Journal of Molecular Modeling, volume 28, issue 4, publication number 81
Molecular modelling and computational studies of peptide diphenylalanine nanotubes, containing waters: structural and interactions analysis
Publication type: Journal Article
Publication date: 2022-03-05
Journal:
Journal of Molecular Modeling
Quartile SCImago
Q3
Quartile WOS
Q3
Impact factor: 2.2
ISSN: 16102940, 09485023
Catalysis
Organic Chemistry
Inorganic Chemistry
Physical and Theoretical Chemistry
Computer Science Applications
Computational Theory and Mathematics
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.
Citations by journals
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1
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Symmetry
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Symmetry
1 publication, 20%
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Journal of Materials Chemistry B
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Journal of Materials Chemistry B
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Mathematical Biology and Bioinformatics
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Advanced Structured Materials
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1
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Citations by publishers
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1
2
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Multidisciplinary Digital Publishing Institute (MDPI)
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Multidisciplinary Digital Publishing Institute (MDPI)
2 publications, 40%
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Royal Society of Chemistry (RSC)
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1 publication, 20%
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Institute of Mathematical Problems of Biology RAS
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Institute of Mathematical Problems of Biology RAS, 1, 20%
Institute of Mathematical Problems of Biology RAS
1 publication, 20%
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Springer Nature
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Springer Nature
1 publication, 20%
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1
2
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- Statistics recalculated weekly.
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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 // Journal of Molecular Modeling. 2022. Vol. 28. No. 4. 81
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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 // Journal of Molecular Modeling. 2022. Vol. 28. No. 4. 81
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TY - JOUR
DO - 10.1007/s00894-022-05074-2
UR - https://doi.org/10.1007%2Fs00894-022-05074-2
TI - Molecular modelling and computational studies of peptide diphenylalanine nanotubes, containing waters: structural and interactions analysis
T2 - Journal of Molecular Modeling
AU - Bystrov, Vladimir S
AU - Filippov, Sergey V.
PY - 2022
DA - 2022/03/05 00:00:00
PB - Springer Nature
IS - 4
VL - 28
SN - 1610-2940
SN - 0948-5023
ER -
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@article{2022_Bystrov,
author = {Vladimir S Bystrov and Sergey V. Filippov},
title = {Molecular modelling and computational studies of peptide diphenylalanine nanotubes, containing waters: structural and interactions analysis},
journal = {Journal of Molecular Modeling},
year = {2022},
volume = {28},
publisher = {Springer Nature},
month = {mar},
url = {https://doi.org/10.1007%2Fs00894-022-05074-2},
number = {4},
doi = {10.1007/s00894-022-05074-2}
}