2'-O-[2-[2-(N,N-dimethylamino)ethoxy]ethyl] modified oligonucleotides: symbiosis of charge interaction factors and stereoelectronic effects

[structure: see text] Oligonucleotides with a novel, 2'-O-[2-[2-(N,N-dimethylamino)ethoxy]ethyl] (2'-O-DMAEOE) modification have been synthesized. This modification, a cationic analogue of the 2'-O-(2-methoxyethyl) (2'-O-MOE) modification, exhibits high binding affinity to target RNA (but not to DNA) and exceptional resistance to nuclease degradation. Analysis of the crystal structure of a self-complementary oligonucleotide containing a single 2'-O-DMAEOE modification explains the importance of charge factors and gauche effects on the observed antisense properties. 2'-O-DMAEOE modified oligonucleotides are ideal candidates for antisense drugs.     

A characterization for spaces of sections

The space of smooth sections of a bundle over a compact smooth manifold can be equipped with a manifold structure, called an -manifold, where represents the Fréchet algebra of real valued smooth functions on . We prove that the -manifold structure characterizes the spaces of sections of bundles over and its open subspaces. We also describe the -maps between -manifolds.

     

Synthesis of spherical polymer and titania photonic crystallites

The fabrication of small structured spherical particles that are essentially small photonic crystals is described. The particles are 1-50 microm in diameter and are porous with nearly close-packed monodisperse pores whose size is comparable to the wavelength of light. The solid matrix of the particles is titania, which provides a large refractive index contrast between the particle matrix and pores. The particles are made by encapsulating polymer colloidal particles in emulsion droplets of hexanes in which a titanium alkoxide precursor is dissolved. Subsequent osmotic removal of the hexanes from the droplets and condensation of the alkoxide precursor leads to spherical aggregates of polymer spheres with titania filling the spaces between the polymer spheres. The polymer particles are then burned out leaving behind the desired porous titania particles. The size and structure of the pores and high refractive index of the titania matrix are expected to produce particles that are very efficient scatterers of light, making them useful as pigments.     

5-Exo-dig radical cyclization of enediynes: the first synthesis of tin-substituted benzofulvenes

[reaction: see text] Bu(3)Sn-mediated 5-exo-dig radical cyclization of diaryl enediynes provides a mild and efficient approach to tin-substituted fulvenes. Further synthetic opportunities opened by this process and general factors responsible for the observed regio- and stereoselectivity are outlined.     

2'-O-[2-[N,N-(dialkyl)aminooxy]ethyl]-modified antisense oligonucleotides

[structure] Oligonucleotides with two novel modifications, 2'-O-?2-[N, N-(dimethyl)aminooxy]ethyl? (2'-O-DMAOE) and 2'-O-?2-[N, N-(diethyl)aminooxy]ethyl? (2'-O-DEAOE), have been synthesized. These modifications exhibit high binding affinity to target RNA (and not to DNA) and enhance the nuclease stability of oligonucleotides considerably with t(1/2) > 24 h as a phosphodiester.     

1,3-Dipolar reactions involving corannulene: how does its rim and spoke addition vary?

[reaction: see text] Corannulene undergoes 1,3-dipolar reactions with the dipoles, diazomethane, nitrile oxide, and nitrone through its rim and spoke pi bonds; the rim addition yields "one possible" adduct whereas two "regioselective" adducts are formed by spoke addition. Mechanisms of these reactions have been investigated at the B3LYP/6-31G(d) level. Computations show that both rim and spoke additions prefer concerted pathways that lie 2-5 kcal/mol lower in energy than stepwise paths. Stepwise additions can take place in two ways and the activation energies of these two modes differ by 1-2 kcal/mol. A close inspection of the energy profiles reveals that rim addition is more favorable kinetically and thermodynamically than spoke addition in view of lower activation energy and higher exothermicity observed for rim addition. The rim bond of corannulene is more flexible for distortion and also has a stronger double bond (i.e. pi-character) than the spoke bond and this facilitates rim addition over spoke addition. Deformation energy analysis also confirms the above through higher deformation in corannulene from the spoke addition when compared to rim addition. In the spoke addition, regio1 reaction is kinetically more favored than regio2 reaction. Attempts to react corannulene in an endohedral fashion have led to the exohedral adduct. Computed activation energies suggest that corannulene acts as a deactivated dipolarophile compared to ethylene. Even more striking is the observation that rim and spoke double bonds in corannulene are part of the local aromatic system but it shows remarkable reactivity compared to benzene despite the loss of aromaticity during the reaction. This is well indicated by computed NICS values. Inclusion of acetonitrile as solvent through the PCM model increases the reaction rate and exothermicity.     

A conformationally preorganized universal solid support for efficient oligonucleotide synthesis

A novel, conformationally preorganized nonnucleosidic universal solid support for oligonucleotide synthesis was developed. The solid support featured two chemically equivalent hydroxy groups locked in syn-periplanar orientation and orthogonally protected with 4,4'-dimethoxytrityl and acetyl groups. The solid support was extensively tested in the preparation of oligonucleotides and their phosphorothioate analogues containing 2'-deoxy, 2'-O-methyl, and 2'-O-methoxyethylnucleoside residues at the 3'-terminus. Upon completion of oligonucleotide chain assembly, the support-bound oligonucleotide material was treated with concentrated ammonium hydroxide, which removed the O-acetyl protection. The deprotected hydroxy group then effected the transesterification of a phosphate linkage between the solid support and the 3'-terminal nucleoside residue to result in a facile release of the oligonucleotide to solution. The kinetics of the release process was studied in a continuous flow of concentrated aqueous ammonium hydroxide at a temperature of 300.15 K. Optimal conditions for the release of oligonucleotides depending on the chemistry of the backbone and 3'-terminal nucleoside residue were formulated.     

5-endo-dig radical cyclizations: "the poor cousins" of the radical cyclizations family

Kinetics and thermodynamics of 5-endo-dig radical cyclizations were studied using a combination of DFT computations and Marcus theory. When the reactant is stabilized by conjugation of the radical center with the bridge pi-system, the cyclization starts with reorientation of the radical orbital needed to reach the in-plane acetylene pi-orbital in the bond-forming step. This reorientation leads to loss of the above conjugative stabilization, increases the activation energy, and renders such cyclizations less exothermic. As a result, even when the radical needed for the 5-endo cyclization is formed efficiently, it undergoes either H-abstraction or equilibration with an isomeric radical. Only when the bridging moiety is saturated or when intramolecular constraints prevent the overlap of the bridge pi-orbital and the radical center, 5-endo cyclizations may be able to proceed with moderate efficiency under conditions when H-abstraction is slow. The main remaining caveat in designing such geometrically constrained 5-endo-dig cyclizations is their sensitivity to strain effects, especially when polycyclic systems are formed. The strain effects can be counterbalanced by increasing the stabilization of the product (e.g., by introducing heteroatoms into the bridging moiety). Electronic effects of such substitutions can be manifested in various ways, ranging from aromatic stabilization to a hyperconjugative beta-Si effect. The 4-exo-dig cyclization is kinetically competitive with the 5-endo-dig process but less favorable thermodynamically. As a result, by proper design of reaction conditions, 5-endo-dig radical cyclizations should be experimentally feasible.     

Conformational and configurational studies on 3-azabicyclo[3.3.1]nonane (3-abn) derivatives and related systems employing carbon-13 NMR spectroscopy

The ¹³C nmr spectra of 4 cis-2,4-diphenyl-3-azabicyclo[3.3.1]nonanes, 11 cis-2,4-diaryl-3-azabicyclo[3.3.1]-nonan-9-ones, 26 cis-2,4-diaryl-3-azabicyclo[3.3.1]-nonan-9-ols or acetates thereof, 5 cis-2,4-diaryl-3-azabi-cyclo[4.3.1]decan-10-ones or -10-ols and 5 cis-2,4-diphenyl-3-aza-7-thiabicyclo[3.3.1]nonan-9-ones, -9-ols or 9-yl acetates have been recorded. Except for the 7-thia compounds, which appear to exist mainly in the configuration and conformation with the nitrogen-containing ring in the boat form, these compounds seem to exist overwhelmingly in chair-chair conformations. The configuration of the 9-ols and their acetates (syn or anti to the nitrogen-containing ring) has been deduced from the spectra. In a number of cases, the structures assigned differ from those earlier postulated. Broadening of one set of aryl signals (probably those due to the ortho carbons) in the case of N-methyl (but not N-H) compounds without ortho substituents is ascribed to restricted phenyl rotation.