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Lee J.S.,KAIST | Yoon I.,KAIST | Kim J.,Center for Time Resolved Diffraction | Ihee H.,Center for Time Resolved Diffraction | And 2 more authors.
Angewandte Chemie - International Edition | Year: 2011

Down to the wire: A simple vapor-transport process using linear diphenylalanine as the starting material has resulted in the self-assembly of cyclodipeptide nanowires with an orthorhombic symmetry. Furthermore, the single-crystalline nanowires exhibit a strong blue luminescence centered at 465 nm and possess semiconducting properties (see picture). © 2010 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Kim J.,Center for Time Resolved Diffraction | Kim T.K.,Pusan National University | Ihee H.,Center for Time Resolved Diffraction
Journal of Physical Chemistry A | Year: 2011

Quantum chemical calculations of CF3Br and the CF3 radical are performed using density functional theory (DFT) and time-dependent DFT (TDDFT). Molecular structures, vibrational frequencies, dipole moment, bond dissociation energy, and vertical excitation energies of CF3Br are calculated and compared with available experimental results. The performance of six hybrid and five hybrid meta functionals in DFT and TDDFT calculations are evaluated. The ωB97X, B3PW91, and M05-2X functionals give very good results for molecular structures, vibrational frequencies, and vertical excitation energies, respectively. The ωB97X functional calculates well the dipole moment of CF3Br. B3LYP, one of the most widely used functionals, does not perform well for calculations of the C - Br bond length, bond dissociation energy, and vertical excitation energies. Potential energy curves of the low-lying excited states of CF3Br are obtained using the multiconfigurational spin-orbit ab initio method. The crossing point between 2A1 and 3E states is located near the C - Br bond length of 2.45 Å. Comparison with CH3Br shows that fluorination does not alter the location of the crossing point. The relation between the calculated potential energy curves and recent experimental result is briefly discussed. © 2011 American Chemical Society.

Ibrahimkutty S.,Karlsruhe Institute of Technology | Kim J.,Center for Time Resolved Diffraction | Cammarata M.,European Synchrotron Radiation Facility | Ewald F.,European Synchrotron Radiation Facility | And 4 more authors.
ACS Nano | Year: 2011

Protein-coated gold nanoparticles in suspension are excited by intense laser pulses to mimic the light-induced effect on biomolecules that occur in photothermal laser therapy with nanoparticles as photosensitizer. Ultrafast X-ray scattering employed to access the nanoscale structural modifications of the protein nanoparticle hybrid reveals that the protein shell is expelled as a whole without denaturation at a laser fluence that coincides with the bubble formation threshold. In this ultrafast heating mediated by the nanoparticles, time-resolved scattering data show that proteins are not denatured in terms of secondary structure even at much higher temperatures than the static thermal denaturation temperature, probably because time is too short for the proteins to unfold and the temperature stimulus has vanished before this motion sets in. Consequently the laser pulse length has a strong influence on whether the end result is the ligand detachment (for example drug delivery) or biomaterial degradation. © 2011 American Chemical Society.

Ramachandran P.L.,University of Oxford | Lovett J.E.,University of Oxford | Lovett J.E.,University of Edinburgh | Carl P.J.,Bruker Biospin Gmbh | And 7 more authors.
Journal of the American Chemical Society | Year: 2011

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 1H-15N 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 I2′ 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. © 2011 American Chemical Society.

Kim K.H.,Center for Time Resolved Diffraction | Ok T.,Institute Pasteur Korea | Ok T.,KAIST | Lee K.,Korea University | And 4 more authors.
Journal of the American Chemical Society | Year: 2010

Herein we present the long-sought quantitative catalyst-substrate association relationships based on experimentally measured quantitative association preferences of diverse metathesis Mo and Ru catalysts (Mo-1, Schrock Mo; Mo-2, Schrock-Hoveyda Mo; Ru-1, Grubbs first generation Ru; Ru-2, Grubbs second generation Ru; Ru-3:, Grubbs-Hoveyda first generation Ru; and Ru-4, Grubbs-Hoveyda second generation Ru) to their substrates (alkenes, alkynes and allenes), determined directly by a general method based on FRET principle. The determined substrate preferences are proved to be dependent on the molecular identity of the catalyst, exhibiting the preference order of alkyne > alkene > allene for Mo-1 and Mo-2, allene > alkene > alkyne for Ru-1 and Ru-3, and alkyne > allene > alkene for Ru-2 and Ru-4. The results enable us to probe metathesis mechanisms by answering issues in metathesis reactions including the controversial reaction initiation in enyne or allenyne metathesis. © 2010 American Chemical Society.

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