Application of molecular dynamics simulations in molecular property prediction II: Diffusion coefficient

Application of molecular dynamics simulations in molecular property prediction II: Diffusion coefficient

In this work, we have evaluated how well the general assisted model building with energy refinement (AMBER) force field performs in studying the dynamic properties of liquids. Diffusion coefficients (D) have been predicted for 17 solvents, five organic compounds in aqueous solutions, four proteins in aqueous solutions, and nine organic compounds in nonaqueous solutions. An efficient sampling st...

Synthesis novel bis-Coumarin derivatives as potential acetylcholinestrase inhibitors: An in vitro, molecular docking, and molecular dynamics simulations study

Alzheimer's disease is an irreversible and progressive brain disorder that slowly destroys memory and thinking skills and ultimately the ability to do the simplest things and can lead to death. Cholinesterases (ChEs) play an important role in controlling cholinergic transmission, and subsequently, by inhibiting CHEs, acetylcholine levels in the brain are elevated. Coumarins have been shown to e...

Molecular dynamics studies of straight-chain alkanes diffusion in SiO2 ceramic versus Bosanquet formula

Molecular Dynamics (MD) simulations were applied to calculate self-diffusion coefficients (Di ) and heats of adsorption for ethane, propane and n-butane. The simulations were done in temperature range of 300-525 K for various concentrations inside the pores of silicalite type zeolite. The calculated values of self-diffusion coefficients and heats of adsorption resulted from the current wo...

Effects of Aluminum Incorporation in Tobermorite Structure on Chloride Diffusion: A Molecular Dynamics Simulation Study

In this paper, the effects of different aluminum to silicon ratios in silicate chains of calcium silicate hydrates (C-S-H) are evaluated on the diffusion coefficient of chloride ions by molecular dynamics method. Tobermorite is a crystalline phase that is used for studying C-S-H properties in nano scale, because of its analogous chemical composition to C-S-H. Aluminum incorporation in C-S-H and...

Diffusion in liquids from molecular dynamics simulations | QuantumWise 2017 Documentation