Novel Single-Molecule Technique by Single-Object Scattering Sampling (SOSS)

Ihee, Hyotcherl Korean Chemical Society 2011 Bulletin of the Korean Chemical Society Vol.32 No.6

Self-Assembled Nanostructures: Role of Water in Directing Diphenylalanine Assembly into Nanotubes and Nanowires (Adv. Mater. 5/2010)

Kim, Jangbae,Han, Tae Hee,Kim, Yong-Il,Park, Ji Sun,Choi, Jungkweon,Churchill, David G.,Kim, Sang Ouk,Ihee, Hyotcherl WILEY-VCH Verlag 2010 Advanced Materials Vol.22 No.5

<B>Graphic Abstract</B> <P>The controllable assembly behavior of diphenylalanine molecules to form nanowires (NWs) and nanotubes (NTs) and their structural details are presented. Hyotcherl Ihee, Sang Ouk Kim and co-workers show on p. 583 that the nanoscale morphologies are closely related to molecular arrangements of diphenylalanine as revealed by Rietveld refinement of powder X-ray diffraction patterns and electron-density distributions in NTs and NWs via the maximum entropy method analysis. <img src='wiley_img/09359648-2010-22-5-ADMA201090007-content.gif' alt='wiley_img/09359648-2010-22-5-ADMA201090007-content'> </P>

Spin–orbit ab initio study of two low-lying states of chloroiodomethane cation

Kim, Joonghan,Ihee, Hyotcherl,Lee, Yoon Sup Springer-Verlag 2011 Theoretical chemistry accounts Vol.129 No.3

Multireference Ab Initio Study of the Ground and Low-Lying Excited States of Cr(CO)₂ and Cr(CO)₃

Kim, Joonghan,Kim, Jeongho,Ihee, Hyotcherl American Chemical Society 2013 The journal of physical chemistry. A, Molecules, s Vol.117 No.18

<P>We investigate the ground and low-lying excited states of unsaturated chromium carbonyls, Cr(CO)<SUB>2</SUB> and Cr(CO)<SUB>3</SUB>, using multiconfigurational ab initio perturbation theory. Unlike other chromium carbonyls, there are discrepancies between the experiment and theory on the identity of the ground states of Cr(CO)<SUB>2</SUB> and Cr(CO)<SUB>3</SUB>. From multireference ab initio calculations considering the full valence orbitals of Cr(CO)<SUB>2</SUB> and Cr(CO)<SUB>3</SUB>, the differences in the molecular structures of their various electronic states are explained by the electronic structure analysis. On the basis of the result from CASPT2 and MS-CASPT2 calculations, we propose that the ground states of Cr(CO)<SUB>2</SUB> and Cr(CO)<SUB>3</SUB> are the <SUP>5</SUP>Π<SUB>g</SUB> and <SUP>1</SUP>A<SUB>1</SUB> states, respectively, addressing the ambiguity regarding their ground states. In addition, the multiconfigurational ab initio perturbation theory calculations reveal that (1) the energy gaps between the ground and first low-lying excited states of Cr(CO)<SUB>2</SUB> and Cr(CO)<SUB>3</SUB> are quite small and (2) the first low-lying excited states of Cr(CO)<SUB>2</SUB> and Cr(CO)<SUB>3</SUB> have the same spin multiplicities as the ground states of CrCO and Cr(CO)<SUB>2</SUB>, respectively, which are the products of ligand dissociation. As a result, the apparent spin-forbidden dissociation of Cr(CO)<SUB>2</SUB> and Cr(CO)<SUB>3</SUB> into CrCO and Cr(CO)<SUB>2</SUB>, respectively, are likely to be facilitated by thermal excitation of the ground states of Cr(CO)<SUB>2</SUB> and Cr(CO)<SUB>3</SUB> into their first low-lying excited states, which then actually undergoes the spin-allowed dissociation to the ground states of CrCO and Cr(CO)<SUB>2</SUB> with the same spin multiplicities.</P><P><B>Graphic Abstract</B> <IMG SRC='http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jpcafh/2013/jpcafh.2013.117.issue-18/jp401128k/production/images/medium/jp-2013-01128k_0003.gif'></P><P><A href='http://pubs.acs.org/doi/suppl/10.1021/jp401128k'>ACS Electronic Supporting Info</A></P>

A Photoconductive Covalent Organic Framework: Self-Condensed Arene Cubes Composed of Eclipsed 2D Polypyrene Sheets for Photocurrent Generation

Wan, Shun,Guo, Jia,Kim, Jangbae,Ihee, Hyotcherl,Jiang, Donglin WILEY-VCH Verlag 2009 Angewandte Chemie. international edition Vol.48 No.30

<B>Graphic Abstract</B> <P>On again, off again: A pyrene-based covalent organic framework (see structure: blue pyrene, white B, red O) facilitates exciton migration and carrier transportation, harvests visible-light photons, and responds quickly to irradiation with light to enable the generation of a significant photocurrent. The framework is capable of repetitive photocurrent switching with a large on–off ratio. <img src='wiley_img/14337851-2009-48-30-ANIE200900881-content.gif' alt='wiley_img/14337851-2009-48-30-ANIE200900881-content'> </P>

Density functional and ab initio studies on structures and energies of the ground state of CrCO

Kim, Joonghan,Lee, Yoon Sup,Ihee, Hyotcherl Wiley 2007 International journal of quantum chemistry Vol.107 No.2

<P>CrCO was studied using density functional theory (DFT) and ab initio methods. We obtained the two-dimensional potential energy surface (PES), geometry, and vibrational frequencies for CrCO in a septet state. Two minimum structures were found in the CCSD(T) calculation, including a local minimum that is a weak van der Waals (vdW) complex. All DFT methods yield only one minimum structure. We demonstrate that the bond dissociation energy (0.50 kcal/mol) and vibrational frequency (1981.1 cm<SUP>−1</SUP>) of CrCO calculated using CCSD(T) are in better agreement with experimental values (<1.5 kcal/mol and 1977 cm<SUP>−1</SUP>) than any of the reported theoretical studies. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007</P>

Ultrafast X-Ray Crystallography and Liquidography

Ki, Hosung,Oang, Key Young,Kim, Jeongho,Ihee, Hyotcherl Annual Reviews 2017 Annual review of physical chemistry Vol.68 No.-

<P>Time-resolved X-ray diffraction provides direct information on three-dimensional structures of reacting molecules and thus can be used to elucidate structural dynamics of chemical and biological reactions. In this review, we discuss time-resolved X-ray diffraction on small molecules and proteins with particular emphasis on its application to crystalline (crystallography) and liquid-solution (liquidography) samples. Time-resolved X-ray diffraction has been used to study picosecond and slower dynamics at synchrotrons and can now access even femtosecond dynamics with the recent arrival of X-ray free-electron lasers.</P>

Recent advances and future prospects of serial crystallography using XFEL and synchrotron X-ray sources

Srinivasan Muniyappan,Seong Ok Kim,Hyotcherl Ihee 한국구조생물학회 2015 Biodesign Vol.3 No.2

Protein structure determination at the atomic level is an essential step for understanding protein functions and developing new drugs. However, growing crystals of sufficient quality and size necessary to obtain good diffraction patterns is a significant bottleneck. The advent of X-ray free electron lasers (XFELs) has made it possible to collect high quality X-ray diffraction patterns from nano- or micro-sized crystals because a typical XFEL pulse is intense enough to provide a diffraction pattern from such small sized crystals and is temporally short (less than 50 femtoseconds) enough to collect the diffraction pattern prior to crystal destruction or significant radiation damage. A combination of this idea and a continuous sample delivery system supplying a fresh crystal for every X-ray pulse provides a nascent field of serial femtosecond crystallography (SFX). The concept of serial crystallography (SX) is also being adapted in conventional micro- and nanofocused synchrotron beamlines, resulting in serial synchrotron crystallography (SSX). In this review, we survey and examine a variety of currently available sample delivery systems in SFX and SSX and discuss their advantages and drawbacks. We also review the protein systems studied by SFX and SSX and various protein crystallization techniques that are particularly useful for membrane proteins in the application with SFX and SSX. Finally, we highlight the applicability of the SFX and SSX methods for time-resolved studies, which offer notable new possibilities for tracking both the reversible and irreversible structural dynamics of proteins at the atomic level in real time. SSX and SFX may revolutionize the field of structural biology.

Chromophore-Removal-Induced Conformational Change in Photoactive Yellow Protein Determined through Spectroscopic and X-ray Solution Scattering Studies

Kim, Youngmin,Ganesan, Prabhakar,Jo, Junbeom,Kim, Seong Ok,Thamilselvan, Kamatchi,Ihee, Hyotcherl American Chemical Society 2018 The journal of physical chemistry. B, Condensed ma Vol.122 No.16

<P>Photoactive yellow protein (PYP) induces negative phototaxis in <I>Halorhodospira halophila</I> via photoactivation triggered by light-mediated chromophore isomerization. Chromophore isomerization proceeds via a volume-conserving isomerization mechanism due to the hydrogen-bond network and steric constraints inside the protein, and causes significant conformational changes accompanied by N-terminal protrusion. However, it is unclear how the structural change of the chromophore affects the remote N-terminal domain. To understand photocycle-related structural changes, we investigated the structural aspect of chromophore removal in PYP because it possesses a disrupted hydrogen-bond network similar to that in photocycle intermediates. A comparison of the structural aspects with those observed in the photocycle would give a clue related to the structural change mechanism in the photocycle<SUB>.</SUB> Chromophore removal effects were assessed via UV-vis spectroscopy, circular dichroism, and X-ray solution scattering. Molecular shape reconstruction and an experiment-restrained rigid-body molecular dynamics simulation based on the scattering data were performed to determine protein shape, size, and conformational changes upon PYP bleaching. Data show that chromophore removal disrupted the holo-PYP structure, resulting in a small N-terminal protrusion, but the extent of conformational changes was markedly less than those in the photocycle. This indicates that disruption of the hydrogen-bond network alone in bleached PYP does not induce the large conformational change observed in the photocycle, which thus must result from the organized structural transition around the chromophore triggered by chromophore photoisomerization along with disruption of the hydrogen-bond network between the chromophore and the PYP core.</P> [FIG OMISSION]</BR>

Regulation of Protein Structural Changes by Incorporation of a Small-Molecule Linker

Kim, Youngmin,Yang, Cheolhee,Kim, Tae Wu,Thamilselvan, Kamatchi,Kim, Yonggwan,Ihee, Hyotcherl MDPI 2018 INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES Vol.19 No.12

<P>Proteins have the potential to serve as nanomachines with well-controlled structural movements, and artificial control of their conformational changes is highly desirable for successful applications exploiting their dynamic structural characteristics. Here, we demonstrate an experimental approach for regulating the degree of conformational change in proteins by incorporating a small-molecule linker into a well-known photosensitive protein, photoactive yellow protein (PYP), which is sensitized by blue light and undergoes a photo-induced N-terminal protrusion coupled with chromophore-isomerization-triggered conformational changes. Specifically, we introduced thiol groups into specific sites of PYP through site-directed mutagenesis and then covalently conjugated a small-molecule linker into these sites, with the expectation that the linker is likely to constrain the structural changes associated with the attached positions. To investigate the structural dynamics of PYP incorporated with the small-molecule linker (SML-PYP), we employed the combination of small-angle X-ray scattering (SAXS), transient absorption (TA) spectroscopy and experiment-restrained rigid-body molecular dynamics (MD) simulation. Our results show that SML-PYP exhibits much reduced structural changes during photo-induced signaling as compared to wild-type PYP. This demonstrates that incorporating an external molecular linker can limit photo-induced structural dynamics of the protein and may be used as a strategy for fine control of protein structural dynamics in nanomachines.</P>