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Molecular modeling of immersion optical clearing of biological tissues

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Abstract

The interaction of six low-molecular tissue-clearing agents (1,2 and 1,3-propanediol, ethylene glycol, glycerol, xylitol, sorbitol) with the collagen mimetic peptide (GPH)3 was studied by applying the methods of classical molecular dynamics (GROMACS), molecular docking (AutoDock Vina) and quantum chemistry (PM6 and B3LYP). The spatial configurations of intermolecular complexes were determined and interaction energies calculated. The dependence of the volume occupied by the collagen peptide on the clearing agent concentration in an aqueous solution was calculated. This dependence is not linear, and has a maximum for almost all the agents in the study. The correlations between the optical clearing potential and intermolecular interactions parameters, such as the time of an agent being in a hydrogen-bonded state, and the relative probability of formation of double hydrogen bonds and interaction energies, were determined. Using the correlations determined, we predicted the numeric value of the optical clearing potential of dextrose molecules in rat skin, which correlates with experimental data. A molecular mechanism of tissue optical clearing within the post-diffusion stage is suggested.

The molecular modeling of the interaction between clearing agents and collagen

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Acknowledgments

The study was supported by the Russian Federation grants: 17.1223.2017/AP of the Ministry of Education and Science, 3.9128.2017/BCh of the Government, 17-02-00358 of RFBR, and the Tomsk State University Competitiveness Improvement Program.

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Authors and Affiliations

  1. Department of Optics and Biophotonics, Saratov State University, 83 Astrakhanskaya Street, Saratov, 410012, Russia

    Kirill V. Berezin, Maria L. Chernavina & Valery V. Tuchin

  2. Department of Medical and Biological Physics, Saratov State Medical University, 112 Bolshaya Kazachya Street, Saratov, 410012, Russia

    Konstantin N. Dvoretski

  3. Department of General Physics, Astrakhan State University, 20A Tatishcheva Street, Astrakhan, 414056, Russia

    Anatoliy M. Likhter, Vladimir V. Smirnov, Ilmira T. Shagautdinova, Ekaterina M. Antonova, Ekaterina Yu. Stepanovich & Elena A. Dzhalmuhambetova

  4. Institute of Precision Mechanics and Control, Russian Academy of Sciences, 24 Rabochaya Street, Saratov, 410028, Russia

    Valery V. Tuchin

  5. Interdisciplinary Laboratory of Biophotonics, Tomsk State University, 36 Lenin Avenue, 634050, Tomsk, Russia

    Valery V. Tuchin

Authors
  1. Kirill V. Berezin
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  2. Konstantin N. Dvoretski
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  3. Maria L. Chernavina
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  4. Anatoliy M. Likhter
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  5. Vladimir V. Smirnov
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  6. Ilmira T. Shagautdinova
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  7. Ekaterina M. Antonova
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  8. Ekaterina Yu. Stepanovich
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  9. Elena A. Dzhalmuhambetova
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  10. Valery V. Tuchin
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Correspondence to Konstantin N. Dvoretski.

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Berezin, K.V., Dvoretski, K.N., Chernavina, M.L. et al. Molecular modeling of immersion optical clearing of biological tissues. J Mol Model 24, 45 (2018). https://doi.org/10.1007/s00894-018-3584-0

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