• Proceedings of the Korean Vacuum Society Conference
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• 2012.02a
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• pp.89-89
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• 2012

Arrangement of individual atoms and molecules with atomic precision and understanding the resulting properties at the molecular level are ultimate goals of chemistry, biology, and materials science. For the past three decades, scanning probe microscopy has made strides towards these goals through the direct observation of individual atoms and molecules, enabling the discovery of new and unexpected phenomena. This talk will discuss the origin of forces governing motion of small organic molecules and their extended self-assembly into two-dimensional surface structures by direct observation of individual molecules using scanning tunneling microscopy (STM).

• Bulletin of the Korean Chemical Society
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• v.18 no.3
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• pp.280-286
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• 1997

Potential energy function sets for some ion-exchanged A-type zeolites, K-A and Rb11Na1-A, were determined by introducing the X-ray crystal structures as constraints. The potential functions reproduced well the X-ray crystal structures of the monovalent ion-exchanged zeolites. The activation energies for the en- or de-capsulation of small molecules (H2, O2, N2, and CH4) and inert gases from the α-cage of model zeolites (Na-A, K-A, Rb11Na1-A, and Cs3Na9-A) were obtained by the molecular mechanical calculations. The calculated activation energies agreed well with experimental results.

• Proceedings of the Korean Institute of Surface Engineering Conference
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• 2012.11a
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• pp.4-4
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• 2012

Proteins enable biology to be viable through molecular interactions (such as in antigen-antibody, ligand-receptor, and drug-target) with

• BMB Reports
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• v.40 no.1
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• pp.58-64
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• 2007

Similar to the other known structures of Bacillus thuringiensis Cry $\delta$-endotoxins, the crystal structure of the 65-kDa activated Cry4Ba toxin comprises three domains which are, from the N- to C-terminus, a bundle of $\alpha$-helices, a three-$\beta$-sheet domain, and a $\beta$-sandwich. To investigate the properties of the C-terminal domain III in isolation from the rest of the toxin, the cloned Cry4Ba-domain III was over-expressed as a 21-kDa soluble protein in Escherichia coli, which cross-reacted with anti-Cry4Ba domain III monoclonal antibody. A highly-purified domain III was obtained in a monomeric form by ion-exchange and size-exclusion FPLC. Circular dichroism spectroscopy indicated that the isolated domain III fragment distinctly exists as a $\beta$-sheet structure, corresponding to the domain III structure embodied in the Cry4Ba crystal structure. In vitro binding analysis via immuno-histochemical assay revealed that the Cry4Ba-domain III protein was able to bind to the apical microvilli of the susceptible Stegomyia aegypti larval midguts, albeit at lower-binding activity when compared with the full-length active toxin. These results demonstrate for the first time that the C-terminal domain III of the Cry4Ba mosquito-larvicidal protein, which can be isolated as a native folded monomer, conceivably participates in toxin-receptor recognition.

• Proceedings of the Korean Vacuum Society Conference
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• 2012.02a
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• pp.130-130
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• 2012

Axial bindings of diatomic molecules to metalloporphyrins involve in the dynamic processes of biological functions such as respiration, neurotransmission, and photosynthesis. The binding reactions are also useful in sensor applications and in control of molecular spins in metalloporphyrins for spintronic applications. Here, we present the binding structures of diatomic molecules to surface- supported Co-porphyrins studied using scanning tunneling microscopy. Upon gasexposure, three-lobed structures of Co-porphyrins transformed to bright ring shapes on Au(111), whereas H2-porphyrins of dark rings remained intact. The bright rings are explained by the structures of reaction complexes where a diatomic ligand, tilted away from the axis normal to the porphyrin plane, is under precession. Our results are consistent with previous bulk experiments using X-ray diffraction and nuclear magnetic resonance spectroscopy.

• Proceedings of the Korean Vacuum Society Conference
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• 2013.08a
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• pp.135-135
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• 2013

The electronic and adsorption structures of Mg and p-tert-butylcalix[4]arene (p-TBCA) adsorbed onto a Ge(100) surface under a variety of sample conditions were characterized using high-resolution photoemission spectroscopy (HRPES) and their corresponding DFT calculation results. Interestingly, after 0.10 ML p-TBCA molecules had been adsorbed onto a Ge(100) surface, subsequent adsorption of a small amount of metallic Mg (~0.10 ML) resulted in the formation of a capped structure inside the pre-adsorbed p-TBCA molecules. The adsorption structures resulting from further deposition of Mg (~0.50 ML) onto the Ge(100) surface were monitored based on the surface charge state and Mg 2s core level spectrum. Work function measurements clearly indicated the electronic structures of the Mg and p-TBCA adsorbed onto the Ge(100) surface. Moreover, we confirmed that three different adsorption structures are experimentally favorable at room temperature through DFT calculation results.

• Bulletin of the Korean Chemical Society
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• v.18 no.11
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• pp.1186-1191
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• 1997

Solvolyses of methanesulfonyl chloride (CH3SO2Cl) in water and methanol have been studied theoretically using ab initio self-consistent reaction field (SCRF) molecular orbital method. All stationary structures including transition state on the potential energy surface in solution have been found and compared with the gas phase structures. The overall reaction occurs via a concerted SN2 mechanism with a non-cyclic trigonal bipyramidal transition state, and the activation barrier is lowered significantly in solution. The transition state for the hydrolysis reaction is looser than that for the methanolysis reaction, and this is in accord with the experimental findings that an SN2 type mechanism, which is shifted toward an SN1 process or an SAN process in the hydrolysis and alcoholysis reaction, respectively, takes place. The catalytic role of additional solvent molecules appears to be a purely general-base catalysis based on the linear transition structures. Experimental barrier can be estimated by taking into account the desolvation energy of nucleophile in the reaction of methanesulfonyl chloride with bulk solvent cluster as a nucleophile.

• Bulletin of the Korean Chemical Society
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• v.18 no.6
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• pp.573-578
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• 1997

Ion fragmentations of fatty acids such as stearic acid, palmitic acid, myristic acid, and lauric acid were studied using mass spectrometry and semiempirical calculations. The mass spectra of fatty acids showed the distributions of CH₃(CH₂)$_n^+$ and $[(CH_2)_nCO_2H]^+$ fragment ions. The relative ion abundance distributions of $[(CH_2)_nCO_2H]^+$ showed the local maxima at n=6, 10, and 14. The local maximum phenomena were also found in the mass spectra of methyl stearate but not in those of normal alcohols. These local maxima could be explained not by heats of reaction for fragmentation but by the cyclic structures of the molecular ions. The AM1 semiempirical calculations for fatty acids clearly show that the linear structures are more favorable than the cyclic ones for neutral molecules while the cyclic structures are more favorable than the linear ones for ionic molecules. The distances between carboxyl group and methylene of the cylic structures of ionized fatty acids were calculated. The methylene carbons with n=6, 10, and 14 were closer to the carboxyl group than adjacent ones.

• The Plant Pathology Journal
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• v.25 no.1
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• pp.86-90
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• 2009

In November 2008, typical powdery mildew symptoms were observed on leaves of Arabidopsis thaliana ecotype Col-0 plants in a growth room under controlled laboratory conditions at Korea University, Seoul. The disease was characterized by the appearance of white powder-like fungal growth on the surface of infected leaves. As the disease progressed, infected leaves exhibited chlorotic or necrotic brown lesions, and leaf distortion and senescence. Conidiophores of the causal fungus were hyaline, unbranched, 3-4 celled, cylindrical, and $80-115{\times}6-9{\mu}m$ in size. Singly produced conidia (pseudoidium type) were hyaline, oblong to cylindrical or oval in shape, and $26-55{\times}15-20{\mu}m$ in size with a length/width ratio of average 3, angular/rectangular wrinkling of outer wall and no distinct fibrosin bodies. Appressoria on the hyphae were multi-lobed. These structures are typical of the powdery mildew Oidium subgenus Pseudoidium, anamorph of the genus Erysiphe. The measurements of the fungal structures coincided with those of Erysiphe cruciferarum. The phylogenetic analysis using ITS rDNA sequences revealed that the causal fungus Erysiphe sp. KUS-F23994 is identical to E. cruciferarum. The isolated fungus incited powdery mildew symptoms on the inoculated Arabidopsis leaves, which proved Koch's postulates. Taken all data together, we first report the occurrence of powdery mildew disease of A. thaliana caused by Erysiphe cruciferarum in Korea.

• Bulletin of the Korean Chemical Society
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• v.33 no.8
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• pp.2508-2512
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• 2012

Cold shock proteins (CSPs) are a family of proteins induced at low temperatures. CSPs bind to single-stranded nucleic acids through the ribonucleoprotein 1 and 2 (RNP 1 and 2) binding motifs. CSPs play an essential role in cold adaptation by regulating transcription and translation via molecular chaperones. The solution nuclear magnetic resonance (NMR) or X-ray crystal structures of several CSPs from various microorganisms have been determined, but structural characteristics of psychrophilic CSPs have not been studied. Therefore, we optimized the purification process to obtain highly pure Lm-Csp and determined the three-dimensional structure model of Lm-Csp by comparative homology modeling using MODELLER on the basis of the solution NMR structure of Bs-CspB. Lm-Csp consists of a ${\beta}$-barrel structure, which includes antiparallel ${\beta}$ strands (G4-N10, F15-I18, V26-H29, A46-D50, and P58-Q64). The template protein, Bs-CspB, shares a similar ${\beta}$ sheet structure and an identical chain fold to Lm-Csp. However, the sheets in Lm-Csp were much shorter than those of Bs-CspB. The Lm-Csp side chains, E2 and R20 form a salt bridge, thus, stabilizing the Lm-Csp structure. To evaluate the contribution of this ionic interaction as well as that of the hydrophobic patch on protein stability, we investigated the secondary structures of wild type and mutant protein (W8, F15, and R20) of Lm-Csp using circular dichroism (CD) spectroscopy. The results showed that solvent-exposed aromatic side chains as well as residues participating in ionic interactions are very important for structural stability. Further studies on the three-dimensional structure and dynamics of Lm-Csp using NMR spectroscopy are required.