Synthesis,Physicochemical Properties,and Hydrogen Bonding of 4(5)‐Substituted 1‐H‐Imidazole‐2‐carboxamide,a Potential Universal Reader for DNA Sequencing by Recognition Tunneling

We have developed a chemical reagent that recognizes all naturally occurring DNA bases, a so called universal reader, for DNA sequencing by recognition tunneling in nanopores. 1 The primary requirements for this type of molecules are the ability to form non‐covalent complexes with individual DNA bases and to generate recognizable electronic signatures under an electrical bias. 1‐H‐imidazole‐2‐carboxamide was designed as such a recognition moiety to interact with the DNA bases through hydrogen bonding. In the present study, we first furnished a synthetic route to 1‐H‐imidazole‐2‐carboxamide containing a short ω‐functionalized alkyl chain at its 4(5) position for its attachment to metal and carbon electrodes. The acid dissociation constants of the imidazole‐2‐carboxamide were then determined by UV spectroscopy. The data show that the 1‐H‐imidazole‐2‐carboxamide exists in a neutral form between pH 6–10. Density functional theory (DFT) and NMR studies indicate that the imidazole ring exists in prototropic tautomers. We propose an intramolecular mechanism for tautomerization of 1‐H‐imidazole‐2‐carboxamide. In addition, the imidazole‐2‐carboxamide can self‐associate to form hydrogen bonded dimers. NMR titration found that naturally occurring nucleosides interacted with 1‐H‐imidazole‐2‐carboxamide through hydrogen bonding in a tendency of dG>dC?dT>dA. These studies are indispensable to assisting us in understanding the molecular recognition that takes place in the nanopore where routinely used analytical tools such as NMR and FTIR cannot be conveniently applied.     

Gas-phase synthesis and structure of monomeric ZnOH: a model species for metalloenzymes and catalytic surfaces

Monomeric ZnOH has been studied for the first time using millimeter and microwave gas-phase spectroscopy. ZnOH is important in surface processes and at the active site of the enzyme carbonic anhydrase. In the millimeter-wave direct-absorption experiments, ZnOH was synthesized by reacting zinc vapor, produced in a Broida-type oven, with water. In the Fourier-transform microwave measurements, ZnOH was produced in a supersonic jet expansion of CH(3)OH and zinc vapor, created by laser ablation. Multiple rotational transitions of six ZnOH isotopologues in their X(2)A' ground states were measured over the frequency range of 22-482 GHz, and splittings due to fine and hyperfine structure were resolved. An asymmetric top pattern was observed in the spectra, showing that ZnOH is bent, indicative of covalent bonding. From these data, spectroscopic constants and an accurate structure were determined. The Zn-O bond length was found to be similar to that in carbonic anhydrase and other model enzyme systems.     

Enantioselective synthesis of tryptophan derivatives by a tandem Friedel-Crafts conjugate addition/asymmetric protonation reaction

The tandem Friedel-Crafts conjugate addition/asymmetric protonation reaction between 2-substituted indoles and methyl 2-acetamidoacrylate is reported. The reaction is catalyzed by (R)-3,3'-dibromo-BINOL in the presence of stoichiometric SnCl(4), and is the first example of a tandem conjugate addition/asymmetric protonation reaction using a BINOL·SnCl(4) complex as the catalyst. A range of indoles furnished synthetic tryptophan derivatives in good yields and high levels of enantioselectivity, even on a preparative scale. The convergent nature of this transformation should lend itself to the preparation of unnatural tryptophan derivatives for use in a broad array of synthetic and biological applications.     

Suicide inhibition of alpha-oxamine synthases: structures of the covalent adducts of 8-amino-7-oxononanoate synthase with trifluoroalanine

The irreversible inhibition of 8-amino-7-oxononanoate synthase by trifluoroalanine involves decarboxylative defluorination of the inhibitor-PLP aldimine followed by attack of the conjugated imine by the amino group of the active site lysine to afford a covalently bound difluorinated intermediate which can subsequently undergo further HF losses and hydrolysis to afford a 2-(pyridoximine phosphate) acetoyl protein adduct.     

A tight-binding method for predicting magnetic ordering in Gd-containing solids: Application to GdB2C2

Herein we present a method to compute d-f mediated exchange coupling in Gd-containing systems with a spin-dependent extended Hückel-tight binding (EHTB) method. EHTB parameters were chosen to exactly reproduce the spin density functional calculation (SDFT) energy gap of the S = 45/2 and 39/2 spin patterns for a model compound, Gd6CoI12(OPH3)6. Comparison between SDFT and EHTB results shows a good match between the spin-pattern energy distribution for the two methods. We applied our EHTB method to the solid-state compound GdB2C2 by considering 6 different variations in the ordering of the 4f7 moments. Calculations indicate that this metallic system should exhibit antiferromagnetic ordering of the 4f7 moments with a magnetic structure consistent with published neutron diffraction results.     

Copper-catalyzed rearrangement of vinyl oxiranes

A novel copper-catalyzed vinyl oxirane ring expansion protocol has been developed. A wide range of vinyl oxiranes can be rearranged to 2,5-dihydrofurans in excellent yields in the presence of electrophilic copper(II) acetylacetonate catalysts. Regioisomeric vinyl oxiranes can be converted to a single dihydrofuran product using these conditions. This method uses low catalyst loadings (0.5-5 mol %), has good tolerance of substitution patterns, and can be done in the absence of solvent.     

High-nuclearity homoleptic and heteroleptic coordination cages based on tetra-capped truncated tetrahedral and cuboctahedral metal frameworks

Two new types of coordination cage have been prepared and structurally characterized: [M16(mu-L1)24]X32 are based on a tetra-capped truncated tetrahedral core and have a bridging ligand L1 along each of the 24 edges; [M12(mu-L1)12(mu3-L2)4]X24 are based on a cuboctahedral core which is supported by a combination of face-capping ligands L2 and edge-bridging ligands L1. The difference between the two illustrates how combinations of ligands with different coordination modes can generate coordination cages which are not available using one ligand type on its own.     

Expanding the scope of the acyl-type radical addition reactions promoted by SmI2

N-acyl oxazolidinones of simple carboxylic acids and amino acids were observed to undergo successful SmI2-promoted couplings with substituted acrylamides and acrylates, affording a variety of functionalized gamma-ketoamides and -esters with yields attaining 85%. As many of these reductive couplings were previously found to be ineffective employing the corresponding 4-pyridylthio esters, the applicability of this methodology has been substantially improved. The methodology has been adapted to prepare structures related to two potent aspartate protease inhibitors, the renin inhibitor aliskiren, and the gamma-secretase inhibitor L-685,458. Finally, a convenient two-step procedure for the preparation of N-acyl oxazolidinones of N-protected amino acids, which provides consistently good yields of the corresponding imide, has been devised.     

High-pressure synthesis, crystal and electronic structures of a new scandium tungstate, Sc0.67WO4

Negative thermal expansion (NTE) materials possess a low-density, open structure that can respond to high pressure conditions, leading to new compounds and/or different physical properties. Here we report that one such NTE material - white, insulating, orthorhombic Sc₂W₃O₁₂ - transforms into a black compound when treated at 4 GPa and 1400 °C. The high pressure phase, Sc_0.67WO₄, crystallizes in a defect-rich wolframite-type structure, a dense, monoclinic structure (space group P2/c) containing 1-D chains of edge-sharing WO₆ octahedra. The chemical bonding of Sc_0.67WO₄ vis-à-vis the ambient pressure Sc₂W₃O₁₂ phase can be understood on the basis of the Sc defect structure. Magnetic susceptibility, resistivity, thermoelectric power and IR spectroscopic measurements suggest that the Sc_0.67WO₄ sample is a paramagnet whose conductivity is that of a metal in the presence of weak localization and electron-electron interactions. Oxygen vacancies are suggested as a potential mechanism for generating the carriers in this defective wolframite material.     

Chaos and oscillations in a loaded plasma-filled diode

A plasma-filled diode can be used as a model for the interaction space in a virtual cathode oscillator (VCO) (vircator). It is shown that depending on the separation of the electrodes xˆ_L, the initial ion/electron ratio αˆ, and the load Zˆ_l , the system may exhibit a cascade of bifurcations leading to chaos. The positioning and extent of chaos can be controlled by a judicious choice of the above parameters. It is also shown that for a range of values of xˆ_L,αˆ, and Zˆ_l the system is capable of generating oscillations of a well-defined frequency. For other ranges, it reaches a stable state or becomes unstable