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At least 19 records

Ultrafast X-ray Transient Absorption Spectroscopy of Gas-Phase Photochemical Reactions: A New Universal Probe of Photoinduced Molecular Dynamics

Time-resolved spectroscopic investigations of light-induced chemical reactions with universal detection capitalize recently on single-photon molecular probing using laser pulses in the extreme ultraviolet or X-ray regimes. Direct and simultaneous mappings of the time-evolving populations of ground-state reactants, Franck-Condon (FC) and transition state regions, excited-state intermediates and conical intersections (CI), and photoproducts in photochemical reactions utilize probe pulses that are broadband and energy-tunable. The limits on temporal resolution are set by the transit- or dwell-time of the photoexcited molecules at specific locations on the potential energy surface, typically ranging from a few femtoseconds to several hundred picoseconds. Femtosecond high-harmonic generation (HHG) meets the stringent demands for a universal spectroscopic probe of large regions of the intramolecular phase-space in unimolecular photochemical reactions. Extreme-ultraviolet and soft X-ray pulses generated in this manner with few-femtosecond or sub-femtosecond durations have enormous bandwidths, allowing the probing of many elements simultaneously through excitation or ionization of core-electrons, creating molecular movies that shed light on entire photochemical pathways. At free electron lasers (FELs), powerful investigations are also possible, recognizing their higher flux and tunability but more limited bandwidths. Femtosecond time-resolved X-ray transient absorption spectroscopy, in particular, is a valuable universal probe of reaction pathways that maps changes via the fingerprint core-to-valence resonances. The particular power of this method over valence-ionization probes lies in its unmatched element and chemical-site specificities. The elements carbon, nitrogen, and oxygen constitute the fundamental building blocks of life; photochemical reactions involving these elements are ubiquitous, diverse, and manifold. However, table-top HHG sources in the "water-window" region (280-550 eV), which encompasses the 1s-absorption edges of carbon (284 eV), nitrogen (410 eV), and oxygen (543 eV), are far from abundant or trivial. Recent breakthroughs in the laboratory have embraced this region by using long driving-wavelength optical parametric amplifiers coupled with differentially pumped high-pressure gas source cells. This has opened avenues to study a host of photochemical reactions in organic molecules using femtosecond time-resolved transient absorption at the carbon K-edge. In this Account, we summarize recent efforts to deploy a table-top carbon K-edge source to obtain crucial chemical insights into ultrafast, ultraviolet-induced chemical reactions involving ring-opening, nonadiabatic excited-state relaxation, bond dissociation and radical formation. Here, the X-ray probe provides a direct spectroscopic viewport into the electronic characters and configurations of the valence electronic states through spectroscopic core-level transitions into the frontier molecular orbitals of the photoexcited molecules, laying fertile ground for the real-time mapping of the evolving valence electronic structure. The profound detail and mechanistic insights emerging from the pioneering experiments at the carbon K-edge are outlined here. Comparisons of the experimental methodology with other techniques employed to study similar reactions are drawn, where applicable and relevant. We show that femtosecond time-resolved X-ray transient absorption spectroscopy blazes a new trail in the study of nonadiabatic molecular dynamics. Despite table-top implementations being largely in their infancy, future chemical applications of the technique will set the stage for widely applicable, universal probes of photoinduced molecular dynamics with unprecedented temporal resolution.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Expression and purification of affinity-tagged variants of the photochemical reaction center from Heliobacterium modesticaldum

The heliobacterial photochemical reaction center (HbRC) from the chlorophototrophic Firmicutes bacterium Heliobacterium modesticaldum is the only homodimeric type I RC whose structure is known. Using genetic techniques recently established in our lab, we have developed a rapid heterologous expression system for the HbRC core polypeptide PshA. Our system relies on rescue of the non-chlorophototrophic ΔpshA::cbp2p - aph3 strain of Hbt. modesticaldum by expression of a heterologous pshA gene from a replicating shuttle vector. Furthermore, we constructed two tagged variants of PshA, one with an N-terminal octahistidine tag and one with an internal hexahistidine tag, which facilitate rapid purification of pure, active HbRC cores in milligram quantities. We constructed a suite of shuttle vectors bearing untagged or tagged versions of pshA driven by various promoters. Surprisingly, we found that the eno and gapDH_2 promoters from Clostridium thermocellum drive better expression of pshA than fragments of DNA derived from the region upstream of the pshA locus on the Hbt. modesticaldum genome. This “ pshA rescue” strategy additionally provided a useful window into how Hbt. modesticaldum regulates pigment synthesis and growth rate when chlorophototrophic output decreases.

59 BASIC BIOLOGICAL SCIENCES↗

Using the Endogenous CRISPR-Cas System of Heliobacterium modesticaldum To Delete the Photochemical Reaction Center Core Subunit Gene

In Heliobacterium modesticaldum , as in many Firmicutes , deleting genes by homologous recombination using standard techniques has been extremely difficult. The cells tend to integrate the introduced plasmid into the chromosome by a single recombination event rather than perform the double recombination required to replace the targeted locus. Transformation with a vector containing only a homologous recombination template for replacement of the photochemical reaction center gene pshA produced colonies with multiple genotypes, rather than a clean gene replacement. To address this issue, we required an additional means of selection to force a clean gene replacement. In this study, we report the genetic structure of the type I-A and I-E CRISPR-Cas systems from H. modesticaldum , as well as methods to leverage the type I-A system for genome editing. In silico analysis of the CRISPR spacers revealed a potential consensus protospacer adjacent motif (PAM) required for Cas3 recognition, which was then tested using an in vivo interference assay. Introduction of a homologous recombination plasmid that carried a miniature CRISPR array targeting sequences in pshA (downstream of a naturally occurring PAM sequence) produced nonphototrophic transformants with clean replacements of the pshA gene with ~80% efficiency. Mutants were confirmed by PCR, sequencing, optical spectroscopy, and growth characteristics. This methodology should be applicable to any genetic locus in the H. modesticaldum genome. The heliobacteria are the only phototrophic members of the largely Gram-positive phylum Firmicutes , which contains medically and industrially important members, such as Clostridium difficile and Clostridium acetobutylicum . Heliobacteria are of interest in the study of photosynthesis because their photosynthetic system is unique and the simplest known. Since their discovery in the early 1980s, work on the heliobacteria has been hindered by the lack of a genetic transformation system. The problem of introducing foreign DNA into these bacteria has been recently rectified by our group; however, issues still remained for efficient genome editing. The significance of this work is that we have characterized the endogenous type I CRISPR-Cas system in the heliobacteria and leveraged it to assist in genome editing. Using the CRISPR-Cas system allowed us to isolate transformants with precise replacement of the pshA gene encoding the main subunit of the photochemical reaction center.

59 BASIC BIOLOGICAL SCIENCES↗

Photochemical reaction of sulfur hexafluoride with water in low-temperature xenon matrices

Sulfur hexafluoride SF{sub 6} is a very stable molecule with which very few reactions with other molecules have been reported. Here, we report a photochemical reaction of SF{sub 6} with water molecules using a matrix-isolation technique, where SF{sub 6} and H{sub 2}O were co-condensed in Xe matrices, and the products were observed using infrared spectroscopy. Irradiation at 193 nm from an ArF excimer laser caused the simultaneous decomposition of SF{sub 6} and H{sub 2}O, which resulted in the production of novel species. Infrared spectra and molecular orbital calculations of the species showed that the product was a SF{sub 4}{center_dot}{center_dot}{center_dot}HF{center_dot}{center_dot}{center_dot}HOF complex, which consists of hydrogen bonds and charge transfer interaction between S and F atoms. The assignment of the species was confirmed by isotope shifts using D and {sup 18}O isotope substitutions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Reconstitution of the heliobacterial photochemical reaction center and cytochrome c 553 into a proteoliposome system

The heliobacterial reaction center (HbRC) is the simplest understood photochemical reaction center, in terms of its polypeptide composition. In the heliobacterial cells, its electron donor is a cytochrome (cyt) c 553 attached to the membrane via a covalent linkage with a diacylglycerol. We have reconstituted purified HbRC into liposomes mimicking the phospholipid composition of heliobacterial membranes. We also incorporated a lipid with a headgroup containing Ni(II):nitrilotriacetate (NTA) to provide a binding site for the soluble version of the heliobacterial cyt c 553 in which the N-terminal membrane attachment site is replaced by a hexahistidine tag. The HbRC was inserted into the liposomes with the donor side preferentially exposed to the exterior; this bias increased to nearly 100% with higher concentrations (≥ 10 mol%) of the Ni(II)-NTA lipid in the membrane, and is most likely due to the net negative charge of the surface of the membrane. The HbRC in proteoliposomes without the Ni(II)-NTA lipid exhibited normal charge separation and subsequent charge recombination of the P + 800 F - X state in 15 ms; however, the oxidized primary donor (P + 800 ) was not significantly reduced by added H 6 -cyt c 553 . In contrast, with proteoliposomes containing the Ni(II)-NTA lipid, addition of H 6 -cyt c 553 resulted in a new kinetic component resulting from fast reduction (2–5 ms) of P + 800 by H 6 -cyt c 553 . The contribution of this kinetic component varied with the concentration of added H 6 -cyt c 553 and could represent 80% or more of the total P + 800 decay. As a result, the HbRC and its interaction with its native electron donor have been reconstituted into an artificial membrane system.

59 BASIC BIOLOGICAL SCIENCES↗

The study of the elementary acts of a reversible photochemical reaction generating quasistationary radio emission in a magnetic field

Constant coherent radio frequency radiation in the course of a reversible photochemical reaction of a 8-hydroxy-6-dibenzofuran—deuteromethanol system was detected and investigated. The observed effect is one of the few examples of the generation of stationary radio emission during a photoreaction and may have a practical application. The elementary stages and the mechanism of these photoreactions are presented.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Mediating Photochemical Reaction Rates at Lewis Acidic Rare Earths by Selective Energy Loss to 4f-Electron States

Manifesting chemical differences in individual rare earth (RE) element complexes is challenging due to the similar sizes of the tripositive cations and the corelike 4f shell. In this work, we disclose a new strategy for differentiating between similarly sized Dy 3+ and Y 3+ ions through a tailored photochemical reaction of their isostructural complexes in which the f-electron states of Dy 3+ act as an energy sink. Complexes RE(hfac) 3 (NMMO) 2 (RE = Dy (2-Dy) and Y (2-Y), hfac = hexafluoroacetylacetonate, and NMMO = N-methylmorpholine-N-oxide) showed variable rates of oxygen atom transfer (OAT) to triphenylphosphine under ultraviolet (UV) irradiation, as monitored by 1 H and 19 F NMR spectroscopies. Ultrafast transient absorption spectroscopy (TAS) identified the excited state(s) responsible for the photochemical OAT reaction or lack thereof. Competing sensitization pathways leading to excited-state deactivation in 2-Dy through energy transfer to the 4f electron manifold ultimately slows the OAT reaction at this metal cation. The measured rate differences between the open-shell Dy 3+ and closed-shell Y 3+ complexes demonstrate that using established principles of 4f ion sensitization may deliver new, selective modalities for differentiating the RE elements that do not depend on cation size.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Photochemical reactions on aerosols at West Antarctica: A molecular case-study of nitrate formation among sea salt aerosols

Environmental implications of climate change are complex and exhibit regional variations both within and between the polar regions. The increase of solar UV radiation flux over Antarctica due to stratospheric ozone depletion creates the optimal conditions for photochemical reactions on the snow. Modeling, laboratory, and indirect field studies suggest that snowpack process release gases to the atmosphere that can react on sea salt particles in remote regions such as Antarctica, modifying aerosol composition and physical properties of aerosols. Here, we present evidence of photochemical processing in West Antarctica aerosols using microscopic and chemical speciation of individual atmospheric particles. Individual aerosol particles collected at the Brazilian module Criosfera 1 were analyzed by scanning transmission X-ray microscopy with near edge X-ray absorption fine structure spectroscopy (STXM/NEXAFS) combined with computer controlled scanning electron microscopy (CCSEM) with energy-dispersive X-ray (EDX) microanalysis. The displacement of chlorine relative to sodium was observed over most of the sea salt particles. Particles with a chemical composition consistent with NaCl-NO3 contributed up to 30% of atmospheric particles investigated. Overall, this study provides evidence that the snowpack and particulate nitrate photolysis should be considered in dynamic partition equilibrium in the troposphere. Finally, these findings may assist in reducing modeling uncertainties and present new insights into the aerosol chemical composition in the polar environment.

54 ENVIRONMENTAL SCIENCES↗

The PshX subunit of the photochemical reaction center from Heliobacterium modesticaldum acts as a low-energy antenna

The anoxygenic phototrophic bacterium Heliobacterium modesticaldum contains a photochemical reaction center protein complex (called the HbRC) consisting of a homodimer of the PshA polypeptide and two copies of a newly discovered polypeptide called PshX, which is a single transmembrane helix that binds two bacteriochlorophyll g molecules. Here, to assess the function of PshX, we produced a ΔpshX strain of Hbt. modesticaldum by leveraging the endogenous Hbt. modesticaldum Type I-A CRISPR-Cas system to aid in mutant selection. We optimized this system by separating the homologous recombination and CRISPR-based selection steps into two plasmid transformations, allowing for markerless gene replacement. Fluorescence and low-temperature absorbance of the purified HbRC from the wild-type and ΔpshX strains showed that the bacteriochlorophylls bound by PshX have the lowest site energies in the entire HbRC. This indicates that PshX acts as a low-energy antenna subunit, participating in entropy-assisted uphill energy transfer towards the P 800 special bacteriochlorophyll g pair. We further discuss the role that PshX may play in stability of the HbRC, its conservation in other heliobacterial species, and the evolutionary pressure to produce and maintain single-TMH subunits in similar locations in other reaction centers.

59 BASIC BIOLOGICAL SCIENCES↗

Photochemical reactions of cyanoacetylene and dicyanoacetylene: Possible processes in Titan's atmosphere

Titan has an atmosphere which is subject to dramatic chemical evolution due mainly to the dramatic effect of the UV flux from the Sun. The energetic solar photons and other particles are converting the methane-nitrogen atmosphere into the unsaturated carbon compounds observed by the Voyager probes. These same solar photons are also converting some of these unsaturated reaction products into the aerosols observed in the atmosphere which obscure the view of the surface of Titan. In particular, the photochemical reactions of cyanoacetylene, dicyanoacetylene, acetylene and ethylene may result in the formation of the higher hydrocarbons and polymers which result in the aerosols observed in Titan's atmosphere. Polymers are the principal reaction products formed by irradiation of cyanoacetylene and dicyanoacetylene. Irradiation of cyanoacetylene with 185 nm of light also yields 1,3,5-tricyanobenzene while irradiation at 254 nm yields 1,2,4-tricyanobenzene and tetracyano cyclooctatetraenes. Photolyses of mixtures of cyanoacetylene and acetylene yields mono- and di- cyanobenzenes. The 1-Cyanocyclobutene is formed from the photochemical addition of cyanoacetylene with ethylene. The photolysis of dicyanoacetylene with acetylene yields 2,3-dicyano-1,3-butadiene and 1,2-dicyanobenzene. Tetracyano cyclooctatetraene products were also observed in the photolysis of mixtures of dicyanoacetylene and acetylene with 254 nm light. The 1,2-Dicyano cyclobutene is obtained from the photolysis dicyanoacetylene and ethylene. Reaction mechanisms will be proposed to explain the observed photoproducts.

Ferris, J. P.↗

Photochemical reactions between mercury (Hg) and dissolved organic matter decrease Hg bioavailability and methylation

Atmospheric deposition of mercury (Hg) to surface water is one of the dominant sources of Hg in aquatic environments and ultimately drives methylmercury (MeHg) toxin accumulation in fish. It is known that freshly deposited Hg is more readily methylated by microorganisms than aged or preexisting Hg; however the underlying mechanism of this process is unclear. Here we report that Hg bioavailability is decreased by photochemical reactions between Hg and dissolved organic matter (DOM) in water. Photo-irradiation of Hg-DOM complexes results in loss of Sn(II)-reducible (i.e. reactive) Hg and up to an 80% decrease in MeHg production by the methylating bacterium Geobacter sulfurreducens PCA. Loss of reactive Hg proceeded at a faster rate with a decrease in the Hg to DOM ratio and is attributed to the possible formation of mercury sulfide (HgS). Lastly, these results suggest a new pathway of abiotic photochemical formation of HgS in surface water and provide a mechanism whereby freshly deposited Hg is readily methylated but, over time, progressively becomes less available for microbial uptake and methylation.

54 ENVIRONMENTAL SCIENCES↗

Constructive Quantum Interference in Photochemical Reactions

Interferences emerge when multiple pathways coexist together, leading toward the same result. Here, we report a theoretical study for a reaction scheme that leads to constructive quantum interference in a photoassociation (PA) reaction of a 87 Rb Bose–Einstein condensate where the reactant spin state is prepared in a coherent superposition of multiple bare spin states. This is achieved by changing the reactive scattering channel in the PA reaction. As the origin of coherent control comes from the spin part of the wavefunction, we show that it is sufficient to use radio frequency (RF) coupling to achieve the superposition state. We simulate the RF coupling on a quantum processor (IBMQ Lima), and our results show that interferences can be used as a resource for the coherent control of photochemical reactions. The approach is general and can be employed to study a wide spectrum of chemical reactions in the ultracold regime.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Photochemical reactions in interstellar grains photolysis of CO, NH3, and H2O

The interstellar grains are currently considered to be the basic building blocks of comets and, possibly, meteorites. To test this theory, a simulation of the organic layer accreted onto interstellar dust particles was prepared by slow deposition of a CO:NH3:H2O gas mixture on an Al block at 10 K, with concomitant irradiation with vacuum UV. The results of the HPLC and IR analyses of the nonvolatile residue formed by photolysis at 10 K are compared with those observed at 77 K and 298 K. Some of the compounds that may be present on the surfaces of interstellar dust particles have been identified, and some specific predictions concerning the types of molecular species present in comets could be drawn. The results also suggest that photochemical reactions may have been important for the formation of meteorite components. The implication of the findings to the questions of the source of organic matter on earth and the origin of life are discussed.

Agarwal, V. K.↗

Predicting encapsulant delamination in photovoltaic modules bridging photochemical reaction kinetics and fracture mechanics

Abstract Photovoltaic (PV) modules are subjected to environmental stressors (UV exposure, temperature, and humidity) that cause degradation within the encapsulant and its interfaces with adjacent glass and cell substrates. To save experimental time and to enable long‐term assessment with intensive degradation only taking place after many years, the development of predictive models is indispensable. Previous works have modeled the delamination of the ethylene vinyl acetate (EVA) encapsulant/glass and encapsulant/cell interfaces under field aging conditions with fundamental photochemical degradation reactions that lead to molecular scission and loss of interfacial adhesion, characterized by the fracture resistance, G c . However, these models were fundamentally limited in that the following aspects were not incorporated: (i) molecular crosslinking in the field, (ii) synergistic autocatalytic interactions of degradation mechanisms, (iii) connection between degraded encapsulant structure and its mechanical properties, and (iv) rigorous treatment of the plasticity contribution to G c with finite element models. Here, we present a time‐dependent multiscale model that addresses these limitations and is applicable to a wide range of encapsulants and interfaces. For the reference EVA encapsulant and its interfaces with the glass and cell, the presented model predicts an initial rise in G c in the first 3 years of field aging from crosslinking, then a subsequent sharp decline from degradation mechanisms. We used nanoindentation to measure the changes in EVA mechanical properties over exposure time to tune the model parameters. The model predictions of G c and mechanical properties match with experimental data and show an improvement compared to previous models. The model can even predict switches in failure interfaces, such as the observed EVA/cell to EVA/glass transition. We also conducted a sensitivity analysis study by varying the degradation and crosslinking kinetic parameters to demonstrate their effects on G c . Model extensions to polyolefin elastomer‐ and silicone‐encapsulants and their interfaces are also demonstrated.

Liu, Kuan↗

Infrared absorption of trans-1-chloromethylallyl and trans-1-methylallyl radicals produced in photochemical reactions of trans-1,3-butadiene and C Script-Small-L {sub 2} in solid para-hydrogen

The reactions of chlorine and hydrogen atoms with trans-1,3-butadiene in solid para-hydrogen (p-H{sub 2}) were investigated with infrared (IR) absorption spectra. When a p-H{sub 2} matrix containing C Script-Small-L {sub 2} and trans-1,3-butadiene was irradiated with ultraviolet light at 365 nm, intense lines at 650.3, 809.0, 962.2, 1240.6 cm{sup -1}, and several weaker ones due to the trans-1-chloromethylallyl radical, Bullet (CH{sub 2}CHCH)CH{sub 2}C Script-Small-L , appeared. Observed wavenumbers and relative intensities agree with the anharmonic vibrational wavenumbers and IR intensities predicted with the B3PW91/6-311++g(2d, 2p) method. That the C Script-Small-L atom adds primarily to the terminal carbon atom of trans-1,3-butadiene is in agreement with the path of minimum energy predicted theoretically, but in contrast to the reaction of C Script-Small-L + propene in solid p-H{sub 2}[J. Amicangelo and Y.-P. Lee, J. Phys. Chem. Lett. 1, 2956 (2010)] in which the addition of C Script-Small-L to the central C atom is favored, likely through steric effects in a p-H{sub 2} matrix. A second set of lines, intense at 781.6, 957.9, 1433.6, 2968.8, 3023.5, 3107.3 cm{sup -1}, were observed when the UV-irradiated C Script-Small-L {sub 2}/trans-1,3-butadiene/p-H{sub 2} matrix was further irradiated with IR light from a SiC source. These lines are assigned to the trans-1-methylallyl radical, Bullet (CH{sub 2}CHCH)CH{sub 3}, produced from reaction of 1,3-butadiene with a H atom resulted from the reaction of C Script-Small-L atoms with solid p-H{sub 2} exposed to IR radiation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Spin-orbit relativistic long-range corrected time-dependent density functional theory for investigating spin-forbidden transitions in photochemical reactions

A long-range corrected (LC) time-dependent density functional theory (TDDFT) incorporating relativistic effects with spin-orbit couplings is presented. The relativistic effects are based on the two-component zeroth-order regular approximation Hamiltonian. Before calculating the electronic excitations, we calculated the ionization potentials (IPs) of alkaline metal, alkaline-earth metal, group 12 transition metal, and rare gas atoms as the minus orbital (spinor) energies on the basis of Koopmans' theorem. We found that both long-range exchange and spin-orbit coupling effects are required to obtain Koopmans' IPs, i.e., the orbital (spinor) energies, quantitatively in DFT calculations even for first-row transition metals and systems containing large short-range exchange effects. We then calculated the valence excitations of group 12 transition metal atoms and the Rydberg excitations of rare gas atoms using spin-orbit relativistic LC-TDDFT. We found that the long-range exchange and spin-orbit coupling effects significantly contribute to the electronic spectra of even light atoms if the atoms have low-lying excitations between orbital spinors of quite different electron distributions.

74 ATOMIC AND MOLECULAR PHYSICS↗

Plasmonic Hot-Carrier-Mediated Tunable Photochemical Reactions

Hot-carrier generation from surface plasmon decay has found applications in many branches of physics, chemistry, materials science, and energy science. Recent reports demonstrated that the hot carriers generated from plasmon decay in nanoparticles can transfer to attached molecules and drive photochemistry which was thought impossible previously. Here, we have computationally explored the atomic-scale mechanism of a plasmonic hot-carrier-mediated chemical process, H 2 dissociation. Numerical simulations demonstrate that, after photoexcitation, hot carriers transfer to the antibonding state of the H 2 molecule from the nanoparticle, resulting in a repulsive-potential-energy surface and H 2 dissociation. This process occurs when the molecule is close to a single nanoparticle. However, if the molecule is located at the center of the gap in a plasmonic dimer, dissociation is suppressed due to sequential charge transfer, which efficiently reduces occupation in the antibonding state and, in turn, reduces dissociation. An asymmetric displacement of the molecule in the gap breaks the symmetry and restores dissociation when the additional charge transfer is significantly suppressed. Furthermore, these models demonstrate the possibility of structurally tunable photochemistry via plasmonic hot carriers.

36 MATERIALS SCIENCE↗