New regioselective multicomponent reaction: one pot synthesis of spiro heterobicyclic aliphatic rings

In the context of our high-throughput organic synthesis program, we have studied the reactivity of special beta-keto esters toward the Biginelli reaction. We have found that a cyclic beta-keto ester reacts with one molecule of urea and two molecules of aldehyde to give a new family of spiro heterobicyclic aliphatic rings in good yields. Interestingly, the Biginelli product was not detected. After analysis of products using HPLC, 1H NMR, and 13C NMR, we have found that the reaction is driven by a regio-specific condensation of two molecules of aldehyde with the other reagents to afford only products harboring substituents exclusively in cis configuration. Monte Carlo minimization studies using MM2 force field suggest that cis products are energetically more stable than the trans counterparts. Together with previously reported data, these results suggest that the trans products were not obtained as result of steric hindrance produced by the equatorial position of one of the ring substituents. This new reaction is useful for high-throughput organic synthesis. Indeed, the new scaffold can be used to introduce additional groups in the molecules through remaining functional groups by a "domino strategy".     

Studies in the field of 2,1,3-thia- and -selenadiazoles

The results of studies on 2,1,3-thiadiazole, benzo-2,1,3-thiadiazole, benzo-2,1,3-selenadiazole, and their derivatives by chemical, physicochemical, and physical methods give no grounds for assuming that they have a quinoid structure. These results permit the statement that these heterocycles containing quatervalent sulfur or selenium are typical heteroaromatic systems satisfying Hückel's (4n+2) rule.For part LV, see [1].     

A new approach to amplified telomerase detection with polyvalent oligonucleotide nanoparticle conjugates

We report a new assay for human telomerase activity that relies on polyvalent oligonucleotide nanoparticle conjugates as diagnostic probes and amplification units. Gold nanoparticles functionalized with specific oligonucleotide sequences can efficiently capture telomerase enzymes and subsequently be elongated. Both the elongated and unmodified oligonucleotide sequences are simultaneously measured. The two strands not only serve as internal positive controls for each other but also provide a way of amplifying signal. At high concentrations, both elongated and unmodified strands exhibit measurable responses. At low telomerase concentrations (e.g., from 10 HeLa cells), elongated strands cannot be detected, but the unmodified sequences, which come from the same probe particles, can be detected because their concentration is higher, providing a novel form of amplification. This new assay rivals the sensitivity of the conventional PCR-based method of telomerase detection.     

"Three-dimensional hybridization" with polyvalent DNA-gold nanoparticle conjugates

We have determined the minimum number of base pairings necessary to stabilize DNA-Au NP aggregates as a function of salt concentration for particles between 15 and 150 nm in diameter. Significantly, we find that sequences containing a single base pair interaction are capable of effecting hybridization between 150 nm DNA-Au NPs. While traditional DNA hybridization involves two strands interacting in one dimension (1D, Z), we propose that hybridization in the context of an aggregate of polyvalent DNA-Au NP conjugates occurs in three dimensions (many oligonucleotides oriented perpendicular to the X, Y plane engage in base pairing), making nanoparticle assembly possible with three or fewer base pairings per DNA strand. These studies enabled us to compare the stability of duplex DNA free in solution and bound to the nanoparticle surface. We estimate that 4-8, 6-19, or 8-33 additional DNA bases must be added to free duplex DNA to achieve melting temperatures equivalent to hybridized systems formed from 15, 60, or 150 nm DNA-Au NPs, respectively. In addition, we estimate that the equilibrium binding constant (K(eq)) for 15 nm DNA-Au NPs (3 base pairs) is approximately 3 orders of magnitude higher than the K(eq) for the corresponding nanoparticle free system.     

Electrochemistry of individual molecules in zeptoliter volumes

Electrochemical experiments were carried out in a nanometer-sized cylindrical thin layer cell (TLC) formed by etching the surface of a disk-type platinum nanoelectrode (5- to 150-nm radius). Using high frequency ac voltage, the surface of such an electrode was etched to remove a very thin (> or = 1-nm-thick) layer of Pt. The resulting zeptoliter-scale cavity inside the glass sheath was filled with aqueous solution containing redox species, and the etched electrode was immersed in a dry (no external solution) pool of mercury to produce a TLC. Several approaches based on steady-state voltammetry and scanning electrochemical microscopy (SECM) were developed to independently evaluate the electrode radius and the etched volume. The number of redox molecules in the TLC could be varied between one and a few hundred by changing its volume and solution concentration. In this way, the transition between a random and deterministic number of trapped molecules was observed. High quality steady-state voltammograms of > or = 1 molecules were obtained for different neutral and charged redox species and different concentrations of supporting electrolyte. The analysis of such voltammograms yields information about mass transfer, adsorption, electron transfer kinetics, and double-layer effects on the nanoscale.     

Peptide C(alpha)D(alpha) stretch frequencies in a hydrated conformation are perturbed mainly by C(alpha)-D(alpha)...O hydrogen bonding

We have shown (J. Phys. Chem. A 2004, 108, 10923; 2007, 111, 5300) that the C(alpha)D(alpha) stretch frequency, nu(CD), can discriminate between uniform alpha(R), beta, and polyproline II conformations of isolated peptides. Similar results for such peptides to which explicit waters are hydrogen bonded exhibit shifts in nu(CD) from those of the isolated structures. We demonstrate that the main source of these frequency shifts is the formation of C(alpha)-D(alpha)...O hydrogen bonds to water. Taking into account C-H...O(water) hydrogen bonding, together with the traditional bonding of peptide groups to water, can be expected to increase our understanding of the interaction of proteins with their aqueous environment.     

Effect of mechanical stress on the kinetics of heterogeneous electron transfer

The scanning electrochemical microscope (SECM) combined with a computerized tensile stage was employed to measure the kinetics of electron transfer (ET) reactions at stainless steel electrodes as a function of the applied mechanical stress. Reproducible current versus distance curves were obtained for different values of the tensile stress applied to a stainless steel (T-316) sample by using hexaammineruthenium as a redox mediator. The dependences of the extracted rate constant on substrate potential (i.e., Tafel plots, ln k versus E) were linear, in agreement with classical electrochemical theory. Possible origins of the stress effect on the ET rate and its implications for studies of stress corrosion cracking are discussed.     

Pyrene-Appended Fluorescent Tweezers Generated via the Weak-Link Approach and Their Halide Recognition Properties

Through the Weak-Link Approach, fluorescent condensed and open Cu(I) tweezer complexes were prepared and characterized. These complexes exhibit fluorescence-sensitive binding properties for halide anions. The solid-state structure of a non-fluorescent Rh(I) tweezer analogue, determined by X-ray crystallography, shows that the counter anion, Cl⁻, is trapped inbetween the two amide groups of the tweezer arms through hydrogen bonds. Although the tweezer binds Cl⁻, the open complex also binds Cl⁻, showing that the main role of the metal is to increase the local concentration of the pyrenyl amide moieties so that 2:1 binding can take place.     

On-wire lithography-generated molecule-based transport junctions: a new testbed for molecular electronics

On-wire lithography (OWL) fabricated nanogaps are used as a new testbed to construct molecular transport junctions (MTJs) through the assembly of thiolated molecular wires across a nanogap formed between two Au electrodes. In addition, we show that one can use OWL to rapidly characterize a MTJ and optimize gap size for two molecular wires of different dimensions. Finally, we have used this new testbed to identify unusual temperature-dependent transport mechanisms for alpha,omega-dithiol terminated oligo(phenylene ethynylene).