Vladimir L. Malinovskii

Capacitance and conductance characterization of ferrocene-containing self-assembled monolayers on silicon surfaces for memory applications

Self-assembled monolayers of 4-ferrocenylbenzyl alcohol attached to silicon provided the basis for electrolyte-molecule-silicon capacitors. Characterization by conventional capacitance and conductance techniques showed very high capacitance and conductance peaks near ∼0.6 V associated with charging and discharging of electrons into and from discrete levels in the monolayer owing to the presence of the redox-active ferrocenes. The reversible charge trapping of these molecules suggest their potential application in memory devices. Due to the molecular scalability and low-power operation, molecular-silicon hybrid devices may be strong candidates for next-generation electronic devices.

Dialkynylpyrenes: Strongly Fluorescent, Environment-Sensitive DNA Building Blocks

Two isomeric dialkynylpyrene phosphoramidites and their incorporation into oligonucleotides are described. The pyrene units closely resemble the well-known perylene bisimide dye PDI with regard to the ability to self-organize within a DNA duplex. In addition, dialkynylpyrenes exhibit significant monomer and remarkably strong excimer fluorescence. The dialkynylpyrene building blocks are promising candidates for applications in diagnostic tools, such as excimer-based molecular beacons, as well as for novel DNA-based materials with special optical properties.

Highly efficient quenching of excimer fluorescence by perylene diimide in DNA.

Pyrene excimer fluorescence is effectively quenched by non-nucleosidic perylene diimides upon DNA duplex formation.

DNA‐Assisted Self‐Assembly of Pyrene Foldamers

The self-organization of oligopyrene foldamers is described. Bi- and tri-segmental oligomers composed of nucleotides and non-nucleosidic, achiral pyrene monomers form double-stranded helical structures, as shown by absorbance, fluorescence, and CD spectroscopy. The mixed nature of alternating aromatic and phosphate groups ensures water solubility which, in turn, favors folding of the aromatic units. Pyrene molecules also assemble though interstrand stacking interactions. Structural organization of the pyrene units is an intrinsic property of the oligoaryl part and takes place independently from the sequence of the attached DNA. Chirality transfer from DNA to the pyrene segment leads to formation of a double helix, in which neighboring pyrene units are, in the present case, twisted in a right-handed manner. Pyrene helicity is most pronounced in a bi-segmental chimera, in which a DNA stem is present only at one end of the pyrene section.

Design, synthesis, and characterization of prototypical multistate counters in three distinct architectures

The storage of multiple bits of information in distinct molecular oxidation states is anticipated to afford extraordinarily high memory densities. Among redox-active molecules, lanthanide porphyrinic triple-decker complexes are attractive candidates for such molecular information storage elements because they provide at least four cationic states over a modest potential range. Our approach toward a molecular multistate counter involves covalently linking two triple deckers with interleaving oxidation potentials to achieve a commensurate increase in the number of oxidation states within a single dyad. We report the design and synthesis of five dyads comprised of triple-decker complexes of the form (Pc)Ln(Pc)Ln(Por) or (Por1)Ln(Pc)Ln(Por2), where Pc = phthalocyaninato, Por = porphyrinato, and Ln = Ce or Eu. The dyads were prepared in a modular building-block fashion by Pd-mediated coupling of an iodophenyl-triple decker and an ethynylphenyl-triple decker. The different dyad architectures examined include a vertical architecture with one linker (V1), a horizontal architecture with one linker (H1), and a horizontal architecture with two linkers (H2). In each dyad, one or two S-acetylthiomethyl groups incorporated on the porphyrinic moiety of the triple decker enables attachment to an electroactive surface viain situ cleavage of the protected thiol linker(s). Three dyads (Dyad1–3) have the V1 architecture but different compositions of triple deckers; three dyads (Dyad3–5) have identical composition but different architectures (V1, H1, H2) for comparison of the properties in self-assembled monolayers (SAMs) on gold. The SAM of each dyad exhibits robust reversible electrochemical behavior; the redox waves are essentially the sum of the waves of the component triple deckers. In contrast, mixtures of the component triple decker monomers form poor quality SAMs with inferior electrochemical characteristics. Accordingly, all three dyad architectures are viable constructs for assembling a multistate counter.

Signal control by self-assembly of fluorophores in a molecular beacon—a model study

Pyrene excimer fluorescence is efficiently regulated through formation of π-stacked aggregates between dialkynylpyrene (Y) and perylenediimide (E) residues located in the stem region of a molecular beacon (MB). The building blocks form organized, multichromophoric complexes in the native form. Hybridization to the target results in a conformational reorganization of the chromophores. The nature of the aggregates was investigated by changing the number of chromophores and natural base pairs in the beacon stem. The formation of different types of complexes (EYEY→YEY→EY) is revealed by characteristic spectroscopic changes. The data show that signal control is an intrinsic property of the interacting chromophores. The directed assembly of non-nucleosidic chromophores can be used for the generation of an on/off switch of a fluorescence signal. The concept may find applications in various types of light-based input/output systems.

Oligopyrenotides: Chiral Nanoscale Templates for Chromophore Assembly

Getting organized: DNA-like supramolecular polymers formed of short oligopyrenotides serve as a helical scaffold for the molecular assembly of ligands. The cationic porphyrin meso-tetrakis(1-methylpyridin-4-yl)porphyrin interacts with the helical polymers in a similar way as with poly(dA:dT).

Triazolylpyrenes: Synthesis, fluorescence properties, and incorporation into DNA

Synthesis of 1,6- and 1,8-triazolylpyrenes and their incorporation into oligonucleotides is described. In hybrids, triazolylpyrenes adopt interstrand stacking interactions. Exciton coupling is observed for the duplex containing a pair of the 1,6-isomer indicating a well-defined helical arrangement of the triazolylpyrene building blocks. Triazole substitution results in pronounced red-shifts of monomer as well as excimer fluorescence. Furthermore, quantum yields of the formed excimers are remarkably high.

Photon harvesting by excimer-forming multichromophores

A light-harvesting system based on a DNA-organized oligopyrene-cyanine complex is described. Energy transfer from the pyrene units to the cyanine dye was found to proceed via FRET from locally confined excimers to the acceptor.

Modulation of chiroptical properties by DNA-guided assembly of fluorenes.

The supramolecular organization of fluorene building blocks in a DNA scaffold is described. The molecular assembly into ordered π-aggregates leads to distinct changes in the electronic properties.