CF_2XCF_2X and CF_2XCF_2• Radicals (X = Cl, Br, I): Ab Initio and DFT Studies and Comparison with Experiments

1,2-dihalotetrafluoroethanes (CF_2XCF_2X, X = I, Br and Cl) and halotetrafluoroethyl radicals (CF_2XCF_2•, X = I, Br, and Cl) have been studied by ab initio molecular-orbital techniques using restricted Hartree−Fock and Density functional theory (DFT-B3PW91). For the optimized HF geometries, we carried out local MP2 calculations to account for electron correlation effects. Each CF_2XCF_2X molecule and CF_2XCF_2• radical has two conformational minima (anti and gauche) and two rotational transition structures in the rotational energy surface along the C−C bond. The rotational barriers of the  radicals are smaller than those of the parent molecules due to the absence of the nonbonded interaction between two halogen atoms. In contrast, the conformational energy difference between two stable rotamers (anti and gauche) of each radical is larger than that in the corresponding parent molecules. This stabilizing effect on the anti conformers of the radicals is rationalized in terms of hyperconjugation between the radical center and the σ^*(C−X) molecular orbital. The dissociation energies for breaking the first and second C−X bonds of CF_2XCF_2X were also calculated and compared with available experimental data. The CF_2XCF_2• radicals show dramatically different behavior compared with haloethyl radicals (CH_2XCH_2•). The CF_2XCF_2• radical has two minima and two saddle points, whereas CH_2XCH_2• radical has only one minimum and one saddle point in the rotational energy surface. In addition, the bridged structures are not stable for CF_2XCF_2• radicals in contrast with CH_2XCH_2• radicals. The origin of these differences is attributed to differences in the environment of the radical center. The calculated structures of the CF_2ICF_2• radical were used in interpreting a recent experimental observation (Cao et al. Proc. Natl. Acad. Sci. 1999, 96, 338) and are compared with quantitative results from a new experiment (Ihee et al. Science 2001, 291, 458) using the ultrafast electron diffraction technique

CF_2XCF_2X and CF_2XCF_2• Radicals (X = Cl, Br, I): Ab Initio and DFT Studies and Comparison with Experiments

1,2-dihalotetrafluoroethanes (CF_2XCF_2X, X = I, Br and Cl) and halotetrafluoroethyl radicals (CF_2XCF_2•, X = I, Br, and Cl) have been studied by ab initio molecular-orbital techniques using restricted Hartree−Fock and Density functional theory (DFT-B3PW91). For the optimized HF geometries, we carried out local MP2 calculations to account for electron correlation effects. Each CF_2XCF_2X molecule and CF_2XCF_2• radical has two conformational minima (anti and gauche) and two rotational transition structures in the rotational energy surface along the C−C bond. The rotational barriers of the  radicals are smaller than those of the parent molecules due to the absence of the nonbonded interaction between two halogen atoms. In contrast, the conformational energy difference between two stable rotamers (anti and gauche) of each radical is larger than that in the corresponding parent molecules. This stabilizing effect on the anti conformers of the radicals is rationalized in terms of hyperconjugation between the radical center and the σ^*(C−X) molecular orbital. The dissociation energies for breaking the first and second C−X bonds of CF_2XCF_2X were also calculated and compared with available experimental data. The CF_2XCF_2• radicals show dramatically different behavior compared with haloethyl radicals (CH_2XCH_2•). The CF_2XCF_2• radical has two minima and two saddle points, whereas CH_2XCH_2• radical has only one minimum and one saddle point in the rotational energy surface. In addition, the bridged structures are not stable for CF_2XCF_2• radicals in contrast with CH_2XCH_2• radicals. The origin of these differences is attributed to differences in the environment of the radical center. The calculated structures of the CF_2ICF_2• radical were used in interpreting a recent experimental observation (Cao et al. Proc. Natl. Acad. Sci. 1999, 96, 338) and are compared with quantitative results from a new experiment (Ihee et al. Science 2001, 291, 458) using the ultrafast electron diffraction technique

Structural dynamics probed by X-ray pulses from synchrotrons and XFELs

This review focuses on how short X-ray pulses from synchrotrons and XFELs can be used to track light-induced structural changes in molecular complexes and proteins via the pump–probe method. The upgrade of the European Synchrotron Radiation Facility to a diffraction-limited storage ring, based on the seven-bend achromat lattice, and how it might boost future pump–probe experiments are described. We discuss some of the first X-ray experiments to achieve 100 ps time resolution, including the dissociation and in-cage recombination of diatomic molecules, as probed by wide-angle X-ray scattering, and the 3D filming of ligand transport in myoglobin, as probed by Laue diffraction. Finally, the use of femtosecond XFEL pulses to investigate primary chemical reactions, bond breakage and bond formation, isomerisation and electron transfer are discussed

Cooperative protein structural dynamics of homodimeric hemoglobin linked to water cluster at subunit interface revealed by time-resolved X-ray solution scattering

Homodimeric hemoglobin (HbI) consisting of two subunits is a good model system for investigating the allosteric structural transition as it exhibits cooperativity in ligand binding. In this work, as an effort to extend our previous study on wild-type and F97Y mutant HbI, we investigate structural dynamics of a mutant HbI in solution to examine the role of well-organized interfacial water cluster, which has been known to mediate intersubunit communication in HbI. In the T72V mutant of HbI, the interfacial water cluster in the T state is perturbed due to the lack of Thr72, resulting in two less interfacial water molecules than in wild-type HbI. By performing picosecond time-resolved X-ray solution scattering experiment and kinetic analysis on the T72V mutant, we identify three structurally distinct intermediates (I1, I2, and I3) and show that the kinetics of the T72V mutant are well described by the same kinetic model used for wild-type and F97Y HbI, which involves biphasic kinetics, geminate recombination, and bimolecular CO recombination. The optimized kinetic model shows that the R-T transition and bimolecular CO recombination are faster in the T72V mutant than in the wild type. From structural analysis using species-associated difference scattering curves for the intermediates, we find that the T-like deoxy I3 intermediate in solution has a different structure from deoxy HbI in crystal. In addition, we extract detailed structural parameters of the intermediates such as E-F distance, intersubunit rotation angle, and heme-heme distance. By comparing the structures of protein intermediates in wild-type HbI and the T72V mutant, we reveal how the perturbation in the interfacial water cluster affects the kinetics and structures of reaction intermediates of HbI. © 2016 Author(s)1571sciescopu

The Short-Lived Signaling State of the Photoactive Yellow Protein Photoreceptor Revealed by Combined Structural Probes

The signaling state of the photoactive yellow protein (PYP) photoreceptor is transiently developed via isomerization of its blue-light-absorbing chromophore. The associated structural rearrangements have large amplitude but, due to its transient nature and chemical exchange reactions that complicate NMR detection, its accurate three-dimensional structure in solution has been elusive. Here we report on direct structural observation of the transient signaling state by combining double electron electron resonance spectroscopy (DEER), NMR, and time-resolved pump-probe X-ray solution scattering (TR-SAXS/WAXS). Measurement of distance distributions for doubly spin-labeled photoreceptor constructs using DEER spectroscopy suggests that the signaling state is well ordered and shows that interspin-label distances change reversibly up to 19 Å upon illumination. The SAXS/WAXS difference signal for the signaling state relative to the ground state indicates the transient formation of an ordered and rearranged conformation, which has an increased radius of gyration, an increased maximum dimension, and a reduced excluded volume. Dynamical annealing calculations using the DEER derived long-range distance restraints in combination with short-range distance information from (1)H-(15)N HSQC perturbation spectroscopy give strong indication for a rearrangement that places part of the N-terminal domain in contact with the exposed chromophore binding cleft while the terminal residues extend away from the core. Time-resolved global structural information from pump-probe TR-SAXS/WAXS data supports this conformation and allows subsequent structural refinement that includes the combined energy terms from DEER, NMR, and SAXS/WAXS together. The resulting ensemble simultaneously satisfies all restraints, and the inclusion of TR-SAXS/WAXS effectively reduces the uncertainty arising from the possible spin-label orientations. The observations are essentially compatible with reduced folding of the I(2)' state (also referred to as the 'pB' state) that is widely reported, but indicates it to be relatively ordered and rearranged. Furthermore, there is direct evidence for the repositioning of the N-terminal region in the I(2)' state, which is structurally modeled by dynamical annealing and refinement calculations

Atomistic characterization of the active-site solvation dynamics of a model photocatalyst

The interactions between the reactive excited state of molecular photocatalysts and surrounding solvent dictate reaction mechanisms and pathways, but are not readily accessible to conventional optical spectroscopic techniques. Here we report an investigation of the structural and solvation dynamics following excitation of a model photocatalytic molecular system [Ir 2 (dimen) 4 ] 2+, where dimen is para-diisocyanomenthane. The time-dependent structural changes in this model photocatalyst, as well as the changes in the solvation shell structure, have been measured with ultrafast diffuse X-ray scattering and simulated with Born-Oppenheimer Molecular Dynamics. Both methods provide direct access to the solute-solvent pair distribution function, enabling the solvation dynamics around the catalytically active iridium sites to be robustly characterized. Our results provide evidence for the coordination of the iridium atoms by the acetonitrile solvent and demonstrate the viability of using diffuse X-ray scattering at free-electron laser sources for studying the dynamics of photocatalysis