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- 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.
- ItemSonopharmacology: controlling pharmacotherapy and diagnosis by ultrasound-induced polymer mechanochemistry(Cambridge : RSC, 2022) Yildiz, Deniz; Göstl, Robert; Herrmann, AndreasActive pharmaceutical ingredients are the most consequential and widely employed treatment in medicine although they suffer from many systematic limitations, particularly off-target activity and toxicity. To mitigate these effects, stimuli-responsive controlled delivery and release strategies for drugs are being developed. Fueled by the field of polymer mechanochemistry, recently new molecular technologies enabled the emergence of force as an unprecedented stimulus for this purpose by using ultrasound. In this research area, termed sonopharmacology, mechanophores bearing drug molecules are incorporated within biocompatible macromolecular scaffolds as preprogrammed, latent moieties. This review presents the novelties in controlling drug activation, monitoring, and release by ultrasound, while discussing the limitations and challenges for future developments.
- ItemInfrared and NMR Spectroscopic Fingerprints of the Asymmetric H7 + O3 Complex in Solution(Weinheim : Wiley-VCH Verl., 2021) Kozari, Eve; Sigalov, Mark; Pines, Dina; Fingerhut, Benjamin P.; Pines, EhudInfrared (IR) absorption in the 1000-3700 cm-1 range and 1 H NMR spectroscopy reveal the existence of an asymmetric protonated water trimer, H7 + O3, in acetonitrile. The core H7 + O3 motif persists in larger protonated water clusters in acetonitrile up to at least 8 water molecules. Quantum mechanics/molecular mechanics (QM/MM) molecular dynamics (MD) simulations reveal irreversible proton transport promoted by propagating the asymmetric H7 + O3 structure in solution. The QM/MM calculations allow for the successful simulation of the measured IR absorption spectra of H7 + O3 in the OH stretch region, which reaffirms the assignment of the H7 + O3 spectra to a hybrid-complex structure: a protonated water dimer strongly hydrogen-bonded to a third water molecule with the proton exchanging between the two possible shared-proton Zundel-like centers. The H7 + O3 structure lends itself to promoting irreversible proton transport in presence of even one additional water molecule. We demonstrate how continuously evolving H7 + O3 structures may support proton transport within larger water solvates.
- ItemThe interaction of chondroitin sulfate with a lipid monolayer observed by using nonlinear vibrational spectroscopy(Cambridge : RSC Publ., 2021) Szekeres, Gergo Peter; Krekic, Szilvia; Miller, Rebecca L.; Mero, Mark; Pagel, Kevin; Heiner, ZsuzsannaThe first vibrational sum-frequency generation (VSFG) spectra of chondroitin sulfate (CS) interacting with dipalmitoyl phosphatidylcholine (DPPC) at air–liquid interface are reported here, collected at a laser repetition rate of 100 kHz. By studying the VSFG spectra in the regions of 1050–1450 cm−1, 2750–3180 cm−1, and 3200–3825 cm−1, it was concluded that in the presence of Ca2+ ions, the head groups together with the head-group-bound water molecules in the DPPC monolayer are strongly influenced by the interaction with CS, while the organization of the phospholipid tails remains mostly unchanged. The interactions were observed at a CS concentration below 200 nM, which exemplifies the potential of VSFG in studying biomolecular interactions at low physiological concentrations. The VSFG spectra recorded in the O–H stretching region at chiral polarization combination imply that CS molecules are organized into ordered macromolecular superstructures with a chiral secondary structure.
- ItemA green solvent-to-polymer upgrading approach to water-soluble LCST poly(N-substituted lactamide acrylate)s(Cambridge : RSC, 2022) Palà, Marc; El Khannaji, Hafssa; Garay-Sarmiento, Manuela; Ronda, Juan Carlos; Cádiz, Virginia; Galià, Marina; Percec, Virgil; Rodriguez-Emmenegger, César; Lligadas, GerardWe report a green solvent-to-polymer upgrading transformation of chemicals of the lactic acid portfolio into water-soluble lower critical solution temperature (LCST)-type acrylic polymers. Aqueous Cu(0)-mediated living radical polymerization (SET-LRP) was utilized for the rapid synthesis of N-substituted lactamide-type homo and random acrylic copolymers under mild conditions. A particularly unique aspect of this work is that the water-soluble monomers and the SET-LRP initiator used to produce the corresponding polymers were synthesized from biorenewable and non-toxic solvents, namely natural ethyl lactate and BASF's Agnique® AMD 3L (N,N-dimethyl lactamide, DML). The pre-disproportionation of Cu(I)Br in the presence of tris[2-(dimethylamino)ethyl]amine (Me6TREN) in water generated nascent Cu(0) and Cu(II) complexes that facilitated the fast polymerization of N-tetrahydrofurfuryl lactamide and N,N-dimethyl lactamide acrylate monomers (THFLA and DMLA, respectively) up to near-quantitative conversion with excellent control over molecular weight (5000 < Mn < 83 000) and dispersity (1.05 < Đ < 1.16). Interestingly, poly(THFLA) showed a degree of polymerization and concentration dependent LCST behavior, which can be fine-tuned (Tcp = 12–62 °C) through random copolymerization with the more hydrophilic DMLA monomer. Finally, covalent cross-linking of these polymers resulted in a new family of thermo-responsive hydrogels with excellent biocompatibility and tunable swelling and LCST transition. These illustrate the versatility of these neoteric green polymers in the preparation of smart and biocompatible soft materials.
- ItemShort-Range Cooperative Slow-down of Water Solvation Dynamics Around SO42--Mg2+ Ion Pairs(Washington, DC : American Chemical Society, 2022) Kundu, Achintya; Mamatkulov, Shavkat I.; Brünig, Florian N.; Bonthuis, Douwe Jan; Netz, Roland R.; Elsaesser, Thomas; Fingerhut, Benjamin P.The presence of ions affects the structure and dynamics of water on a multitude of length and time scales. In this context, pairs of Mg2+ and SO42- ions in water constitute a prototypical system for which conflicting pictures of hydration geometries and dynamics have been reported. Key issues are the molecular pair and solvation shell geometries, the spatial range of electric interactions, and their impact on solvation dynamics. Here, we introduce asymmetric SO42- stretching vibrations as new and most specific local probes of solvation dynamics that allow to access ion hydration dynamics at the dilute concentration (0.2 M) of a native electrolyte environment. Highly sensitive heterodyne 2D-IR spectroscopy in the fingerprint region of the SO42- ions around 1100 cm-1 reveals a specific slow-down of solvation dynamics for hydrated MgSO4 and for Na2SO4 in the presence of Mg2+ ions, which manifests as a retardation of spectral diffusion compared to aqueous Na2SO4 solutions in the absence of Mg2+ ions. Extensive molecular dynamics and density functional theory QM/MM simulations provide a microscopic view of the observed ultrafast dephasing and hydration dynamics. They suggest a molecular picture where the slow-down of hydration dynamics arises from the structural peculiarities of solvent-shared SO42--Mg2+ ion pairs.
- ItemRegulatory impact of the C-terminal tail on charge transfer pathways in drosophila cryptochrome(Basel : MDPI, 2020) Richter, Martin; Fingerhut, Benjamin P.Interconnected transcriptional and translational feedback loops are at the core of the molecular mechanism of the circadian clock. Such feedback loops are synchronized to external light entrainment by the blue light photoreceptor cryptochrome (CRY) that undergoes conformational changes upon light absorption by an unknown photoexcitation mechanism. Light-induced charge transfer (CT) reactions in Drosophila CRY (dCRY) are investigated by state-of-the-art simulations that reveal a complex, multi-redox site nature of CT dynamics on the microscopic level. The simulations consider redox-active chromophores of the tryptophan triad (Trp triad) and further account for pathways mediated by W314 and W422 residues proximate to the C-terminal tail (CTT), thus avoiding a pre-bias to specific W-mediated CT pathways. The conducted dissipative quantum dynamics simulations employ microscopically derived model Hamiltonians and display complex and ultrafast CT dynamics on the picosecond timescale, subtly balanced by the electrostatic environment of dCRY. In silicio point mutations provide a microscopic basis for rationalizing particular CT directionality and demonstrate the degree of electrostatic control realized by a discrete set of charged amino acid residues. The predicted participation of CT states in proximity to the CTT relates the directionality of CT reactions to the spatial vicinity of a linear interaction motif. The results stress the importance of CTT directional charge transfer in addition to charge transfer via the Trp triad and call for the use of full-length CRY models including the interactions of photolyase homology region (PHR) and CTT domains. © 2020 by the authors. Licensee MDPI, Basel, Switzerland.
- ItemTransient spin injection efficiencies at ferromagnet/metal interfaces(Weinheim : Wiley-VCH, 2022-10-19) Elliott, Peter; Eschenlohr, Andrea; Chen, Jinghao; Shallcross, Sam; Bovensiepen, Uwe; Dewhurst, John Kay; Sharma, SangeetaSpin injection across interfaces driven by ultrashort optical pulses on femtosecond timescales constitutes a new way to design spintronics applications. Targeted utilization of this phenomenon requires knowledge of the efficiency of non-equilibrium spin injection. From a quantitative comparison of ab initio time-dependent density functional theory and interface-sensitive, time-resolved non-linear optical experiment, the spin injection efficiency (SIE) at the Co/Cu(001) interface is determined, and its microscopic origin, i.e., the influence of spin-orbit coupling and the interface electronic structure, is discussed. Moreover, we theoretically predict that the SIE at ferromagnetic–metal interfaces can be optimized through laser pulse and materials parameters, namely the fluence, pulse duration, and substrate material.
- ItemTwo-color two-dimensional terahertz spectroscopy: A new approach for exploring even-order nonlinearities in the nonperturbative regime(Melville, NY : American Institute of Physics, 2021) Woerner, Michael; Ghalgaoui, Ahmed; Reimann, Klaus; Elsaesser, ThomasNonlinear two-dimensional terahertz (2D-THz) spectroscopy at frequencies of the emitted THz signal different from the driving frequencies allows for exploring the regime of (off-)resonant even-order nonlinearities in condensed matter. To demonstrate the potential of this method, we study two phenomena in the nonlinear THz response of bulk GaAs: (i) The nonlinear THz response to a pair of femtosecond near-infrared pulses unravels novel fourth- and sixth-order contributions involving interband shift currents, Raman-like excitations of transverse-optical phonon and intervalence-band coherences. (ii) Transient interband tunneling of electrons driven by ultrashort mid-infrared pulses can be effectively controlled by a low-frequency THz field with amplitudes below 50 kV/cm. The THz field controls the electron–hole separation modifying decoherence and the irreversibility of carrier generation.
- ItemZwitterionic Dendrimersomes: A Closer Xenobiotic Mimic of Cell Membranes(Weinheim : Wiley-VCH, 2022-10-31) Joseph, Anton; Wagner, Anna M.; Garay-Sarmiento, Manuela; Aleksanyan, Mina; Haraszti, Tamás; Söder, Dominik; Georgiev, Vasil N.; Dimova, Rumiana; Percec, Virgil; Rodriguez-Emmenegger, CesarBuilding functional mimics of cell membranes is an important task toward the development of synthetic cells. So far, lipid and amphiphilic block copolymers are the most widely used amphiphiles with the bilayers by the former lacking stability while membranes by the latter are typically characterized by very slow dynamics. Herein, a new type of Janus dendrimer containing a zwitterionic phosphocholine hydrophilic headgroup (JDPC) and a 3,5-substituted dihydrobenzoate-based hydrophobic dendron is introduced. JDPC self-assembles in water into zwitterionic dendrimersomes (z-DSs) that faithfully recapitulate the cell membrane in thickness, flexibility, and fluidity, while being resilient to harsh conditions and displaying faster pore closing dynamics in the event of membrane rupture. This enables the fabrication of hybrid DSs with components of natural membranes, including pore-forming peptides, structure-directing lipids, and glycans to create raft-like domains or onion vesicles. Moreover, z-DSs can be used to create active synthetic cells with life-like features that mimic vesicle fusion and motility as well as environmental sensing. Despite their fully synthetic nature, z-DSs are minimal cell mimics that can integrate and interact with living matter with the programmability to imitate life-like features and beyond.