High-temperature shock tube measurements of methyl radical decomposition

We have studied the two-channel thermal decomposition of methyl radicals in argon, involving the reactions CH3 + Ar --> CH + H2 + Ar (1a) and CH3 + Ar --> CH2 + H + Ar (1b), in shock tube experiments over the 2253-3527 K temperature range, at pressures between 0.7 and 4.2 atm. CH was monitored by continuous-wave, narrow-line-width laser absorption at 431.1311 nm. The collision-broadening coefficient for CH in argon, 2gamma(CH-Ar), was measured via repeated single-frequency experiments in the ethane pyrolysis system behind reflected shock waves. The measured 2gamma(CH-Ar) value and updated spectroscopic and molecular parameters were used to calculate the CH absorption coefficient at 431.1311 nm (23194.80 cm(-1)), which was then used to convert raw traces of fractional transmission to quantitative CH concentration time histories in the methyl decomposition experiments. The rate coefficient of reaction 1a was measured by monitoring CH radicals generated upon shock-heating highly dilute mixtures of ethane, C2H6, or methyl iodide, CH3I, in an argon bath. A detailed chemical kinetic mechanism was used to model the measured CH time histories. Within experimental uncertainty and scatter, no pressure dependence could be discerned in the rate coefficient of reaction 1a in the 0.7-4.2 atm pressure range. A least-squares, two-parameter fit of the current measurements, applicable between 2706 and 3527 K, gives k(1a) (cm(3) mol(-1) s(-1)) = 3.09 x 1015 exp[-40700/T (K)]. The rate coefficient of reaction 1b was determined by shock-heating dilute mixtures of C2H6 or CH3I and excess O2 in argon. During the course of reaction, OH radicals were monitored using the well-characterized R(1)(5) line of the OH A-X (0,0) band at 306.6871 nm (32606.52 cm(-1)). H atoms generated via reaction 1b rapidly react with O2, which is present in excess, forming OH. The OH traces are primarily sensitive to reaction 1b, reaction 9 (H + O2 --> OH + O) and reaction 10 (CH3 + O2 --> products), where the rate coefficients of reactions 9 and 10 are relatively well-established. No pressure dependence could be discerned for reaction 1b between 1.1 and 3.9 atm. A two-parameter, least-squares fit of the current data, valid over the 2253-2975 K temperature range, yields the rate expression k(1b) (cm(3) mol(-1) s(-1)) = 2.24 x 10(15) exp[-41600/T (K)]. Theoretical calculations carried out using a master equation/RRKM analysis fit the measurements reasonably well.     

Energy dependence of the roaming atom pathway in formaldehyde decomposition

Recently, a new mechanism of formaldehyde decomposition leading to molecular products CO and H(2) has been discovered, termed the "roaming atom" mechanism. Formaldehyde decomposition from the ground state via the roaming atom mechanism leads to rotationally cold CO and vibrationally hot H(2), whereas formaldehyde decomposition through the conventional molecular channel leads to rotationally hot CO and vibrationally cold H(2). This discovery has shown that it is possible to have multiple pathways for a reaction leading to the same products with dramatically different product state distributions. Detailed investigations of the dynamics of these two pathways have been reported recently. This paper focuses on an investigation of the energy dependence of the roaming atom mechanism up to 1500 cm(-1) above the threshold of the radical channel, H(2)CO-->H+HCO. The influence of excitation energy on the roaming atom and molecular elimination pathways is reported, and the branching fraction between the roaming atom channel and molecular channel is obtained using high-resolution dc slice imaging and photofragment excitation spectroscopy. From the branching fractions and the reaction rates of the radical channel, the overall competition between all three dissociation channels is estimated. These results are compared with recent quasiclassical trajectory calculations on a global H(2)CO potential energy surface.     

In situ fabrication of macroporous polymer networks within microfluidic devices by living radical photopolymerization and leaching

Novel fabrication techniques and polymer systems are being explored to enable mass production of low cost microfluidic devices. In this contribution we discuss a new fabrication scheme for making microfluidic devices containing porous polymer components in situ. Contact lithography, a living radical photopolymer (LRPP) system and salt leaching were used to fabricate multilayer microfluidic devices rapidly with various channel geometries and covalently attached porous polymer plugs made of various photopolymerizable substrates. LRPP systems offer the advantages of covalent attachment of microfluidic device layers and facile surface modification via grafting. Several applications of the porous plugs are also explored, including a static mixer, a high surface area-to-volume reactor and a rapidly responding hydrogel valve. Quantitative and qualitative data show an increase in mixing of a fluorescein and a water stream for channels containing porous plugs relative to channels with no porous plugs. Confocal laser scanning microscopy images demonstrate the ability to graft a functional material onto porous plug surfaces. A reaction was carried out on the grafted pore surfaces, which resulted in fluorescent labelling of the grafted material throughout the pores of the plug. Homogenous fluorescence throughout the depth of the porous plug and along pore surfaces indicated that the porous plugs were surface modified by grafting and that reactions can be carried out on the pore surfaces. Finally, porous hydrogel valves were fabricated which swelled in response to contact with various pH solutions. Results indicate that a porous hydrogel valve will swell and close more rapidly than other valve geometries made with the same polymer formulation. The LRPP-salt leaching method provides a means for rapidly incorporating porous polymer components into microfluidic devices, which can be utilized for a variety of pertinent applications upon appropriate selection of porous plug materials and surface treatments.     

Temperature dependent equilibrium native to unfolded protein dynamics and properties observed with IR absorption and 2D IR vibrational echo experiments

Dynamic and structural properties of carbonmonoxy (CO)-coordinated cytochrome c(552) from Hydrogenobacter thermophilus (Ht-M61A) at different temperatures under thermal equilibrium conditions were studied with infrared absorption spectroscopy and ultrafast two-dimensional infrared (2D IR) vibrational echo experiments using the heme-bound CO as the vibrational probe. Depending on the temperature, the stretching mode of CO shows two distinct bands corresponding to the native and unfolded proteins. As the temperature is increased from low temperature, a new absorption band for the unfolded protein grows in and the native band decreases in amplitude. Both the temperature-dependent circular dichroism and the IR absorption area ratio R(A)(T), defined as the ratio of the area under the unfolded band to the sum of the areas of the native and unfolded bands, suggest a two-state transition from the native to the unfolded protein. However, it is found that the absorption spectrum of the unfolded protein increases its inhomogeneous line width and the center frequency shifts as the temperature is increased. The changes in line width and center frequency demonstrate that the unfolding does not follow simple two-state behavior. The temperature-dependent 2D IR vibrational echo experiments show that the fast dynamics of the native protein are virtually temperature independent. In contrast, the fast dynamics of the unfolded protein are slower than those of the native protein, and the unfolded protein fast dynamics and at least a portion of the slower dynamics of the unfolded protein change significantly, becoming faster as the temperature is raised. The temperature dependence of the absorption spectrum and the changes in dynamics measured with the 2D IR experiments confirm that the unfolded ensemble of conformers continuously changes its nature as unfolding proceeds, in contrast to the native state, which displays a temperature-independent distribution of structures.     

Native and unfolded cytochrome c--comparison of dynamics using 2D-IR vibrational echo spectroscopy

Unfolded vs native CO-coordinated horse heart cytochrome c (h-cyt c) and a heme axial methionine mutant cyt c552 from Hydrogenobacter thermophilus ( Ht-M61A) are studied by IR absorption spectroscopy and ultrafast 2D-IR vibrational echo spectroscopy of the CO stretching mode. The unfolding is induced by guanidinium hydrochloride (GuHCl). The CO IR absorption spectra for both h-cyt c and Ht-M61A shift to the red as the GuHCl concentration is increased through the concentration region over which unfolding occurs. The spectra for the unfolded state are substantially broader than the spectra for the native proteins. A plot of the CO peak position vs GuHCl concentration produces a sigmoidal curve that overlays the concentration-dependent circular dichroism (CD) data of the CO-coordinated forms of both Ht-M61A and h-cyt c within experimental error. The coincidence of the CO peak shift curve with the CD curves demonstrates that the CO vibrational frequency is sensitive to the structural changes induced by the denaturant. 2D-IR vibrational echo experiments are performed on native Ht-M61A and on the protein in low- and high-concentration GuHCl solutions. The 2D-IR vibrational echo is sensitive to the global protein structural dynamics on time scales from subpicosecond to greater than 100 ps through the change in the shape of the 2D spectrum with time (spectral diffusion). At the high GuHCl concentration (5.1 M), at which Ht-M61A is essentially fully denatured as judged by CD, a very large reduction in dynamics is observed compared to the native protein within the approximately 100 ps time window of the experiment. The results suggest the denatured protein may be in a glassy-like state involving hydrophobic collapse around the heme.     

Formaldehyde photodissociation: dependence on total angular momentum and rotational alignment of the CO product

Quasiclassical trajectory calculations are reported to investigate the effects of rotational excitation of formaldehyde on the branching ratios of the fragmentation products, H2+CO and H+HCO. The results of tens of thousands of trajectories show that increased rotational excitation causes suppression of the radical channel and enhancement of the molecular channel. Decomposing the molecular channel into "direct" and "roaming" channels shows that increased rotation switches from suppressing to enhancing the roaming products across our chosen energy range. However, decomposition into these pathways is difficult because the difference between them does not appear to have a distinct boundary. A vector correlation investigation of the CO rotation shows different characteristics in the roaming versus direct channels and this difference is a potentially useful signature of the roaming mechanism, as first speculated by Kable and Houston in their experimental study of photodissociation of acetaldehyde [P. L. Houston and S. H. Kable, Proc. Nat. Acad. Sci. 103, 16079 (2006)].     

Zero-point energy constraint in quasi-classical trajectory calculations

A method to constrain the zero-point energy in quasi-classical trajectory calculations is proposed and applied to the Henon-Heiles system. The main idea of this method is to smoothly eliminate the coupling terms in the Hamiltonian as the energy of any mode falls below a specified value.     

Discovery of fluorescent cyanopyridine and deazalumazine dyes using small molecule macroarrays

[structure: see text] Small molecule macroarrays of cyanopyridines and deazalumazines were generated in high purities via spatially addressed synthesis on planar cellulose supports. Examination of the spectral properties of the heterocycles both on and off of the planar support revealed a set of promising new fluorescent dyes that exhibit high quantum yields, low pH dependence, and high sensitivity to solvent polarity.     

An effervescent reaction micropump for portable microfluidic systems

A water-activated, effervescent reaction was used to transport fluid in a controllable manner on a portable microfluidic device. The reaction between sodium bicarbonate and an organic acid, tartaric acid and/or benzoic acid, was modeled to analyze methods of controlling the generation of carbon-dioxide gas for the purposes of pumping fluids. Integration and testing of the effervescent reaction pump in a microfluidic device was made possible by using elastomeric polymers as both photopolymerizable septa and removable lids. These materials combined to enable facile access to otherwise gas-tight devices. Based on theoretical predictions for 0.33 mg of sodium bicarbonate and a stoichiometric amount of organic acid, the pumping flow rate could be varied from 0.01 microL s(-1) to 70 microL s(-1). The flow rate is controlled by adjusting any or all of the particle size of the least soluble reactant, the amount of reactants used, and the type of organic acid selected. The tartaric acid systems rapidly produce carbon dioxide; however, the gas generation rates dramatically decrease over the course of the reaction. In contrast, carbon dioxide production rate in the benzoic acid systems is lower and nearly constant for several minutes. Water activation and direct placement on a microfluidic device are key features of this micropump, which is therefore useful for portable microfluidic applications.