Chiral peculiar properties of self-organization of diphenylalanine peptide nanotubes: Modeling of structure and properties

The structure and properties of diphenylalanine peptide nanotubes based on phenylalanine were investigated by various molecular modeling methods. The main approaches were semi-empirical quantum-chemical methods (PM3 and AM1), and molecular mechanical ones. Both the model structures and the structures extracted from their experimental crystallographic databases obtained by X-ray methods were examined. A comparison of optimized model structures and structures obtained by naturally-occurring self-assembly showed their important differences depending on D- and L-chirality. In both the cases, the effect of chirality on the results of self-assembly of diphenylalanine peptide nanotubes was established: peptide nanotubes based on the D-diphenylalanine (D-FF) has high condensation energy E 0 in transverse direction and forms thicker and shorter peptide nanotubes bundles, than that based on L-diphenylalanine (L-FF). A topological difference was established: model peptide nanotubes were optimized into structures consisting of rings, while naturally self-assembled peptide nanotubes consisted of helical coils. The latter were different for the original L-FF and D-FF. They formed helix structures in which the chirality sign changes as the level of the macromolecule hierarchy raises. Total energy of the optimal distances between two units are deeper for L-FF (-1.014 eV) then for D-FF (-0.607 eV) for ring models, while for helix coil are approximately the same and have for L-FF (-6.18 eV) and for D-FF (-6.22 eV) by PM3 method; for molecular mechanical methods energy changes are of the order of 2-3 eV for both the cases. A topological transition between a ring and a helix coil of peptide nanotube structures is discussed: self-assembled natural helix structures are more stable and favourable, they have lower energy in optimal configuration as compared with ring models by a value of the order of 1 eV for molecular mechanical methods and 5 eV for PM3 method. © 2019 Mathematical Biology and Bioinformatics.Part of this work was developed as part of the CICECO-Aveiro Materials Institute project, POCI-01-0145-FEDER-007679 funded from Fundação para a Ciência e a Tecnologia (FCT) Ref. UID/CTM/50011/2013, and funded from national funds through FCT/MEC, and co-funded by FEDER in accordance with the PT2020 Partnership Agreement. P.Z. thanks the project FCT PTDC/QEQ-QAN/6373/2014. S.K. thanks the project FCT PTDC/CTM-CTM/31679/2017

FERROELECTRIC DOMAIN PATTERNING BY FOCUSED ION BEAM IRRADIATION OF [100]-CUT [001]-POLED PMN-PT SINGLE CRYSTALS

The formation of domain structure via charge injection controlled by focused ion beam irradiation by means of a lithographic system in PMN-PT single crystals with a surface arti-ficial dielectric layer has been studied experimentally. The results explained in terms of the kinetic approach.The equipment of the Ural Center for Shared Use “Modern nanotechnology” Ural Fed-eral University was used. The research was made possible by the Russian Science Foundation (grant № 19-72-00091)

Molecular packing, piezo- and pyroelectric properties of tert-butyl N-(tert-butoxycarbonyl)-(S)-prolinamide

The work was financially supported by the Russian Foundation for Basic Research (grant no. 16-33-60122). The equipment of the Ural Centre for Shared Use “Modern Nanotechnologies” UrFU and Centre for Joint Use “Spectroscopy and Analysis of Organic Compounds” was used

Polymorphic phase transitions and ferroelectric properties in β-glycine single crystals and micro islands

The research was carried out using equipment of Ural Center for Shared Use "Modern Nanotechnologies" Ural Federal University with the financial support by the Government of the Russian Federation (Resolution 211, Contract 02.A03.21.0006). The reported study was funded by RFBR according to the research project № 18-32-00390

Elastic and piezoelectric properties of diphenylalanine microtubes with different filling of nanochannels

The research was carried out using the equipment of Ural Center for Shared Use "Modern Nanotechnologies", Ural Federal University, under financial support by Russian Science Foundation (grant № 18-72-00052)

Surface piezoelectricity and pyroelectricity in centrosymmetric materials: A case of α-glycine

Surface pyroelectricity and piezoelectricity induced by water incorporation during growth in α-glycine were investigated. Using the periodic temperature change technique, we have determined the thickness (~280 µm) of the near surface layer (NSL) and its pyroelectric coefficient (160 pC/(K × cm2) at 23◦C) independently. The thickness of NSL remains nearly constant till 60◦C and the pyroelectric effect vanishes abruptly by 70◦C. The piezoelectric effect, 0.1 pm/V at 23◦C measured with an interferometer, followed the same temperature dependence as the pyroelectric effect. Abrupt disappearance of both effects at 70◦C is irreversible and suggests that water incorporation to α-glycine forms a well defined near surface phase, which is different form α-glycine because it is polar but it too close to α-glycine to be distinguished by X-ray diffraction (XRD). The secondary pyroelectric effect was found to be <14% of the total, which is unexpectedly small for a material with a large thermal expansion coefficient. This implies that water incorporation infers minimal distortions in the host lattice. This finding suggests a path for the control of the piezoelectric and pyroelectric effects of the crystals using stereospecific incorporation of the guest molecules. © 2020 by the authors. Licensee MDPI, Basel, Switzerland.This work was supported by the collaborative program of the Israeli Ministry of Science with the Russian Foundation for Basic Research, grant № 3-16492. This research was made possible in part by RFBR (Grant No. 19-52-06004 MNTI_a), and the Government of the Russian Federation (Act 211, Agreement 02.A03.21.0006). The work has been supported in part by the Ministry of Science and Higher Education of the Russian Federation under Project № 3.9534.2017/8.9. This work was developed within the scope of the project CICECO-Aveiro Institute of Materials, refs. UIDB/50011/2020 and UIDP/50011/2020, financed by national funds through the Portuguese Foundation for Science and Technology/MCTES. The equipment of the Ural Center for Shared Use “Modern Nanotechnology” UrFU was used. I.L. expresses his gratitude to Estate of Olga Klein–Astrachan fund, grant № 721977

Mechanical and piezoelectric properties of pure and modified microtubes of diphenylalanine

The research was carried out using equipment of Ural Center for Shared Use "Modern Nanotechnologies" Ural Federal University with the financial support by the grant of the President of the Russian Federation for young scientists (Contract 14.Y30.17.2294-MK) and the Government of the Russian Federation (Resolution 211, Contract 02.A03.21.0006). Part of this work was developed in the scope of project CICECO-Aveiro Institute of Materials (ref FCT UID/CTM/50011/2013), financed by national funds through the FCT/MEC and, when applicable, cofinanced by FEDER under the PT2020 Partnership

Modeling of Self-Assembled Peptide Nanotubes and Determination of Their Chirality Sign Based on Dipole Moment Calculations

The chirality quantification is of great importance in structural biology, where the differ-ences in proteins twisting can provide essentially different physiological effects. However, this aspect of the chirality is still poorly studied for helix-like supramolecular structures. In this work, a method for chirality quantification based on the calculation of scalar triple products of dipole moments is suggested. As a model structure, self-assembled nanotubes of diphenylalanine (FF) made of L-and D-enantiomers were considered. The dipole moments of FF molecules were calculated using semi-empirical quantum-chemical method PM3 and the Amber force field method. The obtained results do not depend on the used simulation and calculation method, and show that the D-FF nanotubes are twisted tighter than L-FF. Moreover, the type of chirality of the helix-like nanotube is opposite to that of the initial individual molecule that is in line with the chirality alternation rule general for different levels of hierarchical organization of molecular systems. The proposed method can be applied to study other helix-like supramolecular structures. © 2021 by the authors. Licensee MDPI, Basel, Switzerland.Acknowledgments: The authors are grateful to the Russian Foundation for Basic Researches (RFBR): grants №№ 19–01–00519_A and 20-51-53014_GFEN_A. Part of this work (A.K.) was supported by the Ministry of Science and Higher Education of the Russian Federation (grant No. 075-15-2021-588). P.Z., S.K. and A.K. are grateful to the FCT project “BioPiezo”—PTDC/CTM−CTM/31679/2017 (CENTRO-01-0145-FEDER-031679) and to the project CICECO-Aveiro Institute of Materials, refs. UIDB/50011/2020 and UIDP/50011/2020, financed by national funds through the Portuguese Foundation for Science and Technology/MCTES. Part of this work was funded by national funds (OE), through FCT–Fundação para a Ciência e a Tecnologia, I.P., in the scope of the framework contract foreseen in the numbers 4, 5, and 6 of the article 23, of the Decree-Law 57/2016, of August 29, changed by Law 57/2017, of July 19. A.S. and E.M. are grateful to the the Interdisciplinary Scientific and Educational School of Moscow University “Fundamental and Applied Space Research”

Structures and properties of the self-assembling diphenylalanine peptide nanotubes containing water molecules: Modeling and data analysis

The structures and properties of the diphenylalanine (FF) peptide nanotubes (PNTs), both L-chiral and D-chiral (L-FF and D-FF) and empty and filled with water/ice clusters, are presented and analyzed. DFT (VASP) and semi-empirical calculations (HyperChem) to study these structural and physical properties of PNTs (including ferroelectric) were used. The results obtained show that after optimization the dipole moment and polarization of both chiral type L-FF and D-FF PNT and embedded water/ice cluster are enhanced; the water/ice cluster acquire the helix-like structure similar as L-FF and D-FF PNT. Ferroelectric properties of tubular water/ice helix-like cluster, obtained after optimization inside L-FF and D-FF PNT, as well of the total L-FF and D-FF PNT with embedded water/ice cluster, are discussed. © 2020 by the authors. Licensee MDPI, Basel, Switzerland.This work was partially supported by the Fundacão para a Ciência e a Tecnologia (FCT, Portugal) through project UID/CTM/50025/2013 and UIDB/50011/2020 & UIDP/50011/2020. P.Z. and S.K. are grateful to the FCT (Portugal) through the project “BioPiezo,” PTDC/CTM–CTM/31679/2017 (CENTRO-01-0145-FEDER-031679). The theoretical and computational parts of the study was completed within the framework of the non-commercial Agreement on scientific and technical cooperation between Institute of Mathematical Problems of Biology (IMPB) of KIAM RAS and Department of Physics and I3N institution of the University of Aveiro, Portugal. Part of this work was funded by national funds (OE), through FCT (Portugal), in the scope of the framework contract foreseen in the numbers 4, 5, and 6 of the article 23, of the Decree-Law 57/2016, of August 29, changed by Law 57/2017, of July 19

Local measurements of Young’s moduli of diphenylalanine macrotubes

The study was carried out using the equipment of UCSU "Modern Nanotechnology" UFU with the financial support of the RF President grant for young scientists (MK-2294.2017.2) and the Government of the Russian Federation (Act 211, contract 02.A03.21.0006)