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Molecular modelling and computational studies of peptide diphenylalanine nanotubes, containing waters: structural and interactions analysis

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Abstract

The work is devoted to computer studies of the structural and physical properties of such self-organizing structures as peptide nanotubes (PNT) based on diphenylalanine (FF) dipeptide with different initial isomers of the left (L-FF) and right (D-FF) chiralities of these dipeptides. The structures under study are considered both with empty anhydrous and with internal cavities filled with water molecules. Molecular models of both chiralities are investigated using quantum-chemical DFT and semi-empirical methods, which are in consistent with the known experimental data. To study the effect of nano-sized clusters of water molecules embedded in the inner hydrophilic cavity on the properties of nanotubes (including the changes in their dipole moments and polarizations), as well as the changes in the structure and properties of water clusters themselves (their own dipole moments and polarizations), the surfaces of internal cavities of nanotubes and outer surfaces of water cluster structures for both types of chirality are analyzed. A specially developed method of visual differential analysis of structural features of (bio)macromolecular structures is applied for these studies. The results obtained of a number of physical properties (interacting energies, dipole moments, polarization values) are given for various cases and analyzed in comparison with the known data. These data are necessary for analyzing the interactions of water molecules with hydrophilic parts of nanotube molecules based on FF, such as COO- and NH3 + , since they determine many properties of the structures under study. The data obtained are useful for further analysis of the possible adhesion and capture of medical molecular components by active layers of FF-based PNT, which can be designed for creating capsules for targeted delivery of pharmaceuticals and drugs on their basis.

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Acknowledgements

The authors express their gratitude to V.A. Tverdislov for fruitful discussions and support of this line of research. The authors are grateful to the University of Aveiro (UA, Faculty of Physics), Portugal, for the opportunity to use a multi-processor computer cluster for computational research on this study within the framework of non-commercial scientific agreement between IMPB RAS (the branch of KIAM RAS) and UA for the period 2017–2020 of our collaboration. In addition, the authors thank the Center for Collective Use of the Keldysh Institute of Applied Mathematics RAS for the possibility of the use of a hybrid supercomputer.

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    Vladimir S. Bystrov & Sergey V. Filippov

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V.B. wrote the manuscript and supervised this study. S.F. developed the method of the visual differential analysis and applied it to the FF nanotubes and water clusters.

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Correspondence to Vladimir S. Bystrov.

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Bystrov, V.S., Filippov, S.V. Molecular modelling and computational studies of peptide diphenylalanine nanotubes, containing waters: structural and interactions analysis. J Mol Model 28, 81 (2022). https://doi.org/10.1007/s00894-022-05074-2

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