5 results
Search Results
Now showing 1 - 5 of 5
- 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.
- 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.
- 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.