Ultrafast ring-opening and solvent-dependent product relaxation of photochromic spironaphthopyran.

The ultrafast dynamics of unsubstituted spironaphthopyran (SNP) were investigated using femtosecond transient UV and visible absorption spectroscopy in three different solvents and by semi-classical nuclear dynamics simulations. The primary ring-opening of the pyran unit was found to occur in 300 fs yielding a non-planar intermediate in the first singlet excited state (S1). Subsequent planarisation and relaxation to the product ground state proceed through barrier crossing on the S1 potential energy surface (PES) and take place within 1.1 ps after excitation. Simulations show that more than 90% of the trajectories involving C-O bond elongation lead to the planar, open-ring product, while relaxation back to the S0 of the closed-ring form is accompanied by C-N elongation. All ensuing spectral dynamics are ascribed to vibrational relaxation and thermalisation of the product with a time constant of 13 ps. The latter shows dependency on characteristics of the solvent with solvent relaxation kinetics playing a role.

Oscillatory Photoelectron Signal of N-Methylmorpholine as a Test Case for the Algebraic-Diagrammatic Construction Method of Second Order.

Motivated by recent progress in the application of time-resolved photoelectron spectroscopy (TRPES) to molecular Rydberg states, we report herein a detailed assessment of the performance of the second-order algebraic diagrammatic construction (ADC(2)) method in the simulation of their TRPES spectra. As the test case, we employ the tertiary aliphatic amine N-methylmorpholine (NMM), which is notable for the fact that the signal of its 3s state exhibits long-lived oscillations along the electron binding energy axis. The relaxation process of photoexcited NMM is simulated via the Born-Oppenheimer molecular dynamics method, and the resulting TRPES spectrum is generated on the basis of ionization energies and approximate Dyson orbital norms calculated with the continuum orbital technique. On the whole, the simulated TRPES spectrum achieves satisfactory agreement with experiment, which suggests that the ADC(2) method provides a realistic description of the potential energy surfaces of the relevant excited and ionized states. In particular, the simulations reproduce the fine oscillatory structure of the signal of the 3s state, and provide evidence to the effect that it results from a coherent vibrational wavepacket evolving along the deformation modes of the six-membered ring. However, it is found that ADC(2) underestimates electron binding energies by up to a few tenths of an electronvolt. The case of NMM demonstrates the usefulness of ADC(2) as a tool to aid the interpretation of the TRPES spectra of large organic molecules.

Energy landscapes from cryo-EM snapshots: a benchmarking study.

Biomolecules undergo continuous conformational motions, a subset of which are functionally relevant. Understanding, and ultimately controlling biomolecular function are predicated on the ability to map continuous conformational motions, and identify the functionally relevant conformational trajectories. For equilibrium and near-equilibrium processes, function proceeds along minimum-energy pathways on one or more energy landscapes, because higher-energy conformations are only weakly occupied. With the growing interest in identifying functional trajectories, the need for reliable mapping of energy landscapes has become paramount. In response, various data-analytical tools for determining structural variability are emerging. A key question concerns the veracity with which each data-analytical tool can extract functionally relevant conformational trajectories from a collection of single-particle cryo-EM snapshots. Using synthetic data as an independently known ground truth, we benchmark the ability of four leading algorithms to determine biomolecular energy landscapes and identify the functionally relevant conformational paths on these landscapes. Such benchmarking is essential for systematic progress toward atomic-level movies of continuous biomolecular function.

Time-resolved crystallography reveals allosteric communication aligned with molecular breathing.

A comprehensive understanding of protein function demands correlating structure and dynamic changes. Using time-resolved serial synchrotron crystallography, we visualized half-of-the-sites reactivity and correlated molecular-breathing motions in the enzyme fluoroacetate dehalogenase. Eighteen time points from 30 milliseconds to 30 seconds cover four turnover cycles of the irreversible reaction. They reveal sequential substrate binding, covalent-intermediate formation, setup of a hydrolytic water molecule, and product release. Small structural changes of the protein mold and variations in the number and placement of water molecules accompany the various chemical steps of catalysis. Triggered by enzyme-ligand interactions, these repetitive changes in the protein framework's dynamics and entropy constitute crucial components of the catalytic machinery.