Excited-State Dynamics during Primary C-I Homolysis in Acetyl Iodide Revealed by Ultrafast Core-Level Spectroscopy.

In typical carbonyl-containing molecules, bond dissociation events follow initial excitation to nπC═O* states. However, in acetyl iodide, the iodine atom gives rise to electronic states with mixed nπC═O* and nσC-I* character, leading to complex excited-state dynamics, ultimately resulting in dissociation. Using ultrafast extreme ultraviolet (XUV) transient absorption spectroscopy and quantum chemical calculations, we present an investigation of the primary photodissociation dynamics of acetyl iodide via time-resolved spectroscopy of core-to-valence transitions of the I atom after 266 nm excitation. The probed I 4d-to-valence transitions show features that evolve on sub-100-fs time scales, reporting on excited-state wavepacket evolution during dissociation. These features subsequently evolve to yield spectral signatures corresponding to free iodine atoms in their spin-orbit ground and excited states with a branching ratio of 1.1:1 following dissociation of the C-I bond. Calculations of the valence excitation spectrum via equation-of-motion coupled cluster with single and double substitutions (EOM-CCSD) show that initial excited states are of spin-mixed character. From the initially pumped spin-mixed state, we use a combination of time-dependent density functional theory (TDDFT)-driven nonadiabatic ab initio molecular dynamics and EOM-CCSD calculations of the N4,5 edge to reveal a sharp inflection point in the transient XUV signal that corresponds to rapid C-I homolysis. By examining the molecular orbitals involved in the core-level excitations at and around this inflection point, we are able to piece together a detailed picture of C-I bond photolysis in which d → σ* transitions give way to d → p excitations as the bond dissociates. We also report theoretical predictions of short-lived, weak 4d → 5d transitions in acetyl iodide, validated by weak bleaching in the experimental transient XUV spectra. This joint experimental-theoretical effort has thus unraveled the detailed electronic structure and dynamics of a strongly spin-orbit coupled system.

The Identity and Chemistry of C7H7 Radicals Observed during Soot Formation.

We used aerosol mass spectrometry coupled with tunable synchrotron photoionization to measure radical and closed-shell species associated with particle formation in premixed flames and during pyrolysis of butane, ethylene, and methane. We analyzed photoionization (PI) spectra for the C7H7 radical to identify the isomers present during particle formation. For the combustion and pyrolysis of all three fuels, the PI spectra can be fit reasonably well with contributions from four radical isomers: benzyl, tropyl, vinylcyclopentadienyl, and o-tolyl. Although there are significant experimental uncertainties in the isomeric speciation of C7H7, the results clearly demonstrate that the isomeric composition of C7H7 strongly depends on the combustion or pyrolysis conditions and the fuel or precursors. Fits to the PI spectra using reference curves for these isomers suggest that all of these isomers may contribute to m/z 91 in butane and methane flames, but only benzyl and vinylcyclopentadienyl contribute to the C7H7 isomer signal in the ethylene flame. Only tropyl and benzyl appear to play a role during pyrolytic particle formation from ethylene, and only tropyl, vinylcyclopentadienyl, and o-tolyl appear to participate during particle formation from butane pyrolysis. There also seems to be a contribution from an isomer with an ionization energy below 7.5 eV for the flames but not for the pyrolysis conditions. Kinetic models with updated and new reactions and rate coefficients for the C7H7 reaction network predict benzyl, tropyl, vinylcyclopentadienyl, and o-tolyl to be the primary C7H7 isomers and predict negligible contributions from other C7H7 isomers. These updated models provide better agreement with the measurements than the original versions of the models but, nonetheless, underpredict the relative concentrations of tropyl, vinylcyclopentadienyl, and o-tolyl in both flames and pyrolysis and overpredict benzyl in pyrolysis. Our results suggest that there are additional important formation pathways for the vinylcyclopentadienyl, tropyl, and o-tolyl radicals and/or loss pathways for the benzyl radical that are currently unaccounted for in the present models.

Distinguishing Gas-Phase and Nanoparticle Contributions to Small-Angle X-ray Scattering in Reacting Aerosol Flows.

We have developed a strategy for distinguishing between small-angle X-ray scattering (SAXS) from gas-phase species and newly formed nanoparticles in mixed gas- and particle-phase reacting flows. This methodology explicitly accounts for temperature-dependent scattering from gases. We measured SAXS in situ in a sooting linear laminar partially premixed co-flow ethylene/air diffusion flame. The scattering signal demonstrates a downward curvature as a function of the momentum transfer (q) at q values of 0.2-0.57 Å-1. The q-dependent curvature is consistent with the Debye equation and the independent-atom model for gas-phase scattering. This behavior can also be modeled using the Guinier approximation and could be characterized as a Guinier knee for gas-phase scattering. The Guinier functional form can be fit to the scattering signal in this q range without a priori knowledge of the gas-phase composition, enabling estimation of the gas-phase contribution to the scattering signal while accounting for changes in the gas-phase composition and temperature. We coupled the SAXS measurements with in situ temperature measurements using coherent anti-Stokes Raman spectroscopy. This approach to characterizing the gas-phase SAXS signal provides a physical basis for distinguishing among the contributions to the scattering signal from the instrument function, flame gases, and nanoparticles. The results are particularly important for the analysis of the SAXS signal in the q range associated with particles in the size range of 1-6 nm.

Ultrafast infrared transient absorption spectroscopy of gas-phase Ni(CO)4 photodissociation at 261 nm.

We employ ultrafast mid-infrared transient absorption spectroscopy to probe the rapid loss of carbonyl ligands from gas-phase nickel tetracarbonyl following ultraviolet photoexcitation at 261 nm. Here, nickel tetracarbonyl undergoes prompt dissociation to produce nickel tricarbonyl in a singlet excited state; this electronically excited tricarbonyl loses another CO group over tens of picoseconds. Our results also suggest the presence of a parallel, concerted dissociation mechanism to produce nickel dicarbonyl in a triplet excited state, which likely dissociates to nickel monocarbonyl. Mechanisms for the formation of these photoproducts in multiple electronic excited states are theoretically predicted with one-dimensional cuts through the potential energy surfaces and computation of spin-orbit coupling constants using equation of motion coupled cluster methods (EOM-CC) and coupled cluster theory with single and double excitations (CCSD). Bond dissociation energies are calculated with CCSD, and anharmonic frequencies of ground and excited state species are computed using density functional theory (DFT) and time-dependent density functional theory (TD-DFT).

Ultraviolet photodissociation of gas-phase iron pentacarbonyl probed with ultrafast infrared spectroscopy.

It is well known that ultraviolet photoexcitation of iron pentacarbonyl results in rapid loss of carbonyl ligands leading to the formation of coordinatively unsaturated iron carbonyl compounds. We employ ultrafast mid-infrared transient absorption spectroscopy to probe the photodissociation dynamics of gas-phase iron pentacarbonyl following ultraviolet excitation at 265 and 199 nm. After photoexcitation at 265 nm, our results show evidence for sequential dissociation of iron pentacarbonyl to form iron tricarbonyl via a short-lived iron tetracarbonyl intermediate. Photodissociation at 199 nm results in the prompt production of Fe(CO)3 within 0.25 ps via several energetically accessible pathways. An additional 15 ps time constant extracted from the data is tentatively assigned to intersystem crossing to the triplet manifold of iron tricarbonyl or iron dicarbonyl. Mechanisms for formation of iron tetracarbonyl, iron tricarbonyl, and iron dicarbonyl are proposed and theoretically validated with one-dimensional cuts through the potential energy surface as well as bond dissociation energies. Ground state calculations are computed at the CCSD(T) level of theory and excited states are computed with EOM-EE-CCSD(dT).

The Identification of Cable Bacteria Attached to the Anode of a Benthic Microbial Fuel Cell: Evidence of Long Distance Extracellular Electron Transport to Electrodes.

Multicellular, filamentous, sulfur-oxidizing bacteria, known as cable bacteria, were discovered attached to fibers of a carbon brush electrode serving as an anode of a benthic microbial fuel cell (BMFC). The BMFC had been operated in a temperate estuarine environment for over a year before collecting anode samples for scanning electron microscopy and phylogenetic analyses. Individual filaments were attached by single terminus cells with networks of pilus-like nano-filaments radiating out from these cells, across the anode fiber surface, and between adjacent attachment locations. Current harvesting by the BMFC poised the anode at potentials of ~170-250 mV vs. SHE, and these surface potentials appear to have allowed the cable bacteria to use the anode as an electron acceptor in a completely anaerobic environment. A combination of catalyzed reporter deposition fluorescent in situ hybridization (CARD-FISH) and 16S rRNA gene sequence analysis confirmed the phylogeny of the cable bacteria and showed that filaments often occurred in bundles and in close association with members of the genera Desulfuromonas. However, the Desulfobulbaceae Operational Taxonomic Units (OTUs) from the 16S sequencing did not cluster closely with other putative cable bacteria sequences suggesting that the taxonomic delineation of cable bacteria is far from complete.

Critical Assessment of Photoionization Efficiency Measurements for Characterization of Soot-Precursor Species.

We present a critical evaluation of photoionization efficiency (PIE) measurements coupled with aerosol mass spectrometry for the identification of condensed soot-precursor species extracted from a premixed atmospheric-pressure ethylene/oxygen/nitrogen flame. Definitive identification of isomers by any means is complicated by the large number of potential isomers at masses likely to comprise particles at flame temperatures. This problem is compounded using PIE measurements by the similarity in ionization energies and PIE-curve shapes among many of these isomers. Nevertheless, PIE analysis can provide important chemical information. For example, our PIE curves show that neither pyrene nor fluoranthene alone can describe the signal from C16H10 isomers and that coronene alone cannot describe the PIE signal from C24H12 species. A linear combination of the reference PIE curves for pyrene and fluoranthene yields good agreement with flame-PIE curves measured at 202 u, which is consistent with pyrene and fluoranthene being the two major C16H10 isomers in the flame samples, but does not provide definite proof. The suggested ratio between fluoranthene and pyrene depends on the sampling conditions. We calculated the values of the adiabatic-ionization energy (AIE) of 24 C16H10 isomers. Despite the small number of isomers considered, the calculations show that the differences in AIEs between several of the isomers can be smaller than the average thermal energy at room temperature. The calculations also show that PIE analysis can sometimes be used to separate hydrocarbon species into those that contain mainly aromatic rings and those that contain significant aliphatic content for species sizes investigated in this study. Our calculations suggest an inverse relationship between AIE and the number of aromatic rings. We have demonstrated that further characterization of precursors can be facilitated by measurements that test species volatility.

Photoionization Efficiencies of Five Polycyclic Aromatic Hydrocarbons.

We have measured photoionization-efficiency curves for pyrene, fluoranthene, chrysene, perylene, and coronene in the photon energy range of 7.5-10.2 eV and derived their photoionization cross-section curves in this energy range. All measurements were performed using tunable vacuum ultraviolet (VUV) radiation generated at the Advanced Light Source synchrotron at Lawrence Berkeley National Laboratory. The VUV radiation was used for photoionization, and detection was performed using a time-of-flight mass spectrometer. We measured the photoionization efficiency of 2,5-dimethylfuran simultaneously with those of pyrene, fluoranthene, chrysene, perylene, and coronene to obtain references of the photon flux during each measurement from the known photoionization cross-section curve of 2,5-dimethylfuran.

Formation and emission of large furans and oxygenated hydrocarbons from flames.

Many oxygenated hydrocarbon species formed during combustion, such as furans, are highly toxic and detrimental to human health and the environment. These species may also increase the hygroscopicity of soot and strongly influence the effects of soot on regional and global climate. However, large furans and associated oxygenated species have not previously been observed in flames, and their formation mechanism and interplay with polycyclic aromatic hydrocarbons (PAHs) are poorly understood. We report on a synergistic computational and experimental effort that elucidates the formation of oxygen-embedded compounds, such as furans and other oxygenated hydrocarbons, during the combustion of hydrocarbon fuels. We used ab initio and probabilistic computational techniques to identify low-barrier reaction mechanisms for the formation of large furans and other oxygenated hydrocarbons. We used vacuum-UV photoionization aerosol mass spectrometry and X-ray photoelectron spectroscopy to confirm these predictions. We show that furans are produced in the high-temperature regions of hydrocarbon flames, where they remarkably survive and become the main functional group of oxygenates that incorporate into incipient soot. In controlled flame studies, we discovered ∼100 oxygenated species previously unaccounted for. We found that large alcohols and enols act as precursors to furans, leading to incorporation of oxygen into the carbon skeletons of PAHs. Our results depart dramatically from the crude chemistry of carbon- and oxygen-containing molecules previously considered in hydrocarbon formation and oxidation models and spearhead the emerging understanding of the oxidation chemistry that is critical, for example, to control emissions of toxic and carcinogenic combustion by-products, which also greatly affect global warming.

Ocean Acidification Has Multiple Modes of Action on Bivalve Larvae.

Ocean acidification (OA) is altering the chemistry of the world's oceans at rates unparalleled in the past roughly 1 million years. Understanding the impacts of this rapid change in baseline carbonate chemistry on marine organisms needs a precise, mechanistic understanding of physiological responses to carbonate chemistry. Recent experimental work has shown shell development and growth in some bivalve larvae, have direct sensitivities to calcium carbonate saturation state that is not modulated through organismal acid-base chemistry. To understand different modes of action of OA on bivalve larvae, we experimentally tested how pH, PCO2, and saturation state independently affect shell growth and development, respiration rate, and initiation of feeding in Mytilus californianus embryos and larvae. We found, as documented in other bivalve larvae, that shell development and growth were affected by aragonite saturation state, and not by pH or PCO2. Respiration rate was elevated under very low pH (~7.4) with no change between pH of ~ 8.3 to ~7.8. Initiation of feeding appeared to be most sensitive to PCO2, and possibly minor response to pH under elevated PCO2. Although different components of physiology responded to different carbonate system variables, the inability to normally develop a shell due to lower saturation state precludes pH or PCO2 effects later in the life history. However, saturation state effects during early shell development will carry-over to later stages, where pH or PCO2 effects can compound OA effects on bivalve larvae. Our findings suggest OA may be a multi-stressor unto itself. Shell development and growth of the native mussel, M. californianus, was indistinguishable from the Mediterranean mussel, Mytilus galloprovincialis, collected from the southern U.S. Pacific coast, an area not subjected to seasonal upwelling. The concordance in responses suggests a fundamental OA bottleneck during development of the first shell material affected only by saturation state.

Surplus photosynthetic antennae complexes underlie diagnostics of iron limitation in a cyanobacterium.

Chlorophyll fluorescence from phytoplankton provides a tool to assess iron limitation in the oceans, but the physiological mechanism underlying the fluorescence response is not understood. We examined fluorescence properties of the model cyanobacterium Synechocystis PCC6803 and a ΔisiA knock-out mutant of the same species grown under three culture conditions which simulate nutrient conditions found in the open ocean: (1) nitrate and iron replete, (2) limiting-iron and high-nitrate, representative of natural high-nitrate, low-chlorophyll regions, and (3) iron and nitrogen co-limiting. We show that low variable fluorescence, a key diagnostic of iron limitation, results from synthesis of antennae complexes far in excess of what can be accommodated by the iron-restricted pool of photosynthetic reaction centers. Under iron and nitrogen co-limiting conditions, there are no excess antennae complexes and variable fluorescence is high. These results help to explain the well-established fluorescence characteristics of phytoplankton in high-nutrient, low-chlorophyll ocean regions, while also accounting for the lack of these properties in low-iron, low-nitrogen regions. Importantly, our results complete the link between unique molecular consequences of iron stress in phytoplankton and global detection of iron stress in natural populations from space.

High-throughput screening assay for biological hydrogen production.

This paper describes a screening assay, compatible with high-throughput bioprospecting or molecular biology methods, for assessing biological hydrogen (H2) production. While the assay is adaptable to various physical configurations, we describe its use in a 96-well, microtiter plate format with a lower plate containing H2-producing cyanobacteria strains and controls and an upper, membrane-bottom plate containing a color indicator and a catalyst. H2 produced by cells in the lower plate diffuses through the membrane into the upper plate, causing a color change that can be quantified with a microplate reader. The assay is reproducible, semiquantitative, sensitive down to at least 20 nmol of H2, and largely unaffected by oxygen, carbon dioxide, or volatile fatty acids at levels appropriate to biological systems.

Four-wave mixing in nanosecond pulsed fiber amplifiers.

We present an experimental and theoretical analysis of four-wave mixing in nanosecond pulsed amplifiers based on double-clad ytterbium-doped fibers. This process leads to saturation of the amplified pulse energy at 1064 nm and to distortion of the spectral and temporal profiles. These behaviours are well described by a simple model considering both Raman and four-wave-mixing contributions. The role of seed laser polarization in birefringent fibers is also presented. These results point out the critical parameters and possible tradeoffs for optimization.

High-Power fiber amplifier with widely tunable repetition rate, fixed pulse duration, and multiple output wavelengths.

We report a pulsed, fiber-amplified microchip laser providing widely tunable repetition rate (7.1 - 27 kHz) with constant pulse duration (1.0 ns), pulse energy up to 0.41 mJ, linear output polarization, diffraction-limited beam quality (M(2) < 1.2), and < 1% pulse-energy fluctuations. The pulse duration was shown to minimize nonlinear effects that cause temporal and spectral distortion of the amplified pulses. This source employs passive Q-switching, single-stage single-pass amplification, and cw pumping, thus offering high efficiency, simplicity, and compact, rugged packaging for use in practical applications. The high peak power and high beam quality make this system an ideal pump source for nonlinear frequency conversion, and we demonstrated efficient harmonic generation and optical parametric generation of wavelengths from 213 nm to 4.4 mum with Watt-level output powers.

Coupled abiotic-biotic mineralization of 2,4,6-trinitrotoluene (TNT) in soil slurry.

The explosive 2,4,6-trinitrotoluene (TNT) is a contaminant of soils and ground waters worldwide. To help alleviate such environmental contamination, we investigated a coupled abiotic-biotic treatment scheme for remediating TNT-contaminated soil in slurry solutions. Two types of soil were used (sandy and silt loam) to simulate different soils that might be found at actual sites. These soils were subsequently contaminated with 5000 mg kg(-1) TNT. Mineralization of TNT was initially optimized for minimum reactant use (Fe(3+) and H(2)O(2)) and maximum soil slurry percentage (percent solids) using modified Fenton reactions conducted in the absence of light followed by the addition of an uncharacterized aerobic biomass. Greater than 97% TNT degradation was observed under optimum reaction conditions for both soils. Using two optimum reactant concentrations for each soil, coupled abiotic-biotic reactions showed an increase in TNT mineralization, from 41 to 73% and 34 to 64% in the sandy soil (10 and 20% slurry, respectively, 1470 mM H(2)O(2)), and increases from 12 to 23% and 13 to 28% in the silt loam soil (5% slurry, 294 and 1470 mM H(2)O(2), respectively). These results show promise in the use of combined abiotic-biotic treatment processes for soils contaminated with high concentrations of TNT.

Coupled abiotic-biotic mineralization of 2,4,6-trinitrotoluene (TNT).

Munitions wastes such as TNT are widespread contaminants in soils and ground waters. We investigated a coupled abiotic-biotic treatment scheme for remediation of aqueous solutions of TNT. Mineralization of aqueous TNT (0.22 mM) was initially optimized with minimum reactant use (Fe3+ and H2O2) in light-assisted and dark, modified Fenton reactions at acidic and neutral pH. Complete TNT degradation occurred under all reaction conditions within 24 h. Using the optimum reactant concentrations, coupled abiotic-biotic reactions showed an increase in TNT mineralization, from 47 to 80%, after biomass addition to the acidic, dark Fenton-like reaction. Comparable increases of TNT mineralization were observed under neutral pH with similar reaction conditions. In light-assisted Fenton-like reactions at neutral pH, no increase in cumulative TNT mineralization (66%) was seen in coupled abiotic-biotic reactions. Abiotic photo-Fenton-like reactions alone, at acidic pH, produced complete TNT mineralization and required no biotic assistance. While light-enhanced Fenton reactions alone can provide high levels of TNT mineralization, the dark abiotic-biotic reaction scheme has perhaps a wider use due to a similar extent of TNT mineralization in the absence of light, leading to possible applications in soil slurry and in situ processes in the subsurface.