• YAKHAK HOEJI
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• v.41 no.6
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• pp.765-772
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• 1997

Conformational analyses on thromboxane $A_2$ (Tx$A_2$) and thromboxane $A_2$ receptor antagonists (TxRA) were carried out by molecular mechanics method. Based on the assumption that active conformer is the nonintrahydrogen bonding and more stable former of Tx$A_2$ and TxRA, the molecular structural requirements for potent TxA2 receptor antagonists are like below: 1) The distance is 5.0-5.6${\AA}$ between C atom of carboxyl group and S atom of sulfonyl group or C atom which is bonded to hydroxyl group in the active conformers. 2) The putative active conformers of Tx$A_2$and TxRAs are hairpin-like forms.

• Bulletin of the Korean Chemical Society
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• v.22 no.7
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• pp.689-692
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• 2001

An imprinting technique with labile covalent interactions has been developed in the design of new polymer catalysts. The template monomer 2 was prepared and copolymerized with DVB or EDMA to provide the polymer with a cavity having the shape of th e transition state of the reaction as well as binding sites for the substrate and catalytic functionalities. The rate of hydrolysis of diphenyl carbonate (1) in the presence of the imprinted polymer IP-DVB-THF was found to be 120 times faster than the background uncatalyzed reaction. A Km of 32 mM and a kcat of 1.8 ${\times}$ 10-3min-1 were observed from Michaelis-Menten kinetics with the imprinted polymer IP-DVB-THF.

• Corrosion Science and Technology
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• v.7 no.1
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• pp.50-60
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• 2008

The majority of the described experimental results deal with relatively pure aluminium. Variations were made in the pretreatment of the aluminum substrates and an investigation was performed on the resulting changes in oxide layer composition and chemistry. Subsequently, the bonding behavior of the surfaces was investigated by using model adhesion molecules. These molecules were chosen to represent the bonding functionality of an organic polymer. They were applied onto the pretreated surfaces as a monolayer and the bonding behavior was studied using infrared reflection absorption spectroscopy. A direct and clear relation was found between the hydroxyl fraction on the oxide surfaces and the amount of molecules that subsequently bonded to the surface. Moreover, it was found that most bonds between the oxide surface and organic functional groups are not stable in the presence of water. The best performance was obtained using molecules, which are capable of chemisorption with the oxide surface. Finally, it was found that freshly prepared relatively pure aluminum substrates, which are left in air, rapidly lose their bonding capacity towards organic functional groups. This can be attributed to the adsorption of contamination and water to the oxide surface. In addition the adhesion of a typical epoxy-coated aluminum system was investigated during exposure to water at different temperatures. The coating was found to quite rapidly lose its adhesion upon exposure to water. This rapid loss of adhesion corresponds well with the data where it was demonstrated that the studied epoxy coating only bonds through physisorptive hydrogen bonding, these bonds not being stable in the presence of water. After the initial loss the adhesion of the coating was however found to recover again and even exceeded the adhesion prior to exposure. The improvement could be ascribed to the growth of a thin oxyhydroxide layer on the aluminum substrate, which forms a new, water-stable and stronger bond with the epoxy coating. Two routes for improvement of adhesion are finally decribed including an interphasial polymeric thin layer and a treatment in boiling water of the substrate before coating takes place. The adhesion properties were finely also studied as a function of the Mg content of the alloys. It was shown that an enrichment of Mg in the oxide could take place when Mg containing alloys are heat-treated. It is expected that for these alloys the (hydr)oxide fraction also depends on the pre-treatment and on the distribution of magnesium as compared to the aluminium hydroxides, with a direct impact on adhesive properties.

• Bulletin of the Korean Chemical Society
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• v.33 no.11
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• pp.3601-3606
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• 2012

Structural properties of a small hexapeptide molecule modeled after metal-binding siderochrome immersed in a room-temperature ionic liquid (RTIL) are studied via molecular dynamics simulations. We consider two different RTILs, each of which is made up of the same cationic species, 1-butyl-3-methylimidazolium ($BMI^+$), but different anions, hexafluorophosphate ($PF_6{^-}$) and chloride ($Cl^-$). We investigate how anionic properties such as hydrophobicity/hydrophilicity or hydrogen bonding capability affect the stabilization of the peptide in RTILs. To examine the effect of peptide-RTIL electrostatic interactions on solvation, we also consider a hypothetical solvent $BMI^0Cl^0$, a non-ionic counter-part of $BMI^+Cl^-$. For reference, we investigate solvation structures in common polar solvents, water and dimethylsulfoxide (DMSO). Comparison of $BMI^+Cl^-$ and $BMI^0Cl^0$ shows that electrostatic interactions of the peptide and RTIL play a significant role in the conformational fluctuation of the peptide. For example, strong electrostatic interactions between the two favor an extended conformation of the peptide by reducing its structural fluctuations. The hydrophobicity/hydrophilicity of RTIL anions also exerts a notable influence; specifically, structural fluctuations of the peptide become reduced in more hydrophilic $BMI^+Cl^-$, compared with those in more hydrophobic $BMI^+PF_6{^-}$. This is ascribed to the good hydrogen-bond accepting power of chloride anions, which enables them to bind strongly to hydroxyl groups of the peptide and to stabilize its structure. Transport properties of the peptide are examined briefly. Translations of the peptide significantly slow down in highly viscous RTILs.

• Journal of the Korean Chemical Society
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• v.48 no.3
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• pp.229-235
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• 2004

For the study of hydrogen bonding phenomenon of high energetic compounds, we have been carried out a theoretical calculations for the nitromethane with the program Gaussian-98. The calculations at levels of restricted BLYP/6-311++G(d,p), B3LYP/6-311++G(d,p) and MP2/6-311++G have been performed to obtain molecular structures, hydrogen bonding effects and vibrational spectra of nitromethane monomer and dimer. The results show nitromethane is favored to make two hydrogen bonds between molecules and the nitromethane dimer is more stable than the monomer about 15.2, 19.4 and 32.6 kJ/mol for the BLYP, B3LYP, and MP2 level calculations, respectively.

• BMB Reports
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• v.42 no.12
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• pp.769-775
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• 2009

Periplasmic glucans (PGs) are general constituents in the periplasmic space of Proteobacteria. PGs from bacterial strains are found in larger amounts during growth on medium with low osmolarity and thus are often been specified as osmoregulated periplasmic glucans (OPGs). Furthermore, they appear to play crucial roles in pathogenesis and symbiosis. PGs have been classified into four families based on the structural features of their backbones, and they can be modified by a variety of non-sugar substituents. It has also recently been confirmed that novel PGs with various degrees of polymerization (DPs) and/or different substituents are produced under different growth conditions among Proteobacteria. In addition to their biological functions as regulators of low osmolarity, PGs have a variety of physico-chemical properties due to their inherent three-dimensional structures, hydrogen-bonding and complex-forming abilities. Thus, much attention has recently been focused on their physico-chemical applications. In this review, we provide an updated classification of PGs, as well as a description of the occurrences of novel PGs with substituents under various bacterial growth environments, the genes involved in PG biosynthesis and the various physico-chemical properties of PGs.

• Bulletin of the Korean Chemical Society
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• v.31 no.8
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• pp.2147-2150
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• 2010

c-Jun N-terminal kinase 1 (JNK1) is involved in apoptosis, cell differentiation and proliferation. It has been reported that a flavonol, quercetin, induces cell apoptosis and JNK inhibition. In order to understand the interactions of quercetin and JNK1, we performed receptor-oriented pharmacophore based in silico screening and determined a binding model of human JNK1 and quercetin at the ATP binding site of JNK1. 5-OH of A-ring and carbonyl oxygen of C-ring of quercetin participated in hydrogen bonding interactions with backbone of E109 and M111. Additionally, 3'-OH of quercetin formed a hydrogen bond with backbone of I32. One hydrophobic interaction is related on the binding of quercetin to JNK1 with I32, N114, and V158. Based on this model, we conducted a docking study with other 8 flavonols to find possible flavonoids inhibitors of JNK1. We proposed that one flavonols, rhamnetin, can be a potent inhibitor of JNK and 5-OH of A-ring and 3'-OH of B-ring of flavonols are the essential features for JNK1 inhibition.

• Bulletin of the Korean Chemical Society
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• v.32 no.2
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• pp.455-458
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• 2011

In previous report, with the aid of receptor-oriented pharmacophore-based in silico screening, we characterized three novel hPNMT inhibitors (YPN010, YPN016, and YPN017) and proposed that the hydrogen bonding interaction between inhibitors and side chain of Lys57 is very important to inhibitory activity of hPNMT. To confirm the importance of Lys57, mutant with substitution of Lys57 with Ala was cloned and binding study was performed for a K57A mutant of hPNMT using STD-NMR and fluorescence experiments. The binding constants for three novel inhibitors with mutant hPNMT were dramatically decreased compared to those with wild-type protein. K57A mutant-induced conversion of noradrenaline to adrenaline was suppressed about 95 % compared to wild-type hPNMT. Mutagenic analysis using a K57A mutant confirmed the importance of the Lys57 residue in binding of the inhibitor candidate to hPNMT as well as enzymatic activity of hPNMT, implying that these results are consistent with our binding model.

• Proceedings of the Korean Vacuum Society Conference
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• 2014.02a
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• pp.402.1-402.1
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• 2014

Photonic force microscopy (PFM) is an optical tweezers-based scanning probe microscopy, which measures the forces in the range of fN to pN. The low stiffness leads proper to measure single molecular interaction. We introduce a novel photonic force microscopy to stably map various chemical properties as well as topographic information, utilizing weak molecular bond between probe and object's surface. First, we installed stable optical tweezers instrument, where an IR laser with 1064 nm wavelength was used as trapping source to reduce damage to biological sample. To manipulate trapped material, electric driven two-axis mirrors were used for x, y directional probe scanning and a piezo stage for z directional probe scanning. For resolution test, probe scans with vertical direction repeatedly at the same lateral position, where the vertical resolution is ~25 nm. To obtain the topography of surface which is etched glass, trapped bead scans 3-dimensionally and measures the contact position in each cycle. To acquire the chemical mapping, we design the DNA oligonucleotide pairs combining as a zipping structure, where one is attached at the surface of bead and other is arranged on surface. We measured the rupture force of molecular bonding to investigate chemical properties on the surface with various loading rate. We expect this system can realize a high-resolution multi-functional imaging technique able to acquire topographic map of objects and to distinguish difference of chemical properties between these objects simultaneously.

• Proceedings of the Korean Vacuum Society Conference
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• 2011.02a
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• pp.24-25
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• 2011

Molecular self-assembly has several advantages over other nanofabrication methods. Molecular building blocks ensure ultrafine pattern precision, parallel structure formation allows for mass production and a variety of three-dimensional structures are available for fabricating complex structures. Nevertheless, the molecular interaction for self-assembly generally relies on weak forces such as van der Waals force, hydrogen bonding, or hydrophobic interaction. Due to the weak interaction, the structure formation is usually slow and the degree of ordering is low in a self-assembled structure. To promote self-assembly, directed assembly methods employing prepatterned substrates or external fields have been developed and gathered a great deal of technological attention as a next generation nanofabrication process. In this presentation a variety of directed assembly methods for soft nanomaterials including block copolymers, peptides and carbon nanomaterials will be introduced. Block copolymers are representative self-assembling materials extensively utilized in nanofabrication. In contrast to colloid assembly or anodized metal oxides, various shapes of nanostructures, including lines or interconnected networks, can be generated with a precise tunability over their shape and size. Applying prepatterned substrates$^{1,2}$ or introducing thickness modulation$^3$ to block copolymer thin films allowed for the control over the orientational and positional orderings of self-assembled structures. The nanofabrication processes for metals, semiconductors$^4$, carbon nanotubes$^{5,6}$, and graphene$^{6,7}$ templating block copolymer self-assembly will be presented.