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Hyotcherl Ihee

Publications and source records attributed to Hyotcherl Ihee.

9 recordsLinked to original sources
PubMed2006

Analyzing solution-phase time-resolved x-ray diffraction data by isolated-solute models.

Extracting transient structural information of a solute from time-resolved x-ray diffraction (TRXD) data is not trivial because the signal from a solution contains not only the solute-only term as in the gas phase, but also solvent-related terms. To obtain structural insights, the diffraction signal in q space is often Fourier sine transformed (FT) into r space, and molecular dynamics (MD) simulation-aided signal decomposition into the solute, cage, and solvent terms has so far been indispensable for a clear-cut assignment of structural features. Here we present a convenient method of comparative structural analysis without involving MD simulations by incorporating only isolated-species models for the solute. FT is applied to both the experimental data and candidate isolated-solute models, and comparison of the correlation factors between the experimental FT and the model FTs can distinguish the best candidate among isolated-solute models for the reaction intermediates. The low q region whose influence by solvent-related terms is relatively high can be further excluded, and this mode of truncated Fourier transform (TFT) improves the correlation factors and facilitates the comparison. TFT analysis has been applied to TRXD data on the photodissociation of C(2)H(4)I(2) in two different solvents (methanol and cyclohexane), HgI(2) in methanol, and I(3) (-) in methanol excited at 267 nm. The results are consistent with previous conclusions for C(2)H(4)I(2) in methanol and HgI(2) in methanol, and the new TRXD data reveal that the C(2)H(4)I transient radical has a bridged structure in cyclohexane and I(3) (-) in methanol decomposes into I+I(2) (-) upon irradiation at 267 nm. This TFT method should greatly simplify the analysis because it bypasses MD simulations.

Journal Article↗
PubMed2006

Structure of the photodissociation products of CCl4, CBr4, and CI4 in solution studied by DFT and ab initio calculations.

Various molecular species that can be populated during the photoreaction of carbon tetrahalides CX(4) (X = Cl, Br, I) in the gas phase and in solution have been studied by ab initio and density functional theory (DFT) calculations. Geometries, energies, and vibrational frequencies of CX(4), CX(3), CX(2), C(2)X(6), C(2)X(5), C(2)X(4), X(2), and the isomer X(2)CX-X were calculated and transition states connecting these species were characterized. Spin-orbit DFT (SODFT) computations were also performed to include the relativistic effects, which cannot be neglected for Br and I atoms. The calculated potential energy surfaces satisfactorily describe the reactions of the photoexcited CX(4) molecules. In the gas phase, the initial C-X bond rupture in CX(4) is followed by secondary C-X breakage in the CX(3) radical, leading to CX(2) and 2X, and the formation of C(2)X(6) or C(2)X(4) through bimolecular recombination of the CX(3) or CX(2) radicals is favored thermodynamically. In solution, by contrast, the X(2)CX-X isomer is formed via X-X binding, and two CX(3) radicals recombine nongeminately to form C(2)X(6), which then dissociates into C(2)X(4) and X(2) through C(2)X(5). The Raman intensities and the vibrational frequencies, as well as the absorption spectra and oscillator strengths of the Br(2)CBr-Br isomer in the gas phase and in various solvents were computed and the calculated absorption and Raman spectra of the Br(2)CBr-Br isomer in various solutions are in good agreement with the experimental data. The natural population analysis indicates that the Br(2)CBr-Br isomer corresponds to the recently reported solvent-stabilized solvated ion pair (CBr(3)(+)//Br(-))(solv) in the highly polar alcohol solvent. The singlet-triplet energy separations of the CX(2) radicals in the gas phase and in solution were evaluated with high level computational methods, and the optimized geometric parameters are in good agreement with the experimental results. The geometric and energetic differences between the singlet and triplet states were explained by the electronic properties of the CX(2) radicals. C(2)X(4), C(2)X(5), and C(2)X(6) (X = Br, I) in the gas phase and in solution were optimized at different computational levels, and the optimized geometric parameters of C(2)I(4) are in very good agreement with the experimental data.

Journal Article↗
PubMed2006

Spatiotemporal reaction kinetics of an ultrafast photoreaction pathway visualized by time-resolved liquid x-ray diffraction.

We have studied the reaction dynamics for HgI(2) in methanol by using time-resolved x-ray diffraction (TRXD). Although numerous time-resolved spectroscopic studies have provided ample information about the early dynamics of HgI(2), a comprehensive reaction mechanism in the solution phase spanning from picoseconds up to microseconds has been lacking. Here we show that TRXD can provide this information directly and quantitatively. Picosecond optical pulses triggered the dissociation of HgI(2), and 100-ps-long x-ray pulses from a synchrotron probed the evolving structures over a wide temporal range. To theoretically explain the diffracted intensities, the structural signal from the solute, the local structure around the solute, and the hydrodynamics of bulk solvents were considered in the analysis. The results in this work demonstrate that the determination of transient states in solution is strongly correlated with solvent energetics, and TRXD can be used as an ultrafast calorimeter. It also is shown that a manifold of structural channels can be resolved at the same time if the measurements are accurate enough and that global analysis is applied. The rate coefficients for the reactions were obtained by fitting our model against the experimental data in one global fit including all q-values and time delays. The comparison between all putative reaction channels confirms that two-body dissociation is the dominant dissociation pathway. After this primary bond breakage, two parallel channels proceed. Transient HgI associates nongeminately with an iodine atom to form HgI(2), and I(2) is formed by nongeminate association of two iodine atoms.

Journal Article↗
PubMed2005

Photodissociation reaction of 1,2-diiodoethane in solution: a theoretical and X-ray diffraction study.

Various molecular species are known to form during the photoreaction of C2H4I2 in the gas phase and in solution. We have studied all species involved in this reaction by ab initio and density functional theory (DFT) calculations: Geometries, energies, and vibrational frequencies of C2H4I2, bridged C2H4I*, anti C2H4I*, C4H4, I2, I3-, and the isomer C2H4I-I were calculated. The absorption peaks and oscillator strengths of selected species along the potential energy surface (PES) were calculated using time-dependent DFT and were compared with available experimental results. The calculated PES satisfactorily describes the observed reactions of the photoexcited C2H4I2 molecule. In the gas phase, there is only one reaction pathway: the first C-I bond ruptures followed by a secondary C-I breakage in the haloethyl radical C2H4I*. In solution, by contrast, another reaction channel, which is energetically more favored over the secondary dissociation, is switched on due to a solvation effect: the bridged C2H4I* can bind to the free iodine atom to form a C2H4I-I isomer without any energy barrier. The isomer can then break into C2H4 and I2. The rotational barriers in the gas phase and in solution were also calculated and compared. To provide experimental data on the structure of C2H4I2 in solution, the ground state structure of C2H4I2 in methanol was determined from static X-ray diffraction data using 88 keV (lambda = 0.14 A) X-rays. The structural parameters are compared with those from the theoretical results.

Computer Simulation↗
PubMed2005

Visualizing reaction pathways in photoactive yellow protein from nanoseconds to seconds.

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.

Bacterial Proteins↗
PubMed2005

Protein-ligand interaction probed by time-resolved crystallography.

Time-resolved (TR) crystallography is a unique method for determining the structures of intermediates in biomolecular reactions. The technique reached its mature stage with the development of the powerful third-generation synchrotron X-ray sources, and the advances in data processing and analysis of time-resolved Laue crystallographic data. A time resolution of 100 ps has been achieved and relatively small structural changes can be detected even from only partial reaction initiation. The remaining challenge facing the application of this technique to a broad range of biological systems is to find an efficient and rapid, system-specific method for the reaction initiation in the crystal. Other frontiers for the technique involve the continued improvement in time resolution and further advances in methods for determining intermediate structures and reaction mechanisms. The time-resolved technique, combined with trapping methods and computational approaches, holds the promise for a complete structure-based description of biomolecular reactions.

Bacterial Proteins↗
PubMed2004

Analysis of experimental time-resolved crystallographic data by singular value decomposition.

Singular value decomposition (SVD) separates time-dependent crystallographic data into time-independent and time-dependent components. Procedures for the effective application of SVD to time-resolved macromolecular crystallographic data have yet to be explored systematically. Here, the applicability of SVD to experimental crystallographic data is tested by analyzing 30 time-resolved Laue data sets spanning a time range of nanoseconds to milliseconds through the photocycle of the E46Q mutant of photoactive yellow protein. The data contain random and substantial systematic errors, the latter largely arising from crystal-to-crystal variation. The signal-to-noise ratio of weighted difference electron-density maps is significantly improved by the SVD flattening procedure. Application of SVD to these flattened maps spreads the signal across many of the 30 singular vectors, but a rotation of the vectors partitions the large majority of the signal into only five singular vectors. Fitting the time-dependent vectors to a sum of simple exponentials suggests that a chemical kinetic mechanism can describe the time-dependent structural data. Procedures for the effective SVD analysis of experimental time-resolved crystallographic data have been established and emphasize the necessity for minimizing systematic errors by modification of the data-collection protocol.

Algorithms↗
PubMed2004

Protein kinetics: structures of intermediates and reaction mechanism from time-resolved x-ray data.

We determine the number of authentic reaction intermediates in the later stages of the photocycle of photoactive yellow protein at room temperature, their atomic structures, and a consistent set of chemical kinetic mechanisms, by analysis of a set of time-dependent difference electron density maps spanning the time range from 5 micros to 100 ms. The successful fit of exponentials to right singular vectors derived from a singular value decomposition of the difference maps demonstrates that a chemical kinetic mechanism holds and that structurally distinct intermediates exist. We identify two time-independent difference maps, from which we refine the structures of the corresponding intermediates. We thus demonstrate how structures associated with intermediate states can be extracted from the experimental, time-dependent crystallographic data. Stoichiometric and structural constraints allow the exclusion of one kinetic mechanism proposed for the photocycle but retain other plausible candidate kinetic mechanisms.

Bacterial Proteins↗