Electrostatics of nucleic acid folding under conformational constraint

RNA folding is enabled by interactions between the nucleic acid and its ion atmosphere, the mobile sheath of aqueous ions that surrounds and stabilizes it. Understanding the ion atmosphere requires the interplay of experiment and theory. However, even an apparently simple experiment to probe the ion atmosphere, measuring the dependence of DNA duplex stability upon ion concentration and identity, suffers from substantial complexity, because the unfolded ensemble contains many conformational states that are difficult to treat accurately with theory. To minimize this limitation, we measured the unfolding equilibrium of a DNA hairpin using a single-molecule optical trapping assay, in which the unfolded state is constrained to a limited set of elongated conformations. The unfolding free energy increased linearly with the logarithm of monovalent cation concentration for several cations, such that smaller cations tended to favor the folded state. Mg(2+) stabilized the hairpin much more effectively at low concentrations than did any of the monovalent cations. Poisson-Boltzmann theory captured trends in hairpin stability measured for the monovalent cation titrations with reasonable accuracy, but failed to do so for the Mg(2+) titrations. This finding is consistent with previous work, suggesting that Poisson-Boltzmann and other mean-field theories fail for higher valency cations where ion-ion correlation effects may become significant. The high-resolution data herein, because of the straightforward nature of both the folded and the unfolded states, should serve as benchmarks for the development of more accurate electrostatic theories that will be needed for a more quantitative and predictive understanding of nucleic acid folding.     

Asymmetric formal synthesis of schulzeines A and C

The asymmetric formal synthesis of schulzeines A and C is described. Key features of the synthesis include the efficient and stereoselective construction of the benzoquinolizidine skeleton via the aza-Claisen rearrangement-induced ring expansion of the 1-vinyl-N-glycyl-isoquinoline, which was prepared by the highly enantioselective asymmetric allylation of the 8-benzyloxy-substituted dihydroisoquinoline and by the acid-catalyzed transannulation of the resulting 10-membered lactam.     

Asymmetric syntheses of 1-deoxy-6,8a-di-epi-castanospermine and 1-deoxy-6-epi-castanospermine

Asymmetric syntheses of both 1-deoxy-6,8a-di-epi-castanospermine and 1-deoxy-6-epi-castanospermine, polyhydroxylated indolizidine alkaloids that act as selective glycosidase inhibitors, have been accomplished in seven steps. The key feature of our unique syntheses includes the stereoselective introduction of the C-3 and C-4 hydroxyl groups utilizing the aza-Claisen rearrangement-induced ring expansion of 1-acyl-2-alkoxyvinyl pyrrolidine and a substrate-controlled stereoselective transannulation of the resulting azoninone intermediate.     

Ternary codes from the strongly regular (45, 12, 3, 3) graphs and orbit matrices of 2-(45, 12, 3) designs

The enumeration of strongly regular graphs with parameters (45, 12, 3, 3) has been completed, and it is known that there are 78 non-isomorphic strongly regular (45, 12, 3, 3) graphs. A strongly regular graph with these parameters is a symmetric (45, 12, 3) design having a polarity with no absolute points. In this paper we examine the ternary codes obtained from the adjacency (resp. incidence) matrices of these graphs (resp. designs), and those of their corresponding derived and residual designs. Further, we give a generalization of a result of Harada and Tonchev on the construction of non-binary self-orthogonal codes from orbit matrices of block designs under an action of a fixed-point-free automorphism of prime order. Using the generalized result we present a complete classification of self-orthogonal ternary codes of lengths 12, 13, 14, and 15, obtained from non-fixed parts of orbit matrices of symmetric (45, 12, 3) designs admitting an automorphism of order 3. Several of the codes obtained are optimal or near optimal for the given length and dimension. We show in addition that the dual codes of the strongly regular (45, 12, 3, 3) graphs admit majority logic decoding.     

Portfolio value-at-risk optimization for asymmetrically distributed asset returns

We propose a new approach to portfolio optimization by separating asset return distributions into positive and negative half-spaces. The approach minimizes a newly-defined Partitioned Value-at-Risk (PVaR) risk measure by using half-space statistical information. Using simulated data, the PVaR approach always generates better risk-return tradeoffs in the optimal portfolios when compared to traditional Markowitz mean–variance approach. When using real financial data, our approach also outperforms the Markowitz approach in the risk-return tradeoff. Given that the PVaR measure is also a robust risk measure, our new approach can be very useful for optimal portfolio allocations when asset return distributions are asymmetrical.     

Capillary electrophoresis-mass spectrometry of a new cross-linker with acrylic functionality

Analytical characterization of dimethacrylate-tyrosine-lysine-tyrosine (DMTLT, a new biodegradable acrylic cross-linker synthesized at our laboratory) is carried out using CE-MS. DMTLT is a pseudopeptide composed by tyrosine-lysine-tyrosine amino acids linked through urea bonds with two methacrylic groups, one at each end of the molecule, making this compound an excellent cross-linker for polymerization reactions and for obtaining new biodegradable materials. A new CE-MS method is developed for the characterization of DMTLT and its products of degradation after basic hydrolysis. In order to carry out an exhaustive examination of such degradation products methods based on CE coupled to IT and TOF-MS are employed. Based on CE-IT-MS results and the elemental composition of the degradation products obtained by CE-TOF-MS, conclusions on the mechanism and kinetic of hydrolysis of DMTLT are obtained confirming both the usefulness of CE-MS to characterize new biomaterials and the applicability of DMTLT for preparing new biodegradable polymers. These results are corroborated through the CE-MS detection of the identified products of degradation in a dimethyl acrylamide polymer cross-linked with DMTLT.     

Au nanoparticles encapsulated in Ru carbonyl carboxylate shells

A two-step surface functionalization approach has been used to encase Au nanoparticles in monolayer organometallic Ru-complex shells by the reaction of an intermediate surface-bound mercaptopropanoic acid capping species with Ru dodecacarbonyl (Ru3(CO)12) clusters. Vibrational (infrared and Raman) spectroscopy shows that insertion of carboxylate groups into the Ru clusters results in their fragmentation and the formation of a shell of Ru dicarbonyl carboxylate oligomers that remain attached to the Au nanoparticles through the original Au-alkanethiolate bonds. The structural integrity of the metallic nanoparticulate Au cores has been verified by X-ray photoelectron spectroscopy, X-ray diffraction, and transmission electron microscopy. The organometallic Ru-complex shell may be decomposed thermally to eliminate the mercaptopropanoate and carbonyl groups and leave a mixed phase of Au and RuO2.     

15N NMR spectra of some ionic liquids based on 1,3-disubstituted imidazolium cations

15N NMR spectra of twelve neat ionic liquids derived from 1,3-disubstituted imidazolium salts were measured, and effects of nitrogen atoms substitution, type of anions and influence of solvents used for dilution of neat ionic liquids were studied. Changes in charge distribution are discussed.     

Characterization of quantum dynamically significant paths of bridge-mediated charge transfer systems

In this article, we examine characteristics of quantum dynamically important paths using the on-the-fly filtered propagator functional path integral method, which evaluates a numerically accurate reduced density matrix by ignoring the vast majority of paths with insignificant contribution to the dynamics of interest. Two five-state charge-transfer systems have been considered, such that each system is governed by a different charge-transfer mechanism. It was found that, for the incoherent hopping transfer, the quantum mechanically important paths mimic classical counterparts that show little deviation between forward and backward path. Therefore, it is desirable to take advantage of a priori knowledge of the important path characteristics; in particular, it is possible to evaluate the accurate dynamics of bridge-mediated long-range charge-transfer systems efficiently in a significantly reduced quantum mechanical trajectory space.     

Chemisorption-induced spin symmetry breaking in gold clusters and the onset of paramagnetism in capped gold nanoparticles

We present a simple model to describe the induction of magnetic behavior on gold clusters upon chemisorption of one organic molecule with different chemical linkers. In particular, we address the problem of stability of the lowest lying singlet and show that for some linkers there exists a spin symmetry-breaking that lowers the energy and leads to preferential spin density localization on the gold atoms neighboring the chemisorption site. The model is basically an adaptation of the Stoner model for itinerant electron ferromagnetism to finite clusters and it may have important implications for our understanding of surface magnetism in larger nanosystems and its relevance to electronic transport in electrode-molecule interfaces.