Studying the mechanism of tissue optical clearing using the method of molecular dynamics

The interaction of three tissue-clearing agents (1,2-1,3-propanediol, 1,2-ethanediol) with the collagen mimetic peptide ((GPH)3)9 was studied by applying the method of classical molecular dynamics. The complete conformational analysis of the clearing agents under study was performed using the DFT/B3LYP/6-311+G method (d, p), the most energetically favorable spatial configurations were determined, the values of the Mulliken atomic charges were calculated which were used for the simulation. The research showed that there is a good correlation between the time of the hydrogen binding of a clearing agent with a collagen peptide and the potential of optical clearing. The paper also discusses that the interaction of the tissue-clearing agents with a collagen peptide in a water solution results in the 6% average enlargement of the distance between the alpha peptide chains. It has been suggested that such changes in a collagen structure can affect the refraction index and as a consequence the optical clearing of a biotissue. The dependences of the average distance changing between the alpha chains of a collagen peptide and the concentration of clearing agents in water solution were determined.