Estimation of the Diffusion Coefficients of Small Molecules by Diffusion Measurements with Agar-gel and Theoretical Molecular Modeling

• Published in: Chem-Bio Informatics Journal Vol. 22; pp. 13 - 20
• Main Authors: Miyamoto, Shuichi, Shimono, Kazumi
• Format: Journal Article
• Language: English
• Published: Chem-Bio Informatics Society 30.04.2022
• Subjects: agar-gel; diffusion coefficient agar-gel; molecular modeling; molecular radius; Stokes-Einstein equation; molecular modeling; molecular radius; Stokes-Einstein equation
• ISSN: 1347-6297; 1347-0442
• DOI: 10.1273/cbij.22.13

Diffusion is a spontaneous process and one of the physicochemical phenomena responsible for molecular transport, the rate of which is governed mainly by the diffusion coefficient; however, few coefficients are available for small molecules. We have constructed a simple and convenient experimental system with agar-gel to measure the diffusion coefficients of sugars.A theoretical method has also been developed to estimate diffusion coefficients by a combination of molecular modeling and the Stokes–Einstein equation, by which the coefficients of several sugars, amino acids, and drug molecules have been obtained. This time we have applied both experimental and theoretical approaches to estimate the diffusion coefficients of an additional 10 amino acids. The measured and calculated values are consistent with small deviations, i.e., the diffusion coefficients estimated by molecular modeling correspond well to the experimental data, which suggests that the potential use of the diffusion coefficient as an additional molecular property in drug screening has been enhanced.