Synthesis and Characterization of Quinuclidinium Derivatives of the [closo-1-CB11H12](-) Anion as Potential Polar Components of Liquid Crystal Materials.

Antipodal substitution of the [closo-1-CB11H12](-) anion with a 4-pentylquinuclidinium fragment and alkyl groups in positions C(1) and B(12) gave polar zwitterions 1[n] and 2[n]. The molecular structure of 1[5] was established using X-ray diffraction (XRD) methods: P1̅, a = 15.162(2) Å, b = 16.546(3) Å, c = 19.794(3) Å; α = 84.871(2)°, ß = 84.057(2)°, γ = 84.058(3)°; Z = 8. All compounds exhibit high temperature in-plane ordered smectic phases that are stabilized by dipolar interactions. The ordered phases were investigated by powder XRD methods. Thermal and dielectric parameters for two derivatives, 1[0] and 1[6], were evaluated in nematic hosts, ClEster and BPhF. The dielectric data were analyzed with the Maier-Meier formalism augmented with density functional theory methods, and the results were compared to those for similar zwitterions previously reported.

Phthalocyanine dimerization-based molecular beacons using near-IR fluorescence.

Herein we demonstrate the use of a novel dimerization-based molecular beacon (MB) probe consisting of two metallo-phthalocyanine (Pc) fluorophores that use near-IR fluorescence, appropriate for highly specific and sensitive in vivo and/or in vitro DNA/RNA detection. Pc's possess a propensity to form nonfluorescent H-dimers that is utilized as the molecular "off" switch in the closed MB conformation. The "on" switch, which is generated when the solution target binds to the loop of the MB forming the open form, also provides two fluorophores for transduction resulting in a doubling of the extinction coefficient and improving the resulting fluorescence yield compared to a classical single-fluorophore/quencher MB system. In addition, the Pc-based MBs possess high thermal, photo, and chemical stabilities that are essential for many highly sensitive applications, such as molecular imaging. The dimer-based MBs were obtained using a simple single-step synthesis procedure and demonstrated excellent quenching efficiencies (98%) as well as a high signal-to-background ratio (approximately 60) exceeding the performance characteristics of many conventionally available MB probes.

1-Pyridine- and 1-quinuclidine-1-boraadamantane as models for derivatives of 1-borabicyclo[2.2.2]octane. Experimental and theoretical evaluation of the B-N fragment as a polar isosteric substitution for the C-C group in liquid crystal compounds.

The suitability of 1-borabicyclo[2.2.2]octane (1) as a structural element for liquid crystals was evaluated using computational methods and experimental studies of two complexes of its close analogue 1-boraadamantane (2). The molecular and crystal structures for 1-pyridine-1-boraadamantane [2-P, C(14)H(20)BN, P2(1)/m, a = 8.4404(13) A, b = 6.8469(10) A, c = 10.5269(16) A, beta = 104.712(3) degrees, Z = 2], 1-quinuclidine-1-boraadamantane [2-Q, C(16)H(28)BN, P2(1)/n, a = 6.6529(3) A, b = 10.6665(6) A, c = 19.3817(10) A, beta = 94.689(3) degrees, Z = 4], and 1-pyridine-trimethylborane [3-P, C(8)H(14)BN, C(cma), a = 6.9875(10) A, b = 15.011(2) A, c = 16.556(2) A, Z = 8] were determined by X-ray crystallography and compared with the results of DFT and MP2 calculations. Gas-phase thermodynamic stabilities of complexes 1-P, 1-Q, 2-P, and 2-Q were estimated using a correlation between theoretical (MP2/6-31+G(d)//MP2/6-31G(d) with B3LYP/6-31G(p) thermodynamic corrections) and experimental data for complexes of BMe(3) (3) with amines lacking N-H bonds. The analysis showed the generally higher thermodynamic stability for the quinuclidine (Q) complexes compared to that of the pyridine (P) analogues in the gas phase and an overall order of stability of 1 > 2 > 3. This order is paralleled by high ring strain energy of 1 (SE = 27 kcal/mol) as compared to that of 1-boraadamantane (2, SE = 16.5 kcal/mol). The chemical stability of 2-P and 2-Q, with respect to hydrolytic and oxidative reagents, is high for the pyridine derivative and satisfactory for the quinuclidine complex at ambient temperature, which implies sufficiently high stability of 1-borabicyclo[2.2.2]octane complexes for materials applications. Molecular dipole moments of 6.2 +/- 0.1 and 6.0 +/- 0.15 D were measured for 2-Q and 2-P, respectively.

Metallo-phthalocyanine near-IR fluorophores: oligonucleotide conjugates and their applications in PCR assays.

Water soluble, metallo-pthalocyanine (MPc) near-IR fluorophores were designed, synthesized, and evaluated as highly stable and sensitive reporters for fluorescence assays. Their conjugation to oligonucleotides was achieved via succinimidyl ester-amino coupling chemistry with the conditions for conjugation extensively examined and optimized. In addition, various conjugate purification and isolation techniques were evaluated as well. Results showed that under proper conditions and following purification using reverse-phase ion-pair chromatography, labeling efficiencies near 80% could be achieved using ZnPc (Zn phthalocyanine) as the labeling fluorophore. Absorption and fluorescence spectra accumulated for the conjugates indicated that the intrinsic fluorescence properties of the MPc's were not significantly altered by covalent attachment to oligonucleotides. As an example of the utility of MPc reporters, we used the MPc-oligonucleotide conjugates as primers for PCR (polymerase chain reaction) amplifications with the products sorted via electrophoresis and detected using near-IR fluorescence (lambda ex = 680 nm). The MPc dyes were found to be more chemically stable under typical thermal cycling conditions used for PCR compared to the carbocyanine-based near-IR reporter systems typically used and produced single and narrow bands in the electrophoretic traces, indicative of producing a single PCR product during amplification.

Water soluble metallo-phthalocyanines: the role of the functional groups on the spectral and photophysical properties.

Strategies are reported that produce symmetrical metal-free and metallo-phthalocyanine dyes, Pc and MPc, respectively, containing various numbers of water solubilizing carboxylic acid groups on their periphery that provide a dual role by also serving as functional groups to covalently link primary amine-containing targets to these dyes. In order to induce water compatibility and to minimize the degree of aggregation, the periphery of the macrocycle was decorated with various numbers of water-solubilizing groups and/or altering the identity of the metal center. The influence of the number of solubilizing groups and metal center on the spectral and photophysical properties were evaluated. MPc dyes containing 4, 8, or 16 carboxylic acid groups exhibited similar absorption and emission maxima (677 and 686 nm, respectively) with the molar absorptivity of the Q-band approximately 10(5) M(-1) cm(-1). Results indicated that the fluorescence lifetimes and quantum yields varied as a function of the metal center; the degree of carboxylation did not significantly alter these properties in DMSO, but did mediate the solubility and aggregation states when placed in aqueous solvents. The water solubilizing groups could also serve as labeling moieties for targets bearing primary amines. Results showed that the conjugate, produced by covalently linking an MPc to streptavidin through one of its carboxylate groups, generated a red-shift in the emission maximum with a fluorescence lifetime shorter than that of the native MPc dye.

Chiral tubule self-assembly from an achiral diynoic lipid.

Tubules possessing microm-scale chiral substructure self-assemble from an achiral isomer of the tubule-forming diynoic phosphatidylcholine, 1,2-bis(10,12-tricosadiynoyl)sn-glycero-3-phosphocholine [DC(8,9)PC], showing that molecular chirality is not essential for tubule formation. CD spectroscopy shows that these structures' helical sense of handedness instead originates in a spontaneous cooperative chiral symmetry-breaking process. We conclude that the chiral symmetry-breaking must originate in the unusual feature common to the chiral and achiral tubule-forming molecules, the diynes centered in their hydrocarbon tails.