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 differences 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.

Local Polarization Reversal by Ion Beam Irradiation in SBN Single Crystals Covered by Dielectric Layer.

Formation of the domain structure by ion beam irradiation was studied in thermally depolarized Ce-doped strontium barium niobate single crystals covered by a dielectric layer. Three types of irradiation regimes were used: dot exposure, stripe exposure, and line exposure. The dependences of the domain size and depth on the irradiated dose were measured. The circular shape of the isolated domains with partially switched broad domain boundary was obtained. Isotropic domain growth was attributed to the step generation at the wall by merging with the residual nanodomains that appeared after thermal depolarization. The obtained linear dose dependence of the switched area was attributed to the screening of the depolarization field by the injected charge. The shape distortion of the domains growing in the neighborhood with already created ones was attributed to the electrostatic interaction of the approaching charged domain walls. The obtained results can be applied for the creation of precise domain patterns with arbitrary orientation and shape to produce nonlinear optical devices with improved characteristics, including electrically tunable diffractive optical elements.

Molecular modeling and computational study of the chiral-dependent structures and properties of the self-assembling diphenylalanine peptide nanotubes, containing water molecules.

DFT (VASP) and semi-empirical (HyperChem) calculations for the L- and D-chiral diphenylalanine (L-FF and D-FF) nanotube (PNT) structures, empty and filled with water/ice clusters, are presented and analyzed. 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 and total L-FF and D-FF PNT with embedded water/ice cluster are discussed.

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.

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.

Molecular modeling and computational study of the chiral-dependent structures and properties of self-assembling diphenylalanine peptide nanotubes.

The structure and properties of diphenylalanine (FF) peptide nanotubes (PNT) based on phenylalanine were investigated by various molecular modeling methods. The main approach employed semi-empirical quantum-chemical methods (PM3 and AM1). Ab initio, density functional theory methods and molecular mechanical approaches were also used. Both model structures and structures extracted from experimental crystallographic databases obtained by X-ray methods were examined. A comparison of optimized model structures and structures obtained by natural self-assembly revealed important differences depending on chirality: D and L. In both the cases, the effect of chirality on the results of self-assembly of FF PNT was established: PNT based on the D-FF has large condensation energy E0 in the transverse direction, and form thicker and shorter PNT bundles than those based on L-FF. A topological difference was established: model PNT were optimized into structures consisting of rings, while naturally self-assembled PNT consisted of helical turns. The latter nanotubes differed from the original L-FF and D-FF and formed helix structures of different chirality signs in accordance with the alternation rule of chirality due to macromolecule hierarchy. A topological transition between ring and helix turn PNT structures is discussed: self-assembled natural helix structures are favorable and their energy is lower by a value of the order of one to several eV.

Self-Assembly of Organic Ferroelectrics by Evaporative Dewetting: A Case of ß-Glycine.

Self-assembly of ferroelectric materials attracts significant interest because it offers a promising fabrication route to novel structures useful for microelectronic devices such as nonvolatile memories, integrated sensors/actuators, or energy harvesters. In this work, we demonstrate a novel approach for self-assembly of organic ferroelectrics (as exemplified by ferroelectric ß-glycine) using evaporative dewetting, which allows forming quasi-regular arrays of nano- and microislands with preferred orientation of polarization axes. Surprisingly, self-assembled islands are crystallographically oriented in a radial direction from the center of organic "grains" formed during dewetting process. The kinetics of dewetting process follows the t-1/2 law, which is responsible for the observed polygon shape of the grain boundaries and island coverage as a function of radial position. The polarization in ferroelectric islands of ß-glycine is parallel to the substrate and switchable under a relatively small dc voltage applied by the conducting tip of piezoresponse force microscope. Significant size effect on polarization is observed and explained within the Landau-Ginzburg-Devonshire phenomenological formalism.