Kinetic discrimination in recognition of DNA quadruplex targets by guanine-rich heteroquadruplex-forming PNA probes

Guanine-rich peptide nucleic acid probes hybridize to DNA G quadruplex targets with high affinity, forming PNA-DNA heteroquadruplexes. We report a surprising degree of kinetic discrimination for PNA heteroquadruplex formation with a series of DNA targets. The fastest hybridization is observed for targets folded into parallel morphologies.     

Rainbows and glories in the angular scattering of the state-to-state F + H2 reaction at E(trans)=0.04088 eV

State-of-the-art differential cross sections (DCSs) have been reported by Wang et al. [Proc. Nat. Acad. Sci. (U.S.), 2008, 105, 6227] for the state-to-state F + H(2)→ FH + H reaction using fully quantum-state-selected crossed molecular beams. We theoretically analyze the angular scattering of this reaction, in order to quantitatively understand the physical content of structure in the DCSs. Three transitions are studied, v(i)=0, j(i)=0, m(i)=0 → v(f)=3, j(f)=0, 1, 2, m(f)=0 at a translational energy of 0.04088 eV, where v, j, m are the vibrational, rotational and helicity quantum numbers respectively for the initial and final states. The input to our analyses consists of accurate quantum scattering (S) matrix elements computed for the Fu-Xu-Zhang potential energy surface, as used by Wang et al. in a computational simulation of their experimental DCSs. We prove that the pronounced peak at forward angles observed in the experimental and simulated DCSs for all three transitions is a glory. At larger angles, it is demonstrated that the 000 → 300 and 000 → 310 DCSs both possess a broad farside rainbow, which is accompanied by diffraction oscillations. We confirm the conjecture of Wang et al. that these diffraction oscillations arise from nearside-farside (NF) interference. We find that the reaction is N dominant for all three transitions. The theoretical techniques used to analyze the angular scattering include uniform semiclassical theories of glory and of rainbow scattering. We also make the first application of a semiclassical formula that is uniform for both glory + rainbow scattering. In addition, structure in the DCSs is analyzed using NF theory and local angular momentum theory, in both cases with three resummations of the partial wave series for the scattering amplitude. We make the first explicit application of the Thiele rational interpolation formula to extract the position and residue of the leading Regge pole from a set of S matrix elements, thereby making contact with complex angular momentum theories of DCSs, which interpret the angular scattering in terms of Regge resonances. Our calculations complement the exit-valley vibrationally-adiabatic analysis of Wang et al.     

Semiclassical theory of molecular collisions: Real and complex-valued classical trajectories for collinear atom Morse oscillator collisions

Real and complex-valued classical trajectories have been calculated for the collinear collision of an atom with a Morse oscillator. They are used in three semiclassical approximations for the transition probability: a Bessel uniform approximation, an Airy uniform approximation and a primitive semiclassical approximation. Comparison with exact quantum results shows that the Bessel uniform approximation is accurate even for near elastic collisions where the Airy and primitive approximations break down. The Airy and Bessel approximations agree quite closely for inelastic collisions however. The primitive semiclassical approximation is less accurate than either the Airy or Bessel approximation.     

Evaluation of multidimensional canonical integrals in semiclassical collision theory

The evaluation of the multidimensional canonical integrals that occur in the uniform asymptotic representations of the S matrix in the semiclassical theory of inelastic and reactive molecular collisions is considered. For the non-separable two-dimensional canonical integral considered earlier, an exact series expansion is obtained with the help of convergence factors. This method avoids the complex variable techniques used previously. The uniform asymptotic formulae derived by Miller and Marcus are discussed, and compared with the approach adopted in the present paper.     

Theory of forward glory scattering for chemical reactions: New derivation of a uniform semiclassical formula for the scattering amplitude

The theory of forward glory scattering is investigated for a state-to-state chemical reaction whose scattering amplitude can be written as a Legendre partial wave series. Legendre series occur in the exact quantum theory of reactive scattering when the initial and final helicity quantum numbers are zero, as well as in many approximate theories of chemical reactions. The starting point for the semiclassical theory is a two-dimensional integral representation for the scattering amplitude. A uniform semiclassical approximation is derived that is valid for angles both on, and off, the axial caustic associated with the glory. The derivation is the first application to a concrete problem in molecular physics of a method outlined by J. N. L. Connor and H. R. Mayne in 1979 for the uniform semiclassical evaluation of multidimensional integrals. The approach exploits the theory of singularities of differential mappings. The key step in the derivation is an exact one-to-one change of variables in the neighbourhood of the stationary phase points that locally reduce the two-dimensional phase of the integrand to a non-polynomial canonical form. The derivation complements a different semiclassical glory analysis reported in a companion paper.     

Use of a birefringent filter for tuning a synchronously pumped optical parametric oscillator

Design considerations are presented for birefringent filters suitable for use as tuning elements in synchronously pumped optical parametric oscillators. A particular design aspect that is important, since typical gains are rather high, is the adequate suppression of subsidiary transmission maxima, in order to maximize the tuning range. Results are presented on the performance of a picosecond synchronously pumped optical parametric oscillator based on periodically poled lithium niobate with an appropriately designed four-plate birefringent filter. PACS 42.65.Yj; 42.72.Ai     

The addition of cuprates to vinyltriphenylphosphonium bromide: a synthesis of 1,5-disubstituted Z,Z-penta-1,4-dienes

It is shown that alkyl, alkenyl and aryl cuprates add to vinyl- triphenylphosphonium bromide to provide phosphoranes and that the Z:E ratio of their Wittig condensation products with benzaldehyde and hexanal are strongly influenced by the addition of hexamethyl- phosphoramide. This reaction is applied to the one-pot synthesis of the title compound.     

Effect of container material, storage time and temperature on determinations of cadmium levels in human urine

The effect of container material (polyethylene, polypropylene, polystyrene, borosilicate glass and flint glass), storage time (0-86 days), and temperature (22 degrees and 4 degrees ) on the cadmium content found by graphite-furnace atomic-absorption spectrometry for spiked and unspiked urine samples has been studied. No loss of cadmium occurred for at least 10 and 28 days when unspiked and spiked samples respectively, were stored in polyethylene containers at 22 degrees . For storage up to 3-4 days at 22 degrees , polypropylene, polystyrene, borosilicate glass and flint glass containers were also found suitable. Storage at 4 degrees was not effective in preventing loss of cadmium.     

Molybdenum carbonyl complexes of binucleating pyridine-based ligands

Reaction of [Mo(CO)₄(diene)] with 4,4′-bipyridine (44′B), trans-1,2-bis(2-pyridyl)ethene (2-bpe) and trans-1,2-bis(4-pyridyl)-ethene (4-bpe) gives polymeric [Mo(CO)₄(44′B)]_n, mononuclear cis-[Mo(CO)₄(2-bpe)₂] and binuclear [Mo(CO)₄(4-bpe)]₂ respectively. Reaction of the same ligands with [Mo(CO)₄(bpy)] (bpy is 2,2′-bipyridine) produces the bridged binuclear complexes [{Mo(CO)₃(bpy)}₂(44′B)] and [{Mo(CO)₃(bpy)}₂(4-bpe)]. Products are characterised by microanalysis and spectroscopy (IR, ¹H NMR, UV/vis). Reduction of [{Mo(CO)₃(bpy)}₂(44′B)] produces an anion in which the unpaired electron is localised on the chelating bpy ligand.