Valence bond studies of AH2 molecules

Minimal basis set (STO) molecular orbital and valence-bond calculations are reported for the³ B ₁ and¹ A ₁ states of CH₂. The open-shell molecular orbital calculations used the Roothaan formulation. The valence-bond calculations used the Prosser-Hagstrom biorthogonalisation technique to evaluate the cofactors required in using Löwdin's formulae. Optimisation of geometry and orbital exponents in the molecular orbital calculation on the³ B ₁ state gave a geometry of R_C-H=2.11 a.u. and H-C-H=123.2 °. The energy obtained was ?38.8355 a.u. The molecular orbital and valencebond calculations are compared. In the valence-bond calculations the variation with bond-length and bond-angle of the configuration energies was studied. Valence bond “build-up” studies are also reported. Valence-bond calculations using hybrid orbitals instead of natural atomic orbitals showed that the perfect-pairing approximation is not as good for CH₂ as BeH₂. The nature of the lone-pair and bonding orbitals is found to be significantly different between the³ B ₁ and¹ A ₁ states. In the³ B ₁ state the 2s and 2p orbitals are fairly equally mixed between both types of orbital. However in the¹ A ₁ state the bonding orbitals have mainly 2p character and the lone pair orbitals have mainly 2s character. As was found for H₂O, the bonding hybrid orbitals do not follow the hydrogen nuclei as the bond angle varies but continue to point approximately in their equilibrium directions.     

Lead hopping using SVM and 3D pharmacophore fingerprints

The combination of 3D pharmacophore fingerprints and the support vector machine classification algorithm has been used to generate robust models that are able to classify compounds as active or inactive in a number of G-protein-coupled receptor assays. The models have been tested against progressively more challenging validation sets where steps are taken to ensure that compounds in the validation set are chemically and structurally distinct from the training set. In the most challenging example, we simulate a lead-hopping experiment by excluding an entire class of compounds (defined by a core substructure) from the training set. The left-out active compounds comprised approximately 40% of the actives. The model trained on the remaining compounds is able to recall 75% of the actives from the "new" lead series while correctly classifying >99% of the 5000 inactives included in the validation set.     

Theory of the two step enantiomeric purification of 1,3 dimethylallene

An application of a recently proposed [P. Kral et al., Phys. Rev. Lett. 90, 033001 (2003)] two step optical control scenario to the purification of a racemic mixture of 1,3 dimethylallene is presented. Both steps combine adiabatic and diabatic passage phenomena. In the first step, three laser pulses of mutually perpendicular linear polarizations, applied in a "cyclic adiabatic passage" scheme, are shown to be able to distinguish between the L and D enantiomers due to their difference in matter-radiation phase. In the second step, which immediately follows the first, a sequence of pulses is used to convert one enantiomer to its mirror-imaged form. This scenario, which only negligibly populates the first excited electronic state, proves extremely useful for systems such as dimethylallene, which can suffer losses from dissociation and internal conversion upon electronic excitation. We computationally observe conversion of a racemic mixture of dimethylallene to a sample containing approximately 95% of the enantiomer of choice.     

Synthesis of the Salmonella type E(1) core trisaccharide as a probe for the generality of 1-(benzenesulfinyl)piperidine/triflic anhydride combination for glycosidic bond formation from thioglycosides

A synthesis of a chromogenic glycoside of the Salmonella anatum group E(1) core trisaccharide is presented in which all three glycosidic bonds, a 1,2-cis-equatorial, a 1,2-trans-axial, and a 1,2-trans-equatorial linkage representing three of the four main classes of glycosidic bond, are formed with thioglycoside donors activated under a single set of conditions by the combination of 1-(benzenesulfinyl)piperidine and trifluoromethanesulfonic anhydride. 2,3-O-Carbonyl- and 2,3-O-isopropylidene-alpha-L-rhamnopyranosyl thioglycosides are found to be highly alpha-selective rhamnosyl donors under these conditions.     

Stereoselective synthesis of β-hydroxy-α-methylketones via z- and e-vinyloxyboranes generated directly from cyclohexyl ethyl ketone

$\text{E}$- and $\text{Z}$-dialkylvinyloxyboranes, prepared directly from cyclohexyl ethyl ketone, undergo stereo-selective aldol condensations to provide $\text{threo}$- $\text{erythro}$-β-hydroxy-α-methylketones, respectively.     

Swallowtail porphyrins: synthesis, characterization and incorporation into porphyrin dyads

The incorporation of symmetrically branched tridecyl ("swallowtail") substituents at the meso positions of porphyrins results in highly soluble building blocks. Synthetic routes have been investigated to obtain porphyrin building blocks bearing 1-4 swallowtail groups. Porphyrin dyads have been synthesized in which the zinc or free base (Fb) porphyrins are joined by a 4,4'-diphenylethyne linker and bear swallowtail (or n-pentyl) groups at the nonlinking meso positions. The swallowtail-substituted Zn(2)- and ZnFb-dyads are readily soluble in common organic solvents. Static absorption and fluorescence spectra and electrochemical data show that the presence of the swallowtail groups slightly raises the energy level of the filled a(2u)(pi) HOMO. EPR studies of the pi-cation radicals of the swallowtail porphyrins indicate that the torsional angle between the proton on the alkyl carbon and p-orbital on the meso carbon of the porphyrin is different from that of a porphyrin bearing linear pentyl groups. Regardless, the swallowtail substituents do not significantly affect the photophysical properties of the porphyrins or the electronic interactions between the porphyrins in the dyads. In particular, time-resolved spectroscopic studies indicate that facile excited-state energy transfer occurs in the ZnFb dyad, and EPR studies of the monocation radical of the Zn(2)-dyad show that interporphyrin ground-state hole transfer is rapid.     

Improving resins for solid phase synthesis: incorporation of 1-[2-(2-methoxyethoxy)ethoxy]-4-vinyl-benzene

The preparation, characterisation and application of a series of non-grafted polystyrene (PS) resins containing a styrenic methoxypoly(ethylene glycol) (MPEG) derivative is presented. These novel PS-MPEG resins were designed to balance swelling and solvation with improved handling. The monomer, 1-[2-(2-methoxyethoxy)ethoxy]-4-vinyl-benzene, contained an inert phenyl ether linkage designed to provide broad chemical compatibility and stability, yet imparting all the favourable properties of the PEG group into the new resin, whilst maintaining a high loading capacity. The synthetic performance of the new resins compared very favourably to those of TentaGel™, ArgoGel™ and aminomethyl PS.     

Rearrangement of epoxynitriles: a convenient homologation of acyclic and cyclic ketones to carboxylic acids

A convenient two-step homologation of both aliphatic and aromatic ketones to the corresponding carboxylic acid has been developed. First ketones were converted to epoxynitriles with the Darzens reaction. Second, a Lewis acid mediated rearrangement of these epoxynitriles with lithium bromide was achieved to give homologated secondary alkanoic acids (as well as aryl-alkanoic) in good yields. The mechanism and the scope of the rearrangement reaction were investigated. This strategy constitutes a two-step homologation of ketones to secondary carboxylic acids.     

Synthetic and theoretical studies of cyclobuta[1,2:3,4]dicyclopentene. Organocobalt intermediates in the construction of the unsaturated carbon skeleton and their transformation into novel cobaltacyclic complexes by C-C insertion

Theoretical and synthetic studies of the tricyclic 10pi-electron hydrocarbon cyclobuta[1,2:3,4]dicyclopentene (1), a nominally aromatic structure that has never been synthesized, are described. Geometry optimization by density-functional-theory calculations (B3LYP/6-31G(d,p)) predict that 1 is a D(2h) symmetric structure with nonalternant C-C single and double bonds. The calculations also predict that 1 is 4.7 kcal/mol higher in energy than the isomeric hydrocarbon 1,6-didehydro[10]annulene (2), a molecule known to isomerize to 1,5-didehydronaphthalene (4) above -50 degrees C. Calculated enthalpic changes of homodesmotic reactions support the notion that 1 is an aromatic molecule with a resonance stabilization energy (RSE) about half to two-thirds that of benzene on a per-molecule basis. Investigations of potential synthetic pathways to 1 initially utilized as starting material the tricyclic carbonate 11, the product of an intramolecular [2 + 2]-photocyclization reaction. In these studies, 11 was transformed in several steps to the distannane 12, which upon treatment with boron fluoride ethyl etherate is believed to have formed the unstable hydrocarbon bicyclopentadienylidene (13). In an effort to avoid cleavage of the central, four-membered ring of unsaturated tricyclo[5.3.0.0(2,6)]decane intermediates (perhaps the result of 10-electron electrocyclic ring opening of the tetraene 8), synthetic approaches to 1 employing cobalt-cyclobutadiene complexes 18 and 19 were pursued. Treatment of 18 with excess methyllithium led to the novel cobaltacyclic product 30, and dehydration of 19 in the presence of pyridine produced the ring-opening cobaltacyclic product 35. It is proposed that both processes may occur by a 10-electron electrocyclic ring-opening reaction of eta(2)-organocobalt intermediates. These processes may be related to the hypothetical transformation of tetraene 8 to bicyclopentadienylidene (13).     

The use of comet assay data with a simple reaction mechanism to evaluate the relative effectiveness of free radical scavenging by quercetin, epigallocatechin gallate and N-acetylcysteine in UV-irradiated MRC5 lung fibroblasts

Comet assay data (tail DNA %) have been gathered for the concentration dependent role of three antioxidants (AOs); quercetin (Q), epigallocatechin gallate (EGCG) and N-acetylcysteine (NAC) in reducing UV-induced damage to DNA in normal fetal lung fibroblasts (MRC5). All three compounds demonstrate a concentration dependent reduction maximum with a pro-oxidant effect at higher (though not cytotoxic) concentrations. Manipulation of a simple 4-step reaction mechanism for free radical (FR) scavenging by AOs produced rate constant ratios which allowed the relative effectiveness (Q > EGCG > NAC) of the AOs to be evaluated.