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- ItemUltrafast phosphate hydration dynamics in bulk H2O(Melville, NY : American Institute of Physics, 2015) Costard, Rene; Tyborski, Tobias; Fingerhut, Benjamin P.; Elsaesser, ThomasPhosphate vibrations serve as local probes of hydrogen bonding and structural fluctuations of hydration shells around ions. Interactions of H2PO4− ions and their aqueous environment are studied combining femtosecond 2D infrared spectroscopy, ab-initio calculations, and hybrid quantum-classical molecular dynamics (MD) simulations. Two-dimensional infrared spectra of the symmetric (𝜈𝑆(PO−2)) and asymmetric (𝜈𝐴𝑆(PO−2)) PO−2 stretching vibrations display nearly homogeneous lineshapes and pronounced anharmonic couplings between the two modes and with the δ(P-(OH)2) bending modes. The frequency-time correlation function derived from the 2D spectra consists of a predominant 50 fs decay and a weak constant component accounting for a residual inhomogeneous broadening. MD simulations show that the fluctuating electric field of the aqueous environment induces strong fluctuations of the 𝜈𝑆(PO−2) and 𝜈𝐴𝑆(PO−2) transition frequencies with larger frequency excursions for 𝜈𝐴𝑆(PO−2). The calculated frequency-time correlation function is in good agreement with the experiment. The 𝜈(PO−2) frequencies are mainly determined by polarization contributions induced by electrostatic phosphate-water interactions. H2PO4−/H2O cluster calculations reveal substantial frequency shifts and mode mixing with increasing hydration. Predicted phosphate-water hydrogen bond (HB) lifetimes have values on the order of 10 ps, substantially longer than water-water HB lifetimes. The ultrafast phosphate-water interactions observed here are in marked contrast to hydration dynamics of phospholipids where a quasi-static inhomogeneous broadening of phosphate vibrations suggests minor structural fluctuations of interfacial water.
- ItemTopological protection versus degree of entanglement of two-photon light in photonic topological insulators([London] : Nature Publishing Group UK, 2021) Tschernig, Konrad; Jimenez-Galán, Álvaro; Christodoulides, Demetrios N.; Ivanov, Misha; Busch, Kurt; Bandres, Miguel A.; Perez-Leija, ArmandoTopological insulators combine insulating properties in the bulk with scattering-free transport along edges, supporting dissipationless unidirectional energy and information flow even in the presence of defects and disorder. The feasibility of engineering quantum Hamiltonians with photonic tools, combined with the availability of entangled photons, raises the intriguing possibility of employing topologically protected entangled states in optical quantum computing and information processing. However, while two-photon states built as a product of two topologically protected single-photon states inherit full protection from their single-photon “parents”, a high degree of non-separability may lead to rapid deterioration of the two-photon states after propagation through disorder. In this work, we identify physical mechanisms which contribute to the vulnerability of entangled states in topological photonic lattices. Further, we show that in order to maximize entanglement without sacrificing topological protection, the joint spectral correlation map of two-photon states must fit inside a well-defined topological window of protection.
- ItemTime-resolved photoelectron spectroscopy of adenine and adenosine in aqueous solution(London [u.a.] : Royal Society of Chemistry, 2013) Buchner, F.; Ritze, H.-H.; Lahl, J.; Lübcke, A.Time-resolved photoelectron spectroscopy is applied to study the excited state dynamics of the DNA base adenine and its ribonucleoside adenosine in aqueous solution for pump and probe photon energies in the range between 4.66 eV and 5.21 eV. We follow the evolution of the prepared excited state on the potential energy surface and retrieve lifetimes of the S1 state under different excitation conditions.
- 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.
- ItemCompetition between excited state proton and OH- transport via a short water wire: Solvent effects open the gate(London [u.a.] : Royal Society of Chemistry, 2014) Bekçioǧlu, G.; Allolio, C.; Ekimova, M.; Nibbering, E.T.J.; Sebastiani, D.We investigate the acid-base proton exchange reaction in a microsolvated bifunctional chromophore by means of quantum chemical calculations. The UV/vis spectroscopy shows that equilibrium of the keto-and enol-forms in the electronic ground state is shifted to the keto conformation in the excited state. A previously unknown mechanism involving a hydroxide ion transport along a short water wire is characterized energetically, which turns out to be competitive with the commonly assumed proton transport. Both mechanisms are shown to have a concerted character, as opposed to a step-wise mechanism. The alternative mechanism of a hydrogen atom transport is critically examined, and evidence for strong solvent dependence is presented. Specifically, we observe electrostatic destabilization of the corresponding πσ* state by the aqueous solvent. As a consequence, no conical intersections are found along the reaction pathway.
- ItemX-ray imaging of chemically active valence electrons during a pericyclic reaction(London : Nature Publishing Group, 2014) Bredtmann, T.; Ivanov, M.; Dixit, G.Time-resolved imaging of chemically active valence electron densities is a long-sought goal, as these electrons dictate the course of chemical reactions. However, X-ray scattering is always dominated by the core and inert valence electrons, making time-resolved X-ray imaging of chemically active valence electron densities extremely challenging. Here we demonstrate an effective and robust method, which emphasizes the information encoded in weakly scattered photons, to image chemically active valence electron densities. The degenerate Cope rearrangement of semibullvalene, a pericyclic reaction, is used as an example to visually illustrate our approach. Our work also provides experimental access to the long-standing problem of synchronous versus asynchronous bond formation and breaking during pericyclic reactions.
- ItemRole of electronic correlations in photoionization of NO2 in the vicinity of the 2A1/2B2 conical intersection(Cambridge : The Royal Soc. of Chemistry, 2017) Brambila, Danilo S.; Harvey, Alex G.; Houfek, Karel; Mašín, Zdeněk; Smirnova, OlgaWe present the first ab initio multi-channel photoionization calculations for NO2 in the vicinity of the 2A1/2B2 conical intersection, for a range of nuclear geometries, using our newly developed set of tools based on the ab initio multichannel R-matrix method. Electronic correlation is included in both the neutral and the scattering states of the molecule via configuration interaction. Configuration mixing is especially important around conical intersections and avoided crossings, both pertinent for NO2, and manifests itself via significant variations in photoelectron angular distributions. The method allows for a balanced and accurate description of the photoionization/photorecombination for a number of different ionic channels in a wide range of photoelectron energies up to 100 eV. Proper account of electron correlations is crucial for interpreting time-resolved signals in photoelectron spectroscopy and high harmonic generation (HHG) from polyatomic molecules.
- ItemA general approach for all-visible-light switching of diarylethenes through triplet sensitization using semiconducting nanocrystals(London [u.a.] : RSC, 2022) Hou, Lili; Larsson, Wera; Hecht, Stefan; Andréasson, Joakim; Albinsson, BoCoupling semiconducting nanocrystals (NCs) with organic molecules provides an efficient route to generate and transfer triplet excitons. These excitons can be used to power photochemical transformations such as photoisomerization reactions using low energy radiation. Thus, it is desirable to develop a general approach that can efficiently be used to control photoswitches using all-visible-light aiming at future applications in life- and materials sciences. Here, we demonstrate a simple ‘cocktail’ strategy that can achieve all-visible-light switchable diarylethenes (DAEs) through triplet energy transfer from the hybrid of CdS NCs and phenanthrene-3-carboxylic acid, with high photoisomerization efficiency and improved fatigue resistance. The size-tunable excitation energies of CdS NCs make it possible to precisely match the clear spectral window of the relevant DAE photoswitch. We demonstrate reversible all-visible-light photoisomerization of a series of DAE derivatives both in the liquid and solid state, even in the presence of oxygen. Our general strategy is promising for fabrication of all-visible-light activated optoelectronic devices as well as memories, and should in principle be adaptable to photopharmacology.
- ItemFemtosecond stimulated Raman spectroscopy of the cyclobutane thymine dimer repair mechanism: A computational study(Washington, DC : American Chemical Society, 2014) Ando, H.; Fingerhut, B.P.; Dorfman, K.E.; Biggs, J.D.; Mukamel, S.Cyclobutane thymine dimer, one of the major lesions in DNA formed by exposure to UV sunlight, is repaired in a photoreactivation process, which is essential to maintain life. The molecular mechanism of the central step, i.e., intradimer C-C bond splitting, still remains an open question. In a simulation study, we demonstrate how the time evolution of characteristic marker bands (C=O and C=C/C-C stretch vibrations) of cyclobutane thymine dimer and thymine dinucleotide radical anion, thymidylyl(3′→5′)-thymidine, can be directly probed with femtosecond stimulated Raman spectroscopy (FSRS). We construct a DFT(M05-2X) potential energy surface with two minor barriers for the intradimer C5-C′5 splitting and a main barrier for the C6-C′6 splitting, and identify the appearance of two C5=C6 stretch vibrations due to the C6-C′6 splitting as a spectroscopic signature of the underlying bond splitting mechanism. The sequential mechanism shows only absorptive features in the simulated FSRS signals, whereas the fast concerted mechanism shows characteristic dispersive line shapes. (Figure Presented).
- 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.