• Journal of the Korean Chemical Society
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• v.48 no.4
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• pp.339-350
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• 2004

The simplified cumulant method was applied to diffraction data of $CClF_3$ to study the equilibrium molecular parameters over a range of temperatures. The molecular parameters of $CClF_3$ by the simplified cumulant method were compared with those from the traditional method. Also the instrumentation of picosecond time resolved electron diffraction (TRED) and the experimental details are described. The total experimental temporal resolution was discussed in terms of the electron pulse width. The TRED system was applied to study the molecular structures for $CClF_3$ at room temperature. The molecular structural parameters $CClF_3$ from TRED are compared with those from GED/RT. The molecular parameters ($r_e$)of bonded C-F and C-Cl for $CClF_3$ by simplified CA are 132.00(2) pm and 175.20(3) pm, respectively, by using GED/RT. From the results of TRED experiments $r_a$ for bonded C-F and C-Cl are 132.23(13) pm and 177.23(19) pm.

• Bulletin of the Korean Chemical Society
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• v.29 no.8
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• pp.1505-1509
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• 2008

Comparative molecular simulations were performed to establish molecular interaction and inhibitory effect of flavonoid myricetin on formation of amyloid fibris. For computational comparison, the conformational stability of myricetin with amyloid $\beta$ -peptide (A$\beta$ ) and $\beta$ -amyloid fibrils (fA$\beta$) were traced with multiple molecular dynamics simulations (MD) using the CHARMM program from Monte Carlo docked structures. Simulations showed that the inhibition by myricetin involves binding of the flavonoid to fA$\beta$ rather than A$\beta$ . Even in MD simulations over 5 ns at 300 K, myricetin/fA$\beta$ complex remained stable in compact conformation for multiple trajectories. In contrast, myricetin/A$\beta$ complex mostly turned into the dissociated conformation during the MD simulations at 300 K. These multiple MD simulations provide a theoretical basis for the higher inhibitory effect of myricetin on fibrillogenesis of fA$\beta$ relative to A$\beta$ . Significant binding between myricetin and fA$\beta$ observed from the computational simulations clearly reflects the previous experimental results in which only fA$\beta$ had bound to the myricetin molecules.

• Bulletin of the Korean Chemical Society
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• v.34 no.2
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• pp.475-481
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• 2013

By using ionic liquid 1-hexylpyridinium hexafluorophosphate ($HPPF_6$) based carbon ionic liquid electrode (CILE) as the substrate electrode, a $CoMoO_4$ nanorods and myoglobin (Mb) composite was casted on the surface of CILE with chitosan (CTS) as the film forming material to obtain the modified electrode (CTS/$CoMoO_4$-Mb/CILE). Spectroscopic results indicated that Mb retained its native structures without any conformational changes after mixed with $CoMoO_4$ nanorods and CTS. Electrochemical behaviors of Mb on the electrode were carefully investigated by cyclic voltammetry with a pair of well-defined redox peaks from the heme Fe(III)/Fe(II) redox center of Mb appeared, which indicated that direct electron transfer between Mb and CILE was realized. Electrochemical parameters such as the electron transfer number (n), charge transfer coefficient (${\alpha}$) and electron transfer rate constant ($k_s$) were estimated by cyclic voltammetry with the results as 1.09, 0.53 and 1.16 $s^{-1}$, respectively. The Mb modified electrode showed good electrocatalytic ability toward the reduction of trichloroacetic acid in the concentration range from 0.1 to 32.0 mmol $L^{-1}$ with the detection limit as 0.036 mmol $L^{-1}$ ($3{\sigma}$), and the reduction of $H_2O_2$ in the concentration range from 0.12 to 397.0 ${\mu}mol\;L^{-1}$ with the detection limit as 0.0426 ${\mu}mol\;L^{-1}$ ($3{\sigma}$).

• Molecules and Cells
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• v.42 no.7
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• pp.503-511
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• 2019

As sessile organisms, plants have developed sophisticated system to defend themselves against microbial attack. Since plants do not have specialized immune cells, all plant cells appear to have the innate ability to recognize pathogens and turn on an appropriate defense response. The plant innate immune system has two major branches: PAMPs (pathogen associated molecular patterns)-triggered immunity (PTI) and effector-triggered immunity (ETI). The ability to discriminate between self and non-self is a fundamental feature of living organisms, and it is a prerequisite for the activation of plant defenses specific to microbial infection. Arabidopsis cells express receptors that detect extracellular molecules or structures of the microbes, which are called collectively PAMPs and activate PTI. However, nucleotidebinding site leucine-rich repeats (NB-LRR) proteins mediated ETI is induced by direct or indirect recognition of effector molecules encoded by avr genes. In Arabidopsis, plasmamembrane localized multifunctional protein RIN4 (RPM1-interacting protein 4) plays important role in both PTI and ETI. Previous studies have suggested that RIN4 functions as a negative regulator of PTI. In addition, many different bacterial effector proteins modify RIN4 to destabilize plant immunity and several NB-LRR proteins, including RPM1 (resistance to Pseudomonas syringae pv. maculicola 1), RPS2 (resistance to P. syringae 2) guard RIN4. This review summarizes the current studies that have described signaling mechanism of RIN4 function, modification of RIN4 by bacterial effectors and different interacting partner of RIN4 in defense related pathway. In addition, the emerging role of the RIN4 in plant physiology and intercellular signaling as it presents in exosomes will be discussed.

• Journal of Microbiology and Biotechnology
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• v.12 no.1
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• pp.130-136
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• 2002

The internal transcribed spacer (ITS) region in the genus Tricholoma was analyzed, including for its primary nucleotide sequence and secondary structural characterization. The secondary structures of the ITS2 region in the genus Tricholoma were identified for use in bioinformatic processes to study molecular evolution and compare secondary structures. Ten newly sequenced ITS regions were added to the analysis and submitted to the GenBank database. The resulting structure from a minimum energy algorithm indicated the four-domain model, as previously suggested by others. The conserved secondary structure of the ITS2 sequences of the genus Tricholoma exhibited certain unique features, including pyrimidine tracts in the loops of domain A and a complete structure containing four domains, with motifs identified in other ITS2 secondary structures. A phylogenetic tree was derived from sequence alignment based on the secondary structures. From the resulting maximum parsimonious tree, it was found that the species in the genus Tricholoma had evolved monophyletically and were composed of four groups, as supported by the bootstrapping values and pileus color.

• Proceedings of the Korean Vacuum Society Conference
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• 2011.02a
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• pp.337-337
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• 2011

The elecronic absorption and surface morphology evolution of two types of molecular double layer thin films, copper phthalocyanine(CuPc) layer deposited on top of chloro[subphtalocyaninato]boron(III) (SubPc) layer, denoted as SubPc/CuPc, and vice versa, at various thicknesses were invertigated using ultraviolet(UV)-visible spectroscopy and atomic force microscopy (AFM). Both types of double layer structures showed similar broadened absorption patterns in UV-visible region which were well consistent with fitted spectra by a simple linear combination of single layer absorption spectra of two materials. In contrast, the surface morphology of double layer structures was dependent on the order of deposition. For CuPc/SubPc structures, the surface morphology was characterized by elongated grains, characteristic of SubPc thin films, indicating the morphological influence of underlying CuPc layer on subsequent SubPc layer was not large. For SubPc/CuPc structures, however, the underlying SubPc layer acted as a morphological template for the subsequently deposited CuPc layer. It was also observed that the grain size of CuPc layer varied by the thickness of underlying SubPc layer.

• Proceedings of the Korean Vacuum Society Conference
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• 2011.02a
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• pp.302-302
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• 2011

Fabrications of metal-organic hybrid networks attracted much attention due to possible applications in gas storages, heterogeneous catalyses, information storages, and opto-electronic devices. One way to construct three-dimensional hybrid structures is to make the arrays of planar or linear metal-organic hybrid structures which are linked through electrostatic interactions. As a model study, we fabricated the arrays of one-dimensional hybrid chains and investigated inter-chain interactions between adjacent hybrid chains using scanning tunneling microscopy (STM) and spectroscopy (STS) on Ag(111). Brominated anthracene molecules were used to grow the arrays of hybrid chains on Ag(111). We proposed atomic models for the observed structures. Linear chains are made of repetition of Ag-anthracene units. Br atoms are attached to anthracene molecules through Br-H structures which mediate inter-chain interactions. Two different apparent heights were observed in anthracene molecules. Molecules having a Br-H connection look brighter than those with two connections due to electronic effect. When a chain is laterally manipulated with STM tip, Br atoms move together with the chain implying that Br-H inter-chain interactions are quite strong.

• Bulletin of the Korean Chemical Society
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• v.31 no.11
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• pp.3247-3251
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• 2010

Molecular structures of the various conformers for the four stereoisomers of tetra-t-butyl-tetra-O-methylsulfinylcalix[4]arene (1) were optimized using DFT BLYP and mPW1PW91/6-31G(d,p) (hybrid HF-DF) calculation methods. We have analyzed the total electronic and Gibbs free energies and normal vibrational frequencies of 16 different structures from four major conformations (cone (CONE), partial cone (PC), 1,2-alternate (1,2-A), 1,3-alternate (1,3-A)) of the four stereoisomers [1(rccc), 1(rcct), 1(rctt), 1(rtct)]. The mPW1PW91/6-31G(d,p) calculations suggested that the $1(rccc)_{CONE}$, $1(rcct)_{PC}$, $1(rctt)_{PC}$, and $1(rtct)_{1,3-A}$ were the most stable conformations of the respective stereoisomers. These outcomes are in accordance with the experimental structures obtained from X-ray crystallography. The electrostatic repulsion between the sulfinyl and methoxy groups is a primary factor for the relative stabilities of the four different conformations. The IR spectra of the most stable conformers [$1(rccc)_{CONE}$, $1(rcct)_{PC}$, $1(rctt)_{PC}$, $1(rtct)_{1,3-A}$] of each stereoisomer were compared to each other.

• Bulletin of the Korean Chemical Society
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• v.35 no.2
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• pp.581-586
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• 2014

The most stable adsorption structures and their corresponding energies of 4-pyridone, 4-hydroxypyridine, 2-pyridone and 2-hydroxypyridine have been investigated by Density Functional Theory (DFT) calculation and high-resolution photoemission spectroscopy (HRPES). We confirmed that between the two reaction centers of 4- and 2-pyridone, only O atom of carbonyl functional group can act as a Lewis base while both the two reaction centers of 4- and 2-hydroxypyridine (tautomers of 4- and 2-pyridone) can successfully function as a Lewis base. On the other hand, owing to their molecular structures, there is a remarkable difference between the adsorption structures of 4- and 2-hydroxypyridine. Through the analysis of the N 1s and O 1s core level spectra obtained using HRPES, we also could corroborate that two different adducts coexist on the surface at room temperature due to their activation energy investigating the coverage dependent variation of bonding configurations when these molecules are adsorbed on the Ge(100) surface.

• Bulletin of the Korean Chemical Society
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• v.32 no.3
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• pp.943-946
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• 2011

The electronic absorption and surface morphology evolution of two types of molecular double layer thin films, copper phthalocyanine (CuPc) layer deposited on chloro[subphthalocyaninato]boron(III) (SubPc) layer, denoted as SubPc/CuPc, and vice versa, with various thicknesses were investigated using ultraviolet (UV)-visible spectroscopy and atomic force microscopy (AFM). Both types of double layer structures showed similar broadened absorption patterns in the UV-visible region that were consistent with the fitted spectra following simple linear combination of the single layer absorption spectra of the two materials. In contrast, the surface morphology of double layer structures was dependent on the order of deposition. For the CuPc/SubPc structures, surface morphology was characterized by elongated grains, which are characteristic of SubPc thin films, indicating that the morphological influence of the underlying CuPc layer on the subsequent SubPc layer was not large. For the SubPc/CuPc structures, however, the underlying SubPc layer acted as a morphological template for the subsequently deposited CuPc layer. It was also observed that the grain size of the CuPc layer varied according to the thickness of the underlying SubPc layer.