Determining 3D intermediate structures during the biological action of proteins in real time under ambient conditions is essential for understanding how proteins function. Here we use time-resolved Laue crystallography to extract short-lived intermediate structures and thereby unveil signal transduction in the blue light photoreceptor photoactive yellow protein (PYP) from Halorhodospira halophila . By analyzing a comprehensive set of Laue data during the PYP photocycle (forty-seven time points from one nanosecond to one second), we track all atoms in PYP during its photocycle and directly observe how absorption of a blue light photon by its p -coumaric acid chromophore triggers a reversible photocycle. We identify a complex chemical mechanism characterized by five distinct structural intermediates. Structural changes at the chromophore in the early, red-shifted intermediates are transduced to the exterior of the protein in the late, blue-shifted intermediates through an initial “volume-conserving” isomerization of the chromophore and the progressive disruption of hydrogen bonds between the chromophore and its surrounding binding pocket. These results yield a comprehensive view of the PYP photocycle when seen in the light of previous biophysical studies on the system.

We report direct structural evidence of the bridged radical (CH ₂ ICH ₂ ·) in a polar solution, obtained using time-resolved liquid-phase x-ray diffraction. This transient intermediate has long been hypothesized to explain stereo-chemical control in many association and/or dissociation reactions involving haloalkanes. Ultrashort optical pulses were used to dissociate an iodine atom from the haloethane molecule (C ₂ H ₄ I ₂ ) dissolved in methanol, and the diffraction of picosecond x-ray pulses from a synchrotron supports the following structural dynamics, with ∼0.01 angstrom spatial resolution and ∼100 picosecond time resolution: The loss of one iodine atom from C ₂ H ₄ I ₂ leads to the C-I-C triangular geometry of CH ₂ ICH ₂ ·. This transient C ₂ H ₄ I then binds to an iodine atom to form a new species, the C ₂ H ₄ I-I isomer, which eventually decays into C ₂ H ₄ + I ₂ . Solvent dynamics were also extracted from the data, revealing a change in the solvent cage geometry, heating, and thermal expansion.

Covalent organic frameworks (COFs) have emerged as a promising light-harvesting module for artificial photosynthesis and photovoltaics. For efficient generation of free charge carriers, the donor–acceptor (D-A) conjugation has been adopted for two-dimensional (2D) COFs recently. In the 2D D-A COFs, photoexcitation would generate a polaron pair, which is a precursor to free charge carriers and has lower binding energy than an exciton. Although the character of the primary excitation species is a key factor in determining optoelectronic properties of a material, excited-state dynamics leading to the creation of a polaron pair have not been investigated yet. Here, we investigate the dynamics of photogenerated charge carriers in 2D D-A COFs by combining femtosecond optical spectroscopy and non-adiabatic molecular dynamics simulation. From this investigation, we elucidate that the polaron pair is formed through ultrafast intra-layer hole transfer coupled with coherent vibrations of the 2D lattice, suggesting a mechanism of phonon-assisted charge transfer.