Ru(TAP)2(dppz)]2+: a DNA intercalating complex, which luminesces strongly in water and undergoes photo-induced proton-coupled electron transfer with guanosine-5'-monophosphate

The lowest excited state of [Ru(TAP)2(dppz)]2+ (TAP = 1,4,5,8-tetraazaphenanthrene, dppz = dipyrido[3,2-a:2',3'-c]phenazine) 1 is strongly luminescent, even in water, and very oxidizing. Therefore it is able to oxidise not only guanosine-5'-monophosphate (GMP), as demonstrated by laser flash photolysis, but also guanine-containing polynucleotides such as calf thymus DNA and [poly(dG-dC)]2. The luminescence quenching was found to be faster in H2O than in D2O, as is the back reaction, indicating that both processes probably proceed by proton-coupled electron transfer. These properties, that are controlled by the triplet MLCT state in which the charge has been transferred from the Ru to a TAP ligand, contrast with those of the well known [Ru(phen)2(dppz)]2+ 2.     

Quantification and evaluation of Joule heating in on-chip capillary electrophoresis

We present the use of a novel, picoliter volume interferometer to measure, for the first time, the extent of Joule heating in chip-scale capillary electrophoresis (CE). The simple optical configuration for the on-chip interferometric backscatter detector (OCIBD) consists of an unfocused laser, an unaltered silica chip with a half-cylinder channel and a photodetector. Using OCIBD for millidegree-level noninvasive thermometry, temperature changes associated with Joule heating (2.81 degrees C above ambient) in on-chip CE have been observed in 90 microm wide and 40 microm deep separation channels. The temporal response of Joule heating in isotropically etched channels was exponential, with it taking an excess of 2.7 s to reach equilibrium. Buffer viscosity changes have also been derived from empirical on-chip thermometry data, allowing for the determination of diffusion coefficients for solutes when separated in heated buffers. In addition, OCIBD has allowed the reduction in separation efficiency to be estimated in the absence of laminar flow and due to increased molecular diffusion and lower buffer viscosity. A 7% reduction in separation efficiency was determined for a high current drawing buffer such as Tris-boric acid under an applied field of just 400 V/cm. Results indicate that heating effects in on-chip CE have been underestimated and there is a need to readdress the theoretical model.     

Sol-gel-derived micron scale optical fibers for chemical sensing

We report for the first time on the preparation of organically-doped room temperature processed sol-gel-derived micron scale optical fibers as platforms for chemical- and bio-sensors. Micron scale optical fibers are drawn from fluorescent dye-doped tetraethoxysilane (TEOS)-derived sol-gel solution processed under ambient conditions. Such a simple methodology to entrap organic and even bioactive species within the optical fiber offers many advantages over more conventional ways of immobilizing organic probes for the development of optical sensors. Specifically, we report on the photophysical properties of fluorescein (a pH sensitive fluorescent dye) and rhodamine 6G (R6G; laser dye) entrapped within sol-gel-derived optical fibers. We present the preliminary results on the viability of such doped optical fibers for chemical sensing. Our results demonstrate that a fluorescein-doped sol-gel-derived optical fiber responds to ammonia and acid vapors with a response time of 1–2 seconds.     

Dendrimeric organochalcogen catalysts for the activation of hydrogen peroxide: origins of the "dendrimer effect" with catalysts terminating in phenylseleno groups

Several scenarios were evaluated to explain the large "dendrimer effect" observed in the bromination of cyclohexene with H(2)O(2) and NaBr catalyzed by the addition of Frechét-type dendrimers terminating in -O(CH(2))(3)SePh groups. Although phenylseleninic acid was an efficient catalyst for the oxidation of NaBr with H(2)O(2), first-order rate constants for the selenoxide elimination were too small to produce PhSeO(2)H at a rate sufficient to explain the rates of catalysis and no dendrimer effect was observed in the rates of selenoxide elimination. An induction period was observed using 1-SePh as a catalyst for the oxidation of Br(-) with H(2)O(2). The addition of preformed selenoxide 1-Se(=O)Ph gave immediate catalysis with no induction period. However, rates of oxidation of the selenides with H(2)O(2) under homogeneous or biphasic conditions or with t-BuOOH under homogeneous conditions were too slow to account for the rates of catalysis, and no dendrimer effect was observed in the rates of oxidation. The primary oxidant for converting selenides to selenoxides was "Br(+)" produced initially by the uncatalyzed background reaction of H(2)O(2) with NaBr and then produced catalytically following formation of selenoxide groups. Autocatalysis is observed, and the rate of oxidation increases with the number of SePh groups. Autocatalysis is the source of the large dendrimer effect observed with the SePh series of catalysts.     

Regiospecific photoisomerization of fluorinated (E,E)-1,4-diphenyl-1,3-butadienes

Photoisomerization of five fluorinated E,E-1-(R-phenyl)-4-phenyl-1,3-butadienes in solution (R = 1: p-monofluoro, 2: m,m′-difluoro, 3: m,m′,p-trifluoro, 4: o,o′,m,m′-tetrafluoro, 5: o,o′,m,m′,p-pentafluoro) was investigated via direct irradiation. Our results indicated that cis-trans photoisomerization of the fluorinated 1,4-diphenyl-1,3-butadienes in the excited singlet state took place exclusively at the CC bonds closer to the fluorine substituents.     

PHOTOLYSIS OF PHOSPHODIESTER BONDS IN PLASMID DNA BY HIGH INTENSITY UV LASER IRRADIATION

Abstract— The cleavage of phosphodiester bonds in DNA exposed to high intensity UV laser pulses in aerated aqueous solution has been investigated using a krypton fluoride excimer laser (248 nm) and bacterial plasmid DNA. The dependence of strand breakage on fluence and intensity has been studied in detail and shows that the process is non-linear with respect to intensity. The relationship between the quantum yield for strand breakage and intensity shows that the strand breakage reaction involves two-photon excitation of DNA bases. The quantum yield rises with intensity from a lower value of 7 times 10^-5 until a maximum value of 4.5 times 10^-4 is attained at intensities of 10¹¹ W m^-2 and above. This value is approximately fifty-fold higher than the quantum yield for strand breakage induced by exposure to low density UV irradiation (254 nm, 12 W m^-2). DNA sequencing experiments have shown that strand breakage occurs by the specific cleavage of the phosphodiester bond which lies immediately 3' to guanine residues in the DNA, leaving some alkali-labile remnant attached to the terminal phosphate. A mechanism for DNA strand breakage which involves the generation of guanine radical cations is proposed.     

Enantiomeric resolution of 2-aryl propionic esters with hyperthermophilic and mesophilic esterases: contrasting thermodynamic mechanisms

The enantiomeric resolution of 2-aryl propionic esters by hyperthermophilic and mesophilic esterases was found to be governed by contrasting thermodynamic mechanisms. Entropic contributions predominated for mesophilic esterases from Candida rugosa and Rhizomucor miehei, while enthalpic forces controlled this resolution by the esterase from the extremely thermoacidophilic archaeon, Sulfolobus solfataricus P1. This disparity in thermodynamic mechanism can be attributed to the differences in conformational flexibility of mesophilic and thermophilic enzymes as they relate to the temperature range (4-70 degrees C) examined.     

Protofilaments, filaments, ribbons, and fibrils from peptidomimetic self-assembly: implications for amyloid fibril formation and materials science

Deciphering the mechanism(s) of β-sheet mediated self-assembly is essential for understanding amyloid fibril formation and for the fabrication of polypeptide materials. Herein, we report a simple peptidomimetic that self-assembles into polymorphic β-sheet quaternary structures including protofilaments, filaments, fibrils, and ribbons that are reminiscent of the highly ordered structures displayed by the amyloidogenic peptides Aβ, calcitonin, and amylin. The distribution of quaternary structures can be controlled by and in some cases specified by manipulating the pH, buffer composition, and the ionic strength. The ability to control β-sheet-mediated assembly takes advantage of quaternary structure dependent pK(a) perturbations. Biophysical methods including analytical ultracentrifugation studies as well as far-UV circular dichroism and FT-IR spectroscopy demonstrate that linked secondary and quaternary structural changes mediate peptidomimetic self-assembly. Electron and atomic force microscopy reveal that peptidomimetic assembly involves numerous quaternary structural intermediates that appear to self-assemble in a convergent fashion affording quaternary structures of increasing complexity. The ability to control the assembly pathway(s) and the final quaternary structure(s) afforded should prove to be particularly useful in deciphering the quaternary structural requirements for amyloid fibril formation and for the construction of noncovalent macromolecular structures.     

Synthesis of porritoxin

A total synthesis following the sequence in Scheme 1 confirms that porritoxin possesses revised structure 3, not the originally assigned 1. A key reaction was the use of iron pentacarbonyl to formylate an aryllithium when DMF and methyl formate proved insufficiently reactive.     

On the direct observation of the gas-dynamics of laser-pulse sputtering of polymers

We bring together a wide range of ideas relating to the gas-dynamic effects that are now recognized to play a leading role in laser-pulse sputtering. The ideas are grouped according to three basic models. (a) In the effusion model one deals with particles which are released from a target surface, form a Knudsen layer (KL), and then enter an unsteady adiabatic expansion (UAE). When the release terminates at time t=_r there is an abrupt change at the surface from positive to zero flow velocity, which means that particles moving towards the surface are reflected. The flow breaks up into three regions and analytical solutions exist for all aspects of this flow. (b) In the recondensation model the comportment of the target is initially like that of the effusion model but when the release terminates at t=_r the change at the surface is from positive to negative flow velocity, meaning that particles which move towards the surface recondense. Only numerical solutions presently exist (due to Sibold and Urbassek) but they are sufficient to show that the flow breaks up into two (not three) regions. (c) The outflow model could be described as the escape of gas from a finite reservoir, a well-known problem since it describes some aspects of guns. In its application to laser sputtering it is assumed that bond-breakage occurs rapidly over a characteristic depth and the resulting gas-like particles then flow out in a UAE; there is no formal KL.For part II, in which explicit photographs of laser-sputtered particles are analyzed, see [1]