Dual-Lifetime Referencing (t-DLR) Optical Fiber Fluorescent pH Sensor for Microenvironments.

The pH behavior in the µm to cm thick diffusion boundary layer (DBL) surrounding many aquatic species is dependent on light-controlled metabolic activities. This DBL microenvironment exhibits different pH behavior to bulk seawater, which can reduce the exposure of calcifying species to ocean acidification conditions. A low-cost time-domain dual-lifetime referencing (t-DLR) interrogation system and an optical fiber fluorescent pH sensor were developed for pH measurements in the DBL interface. The pH sensor utilized dual-layer sol-gel coatings of pH-sensitive iminocoumarin and pH-insensitive Ru(dpp)3-PAN. The sensor has a dynamic range of 7.41 (±0.20) to 9.42 ± 0.23 pH units (95% CI, T = 20 °C, S = 35), a response time (t90) of 29 to 100 s, and minimal salinity dependency. The pH sensor has a precision of approximately 0.02 pHT units, which meets the Global Ocean Acidification Observing Network (GOA-ON) "weather" measurement quality guideline. The suitability of the t-DLR optical fiber pH sensor was demonstrated through real-time measurements in the DBL of green seaweed Ulva sp. This research highlights the practicability of optical fiber pH sensors by demonstrating real-time pH measurements of metabolic-induced pH changes.

Simulation of Cocrystal Formation in Planetary Atmospheres: The C6H6:C2H2 Cocrystal Produced by Gas Deposition.

The formation of molecular cocrystals in condensed aerosol particles has been recently proposed as an efficient pathway for generation of complex organics in Titan's atmosphere. It follows that cocrystal precipitation may facilitate the transport of biologically important precursors to the surface to be sequestered in an organic karstic and sand environment. Recent laboratory studies on these planetary minerals have predominantly synthesized cocrystals by the controlled freezing of binary mixtures from the liquid phase, allowing for their structural and spectroscopic characterization. However, these techniques are perhaps not best representative of aerosol nucleation and growth microphysics in planetary atmospheres. Herein, we report the first synthesis of the known 1:1 C6H6:C2H2 cocrystal using vapor deposition methods onto a cryogenically cooled substrate. Subsequent transmission FTIR spectroscopy has confirmed the formation of the empirical C6H6:C2H2 cocrystal structure via the observation of diagnostic infrared spectral features. Predicted by periodic-DFT calculations, altered vibrational profiles depict a changing site symmetry of the C6H6 and C2H2 components after transition to the cocrystal unit cell geometry. The 80 K temperature of the cocrystal phase transition overlaps with the condensation curves obtained for both species in Titan's lower stratosphere, revealing that the cocrystal may act as an important environment for photo- and radio-lytic processes leading to the formation of higher order organics in Titan's atmosphere. Such solid-state astrochemistry can now be pursued in oxygen-free laboratory settings under (ultra)high vacuum using standard surface science setups.

Water Sorption Controls Extreme Single-Crystal-to-Single-Crystal Molecular Reorganization in Hydrogen Bonded Organic Frameworks.

As hydrogen bonded frameworks are held together by relatively weak interactions, they often form several different frameworks under slightly different synthesis conditions and respond dynamically to stimuli such as heat and vacuum. However, these dynamic restructuring processes are often poorly understood. In this work, three isoreticular hydrogen bonded organic frameworks assembled through charge-assisted amidinium⋅⋅⋅carboxylate hydrogen bonds (1C/C , 1Si/C and 1Si/Si ) are studied. Three distinct phases for 1C/C and four for 1Si/C and 1Si/Si are fully structurally characterized. The transitions between these phases involve extreme yet recoverable molecular-level framework reorganization. It is demonstrated that these transformations are related to water content and can be controlled by humidity, and that the non-porous anhydrous phase of 1C/C shows reversible water sorption through single crystal to crystal restructuring. This mechanistic insight opens the way for the future use of the inherent dynamism present in hydrogen bonded frameworks.

Vibrational mode analysis of hydrogen-bonded organic frameworks (HOFs): synchrotron infrared studies.

Hydrogen-bonded organic frameworks (HOFs) are a promising class of porous crystalline materials for gas sorption and gas separation technologies that can be constructed under mild synthetic conditions. In forming three-dimensional networks of flexible hydrogen bonds between donor/acceptor subunits, these materials have displayed high stability at elevated temperature and under vacuum. Although the structural properties of HOFs are commonly characterized by diffraction techniques, new complimentary methods to elucidate phase behaviour and host-guest interactions at the molecular level are sought, particularly those that can be applied under changing physical conditions or solvent environment. To this end, this study has applied synchrotron far-IR and mid-IR spectroscopy to probe the properties of two known and one new HOF system assembled from tetrahedral amidinium and carboxylate building blocks. All three frameworks produce feature-rich and resolved infrared profiles from 30 to 4000 cm-1 that provide information on hydrogen-bonded water solvent networks and the HOF channel topography via lattice and torsional bands. Comparison of experimental peaks to frequencies and atomic displacements (eigenvectors) predicted by high-level periodic DFT calculations have allowed for the assignment of vibrational modes associated with the aforementioned physicochemical properties. Now compiled, the specific vibrational modes identified as common to charge-assisted hydrogen-bonding motifs, as well as low frequency lattice and torsional bands attributed to HOF pore morphology and water-of-hydration networks, can act as diagnostic features in future spectroscopic investigations of HOF properties, such as those toward the design and tuning of host-guest properties for targeted applications.

The crystal structure, thermal expansion and far-IR spectrum of propanal (CH3CH2CHO) determined using powder X-ray diffraction, neutron scattering, periodic DFT and synchrotron techniques.

The crystal structure of propanal has been determined using powder X-ray diffraction (PXRD), where this common laboratory aldehyde is measured to crystallise in spacegroup P21/a, Z = 4 with a unit cell a = 8.9833(6) Å, b = 4.2237(2) Å, c = 9.4733(6) Å and ß = 97.508(6)°, resulting in a volume of 356.37(4) Å3 at 100 K and atmospheric pressure. The thermal expansion observed from 100 K until the sample melted (∼164 K) was found to be anisotropic. An additional neutron diffraction study was carried out, reaching a temperature of 3 K and found no further phase transformations from the determined structure at lower temperatures. The investigated temperature regime correlates to astronomical surfaces, including outer Solar System bodies and interstellar dust mantles, where propanal is thought to be generated by energetic processing of composite molecular ices. Results from the structure determination were applied to model propanal ice using periodic density functional theory for the calculation of intermolecular frequencies, where the simulated far-infrared spectrum of solid propanal can now be used for future molecular astronomy.

Rigid, biconical hydrogen-bonded dimers that strongly encapsulate cationic guests in solution and the solid state.

The octol of a new rigid, tetraarylene-bridged cavitand was investigated for self-assembly behaviour in solution. 1H and DOSY NMR spectroscopic experiments show that the cavitand readily dimerizes through an unusual seam of interdigitated hydrogen-bonds that is resistant to disruption by polar co-solvents. The well-defined cavity encapsulates small cationic guests, but not their neutral counterparts, restricting the conformation of sequestered tetraethylammonium in solution and the solid state.

Crystal structure of propionitrile (CH3CH2CN) determined using synchrotron powder X-ray diffraction.

The structure and thermal expansion of the astronomical molecule propionitrile have been determined from 100 to 150 K using synchrotron powder X-ray diffraction. This temperature range correlates with the conditions of Titan's lower stratosphere, and near surface, where propionitrile is thought to accumulate and condense into pure and mixed-nitrile phases. Propionitrile was determined to crystallize in space group, Pnma (No. 62), with unit cell a = 7.56183 (16) Å, b = 6.59134 (14) Å, c = 7.23629 (14), volume = 360.675 (13) Å3 at 100 K. The thermal expansion was found to be highly anisotropic with an eightfold increase in expansion between the c and b axes. These data will prove crucial in the computational modelling of propionitrile-ice systems in outer Solar System environments, allowing us to simulate and assign vibrational peaks in the infrared spectra for future use in planetary astronomy.

Single and double addition of oxygen atoms to propyne on surfaces at low temperatures.

Experiments designed to simulate the low temperature surface chemistry occurring in interstellar clouds provide clear evidence of a reaction between oxygen atoms and propyne ice. The reactants are dosed onto a surface held at a fixed temperature between 14 and 100 K. After the dosing period, temperature programmed desorption (TPD), coupled with time-of-flight mass spectrometry, are used to identify two reaction products with molecular formulae C3H4O and C3H4O2. These products result from the addition of a single oxygen atom, or two oxygen atoms, to a propyne reactant. A simple model has been used to extract kinetic data from the measured yield of the single-addition (C3H4O) product at surface temperatures from 30-100 K. This modelling reveals that the barrier of the solid-state reaction between propyne and a single oxygen atom (160 +/- 10 K) is an order of magnitude less than that reported for the gas-phase reaction. In addition, estimates for the desorption energy of propyne and reaction rate coefficient, as a function of temperature, are determined for the single addition process from the modelling. The yield of the single addition product falls as the surface temperature decreases from 50 K to 30K, but rises again as the surface temperature falls below 30 K. This increase in the rate of reaction at low surface temperatures is indicative of an alternative, perhaps barrierless, pathway to the single addition product which is only important at low surface temperatures. The kinetic model has been further developed to characterize the double addition reaction, which appears to involve the addition of a second oxygen atom to C3H4O. This modelling indicates that this second addition is a barrierless process. The kinetic parameters we extract from our experiments indicate that the reaction between atomic oxygen and propyne could occur under on interstellar dust grains on an astrophysical time scale.

On the chemical processing of hydrocarbon surfaces by fast oxygen ions.

Solid methane (CH(4)), ethane (C(2)H(6)), and ethylene (C(2)H(4)) ices (thickness: 120 ± 40 nm; 10 K), as well as high-density polyethylene (HDPE: [C(2)H(4)](n)) films (thickness: 130 ± 20 nm; 10, 100, and 300 K), were irradiated with mono-energetic oxygen ions (Φ ~ 6 × 10(15) cm(-2)) of a kinetic energy of 5 keV to simulate the exposure of Solar System hydrocarbon ices and aerospace polymers to oxygen ions sourced from the solar wind and planetary magnetospheres. On-line Fourier-transform infrared spectroscopy (FTIR) was used to identify the following O(+) induced reaction pathways in the solid-state: (i) ethane formation from methane ice via recombination of methyl (CH(3)) radicals, (ii) ethane conversion back to methane via methylene (CH(2)) retro-insertion, (iii) ethane decomposing to acetylene via ethylene through successive hydrogen elimination steps, and (iv) ethylene conversion to acetylene via hydrogen elimination. No changes were observed in the irradiated PE samples via infrared spectroscopy. In addition, mass spectrometry detected small abundances of methanol (CH(3)OH) sublimed from the irradiated methane and ethane condensates during controlled heating. The detection of methanol suggests an implantation and neutralization of the oxygen ions within the surface where atomic oxygen (O) then undergoes insertion into a C-H bond of methane. Atomic hydrogen (H) recombination in forming molecular hydrogen and recombination of implanted oxygen atoms to molecular oxygen (O(2)) are also inferred to proceed at high cross-sections. A comparison of the reaction rates and product yields to those obtained from experiments involving 5 keV electrons, suggests that the chemical alteration of the hydrocarbon ice samples is driven primarily by electronic stopping interactions and to a lesser extent by nuclear interactions.

On the formation of ozone in oxygen-rich solar system ices via ionizing radiation.

The irradiation of pure molecular oxygen (O(2)) and carbon dioxide (CO(2)) ices with 5 keV H(+) and He(+) ions was investigated experimentally to simulate the chemical processing of oxygen rich planetary and interstellar surfaces by exposure to galactic cosmic ray (GCR), solar wind, and magnetospheric particles. Deposited at 12 K under ultra-high vacuum conditions (UHV), the irradiated condensates were monitored on-line and in situ in the solid-state by Fourier transform infrared spectroscopy (FTIR), revealing the formation of ozone (O(3)) in irradiated oxygen ice; and ozone, carbon monoxide (CO), and cyclic carbon trioxide (c-CO(3)) in irradiated carbon dioxide. In addition to these irradiation products, evolution of gas-phase molecular hydrogen (H(2)), atomic helium (He) and molecular oxygen (O(2)) were identified in the subliming oxygen and carbon dioxide condensates by quadrupole mass spectrometry (QMS). Temporal abundances of the oxygen and carbon dioxide precursors and the observed molecular products were compiled over the irradiation period to develop reaction schemes unfolding in the ices. These reactions were observed to be dependent on the generation of atomic oxygen (O) by the homolytic dissociation of molecular oxygen induced by electronic, S(e), and nuclear, S(n), interaction with the impinging ions. In addition, the destruction of the ozone and carbon trioxide products back to the molecular oxygen and carbon dioxide precursors was promoted over an extended period of ion bombardment. Finally, destruction and formation yields were calculated and compared between irradiation sources (including 5 keV electrons) which showed a surprising correlation between the molecular yields (∼10(-3)-10(-4) molecules eV(-1)) created by H(+) and He(+) impacts. However, energy transfer by isoenergetic, fast electrons typically generated ten times more product molecules per electron volt (∼10(-2)-10(-3) molecules eV(-1)) than exposure to the ions. Implications of these findings to Solar System chemistry are also discussed.

Mechanistical studies on the electron-induced degradation of polymethylmethacrylate and Kapton.

Mechanisms for the electron-induced degradation of poly(methyl methacrylate) (PMMA) and Kapton polyimide (PMDA-ODA), both of which are commonly used in aerospace applications, were examined over a temperature range of 10 K to 300 K under ultra high vacuum (∼10(-11) Torr). The experiments were designed to simulate the interaction between the polymer materials and secondary electrons produced by interaction with galactic cosmic ray particles in the near-Earth space environment. Chemical alterations of the samples were monitored on line and in situ by Fourier-transform infrared spectroscopy and mass spectrometry during irradiation with 5 keV electrons and also prior and after the irradiation exposure via UV-vis. The irradiation-induced degradation of PMMA resulted in the formation and unimolecular decomposition of methyl carboxylate radicals (CH(3)OCO) forming carbon monoxide (k = 4.60 × 10(-3) s(-1)) and carbon dioxide (k = 1.29 × 10(-3) s(-1)). Temperature dependent gas-phase abundances for carbon monoxide, carbon dioxide, and molecular hydrogen were also obtained for the PMMA and Kapton samples. The lower gas yields detected for irradiated Kapton were typically one or two orders of magnitude less than PMMA suggesting a higher degradation resistance to energetic electrons. In addition, UV-vis spectroscopy revealed the propagation of conjugated bonds induced by the irradiation of PMMA and indicated a decrease in the optical band gap by an increase in absorbance above 500 nm in irradiated Kapton.

Mechanistical studies on the electron-induced degradation of polymers: polyethylene, polytetrafluoroethylene, and polystyrene.

Mechanisms of the electron-induced degradation of three polymers utilized in aerospace applications (polyethylene (PE), polytetrafluoroethylene (PTFE), and polystyrene (PS)) were examined over a temperature range of 10 K to 300 K at ultra high vacuum conditions (∼10(-11) Torr). These processes simulate the interaction of secondary electrons generated in the track of galactic cosmic ray particles in the near-Earth space environment with polymer material. The chemical alterations at the macromolecular level were monitored on-line and in situ by Fourier-transform infrared spectroscopy and mass spectrometry. These data yielded important information on the temperature dependent kinetics on the formation of, for instance, trans-vinylene groups (-CH=CH-) in PE, benzene (C(6)H(6)) production in PS, fluorinated trans-vinylene (-CF=CF-) and terminal vinyl (-CF=CF(2)) groups in PTFE together with molecular hydrogen release in PE and PS. Additional data on the radiation-induced development of unsaturated, conjugated bonds were collected via UV-vis spectroscopy. Temperature dependent G-values for trans-vinylene formation (G(-CH=CH-) ≈ 25-2.5 × 10(-4) units (100 eV)(-1) from 10-300 K) and molecular hydrogen evolution (G(H(2)) ≈ 8-80 × 10(-5) molecules (100 eV)(-1) from 10-300 K) for irradiated PE were calculated to quantify the degree of polymer degradation following electron irradiation. These values are typically two to three orders of magnitude less than G-values previously published for the irradiation of polymers with energetic particles of higher mass.

Untangling the chemical evolution of Titan's atmosphere and surface--from homogeneous to heterogeneous chemistry.

In this article, we first explored the chemical dynamics of simple diatomic radicals (dicarbon, methylidyne) utilizing the crossed molecular beams method. This versatile experimental technique can be applied to study reactions relevant to the atmospheres of planets and their moons as long as intense and stable supersonic beam sources of the reactant species exist. By focusing on reactions of dicarbon with hydrogen cyanide, we untangled the contribution of dicarbon in its singlet ground and first excited triplet states. These results were applied to understand and re-analyze the data of crossed beam reactions of the isoelectronic dicarbon plus acetylene reaction. Further, we investigated the interaction of ionizing radiation in form of energetic electrons with organic molecules ethane and propane sequestered on Titan's surface. These experiments presented compelling evidence that even at irradiation exposures equivalent to about 44 years on Titan's surface, aliphatic like organic residues can be produced on Titan's surface with thicknesses up to 1.5 m. Finally, we investigated how Titan's nascent chemical inventory can be altered by an external influx of matter as supplied by (micro)meteorites and possibly comets. For this, we simulated the ablation process in Titan's atmosphere, which can lead to ground and electronically excited atoms of, for instance, the principal constituents of silicates like iron, silicon, and magnesium, in laboratory experiments. By ablating silicon species and seeding the ablated species in acetylene carrier gas, which also acts as a reactant, we produced organo silicon species, which were then photoionized utilizing tunable VUV radiation from the Advanced Light Source. In combination with electronic structure calculations, the structures and ionization energies of distinct organo-silicon species were elucidated.

Identification of the water amidogen radical complex.

The water amidogen radical complex (H(2)O-NH(2)) is a reactive intermediate in the atmospheric oxidation of ammonia by a hydroxyl radical. In the present study, we identify for the first time the H(2)O-NH(2) complex using matrix isolation infrared spectroscopy. We corroborate our experimental findings with high level coupled cluster ab initio calculations.