Structural Characterization of Nanoscale Meshworks within a Nucleoporin FG Hydrogel

The permeability barrier of nuclear pore complexes (NPCs) controls all exchange of macromolecules between the cytoplasm and the cell nucleus. It consists of phenylalanine–glycine (FG) repeat domains apparently organized as an FG hydrogel. It has previously been demonstrated that an FG hydrogel derived from the yeast nucleoporin Nsp1p reproduces the selectivity of authentic NPCs. Here we combined time-resolved optical spectroscopy and X-ray scattering techniques to characterize such a gel. The data suggest a hierarchy of structures that form during gelation at the expense of unstructured elements. On the largest scale, protein-rich domains with a correlation length of ∼16.5 nm are evident. On a smaller length scale, aqueous channels with an average diameter of ∼3 nm have been found, which possibly represent the physical structures accounting for the passive sieving effect of nuclear pores. The protein-rich domains contain characteristic β-structures with typical inter-β-strand and inter-β-sheet distances of 1.3 and 0.47 nm, respectively. During gelation, the formation of oligomeric associates is accompanied by the transfer of phenylalanines into a hydrophobic microenvironment, supporting the view that this process is driven by a hydrophobic collapse

Ultrafast Dynamical Study of Pyrene-<i>N,N</i>-dimethylaniline (PyDMA) as an Organic Molecular Diode in Solid State

Femtosecond optical pump–probe spectroscopy has been employed for studying the directly linked electron donor–acceptor system pyrene-<i>N,N</i>-dimethylaniline (PyDMA) in solid state. This DMA-pyrene derivative discussed is being applied as a molecular diode system switching on an ultrafast time scale. Our ultrafast solid-state studies reveal a complex photochemistry of this molecular crystal system. Strong couplings of the optically induced charge-transfer state with the radical ion pair state allow a femtosecond transition of the latter. One could see on the highest occupied molecular orbital–lowest unoccupied molecular orbital (HOMO–LUMO) description that a pure optical transition switches the system from a conducting to a blocked system because the molecular orbitals (MOs) of DMA moiety lie in a node plane of the LUMO. Within 800 fs the system relaxes back to the ground state and/or forms a radical ion pair, which is the surprising result of our study; when the system was probed further, the system underwent vibrational cooling and enhanced population inversion of the radical ion pair

Evidence for Point Transformations in Photoactive Molecular Crystals by the Photoinduced Creation of Diffuse Diffraction Patterns

Time-resolved diffuse X-ray scattering is one powerful method for monitoring the progression from the creation of local structural changes inside a crystalline material up to the transformation of the whole crystalline bulk. In this work, we study the mechanism of phototransformation of a molecular crystal by time-resolved diffuse X-ray scattering. Here, an optical excitation source, like a pulsed laser, initiates structural transformations which are monitored by X-ray scattering techniques. We have studied the dimerization process of the molecular switch α-styrylpyrylium (trifluoromethanesulfonate) TFMS, in particular for understanding whether cooperative effects influence the changes of the structure in the bulk and its periodicity. Upon illumination with optical light, α-styrylpyrylium TFMS instantaneously photoswitches. Depending on the optical fluence, X-ray diffuse planes are observed prior to phototransformation of the bulk. In the early stages of transformation, the analysis reveals systems of randomly distributed islands of product clusters with gradual growth in size and amount. The degree of transformation follows the optical excitation profile, i.e., the spatial absorption of the laser beam. In the present studies, no influence of cooperativity on the photodimerization process has been found

Dissecting Local Atomic and Intermolecular Interactions of Transition-Metal Ions in Solution with Selective X‑ray Spectroscopy

Determining covalent and charge-transfer contributions to bonding in solution has remained an experimental challenge. Here, the quenching of fluorescence decay channels as expressed in dips in the L-edge X-ray spectra of solvated 3d transition-metal ions and complexes was reported as a probe. With a full set of experimental and theoretical ab initio L-edge X-ray spectra of aqueous Cr³⁺, including resonant inelastic X-ray scattering, we address covalency and charge transfer for this prototypical transition-metal ion in solution. We dissect local atomic effects from intermolecular interactions and quantify X-ray optical effects. We find no evidence for the asserted ultrafast charge transfer to the solvent and show that the dips are readily explained by X-ray optical effects and local atomic state dependence of the fluorescence yield. Instead, we find, besides ionic interactions, a covalent contribution to the bonding in the aqueous complex of ligand-to-metal charge-transfer character

From Ligand Fields to Molecular Orbitals: Probing the Local Valence Electronic Structure of Ni²⁺ in Aqueous Solution with Resonant Inelastic X‑ray Scattering

Bonding of the Ni²⁺(aq) complex is investigated with an unprecedented combination of resonant inelastic X-ray scattering (RIXS) measurements and ab initio calculations at the Ni L absorption edge. The spectra directly reflect the relative energies of the ligand-field and charge-transfer valence-excited states. They give element-specific access with atomic resolution to the ground-state electronic structure of the complex and allow quantification of ligand-field strength and 3d–3d electron correlation interactions in the Ni²⁺(aq) complex. The experimentally determined ligand-field strength is 10<i>Dq</i> = 1.1 eV. This and the Racah parameters characterizing 3d–3d Coulomb interactions <i>B</i> = 0.13 eV and <i>C</i> = 0.42 eV as readily derived from the measured energies match very well with the results from UV–vis spectroscopy. Our results demonstrate how L-edge RIXS can be used to complement existing spectroscopic tools for the investigation of bonding in 3d transition-metal coordination compounds in solution. The ab initio RASPT2 calculation is successfully used to simulate the L-edge RIXS spectra

L‑Edge X‑ray Absorption Spectroscopy of Dilute Systems Relevant to Metalloproteins Using an X‑ray Free-Electron Laser

L-edge spectroscopy of 3d transition metals provides important electronic structure information and has been used in many fields. However, the use of this method for studying dilute aqueous systems, such as metalloenzymes, has not been prevalent because of severe radiation damage and the lack of suitable detection systems. Here we present spectra from a dilute Mn aqueous solution using a high-transmission zone-plate spectrometer at the Linac Coherent Light Source (LCLS). The spectrometer has been optimized for discriminating the Mn L-edge signal from the overwhelming O K-edge background that arises from water and protein itself, and the ultrashort LCLS X-ray pulses can outrun X-ray induced damage. We show that the deviations of the partial-fluorescence yield-detected spectra from the true absorption can be well modeled using the state-dependence of the fluorescence yield, and discuss implications for the application of our concept to biological samples