Design considerations and computer modeling related to the development of molecular scaffolds and peptide mimetics for combinatorial chemistry

Summary A critical issue in drug discovery utilizing combinatorial chemistry as part of the discovery process is the choice of scaffolds to be used for a proper presentation, in a three-dimensional space, of the critical elements of structure necessary for molecular recognition (binding) and information transfer (agonist/ antagonist). In the case of polypeptide ligands, considerations related to the properties of various backbone structures (-helix, -sheets, etc.; , space) and those related to three-dimensional presentation of side-chain moieties (topography; (chi) space) must be addressed, although they often present quite different elements in the molecular recognition puzzle. We have addressed aspects of this problem by examining the three-dimensional structures of chemically different scaffolds at various distances from the scaffold to evaluate their putative diversity. We find that chemically diverse scaffolds can readily become topographically similar. We suggest a topographical approach involving design in chi space to deal with these problems.     

β-lithiations of carboxamides. Synthesis of β-substituted-α,β-unsaturated amides

N-Methyl-2-methyl-3-(benzotriazol-l-yl)propanamide, on treatment with butyllithium forms a dianion which on treatment with alkyl and benzyl halides, aldehydes and ketones affords monosubstituted products; with ethyl p-toluate, a lactam is formed. The alkylated derivatives eliminate benzotriazole in the presence of base to afford trisubstituted α,β-unsaturated amides.     

Solid-phase synthesis of pyrazolines and isoxazolines with sodium benzenesulfinate as a traceless linker

[reaction: see text] The preparation of pyrazoline and isoxazoline derivatives with traceless solid-phase sulfone linker strategy is described. Key steps involved in the solid-phase synthetic procedure include (i) sulfinate S-alkylation, (ii) sulfone anion alkylation, (iii) gamma-hydroxy sulfone --> gamma-ketosulfone oxidation, and (iv) traceless product release via elimination-cyclization. A library of 12 pyrazolines and isoxazolines was synthesized.     

Ruthenium Cluster Chemistry with Ph2PC6H4-4-C≡CH

The new phosphines Ph₂PC₆H₄-4-CCR [R=SiMe₃ (1), H (2)] have been used to prepare Ru₃(CO)₉(Ph₂PC₆H₄-4-CCSiMe₃)₃ (4) and Ru(CCC₆H₄-4-PPh₂)(PPh₃)₂(-C₅H₅) (3), respectively, the latter with a pendent phosphine. Reaction of 4 with carbonate or fluoride affords Ru₃(CO)₉(Ph₂PC₆H₄-4-CCH)₃ (5) with pendent terminal alkynyl groups, the identity of which was confirmed by a structural study. Reaction of 5 with [Ru(NCMe)(PPh₃)₂(-C₅H₅)]PF₆ or reaction of Ru₃(CO)₁₂ with 3 gives Ru₃(CO)₉{(Ph₂PC₆H₄-4-CC)Ru(PPh₃)₂(-C₅H₅)}₃ (6). Complexes 3–6 have been studied by cyclic voltammetry. Proceeding from Ru₃(CO)₁₂ to 4 or 5 shifts the cluster-centred reduction to more negative potential and affords facile cluster-centred oxidation. Proceeding from 4/5 and 3 to 6 results in similarly-located cluster-centred reduction and peripheral ruthenium-centred oxidation, but results in a lack of observable cluster-centred oxidation. Crystal data for 5·C₆H₁₄: space group P¯1, a=12.760(1) Å, b=17.077(1) Å, c=17.924(2) Å, =108.656(5)°, =96.344(5)°, =93.523(5)°, V=3658.4(6) ų, Z=2, R=0.078, R_w=0.105 for 5008 reflections [I>2.00(I)].     

Autoxidation of cyclohexane: conventional views challenged by theory and experiment.

In spite of its industrial importance, the detailed reaction mechanism of cyclohexane autoxidation by O2 is still insufficiently known. Based on quantum chemical potential energy surfaces, rate coefficients of the primary and secondary chain propagation steps involving the cyclohexylperoxyl (CyOO) radical were evaluated using multiconformer transition-state theory. Including tunneling and hindered-internal-rotation effects, the rate coefficient for hydrogen-atom abstraction from cyclohexane (CyH) by CyOO was calculated to be k(T)= 1.46 x 10(-11) x exp(-17.8 kcal mol(-1)/ RT) cm3s(-1) (300-600K), close to the experimental data. A "Franck-Rabinowitch cage" reaction between the nascent cyclohexylhydroperoxide (CyOOH) and cyclohexyl radical, products from CyOO + CyH, is put forward as an initially important cyclohexanol (CyOH) formation channel. alphaH abstraction by CyOO. from cyclohexanone was calculated to be only about five times faster than that from CyH, too slow to explain all the observed side products. The a-hydrogen (alphaH) abstractions from CyOH and CyOOH by CyOO. are predicted to be about 10 and 40 times faster, respectively, than the CyOO. +CyH reaction. The very fast CyOO.+CyOOH reaction proceeds through the unstable Cy-alphaH .OOH radical that decomposes spontaneously into the ketone (Q=O) plus the OH radical; the "hot" .OH is found to produce the bulk of the alcohol via a second, "activated cage" reaction analogous to that above. It is thus shown how the very reactive CyOOH intermediate is the predominant source of ketone and alcohol, while it also leads to some side products. The alpha-hydroxycyclohexylperoxyl radical formed during the moderately fast oxidation of CyOH is shown to decompose fast into HO2 + cyclohexanone in a rapidly equilibrated reaction, which constitutes a smaller, second ketone source. These two fast cyclohexanone forming routes avoid the need for unfavorable molecular routes hitherto invoked as ketone sources. The theoretical predictions are supported and complemented by experimental findings. The newly proposed scheme is also largely applicable to the oxidation of other hydrocarbons, such as toluene, xylene, and ethylbenzene.     

Solid-phase synthesis of quinoxaline, thiazine, and oxazine analogs through a benzyne intermediate

A solid-phase synthetic route to quinoxaline, thiazine, and oxazine analogs is described. N-Alloc-3-amino-3-(2,4-difluoro-5-nitrophenyl)propanoic acid was tethered to Rink resin via its carboxylic acid group. The 4-arylfluorine was displaced with a primary amine, alcohol, or thiol to create, respectively, a resin bound aniline, phenol, or thiophenol derivative with one diversity element and one single atom (e.g., N, S, or O) diversity point. A fused heterocyclic system was subsequently created via a benzyne heterocyclization initiated by dehydrofluorination with strong base. Acid treatment released the desired products in high yield and moderate purity.     

Semiclassical approach to collision-induced emission in the presence of intense laser radiation: An aspect in the study of cooperative chemical and optical pumping

Collion-induced emission in molecular systems in an intense laser field is studied using the semiclassical approach, with a view towards cooperative chemical and optical pumping in laser production. The formalism is developed with the electronic-field representation, which treats collision and radiative interaction on the same footing. Electronic-field surfaces can be regarded as forming spectra for spontaneous emission; and particular emission events can be accounted for by propagating classical trajectories on emission electronic-field surfaces. Pre-emission loss from the excited state is dealt with by propagating classical trajectories on a loss surface along a complex contour of emission branch points. This loss surface is derived on the basis of localized radiative couplings between electronic-field states and provides a framework to treat the general problem of discrete state-continuum interactions. The formalism is applied to a two-state, collinear exponential model to compute S-matrix elements and transition probabilities between asymptotic states.