Water Molecules ◽  
Interaction Patterns ◽  
Conceptual Density Functional Theory ◽  
Functional Theory

The interactions between DPPC lipid bilayers in different phases with ectoine, amino ectoine and water molecules are studied by means of atomistic molecular dynamics (MD) simulations and conceptual density functional theory (DFT) calculations.

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.

scholarly journals Hydration interactions beyond the first solvation shell in aqueous phenolate solution

2020 ◽  
Vol 22 (35) ◽  
pp. 19940-19947
Author(s):  
Roberto Cota ◽  
Ambuj Tiwari ◽  
Bernd Ensing ◽  
Huib J. Bakker ◽  
Sander Woutersen
Keyword(s):  
Molecular Dynamics ◽  
Density Functional Theory ◽  
Molecular Dynamics Simulations ◽  
Vibrational Spectroscopy ◽  
Density Functional ◽  
Solvation Shell ◽  
Water Molecules ◽  
Functional Theory ◽  
Ultrafast Vibrational Spectroscopy ◽  
Dynamics Simulations

We investigate the orientational dynamics of water molecules solvating phenolate ions using ultrafast vibrational spectroscopy and density functional theory-based molecular dynamics simulations.

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>

C2N: an excellent two-dimensional monolayer membrane for He separation

2015 ◽  
Vol 3 (42) ◽  
pp. 21351-21356 ◽  
Author(s):  
Lei Zhu ◽  
Qingzhong Xue ◽  
Xiaofang Li ◽  
Tiantian Wu ◽  
Yakang Jin ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Density Functional Theory ◽  
First Principles ◽  
Density Functional ◽  
Md Simulations ◽  
Separation Performance ◽  
Two Dimensional ◽  
Functional Theory

Using the first-principles density functional theory (DFT) and molecular dynamics (MD) simulations, we investigate the He separation performance of a porous C2N monolayer synthesized recently.

Molecular motions in a fluxional (η6-indenyl)tricarbonylchromium hemichelate: a density functional theory molecular dynamics study

2018 ◽  
Vol 47 (27) ◽  
pp. 8906-8920 ◽  
Author(s):  
Nicolas Sieffert
Keyword(s):  
Molecular Dynamics ◽  
Density Functional Theory ◽  
Density Functional ◽  
Md Simulations ◽  
Atomic Level ◽  
Molecular Motions ◽  
Comprehensive Understanding ◽  
Intramolecular Dynamics ◽  
Functional Theory

DFT-MD simulations provided atomic-level insights into the intramolecular dynamics of a highly fluxional Pd(ii) hemichelate and a comprehensive understanding of the thermodynamics and the kinetics associated with each motion.

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>

Interaction of Water Molecules with Graphene: A Density Functional Theory and Molecular Dynamics Study

2010 ◽  
Vol 49 (1) ◽  
pp. 01AH07 ◽  
Author(s):  
Shigeaki Abe ◽  
Yoshinori Nagoya ◽  
Fumio Watari ◽  
Hiroto Tachikawa
Keyword(s):  
Molecular Dynamics ◽  
Density Functional Theory ◽  
Density Functional ◽  
Water Molecules ◽  
Functional Theory

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.

Solvent Effect on Xylose-to-Furfural Reaction in Biphasic Systems: Combined Experiments with Theoretical Calculations

2021 ◽  
Author(s):  
Qixuan Lin ◽  
Qiwen Zhan ◽  
Rui Li ◽  
Shouwei Liao ◽  
Junli Ren ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Density Functional Theory ◽  
Solvent Effect ◽  
Density Functional ◽  
Theoretical Calculations ◽  
Present Report ◽  
Md Simulations ◽  
Functional Theory ◽  
Biphasic Systems ◽  
Furfural Production

The present report focuses on the solvent effect on furfural production from xylose in biphasic systems with the methods combined experiments, molecular dynamics (MD) simulations and density functional theory (DFT)...

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