Three-dimensional (3-D) structural models of RNA are essential for understanding of the cellular roles played by RNA. Such models have been obtained by a technique based on a constraint satisfaction algorithm that allows for the facile incorporation of secondary and other structural information. The program generates 3-D structures of RNA with atomic-level resolution that can be refined by numerical techniques such as energy minimization. The precision of this technique was evaluated by comparing predicted transfer RNA loop and RNA pseudoknot structures with known or consensus structures. The root-mean-square deviation (2.0 to 3.0 angstroms before minimization) between predicted and control structures reveal this system to be an effective method in modeling RNA.

Meldrum's acid (2,2-dimethyl-1,3-dioxane-4,6-dione) is a molecule with a unique history, owing to its originally misassigned structure, as well as a unique place among acylating agents, owing to its high acidity and remarkable electrophilicity. In this Account, we outline the work of our group and others toward harnessing the reactivity of Meldrum's acid derivatives in catalytic C-C bond-forming reactions. Taking advantage of the ability of Meldrum's acid to decompose to CO(2) and acetone following acyl substitution, we have shown that intramolecular Friedel-Crafts acylations can be performed under mild Lewis acidic conditions to yield a variety of benzocyclic ketones. In a further expansion of this method, a domino Friedel-Crafts acylation/alpha-tert alkylation reaction was used to complete the first total synthesis of (+/-)-taiwaniaquinol B. The unique characteristics of Meldrum's acid extend to its alkylidene derivatives, which have also proven exceptionally useful for the development of new reactions not readily accessible from other unsaturated carbonyl electrophiles. By combining the electrophilicity and dienophilicity of alkylidene Meldrum's acid with our Friedel-Crafts chemistry, we have demonstrated new domino syntheses of coumarin derivatives and tetrahydrofluorenones by conjugate additions, Diels-Alder cycloadditions, and C-H functionalizations. Additionally, we have used these powerful acceptors to allow conjugate alkenylation with functionalized organostannanes, and conjugate allylation under very mild conditions. We have also shown that these molecules permit the asymmetric formation of all-carbon quaternary stereocenters via enantioselective conjugate additions. These reactions employ dialkylzinc nucleophiles, maximizing functional group compatibility, while the presence of a Meldrum's acid moiety in the product allows a variety of postaddition modifications. A full investigation of this reaction has determined the structural factors of the alkylidene that contribute to optimal enantioselectivity. We have also used these acceptors to form tertiary propargylic stereocenters in very high enantiomeric excess by an extremely mild, Rh(I)-catalyzed addition of TMS-acetylene. Overall, we demonstrate that Meldrum's acid and its derivatives provide access to a broad range of reactivities that, combined with their ease of handling and preparation, make them ideal electrophiles.

Experiments have been carried out in which electrospray ionization has been used to generate ionic complexes of all-cis 1,2,3,4,5,6 hexafluorocyclohexane. These complexes were subsequently mass isolated in a quadrupole ion trap mass spectrometer and then irradiated by the tunable infrared output of a free electron laser in the 800-1600 cm(-1) range. From the frequency dependence of the fragmentation of the complexes, vibrational signatures of the complexes were obtained. Computational work carried out in parallel reveals that the complexes formed are very strongly bound and are among the most strongly bound complexes of Na(+) and Cl(-) ever observed with molecular species. The dipole moment calculated for the heaxafluorocyclohexane is very large (∼7 D), and it appears that the bonding in each of the complexes has a significant electrostatic contribution.

[reaction: see text] The intramolecular Friedel-Crafts acylation of aromatics with Meldrum's acid derivatives catalyzed by metal trifluoromethanesulfonates is reported. Meldrum's acids are easily prepared, functionalized, handled, and purified. The synthesis of polysubstituted 1-indanones from benzyl Meldrum's acids was investigated thoroughly, and it was shown that a variety of catalysts were effective, while accommodating a diversity of functional groups under mild conditions. The scope, limitations, and functional group tolerance (terminal alkene and alkyne, ketal, dialkyl ether, dialkyl thioether, aryl methyl ether, aryl TIPS and TBDPS ethers, nitrile- and nitro-substituted aryls, alkyl and aryl halides) for a variety of 5-benzyl (enolizable Meldrum's acids) and 5-benzyl-5-substituted Meldrum's acids (quaternized Meldrum's acids), forming 1-indanones and 2-substituted-1-indanones, respectively, are delineated. This method was further applied to the synthesis of 1-tetralones, 1-benzosuberones, and the potent acetylcholinesterase inhibitor donepezil. Rate of cyclization as a function of ring size was established for various benzocyclic ketones via competition experiments: 1-tetralones form faster than both 1-indanones and 1-benzosuberones, and 1-benzosuberones cyclize faster than 1-indanones.

The first synthesis of taiwaniaquinol B, a 6-nor-5(6-->7)abeoabietane-type diterpenoid exhibiting the uncommon fused 6-5-6 tricyclic carbon skeleton, was accomplished in 15 steps. A Lewis acid-promoted tandem intramolecular Friedel-Crafts/carbonyl alpha-tert-alkylation reaction was exploited as the core strategy for the synthesis of the sterically congested 1-indanone-containing tricyclic structure. This multiple carbon-carbon bond forming reaction exploits the unique reactivity of Meldrum's acid. The facile precursor synthesis makes this a useful methodology for the expedient modification and assembly of sterically congested 1-indanone-containing ring systems.