Hexachloroiridate(IV) as a redox probe for the electrochemical discrimination of B-DNA and M-DNA monolayers on gold

This paper demonstrates the effectiveness of using the redox couple to investigate DNA monolayers, and compares the potential advantages of this system to the standard redox couple. B-DNA monolayers were converted to M-DNA by incubation in buffer containing 0.4 mM Zn²⁺ at pH 8.6 and studied by cyclic voltammetry (CV), impedance spectroscopy (IS) and chronoamperometry (CA) with . Compared to B-DNA, M-DNA showed significant changes in CV, IS and CA spectra. However, only small changes were observed when the monolayers were incubated in Mg²⁺ at pH 8.6 or in Zn²⁺ at pH 6.0. The heterorgeneous electron-transfer rate (k_ET) between the redox probe and the surface of a bare gold electrode was determined to be 5.7 × 10⁻³ cm/s. For a B-DNA modified electrode, the k_ET through the monolayer was too slow to be measured. However, under M-DNA conditions, a k_ET of 1.5 × 10⁻³ cm/s was reached. As well, the percent change in resistance to charge transfer, measured by IS, was used to illustrate the dependence of M-DNA formation on pH. This result is consistent with Zn²⁺ ions replacing the imino protons on thymine and guanine residues. The redox couple was also effective in differentiating between single-stranded and double-stranded DNA during de-hybridization and rehybridization experiments.     

Monoprotection of diols as a key step for the selective synthesis of unequally disubstituted diamondoids (nanodiamonds)

The monoprotection (desymmetrization) of diamondoid, benzylic, and ethynyl diols has been achieved using fluorinated alcohols such as 2,2,2-trifluoroethanol (TFE) under acidic conditions. This practical acid-catalyzed S(N)1 reaction opens the door for the synthesis of novel bifunctional diamondoids. With diamantane as an example, we show that the resulting monoethers can be used to prepare selectively, for instance, amino or nitro alcohols and unnatural amino acids. These are important compounds in terms of the exploration of electronic, pharmacological, and material properties of functionalized nanodiamonds.     

Probing the mechanical stability of DNA in the presence of monovalent cations

We examine the interaction between monovalent cations and DNA using several different assays that measure the stability of double-stranded DNA (dsDNA). The thermal melting of dsDNA and the mechanical separation of dsDNA into two single strands both depend on the stability of dsDNA with respect to ssDNA and are sensitive to the interstrand phosphate repulsion. We find that the experimentally measured melting temperatures and unzipping forces are approximately the same for all of the ions considered in this study. Likewise, the force required to transform B-DNA into the overstretched form is also similar for all of the ions. In contrast, for a given ion concentration, the force at which the overstretched state fully relaxes back to the canonical B-DNA form depends on the cation; however, for all cations, the overstretching force decreases with decreasing ion concentration, suggesting that this force is sensitive to screening. We observe a general trend for smaller ions to produce more efficient relaxation. Finally, for a given cation, the relaxation can also depend on the anion.     

Rotationally resolved IR-diode laser studies of ground-state CO2 excited by collisions with vibrationally excited pyridine

Relaxation of highly vibrationally excited pyridine (C5NH5) by collisions with carbon dioxide has been investigated using diode laser transient absorption spectroscopy. Vibrationally hot pyridine (E' = 40,660 cm(-1)) was prepared by 248 nm excimer laser excitation followed by rapid radiationless relaxation to the ground electronic state. Pyridine then collides with CO2, populating the high rotational CO2 states with large amounts of translational energy. The CO2 nascent rotational population distribution of the high-J (J = 58-80) tail of the 00(0)0 state was probed at short times following the excimer laser pulse to measure rate constants and probabilities for collisions populating these CO2 rotational states. Doppler spectroscopy was used to measure the CO2 recoil velocity distribution for J = 58-80 of the 00(0)0 state. The energy-transfer distribution function, P(E,E'), from E' - E approximately 1300-7000 cm(-1) was obtained by re-sorting the state-indexed energy-transfer probabilities as a function of DeltaE. P(E,E') is fit to an exponential or biexponential function to determine the average energy transferred in a single collision between pyridine and CO2. Also obtained are fit parameters that can be compared to previously studied systems (pyrazine, C6F6, methylpyrazine, and pyrimidine/CO2). Although the rotational and translational temperatures that describe pyridine/CO2 energy transfer are similar to previous systems, the energy-transfer probabilities are much smaller. P(E,E') fit parameters for pyridine/CO2 and the four previously studied systems are compared to various donor molecular properties. Finally, P(E,E') is analyzed in the context of two models, one indicating that P(E,E') shape is primarily determined by the low-frequency out-of-plane donor vibrational modes, and the other that indicates that P(E,E') shape can be determined from how the donor molecule final density of states changes with DeltaE.     

Synthesis, structure, and spectroscopy of an oxodiiron(II) complex

Bridging oxo species are important in the synthetic and biological chemistry of iron, and are found with iron oxidation states from +2 to +4. We report the first oxodiiron(II) complex that has been crystallographically characterized. It has been examined by NMR, IR, and M?ssbauer spectroscopies as well as density-functional calculations.     

Magnetic exchange interactions in perfluorophenyl dithiadiazolyl radicals

EPR, electrochemical studies and neutron diffraction studies on a large range of 1,2,3,5-dithiadiazolyl radicals have shown that the spin density distribution is essentially unaffected by substituent effects. The variation of magnetic properties previously reported for a series of perfluorophenyl-dithiadiazolyl radicals p-XC₆F₄CNSSN (X = CN, Br, NO₂ and NCC₆F₄) is therefore due to differences in molecular packing. The nearest-neighbour magnetic exchange interactions in these radicals are probed through DFT studies (B3LYP/6-311G**) and are shown to exhibit a variety of both ferromagnetic and antiferromagnetic interactions. All exchange interactions with |J| > 1 cm⁻¹ coincide with close heterocyclic contacts between dithiadiazolyl rings (3.18-4.00 Å) and produce |J| values up to 40 K. An analysis of these interactions indicates that the dominant exchange pathway would appear to be a direct exchange mechanism between radical centres, with orthogonality of the singly-occupied molecular orbitals (SOMOs) favouring ferromagnetic interactions.     

Formation of para-substituted triphenylboroxines: a computational study

Density functional theory (B3LYP//6-311+G) calculations including Poisson-Boltzmann (PB) implicit solvent were applied to study the relative stability of triphenylboroxine (PhBO)(3) with respect to its phenylboronic acid monomers. In solution, formation of (PhBO)(3) is thermodynamically unfavorable; however, addition of an amine base results in the formation of stable 1:1 adducts of (PhBO)(3) and amine. Formation of 1:2 adducts is energetically unfavorable. We find that adduct formation is more exothermic than cleavage of the boroxine ring back to its monomers. pi-Electron-withdrawing groups in the para-position of the phenyl ring destabilize the boroxine ring with respect to its monomers. However, para-substituents that are net electron-withdrawing are found to stabilize formation of the 1:1 adduct.     

Progress in the synthesis of the lituarines: stereocontrol in sequential C-C bond formation on a spirobutenolide template

[structure: see text] We describe elaboration of a tricyclic spirobutenolide corresponding to the C(7-18) tricyclic substructure common to lituarines A-C. Conjugate addition, to install the C(16) methyl, is followed by construction of the crucial C(18-19) bond by silyl enol ether addition to the derived spiroacetal C(18)-O oxonium ion. Esterification with a C(1-6) acid, and selective ozonolysis to release the C(23) carbonyl, complete the assembly of all the carbons present in the lituarine macrocyclic core.     

On the topology of graph picture spaces

We study the space of pictures of a graph G in complex projective d-space. The main result is that the homology groups (with integer coefficients) of are completely determined by the Tutte polynomial of G. One application is a criterion in terms of the Tutte polynomial for independence in the d-parallel matroids studied in combinatorial rigidity theory. For certain special graphs called orchards, the picture space is smooth and has the structure of an iterated projective bundle. We give a Borel presentation of the cohomology ring of the picture space of an orchard, and use this presentation to develop an analogue of the classical Schubert calculus.