Abstract
Diffusion, transport of mass in response to concentration and thermal energy gradient, is an important transport property, vital in material science and life science. In the present work, we have studied about the diffusion of zwitterion glycine, zwitterion diglycine and zwitterion triglycine in SPC/E model of water using classical molecular dynamics. Self and binary diffusion coefficients of aqueous solution of these molecules have been estimated using Einstein’s method. Our results agree with experimental data reported in literatures. Temperature dependency of diffusion of glycine in water has been explored using estimated values of self and binary diffusion coefficients at four different temperature. Effects of peptide bond formation in diffusion has been studied using peptide chain composed of up to three monomers of glycine. The system-size dependence of diffusion coefficient has been studied and the shear viscosity of solvent and system has been calculated. Also, the diffusion coefficient of zwitterion glycine in other water model TIP4P/2005 has been estimated. The structure of the system has been analyzed using radial distribution function of different atoms.
Highlights
Amino acids, the fundamental building blocks of proteins, are the organic substances which contain both amine (-NH2) and acidic (-COOH) functional groups
Self and binary diffusion coefficient of aqueous solution of zwitterion glycine has been estimated at different temperatures from molecular dynamics simulation, as per mole fraction matching to the experimental values reported by Umecky et al.,4 and Longsworth
As statistics is better at beginning than ending region, certain portion has been taken and linear fit of Mean squared displacement (MSD) of different molecules at different temperature are plotted as a function of time for 5 ns
Summary
The fundamental building blocks of proteins, are the organic substances which contain both amine (-NH2) and acidic (-COOH) functional groups. Diffusion provides information about the inter and intra atomic/molecular interactions It helps in the understanding of the dynamics of amino acids, other bio-molecules, protein and protein folding.. Inspite of having many experimental works been done to study about the diffusion of glycine in aqueous medium, it is important to study about the diffusion phenomenon of the system by using molecular dynamics simulations. Self and binary diffusion coefficient of aqueous solution of zwitterion glycine has been estimated at different temperatures from molecular dynamics simulation, as per mole fraction matching to the experimental values reported by Umecky et al., and Longsworth.. Self diffusion coefficients of zwitterion glycine and water have been calculated using other water model TIP4P/2005,17 for the dynamical properties significantly depends upon water models taken during simulations..
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