V. V. Prokhorov

High-Resolution Atomic Force Microscopy Study of Hexaglycylamide Epitaxial Structures on Graphite

Two types of hexaglycylamide (HGA) epitaxial lamellar structures coexisting on the surface of highly oriented pyrolytic graphite (HOPG) exposed to water solutions were studied by high-resolution atomic force microscopy (AFM). Lamellae are distinguished by growth direction and by morphology. The lamellae of the first type (L1) produced by depositions from more dilute solutions are close-packed with a period of ∼5.2 nm, twice the HGA molecular length, and form highly ordered domains morphologically similar to the lamellar domains of alkanes. The less-ordered lamellae of the second type (L2) appear at intermediate and large HGA concentrations and demonstrate variable lamellar width, morphological diversity, and a tendency to merge. The interlamellar separation in the domains of close-packed L2 lamellae varies with the discrete increment ∼2.5 nm; the most frequently observed value is ∼7.5-8.0 nm corresponding to the triple HGA molecular length. The growth directions of lamellae of each type have sixfold rotational symmetry indicating epitaxy with graphite; however, the rosettes of L1 and L2 lamellae orientations are misaligned by 30°. The molecular modeling of possible HGA epitaxial packing arrangements on graphite and their classification have been conducted, and the energetically preferable structures are selected. On this basis, the structural models of the L1 and L2 lamellae are proposed explaining the experimentally observed peculiarities as follows: (1) the L1 and L2 lamellae are respectively parallel and antiparallel β-sheets with two HGA molecules in the unit cell oriented normally to the lamellae boundaries, (2) HGA molecules in L1 and L2 lamellae have different orientations with respect to the graphite lattice, respectively along the directions <1120> and <1010>, (3) L1 lamella is the assembly of two hydrogen-bonded parallel β-sheets oriented head-to-head, (4) L2 lamellae are assemblies of several molecular rows (antiparallel β-sheets) cross-linked by hydrogen bonds. The AFM observations indicate that the covering of the hydrophobic graphite by the dense, closely packed, well-ordered monolayers of hydrophilic oligopeptide is possible.

High-resolution atomic force microscopy of DNA

A method using high resolution atomic force microscopy for imaging DNA has been elaborated. Using super-sharp probes and modified graphite as support for molecule adsorption, DNA molecule images were obtained whose resolution made possible the observation of their fine structure with repeated helical motifs. The method can be used to visualize individual spread molecules of single-stranded DNA.

Multilayer J-aggregates of cyanine dyes

It is shown that the introduction into the aqueous solution of anionic thiamonomethinecyanine of the Mg2+ cation promotes the formation of the multilayer dye J-aggregates. It is also established that, on the J-aggregates or on the metallocomplex J-aggregates of anionic thiamonomethinecyanine, a multilayer and simultaneously multichrome system of new J-aggregate is formed due to the additional introduction of cationic cyanine dye into the solution, which absorbs light in a different region of the spectrum than anionic dye.

High precision nanoscale AFM height measurements of J-aggregates

Atomic force microscopy (AFM) was used to obtain high-resolution images of nanosized organic J-aggregate molecular crystals of 3,3′-di(gamma-sulfopropyl)-5,5-dichlorotiamonomethinecyanine (TC) and 3,3′-bis(2-sulfopropyl)-5,5′,6,6′-tetrachloro-1,1′-dioctylbenzimidacarbocyanine (C8S3) and precise height measurements of J-aggregates monolayers were conducted. It was found that TC J-aggregates obtained both in the solution bulk and by self-assembly on the mica surface are extended monolayer sheets of high mechanical flexibility. The height of TC is 1.05 ± 0.05 nm, which corresponds to the crystallographic size of a single molecule along the short axis. A model of asymmetric single-layer molecular packing is suggested in which sulfopropyl groups are located on the same side of the layer plane. In the case of C8S3, narrow multilayer ribbonlike structures with heights of 3 to 30 nm were observed. The heights are strictly quantized with a step of 3 nm. A bilayer model of C8S3 molecular packing in J-aggregates is discussed with partially interpenetrating monolayers with hydrophobic sides oriented face to face. A model of structural C8S3 units as “elementary ribbons” with the transverse dimensions of 3 × 4 nm is suggested on the basis of the comparison of AFM data with electron microscopy data from other works.

Tubular structure of J-aggregates of cyanine dye

1 A heightened interest in certain supramolecular organic structures is associated with their unusual optical and electronic properties. These structures include J aggregates of cyanine dyes that represent a variation of micro and nanosized molecular crystals with strong and narrow absorption band (J band) in the visible range shifted toward longer wavelengths as compared with the spectrum of monomers [1, 2]. Owing to high electron–hole conductivity and special spectral properties caused by excitation of delocalized Frenkel excitons, J aggregates are promising organic systems for application in different optoelectronic devices [3–7].

Crystalline structure of two-dimensional cyanine dye J-aggregates

A crystallographic analysis of optical fluorescent images of two-dimensional polygonal structures of J-aggregates of 3,3′-di(γ-sulfopropyl)-5,5′-dichlorothiamonomethinecyanine (MCD) cyanine dye has been performed. In aqueous solutions, MCD forms striplike J-aggregates in the form of extended strips with parallel sides and an oblique or right-angled end. It is found that the acute angle in oblique J-aggregates has a single value close to 45°. The staircase model of molecular packing in oblique J-aggregates is proposed with a slippage angle of 25° expected from the molecular simulation. Within this model the sides of aggregates are formed by the [100] and

Crystallography and Molecular Arrangement of Polymorphic Monolayer J-Aggregates of a Cyanine Dye: Multiangle Polarized Light Fluorescence Optical Microscopy Study

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High resolution mapping DNAs by R-loop atomic force microscopy

faces, and the acute angle between them is equal to the experimentally observed angle. Right-angled rectangular J-aggregates are presumably described by the ladder model.