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7. Ultrafast myoglobin structural dynamics observed with an X-ray free-electron laser

Author

LEVANTINO, Matteo, Schirò, G, Lemke, HT, COTTONE, Grazia, Glownia, JM, Zhu, D, Chollet, M, Ihee, H, CUPANE, Antonio, Cammarata, M., Department of Physics and Chemistry, Università degli studi di Palermo - University of Palermo, Institut de biologie structurale (IBS - UMR 5075 ), Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), SLAC National Accelerator Laboratory (SLAC), Stanford University, Korea Advanced Institute of Science and Technology (KAIST), Center for Nanomaterials and Chemical Reactions, Institute for Basic Science [Daejeon] (IBS), Institut de Physique de Rennes (IPR), Université de Rennes (UR)-Centre National de la Recherche Scientifique (CNRS), Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Centre National de la Recherche Scientifique (CNRS), Levantino, M, Schirò, G, Lemke, HT, Cottone, G, Glownia, JM, Zhu, D, Chollet, M, Ihee, H, Cupane, A, and Cammarata, M

Subjects
Biologia Strutturale, [PHYS]Physics [physics], Quantitative Biology::Biomolecules, Photolysis, Time Factors, Light, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], Biofisica, Myoglobin, Protein Conformation, Lasers, [PHYS.PHYS.PHYS-BIO-PH]Physics [physics]/Physics [physics]/Biological Physics [physics.bio-ph], Dinamica delle Proteine, Molecular Dynamics Simulation, Crystallography, X-Ray, Biological sciences Biochemistry Biophysics, Settore FIS/07 - Fisica Applicata(Beni Culturali, Ambientali, Biol.e Medicin), Article, [PHYS.PHYS.PHYS-GEN-PH]Physics [physics]/Physics [physics]/General Physics [physics.gen-ph], [SDV.BBM.BP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biophysics, Animals, Horses, sense organs, Physics::Chemical Physics
Abstract

Light absorption can trigger biologically relevant protein conformational changes. The light-induced structural rearrangement at the level of a photoexcited chromophore is known to occur in the femtosecond timescale and is expected to propagate through the protein as a quake-like intramolecular motion. Here we report direct experimental evidence of such ‘proteinquake’ observed in myoglobin through femtosecond X-ray solution scattering measurements performed at the Linac Coherent Light Source X-ray free-electron laser. An ultrafast increase of myoglobin radius of gyration occurs within 1 picosecond and is followed by a delayed protein expansion. As the system approaches equilibrium it undergoes damped oscillations with a ~3.6-picosecond time period. Our results unambiguously show how initially localized chemical changes can propagate at the level of the global protein conformation in the picosecond timescale., Localized chemical events such as the breakage of a bond between a protein and a ligand may trigger a global protein conformational change. Here, the authors use an X-ray free-electron laser to track the motion of myoglobin in response to photoinduced ligand release, and observe a picosecond proteinquake.

Published
2015

8. Impulsive solvent heating probed by picosecond x-ray diffraction.

Author

Cammarata, M., Lorenc, M., Kim, T. K., Lee, J. H., Kong, Q. Y., Pontecorvo, E., Lo Russo, M., Schiró, G., Cupane, A., Wulff, M., and Ihee, H.

Subjects
X-ray diffraction, OPTICAL diffraction, THERMAL expansion, CHEMICAL reactions, SOLVENTS, SOLUTION (Chemistry), MOLECULAR dynamics
Abstract

The time-resolved diffraction signal from a laser-excited solution has three principal components: the solute-only term, the solute-solvent cross term, and the solvent-only term. The last term is very sensitive to the thermodynamic state of the bulk solvent, which may change during a chemical reaction due to energy transfer from light-absorbing solute molecules to the surrounding solvent molecules and the following relaxation to equilibrium with the environment around the scattering volume. The volume expansion coefficient α for a liquid is typically ∼1×10-3 K-1, which is about 1000 times greater than for a solid. Hence solvent scattering is a very sensitive on-line thermometer. The decomposition of the scattered x-ray signal has so far been aided by molecular dynamics (MD) simulations, a method capable of simulating the solvent response as well as the solute term and solute/solvent cross terms for the data analysis. Here we present an experimental procedure, applicable to most hydrogen containing solvents, that directly measures the solvent response to a transient temperature rise. The overtone modes of OH stretching and CH3 asymmetric stretching in liquid methanol were excited by near-infrared femtosecond laser pulses at 1.5 and 1.7 μm and the ensuing hydrodynamics, induced by the transfer of heat from a subset of excited CH3OH* to the bulk and the subsequent thermal expansion, were probed by 100 ps x-ray pulses from a synchrotron. The time-resolved data allowed us to extract two key differentials: the change in the solvent diffraction from a temperature change at constant density, seen at a very short time delay ∼100 ps, and a term from a change in density at constant temperature. The latter term becomes relevant at later times ∼1 μs when the bulk of liquid expands to accommodate its new temperature at ambient pressure. These two terms are the principal building blocks in the hydrodynamic equation of state, and they are needed in a self-consistent reconstruction of the solvent response during a chemical reaction. We compare the experimental solvent terms with those from MD simulations. The use of experimentally determined solvent differentials greatly improved the quality of global fits when applied to the time-resolved data for C2H4I2 dissolved in methanol. [ABSTRACT FROM AUTHOR]

Published
2006
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9. Recombination of photodissociated iodine: A time-resolved x-ray-diffraction study.

Author

Wulff, M., Bratos, S., Plech, A., Vuilleumier, R., Mirloup, F., Lorenc, M., Kong, Q., and Ihee, H.

Subjects
X-ray diffractometers, X-ray diffraction, PHYSICAL & theoretical chemistry, OPTICAL diffraction, THERMODYNAMICS, NUCLEAR physics
Abstract

A time-resolved x-ray-diffraction experiment is presented that aims to study the recombination of laser-dissociated iodine molecules dissolved in CCl4. This process is monitored over an extended time interval from pico- to microseconds. The variations of atom-atom distances are probed with a milliangstrom resolution. A recent theory of time-resolved x-ray diffraction is used to analyze the experimental data; it employs the correlation function approach of statistical mechanics. The most striking outcome of this study is the experimental determination of time-dependent I–I atom-atom distribution functions. The structure of the CCl4 solvent changes simultaneously; the solvent thus appears as a reaction partner rather than an inert medium hosting it. Thermal expansion of the system is nonuniform in time, an effect due to the presence of the acoustic horizon. One concludes that a time-resolved x-ray diffraction permits real-time visualization of solvent and solute motions during a chemical reaction. [ABSTRACT FROM AUTHOR]

Published
2006
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10. Hemoglobin dynamics probed by picosecond wide-angle x-ray scattering

Author

CAMMARATA M, SCHOTTE F, EWALD F, IHEE H, ANFINRUD PA, WULFF M., LEVANTINO, Matteo, CUPANE, Antonio, CAMMARATA M, LEVANTINO M, SCHOTTE F, EWALD F, IHEE H, CUPANE A, ANFINRUD PA, and WULFF M

Subjects
conformational change, protein dynamic, X-ray scattering
Published
2008

11. Tracking the structural dynamics of proteins in solution using time-resolved wide-angle X-ray scattering (vol 5, pg 881, 2008)

Author

Cammarata, M, Schotte, F, Anfinrud, PA, Ewald, F, Choi, J, Wulff M, Ihee H., LEVANTINO, Matteo, CUPANE, Antonio, Cammarata, M, Levantino, M, Schotte, F, Anfinrud, PA, Ewald, F, Choi, J, Cupane A, Wulff M, and Ihee H

Subjects
CONFORMATIONAL-CHANGES, BIOLOGICAL MACROMOLECULES, QUATERNARY STRUCTURE, LASER PHOTOLYSIS, Settore FIS/07 - Fisica Applicata(Beni Culturali, Ambientali, Biol.e Medicin)
Published
2008

12. Tracking protein motions in solution

Author

CAMMARATA M, SCHOTTE F, IHEE H, WULFF M, ANFINRUD PA, LEVANTINO, Matteo, CUPANE, Antonio, CAMMARATA M, LEVANTINO M, SCHOTTE F, IHEE H, WULFF M, CUPANE A, and ANFINRUD PA

Published
2007

15. XFEL: The European X-Ray Free-Electron Laser - Technical Design Report

Author

Abela, R., Aghababyan, A., Altarelli, M., Altucci, C., Amatuni, G., Anfinrud, P., Audebert, P., Ayvazyan, V., Baboi, N., Baehr, J., Balandin, V., Bandelmann, R., Becker, J., Beutner, B., Blome, C., Bohnet, I., Bolzmann, A., Bostedt, C., Bozhko, Y., Brandt, A., Bratos, S., Bressler, C., Brovko, O., Brück, H., Carneiro, J.-P., Casalbuoni, S., Castellano, M., Castro, P., Catani, L., Cavalleri, A., Celik, S., Chapman, H., Charalambidis, D., Chen, J., Chergui, M., Choroba, S., Cianchi, A., Clausen, M., Collet, E., Danared, H., David, C., Decking, W., Dehler, M., Delsim-Hashemi, H., Dipirro, G., Dobson, B., Dohlus, M., Duesterer, S., Eckhardt, A., Eckoldt, H.-J., Edwards, H., Faatz, B., Fajardo, M., Fateev, A., Feldhaus, J., Filipov, Y., Floettmann, K., Follath, R., Fominykh, B., French, M., Frisch, J., Froehlich, L., Gadwinkel, E., García-Tabarés, L., Gareta, J. J., Garvey, T., Gel'mukhanov, F., Gensch, U., Gerth, C., Goerler, M., Golubeva, N., Graafsma, H., Graeff, W., Grimm, O., Griogoryan, B., Grübel, G., Gutt, C., Hacker, K., Haenisch, L., Hahn, U., Hajdu, J., Han, J. H., Hartrott, M., Havlicek, J., Hensler, O., Honkavaara, K., Honkimäki, V., Hott, T., Howells, M. R., Huening, M., Ihee, H., Ilday, F. Ö., Ischebeck, R., Jablonka, M., Jaeschke, E., Jensch, K., Jensen, J.-P., Johnson, S., Juha, L., Kaerntner, F., Kammering, R., Kapitza, H., Katalev, V., Keil, B., Khodyachykh, S., Kienberger, R., Kim, J.-W., Kim, Y., Klose, K., Kocharyan, V., Koehler, W., Koerfer, M., Kollewe, M., Kong, Q., Kook, W., Kostin, D., Kozlov, O., Kraemer, D., Krasilnikov, M., Krause, B., Krebs, O., Krzywinski, J., Kube, G., Kuhlmann, M., Laich, H., Lange, R., Larsson, M., Lee, R. W., Leuschner, A., Lierl, H., Lilje, L., Limberg, T., Lindenberg, A., Lipka, D., Loehl, F., Ludwig, K., Luong, M., Magne, C., Maquet, A., Marangos, J., Masciovecchio, C., Maslov, M., Matheisen, A., Matyushevskiy, E., Matzen, O., May, H.-J., McNulty, I., McCormick, D., Meulen, P., Meyners, N., Michelato, P., Mildner, N., Miltchev, V., Minty, M., Moeller, W.-D., Möller, T., Monaco, L., Nagl, M., Napoly, O., Neubauer, G., Nicolosi, P., Nienhaus, A., Noelle, D., Nunez, T., Obier, F., Oppelt, A., Pagani, C., Paparella, R., Pedersen, H. B., Petersen, B., Petrosyan, B., Petrosyan, L., Petrov, A., Pflueger, J., Piot, P., Plech, A., Ploenjes, E., Poletto, L., Pöplau, G., Prat, E., Prat, S., Prenting, J., Proch, D., Pugachov, D., Quack, H., Racky, B., Ramert, D., Redlin, H., Rehlich, K., Reininger, R., Remde, H., Reschke, D., Richter, D., Richter, M., Riemann, S., Riley, D., Robinson, I., Roensch, J., Rosmej, F., Ross, M., Rossbach, J., Rybnikov, V., Sachwitz, M., Saldin, E., Sandner, W., Schäfer, J., Schilcher, T., Schlarb, H., Schloesser, M., Schlott, V., Schmidt, B., Schmitz, M., Schmueser, P., Schneider, J., Schneidmiller, E., Schotte, F., Schrader, S., Schreiber, S., Schroer, C., Schuch, R., Schulte-Schrepping, H., Schwarz, A., Seidel, M., Sekutowicz, J., Seller, P., Sellmann, D., Senf, F., Sertore, D., Shabunov, A., Simrock, S., Singer, W., Sinn, H., Smith, R., Sombrowski, E., Sorokin, A. A., Springate, E., Staack, M., Staykov, L., Steffen, B., Stephenson, B., Stephan, F., Stulle, F., Syresin, E., Sytchev, K., Sytchev, V., Tallents, G., Techert, S., Tesch, N., Thom, H., Tiedtke, K., Tischer, M., Tolan, M., Toleikis, S., Toral, F., Treusch, R., Trines, D., Tsakanov, V., Tsakov, I., Tschentscher, T., Ullrich, F.-R., van Rienen, U., Variola, A., Vartaniants, I., Vogel, E., Vogel, J., Vuilleumier, R., Wabnitz, H., Wanzenberg, R., Wark, J. S., Weddig, H., Weiland, T., Weise, H., Wendt, M., Wenndorff, R., Wichmann, R., Will, I., Winter, A., Witte, K., Wittenburg, K., Wochner, P., Wohlenberg, T., Wojtkiewicz, J., Wolf, A., Wulff, M., Yurkov, M., Zagorodnov, I., Zambolin, P., Zapfe, K., Zeitoun, P., Ziemann, V., Zolotov, A., Brinkmann, R., and Grabosch, H.-J.

Subjects
Physics
Abstract

This report contains a comprehensive technical description of a new international research infrastructure, the European X-Ray Free-Electron Laser (XFEL) Facility. It was written between October 2005 and June 2006 and provides a realistic cost estimate and a compelling assessment of the scientific pay-off. The report has been prepared with the contribution of hundreds of people from many laboratories in Europe and even beyond. Their contributions have been harmonised and merged by many editors, and the whole effort has been coordinated by the European Project Team, generously supported and hosted by the Deutsches Elektronen-Synchrotron (DESY) laboratory.

Published
2006
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23. Signaling state of Photoactive Yellow Protein

Author

Ramachandran, P.L., primary, Lovett, J.E., additional, Carl, P.J., additional, Cammarata, M., additional, Lee, J.H., additional, Yang, J.O., additional, Ihee, H., additional, Timmel, C.R., additional, and van Thor, J., additional

Published
2011
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32. Time-resolved macromolecular crystallography: molecular movies?

Author

Moffat, K., primary, Srajer, V., additional, Pahl, R., additional, Ren, Z., additional, Schmidt, M., additional, Anderson, S., additional, Crosson, S., additional, Perman, B., additional, Rajagopal, S., additional, Ihee, H., additional, Bourgeois, D., additional, and Wulff, M., additional

Published
2002
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38. Ultrafast Electron Diffraction and Structural Dynamics:  Transient Intermediates in the Elimination Reaction of C<INF>2</INF>F<INF>4</INF>I<INF>2</INF>

Author

Ihee, H., Goodson, B. M., Srinivasan, R., Lobastov, V. A., and Zewail, A. H.

Abstract

We give a full account of our earlier report on the structural dynamics in the elimination reaction of C2F4I2, as studied with the newly constructed third-generation apparatus for ultrafast electron diffraction (UED3) at Caltech (Ihee, H.; Lobastov, V. A.; Gomez, U., Goodson B. M.; Srinivasan, R.; Ruan, C.-Y.; Zewail, A. H. Science 2000, 291, 458). Improvements in experimental stability, sensitivity, resolution, and versatility provided by UED3 permitted the reaction to be probed with spatial and temporal resolution of ~1 ps and ~0.01 Å, respectively, and with a sensitivity to chemical change of ~1%. In addition to the improvements in apparatus design, a number of advancements in data processing, analysis, and modeling were developed which are described here in detail for the first time. With UED, we directly observed the prompt (within 5 ps) formation of the C2F4I transient structure, and its subsequent decay with a rate of (25 ± 7 ps)-1. The molecular structure of the C2F4I radical was determined to be classical, not bridged&sbd;and was refined via a least-squares fitting procedure. These experimental results are compared with recent predictions obtained from ab initio and density functional theory calculations (Ihee, H.; Kua, J.; Goddard, W. A.; Zewail A. H. J. Phys. Chem. A 2001, 105, 3623), yielding quantitative agreement to within 0.03 Å between the experimental and theoretical structures for the transient intermediate.

Published
2002
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39. CF<INF>2</INF>XCF<INF>2</INF>X and CF<INF>2</INF>XCF<INF>2</INF>• Radicals (X = Cl, Br, I):  Ab Initio and DFT Studies and Comparison with Experiments

Author

Ihee, H., Kua, J., Goddard, W. A.; III, and Zewail, A. H.

Abstract

1,2-dihalotetrafluoroethanes (CF2XCF2X, X = I, Br and Cl) and halotetrafluoroethyl radicals (CF2XCF2•, 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 CF2XCF2X molecule and CF2XCF2• 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 CF2XCF2X were also calculated and compared with available experimental data. The CF2XCF2• radicals show dramatically different behavior compared with haloethyl radicals (CH2XCH2•). The CF2XCF2• radical has two minima and two saddle points, whereas CH2XCH2• radical has only one minimum and one saddle point in the rotational energy surface. In addition, the bridged structures are not stable for CF2XCF2• radicals in contrast with CH2XCH2• radicals. The origin of these differences is attributed to differences in the environment of the radical center. The calculated structures of the CF2ICF2• 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.

Published
2001

40. Conformations and Barriers of Haloethyl Radicals (CH<INF>2</INF>XCH<INF>2</INF>, X = F, Cl, Br, I):  Ab Initio Studies

Author

Ihee, H., Zewail, A. H., and Goddard, W. A., III

Abstract

Radicals such as CH2XCH2•, where X is a halogen, play an important role in the stereochemical control observed in many chemical reactions. To elucidate the origin of the stereoselectivity, we calculated the structures and potential energy surfaces of the haloethyl radicals (CH2XCH2•, X = F, Cl, Br, I) using ab initio quantum mechanics [HF, local MP2, DFT (both B3PW91 and B3LYP)]. We find that the CH2BrCH2• and CH2ICH2• radicals strongly favor the symmetrically bridged structures while the CH2ClCH2• radical leads to similar energy for symmetric bridging and classical structures. (In contrast, X = H and F leads to dramatically different structures). This confirms the Skell hypothesis of symmetric bridging to explain the stereochemical control of the CH2BrCH2• and CH2ICH2• radicals, indicating that such bridged structures play an important role in the dissociation processes involving CH2XCH2• with X = Cl, Br, and I. The trends in the rotational barriers and structural parameters are consistent with hyperconjugation between the singly occupied carbon 2p orbital and the σ*(C-X) MO. We find that the rotational barrier, bridged structure, and dissociation of the radicals are described much more accurately using DFT (with GGA) than with HF or LMP2.

Published
1999

45. Tracking the structural dynamics of proteins in solution using time-resolved wide-angle X-ray scattering

Author

Michael Wulff, Jungkweon Choi, Antonio Cupane, Friedrich Schotte, Hyotcherl Ihee, Friederike Ewald, Matteo Levantino, Philip A. Anfinrud, Marco Cammarata, CAMMARATA, M, LEVANTINO, M, SCHOTTE, F, ANFINRUD, PA, EWALD, F, CHOI, J, CUPANE, A, WULFF, M, and IHEE, H

Subjects
Materials science, Protein Conformation, Crystallography, X-Ray, Biochemistry, Sensitivity and Specificity, Article, chemistry.chemical_compound, Hemoglobins, Protein structure, Scattering, Radiation, Spectroscopy, Wide-angle X-ray scattering, Molecular Biology, protein dynamics, conformational changes, hemoglobin, myoglobin, cytochrome c, Scattering, Myoglobin, X-Rays, Resolution (electron density), Cytochromes c, Cell Biology, Nanosecond, chemistry, Chemical physics, Protein quaternary structure, sense organs, Biotechnology
Abstract

We demonstrate tracking of protein structural changes with time-resolved wide-angle X-ray scattering (TR-WAXS) with nanosecond time resolution. We investigated the tertiary and quaternary conformational changes of human hemoglobin under nearly physiological conditions triggered by laser-induced ligand photolysis. We also report data on optically induced tertiary relaxations of myoglobin and refolding of cytochrome c to illustrate the wide applicability of the technique. By providing insights into the structural dynamics of proteins functioning in their natural environment, TR-WAXS complements and extends results obtained with time-resolved optical spectroscopy and X-ray crystallography.

Published
2008

46. Impulsive solvent heating probed by picosecond x-ray diffraction

Author

Jae Hyuk Lee, Marco Cammarata, Qingyu Kong, Maciej Lorenc, M. Lo Russo, E. Pontecorvo, Hyotcherl Ihee, Antonio Cupane, Giorgio Schirò, Michael Wulff, Tae Kyu Kim, CAMMARATA M, LORENC M, KIM TK, LEE JH, KONG QY, PONTECORVO E, LO RUSSO M, SCHIRO G, CUPANE A, WULFF M, and IHEE H

Subjects
Hot Temperature, Time Factors, Light, Analytical chemistry, Theta solvent, General Physics and Astronomy, Thermal expansion, Molecular dynamics, X-Ray Diffraction, Scattering, Radiation, Physics::Chemical Physics, Physical and Theoretical Chemistry, Spectroscopy, Near-Infrared, Chemistry, Physical, Chemistry, Lasers, Methanol, scattering, Relaxation (NMR), Temperature, Solvation, x rays, Solutions, Solvent, Chemical physics, Excited state, X ray absorption spectroscopy, Solvents, Thermodynamics, Spectrophotometry, Ultraviolet, Solvent effects
Abstract

The time-resolved diffraction signal from a laser-excited solution has three principal components: the solute-only term, the solute-solvent cross term, and the solvent-only term. The last term is very sensitive to the thermodynamic state of the bulk solvent, which may change during a chemical reaction due to energy transfer from light-absorbing solute molecules to the surrounding solvent molecules and the following relaxation to equilibrium with the environment around the scattering volume. The volume expansion coefficient alpha for a liquid is typically approximately 1 x 10(-3) K(-1), which is about 1000 times greater than for a solid. Hence solvent scattering is a very sensitive on-line thermometer. The decomposition of the scattered x-ray signal has so far been aided by molecular dynamics (MD) simulations, a method capable of simulating the solvent response as well as the solute term and solute/solvent cross terms for the data analysis. Here we present an experimental procedure, applicable to most hydrogen containing solvents, that directly measures the solvent response to a transient temperature rise. The overtone modes of OH stretching and CH3 asymmetric stretching in liquid methanol were excited by near-infrared femtosecond laser pulses at 1.5 and 1.7 microm and the ensuing hydrodynamics, induced by the transfer of heat from a subset of excited CH3OH* to the bulk and the subsequent thermal expansion, were probed by 100 ps x-ray pulses from a synchrotron. The time-resolved data allowed us to extract two key differentials: the change in the solvent diffraction from a temperature change at constant density, seen at a very short time delay approximately 100 ps, and a term from a change in density at constant temperature. The latter term becomes relevant at later times approximately 1 mus when the bulk of liquid expands to accommodate its new temperature at ambient pressure. These two terms are the principal building blocks in the hydrodynamic equation of state, and they are needed in a self-consistent reconstruction of the solvent response during a chemical reaction. We compare the experimental solvent terms with those from MD simulations. The use of experimentally determined solvent differentials greatly improved the quality of global fits when applied to the time-resolved data for C2H4I2 dissolved in methanol.

Published
2006

47. Photoinduced Group Transposition via Iridium-Nitrenoid Leading to Amidative Inner-Sphere Aryl Migration.

Author

Jung H, Choi J, Kim D, Lee JH, Ihee H, Kim D, and Chang S

Abstract

We herein report a fundamental mechanistic investigation into photochemical metal-nitrenoid generation and inner-sphere transposition reactivity using organometallic photoprecursors. By designing Cp*Ir(hydroxamate)(Ar) complexes, we induced photo-initiated ligand activation, allowing us to explore the amidative σ(Ir-aryl) migration reactivity. A combination of experimental mechanistic studies, femtosecond transient absorption spectroscopy, and density functional theory (DFT) calculations revealed that the metal-to-ligand charge transfer enables the σ(N-O) cleavage, followed by Ir-acylnitrenoid generation. The final inner-sphere σ(Ir-aryl) group migration results in a net amidative group transposition., (© 2024 Wiley-VCH GmbH.)

Published
2024
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48. Ultrafast Interfacial Charge Transfer Initiates Mechanical Stress and Heat Transport at the Au-TiO 2 Interface.

Author

Heo J, Segalina A, Kim D, Ahn DS, Oang KY, Park S, Kim H, and Ihee H

Abstract

Metal-semiconductor interfaces are crucial components of optoelectronic and electrical devices, the performance of which hinges on intricate dynamics involving charge transport and mechanical interaction at the interface. Nevertheless, structural changes upon photoexcitation and subsequent carrier transportation at the interface, which crucially impact hot carrier stability and lifetime, remain elusive. To address this long-standing problem, they investigated the electron dynamics and resulting structural changes at the Au/TiO 2 interface using ultrafast electron diffraction (UED). The analysis of the UED data reveals that interlayer electron transfer from metal to semiconductor generates a strong coupling between the two layers, offering a new way for ultrafast heat transfer through the interface and leading to a coherent structural vibration that plays a critical role in propagating mechanical stress. These findings provide insights into the relationship between electron transfer and interfacial mechanical and thermal properties., (© 2024 The Author(s). Advanced Science published by Wiley‐VCH GmbH.)

Published
2024
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49. Time-resolved serial femtosecond crystallography for investigating structural dynamics of chemical systems.

Author

Moon J, Lee Y, and Ihee H

Abstract

Time-resolved serial femtosecond crystallography (TR-SFX) has emerged as a crucial tool for studying the structural dynamics of proteins. In principle, TR-SFX has the potential to be a powerful tool not only for studying proteins but also for investigating chemical reactions. However, non-protein systems generally face challenges in indexing due to sparse Bragg spots and encounter difficulties in effectively exciting target molecules. Nevertheless, successful TR-SFX studies on chemical systems have been recently reported in a few instances, boding well for the application of TR-SFX to study chemical reactions in the future. In this context, we review the static SFX and TR-SFX studies conducted on chemical systems reported to date and suggest prospects for future research directions.

Published
2024
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50. Structural dynamics of protein-protein association involved in the light-induced transition of Avena sativa LOV2 protein.

Author

Kim C, Yun SR, Lee SJ, Kim SO, Lee H, Choi J, Kim JG, Kim TW, You S, Kosheleva I, Noh T, Baek J, and Ihee H

Subjects
Models, Molecular, Protein Binding, Protein Domains, Avena metabolism, Plant Proteins metabolism, Plant Proteins chemistry, Light, Protein Multimerization
Abstract

The Light-oxygen-voltage-sensing domain (LOV) superfamily, found in enzymes and signal transduction proteins, plays a crucial role in converting light signals into structural signals, mediating various biological mechanisms. While time-resolved spectroscopic studies have revealed the dynamics of the LOV-domain chromophore's electronic structures, understanding the structural changes in the protein moiety, particularly regarding light-induced dimerization, remains challenging. Here, we utilize time-resolved X-ray liquidography to capture the light-induced dimerization of Avena sativa LOV2. Our analysis unveils that dimerization occurs within milliseconds after the unfolding of the A'α and Jα helices in the microsecond time range. Notably, our findings suggest that protein-protein interactions (PPIs) among the β-scaffolds, mediated by helix unfolding, play a key role in dimerization. In this work, we offer structural insights into the dimerization of LOV2 proteins following structural changes in the A'α and Jα helices, as well as mechanistic insights into the protein-protein association process driven by PPIs., (© 2024. The Author(s).)

Published
2024
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