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- ItemSwitching between Proton Vacancy and Excess Proton Transfer Pathways in the Reaction between 7-Hydroxyquinoline and Formate(Washington, DC : Soc., 2021) Codescu, Marius-Andrei; Weiß, Moritz; Brehm, Martin; Kornilov, Oleg; Sebastiani, Daniel; Nibbering, Erik T. J.Bifunctional or amphoteric photoacids simultaneously present donor (acidic) and acceptor (basic) properties making them useful tools to analyze proton transfer reactions. In protic solvents, the proton exchange between the acid and the base is controlled by the acidity or basicity strength and typically occurs on two different pathways known as protolysis and hydrolysis. We report here how the addition of a formate base will alter the relative importance of the possible reaction pathways of the bifunctional photoacid 7-hydroxyquinoline (7HQ), which has been recently understood to predominantly involve a hydroxide/methoxide transport mechanism between the basic proton-accepting quinoline nitrogen site toward the proton-donating OH group with a time constant of 360 ps in deuterated methanol (CD3OD). We follow the reaction dynamics by probing the IR-active marker modes of the different charged forms of photoexcited 7HQ, and of formic acid (HCOOD) in CD3OD solution. A comparison of the transient IR spectra as a function of formate concentration, and classical molecular dynamics simulations enables us to identify distinct contributions of “tight” (meaning “contact”) and “loose” (i.e., “solvent-separated”) 7HQ–formate reaction pairs in our data. Our results suggest that depending on the orientation of the OH group with respect to the quinoline aromatic ring system, the presence of the formate molecule in a proton relay pathway facilitates a net proton transfer from the proton-donating OH group of 7HQ-N* via the methanol/formate bridge toward the quinoline N site.
- ItemDifferential Cross Sections for the H + D2 → HD(v′ = 3, j′ = 4-10) + D Reaction above the Conical Intersection(Washington, DC : Soc., 2015) Gao, Hong; Sneha, Mahima; Bouakline, Foudhil; Althorpe, Stuart C.; Zare, Richard N.We report rovibrationally selected differential cross sections (DCSs) of the benchmark reaction H + D2 → HD(v′ = 3, j′ = 4–10) + D at a collision energy of 3.26 eV, which exceeds the conical intersection of the H3 potential energy surface at 2.74 eV. We use the PHOTOLOC technique in which a fluorine excimer laser at 157.64 nm photodissociates hydrogen bromide (HBr) molecules to generate fast H atoms and the HD product is detected in a state-specific manner by resonance-enhanced multiphoton ionization. Fully converged quantum wave packet calculations were performed for this reaction at this high collision energy without inclusion of the geometric phase (GP) effect, which takes into account coupling to the first excited state of the H3 potential energy surface. Multimodal structures can be observed in most of the DCSs up to j′ = 10, which is predicted by theory and also well-reproduced by experiment. The theoretically calculated DCSs are in good overall agreement with the experimental measurements, which indicates that the GP effect is not large enough that its existence can be verified experimentally at this collision energy.
- ItemActive Plasmonic Colloid-to-Film-Coupled Cavities for Tailored Light-Matter Interactions(Washington, DC : Soc., 2019) Goßler, Fabian R.; Steiner, Anja Maria; Stroyuk, Oleksandr; Raevskaya, Alexandra; König, Tobias A.F.For large-scale fabrication of optical circuits, tailored subwavelength structures are required to modulate the refractive index. Here, we introduce a colloid-to-film-coupled nanocavity whose refractive index can be tailored by various materials, shapes, and cavity volumes. With this colloidal nanocavity setup, the refractive index can be adjusted over a wide visible wavelength range. For many nanophotonic applications, specific values for the extinction coefficient are crucial to achieve optical loss and gain. We employed bottom-up self-assembly techniques to sandwich optically active ternary metal-chalcogenides between a metallic mirror and plasmonic colloids. The spectral overlap between the cavity resonance and the broadband emitter makes it possible to study the tunable radiative properties statistically. For flat cavity geometries of silver nanocubes with sub-10 nm metallic gap, we found a fluorescence enhancement factor beyond 1000 for 100 cavities and a 112 meV Rabi splitting. In addition, we used gold spheres to extend the refractive index range. By this easily scalable colloidal nanocavity setup, gain and loss building blocks are now available, thereby leading to new generation of optical devices. Copyright © 2019 American Chemical Society.
- ItemMagnesium Contact Ions Stabilize the Tertiary Structure of Transfer RNA: Electrostatics Mapped by Two-Dimensional Infrared Spectra and Theoretical Simulations(Washington, DC : Soc., 2021) Schauss, Jakob; Kundu, Achintya; Fingerhut, Benjamin P.; Elsaesser, ThomasIons interacting with hydrated RNA play a central role in defining its secondary and tertiary structure. While spatial arrangements of ions, water molecules, and phosphate groups have been inferred from X-ray studies, the role of electrostatic and other noncovalent interactions in stabilizing compact folded RNA structures is not fully understood at the molecular level. Here, we demonstrate that contact ion pairs of magnesium (Mg2+) and phosphate groups embedded in local water shells stabilize the tertiary equilibrium structure of transfer RNA (tRNA). Employing dialyzed tRNAPhe from yeast and tRNA from Escherichia coli, we follow the population of Mg2+ sites close to phosphate groups of the ribose-phosphodiester backbone step by step, combining linear and nonlinear infrared spectroscopy of phosphate vibrations with molecular dynamics simulations and ab initio vibrational frequency calculations. The formation of up to six Mg2+/phosphate contact pairs per tRNA and local field-induced reorientations of water molecules balance the phosphate-phosphate repulsion in nonhelical parts of tRNA, thus stabilizing the folded structure electrostatically. Such geometries display limited sub-picosecond fluctuations in the arrangement of water molecules and ion residence times longer than 1 µs. At higher Mg2+ excess, the number of contact ion pairs per tRNA saturates around 6 and weakly interacting ions prevail. Our results suggest a predominance of contact ion pairs over long-range coupling of the ion atmosphere and the biomolecule in defining and stabilizing the tertiary structure of tRNA. © 2020 American Chemical Society.
- ItemPhosphate Vibrations Probe Electric Fields in Hydrated Biomolecules: Spectroscopy, Dynamics, and Interactions(Washington, DC : Soc., 2021) Elsaesser, Thomas; Schauss, Jakob; Kundu, Achintya; Fingerhut, Benjamin P.Electric interactions have a strong impact on the structure and dynamics of biomolecules in their native water environment. Given the variety of water arrangements in hydration shells and the femto- to subnanosecond time range of structural fluctuations, there is a strong quest for sensitive noninvasive probes of local electric fields. The stretching vibrations of phosphate groups, in particular the asymmetric (PO2)− stretching vibration νAS(PO2)−, allow for a quantitative mapping of dynamic electric fields in aqueous environments via a field-induced redshift of their transition frequencies and concomitant changes of vibrational line shapes. We present a systematic study of νAS(PO2)− excitations in molecular systems of increasing complexity, including dimethyl phosphate (DMP), short DNA and RNA duplex structures, and transfer RNA (tRNA) in water. A combination of linear infrared absorption, two-dimensional infrared (2D-IR) spectroscopy, and molecular dynamics (MD) simulations gives quantitative insight in electric-field tuning rates of vibrational frequencies, electric field and fluctuation amplitudes, and molecular interaction geometries. Beyond neat water environments, the formation of contact ion pairs of phosphate groups with Mg2+ ions is demonstrated via frequency upshifts of the νAS(PO2)− vibration, resulting in a distinct vibrational band. The frequency positions of contact geometries are determined by an interplay of attractive electric and repulsive exchange interactions.
- ItemRevealing Fast Proton Transport in Condensed Matter by Means of Density Scaling Concept(Washington, DC : Soc., 2020) Wojnarowska, Zaneta; Musiał, Małgorzata; Cheng, Shinian; Gapinski, Jacek; Patkowski, Adam; Pionteck, Jürgen; Paluch, MarianHerein, we investigate the charge transport and structural dynamics in the supercooled and glassy state of protic ionic material with an efficient interionic Grotthuss mechanism. We found that superprotonic properties of studied acebutolol hydrochloride (ACB-HCl) depend on thermodynamic conditions with the most favorable regions being close to the glass-transition temperature (Tg) and glass-transition pressure (Pg). To quantify the contribution of fast proton hopping to overall charge transport over a broad T–P space, we employed the density scaling concept, one of the most important experimental findings in the field of condensed matter physics. We found that isothermal and isobaric dc-conductivity (σdc) and dynamic light scattering (τα) data of ACB-HCl plotted as a function of (TVγ)−1 satisfy the thermodynamic scaling criterion with the ratio γσ/γα appearing as a new measure of fast charge transport in protic ionic glass-formers in the T–P plane. Such a universal factor becomes an alternative to the well-known Walden rule being limited to ambient pressure conditions.
- ItemTropospheric Aqueous-Phase Oxidation of Isoprene-Derived Dihydroxycarbonyl Compounds(Washington, DC : Soc., 2017) Otto, Tobias; Stieger, Bastian; Mettke, Peter; Herrmann, HartmutThe dihydroxycarbonyls 3,4-dihydroxy-2-butanone (DHBO) and 2,3-dihydroxy-2-methylpropanal (DHMP) formed from isoprene oxidation products in the atmospheric gas phase under low-NO conditions can be expected to form aqSOA in the tropospheric aqueous phase because of their solubility. In the present study, DHBO and DHMP were investigated concerning their radical-driven aqueous-phase oxidation reaction kinetics. For DHBO and DHMP the following rate constants at 298 K are reported: k(OH + DHBO) = (1.0 ± 0.1) × 109 L mol-1 s-1, k(NO3 + DHBO) = (2.6 ± 1.6) × 106 L mol-1 s-1, k(SO4-+ DHBO) = (2.3 ± 0.2) × 107 L mol-1 s-1, k(OH + DHMP) = (1.2 ± 0.1) × 109 L mol-1 s-1, k (NO3 + DHMP) = (7.9 ± 0.7) × 106 L mol-1 s-1, k(SO4- + DHMP) = (3.3 ± 0.2) × 107 L mol-1 s-1, together with their respective temperature dependences. The product studies of both DHBO and DHMP revealed hydroxydicarbonyls, short chain carbonyls, and carboxylic acids, such as hydroxyacetone, methylglyoxal, and lactic and pyruvic acid as oxidation products with single yields up to 25%. The achieved carbon balance was 75% for DHBO and 67% for DHMP. An aqueous-phase oxidation scheme for both DHBO and DHMP was developed on the basis of the experimental findings to show their potential to contribute to the aqSOA formation. It can be expected that the main contribution to aqSOA occurs via acid formation while other short-chain oxidation products are expected to back-partition into the gas phase to undergo further oxidation there.
- ItemIn Situ Transmission Electron Microscopy of Disorder–Order Transition in Epitaxially Stabilized FeGe2(Washington, DC : Soc., 2021) Terker, Markus; Nicolai, Lars; Gaucher, Samuel; Herfort, Jens; Trampert, AchimIsothermal crystallization of amorphous Ge deposited on a cubic Fe3Si/GaAs(001) substrate is performed by in situ annealing within a transmission electron microscope. It was found that the formation of epitaxially aligned tetragonal FeGe2 is associated with a disorder–order phase transition mainly consisting of a rearrangement of the Fe/vacancy sublattice from a random distribution to alternating filled and empty layers. Additionally, atomically resolved high-angle annular dark-field scanning transmission electron microscopy and energy-dispersive X-ray spectroscopy demonstrated that the vertical lattice spacing of the Ge sublattice reduces across vacancy layers, indicating that strain minimization plays a role in the phase transition process. Crystallization and ordering are both found to proceed layer-by-layer and with square-root-shaped kinetics with a smaller transition rate for the latter.