• Proceedings of the Korean Society for Bioinformatics Conference
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• 2003.10a
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• pp.17-25
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• 2003

Determining the binding sites in protein-nucleic acid complexes is essential to the complete understanding of protein-nucleic acid interactions and to the development of new drugs. We have developed a set of algorithms for analyzing protein-nucleic acid interactions and for predicting potential binding sites in protein-nucleic acid complexes. The algorithms were used to analyze the hydrogen-bonding interactions in protein-RNA and protein-DNA complexes. The analysis was done both at the atomic and residue level, and discovered several interesting interaction patterns and differences between the two types of nucleic acids. The interaction patterns were used for predicting potential binding sites in new protein-RNA complexes.

• Advances in nano research
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• v.6 no.4
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• pp.357-375
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• 2018

Two dimensional (2D) atomic layered nanomaterials exhibit some of the most striking phenomena in modern materials research and hold promise for a wide range of applications including energy and biomedical technologies. Graphene has received much attention for having extremely high surface area to mass ratio and excellent electric conductivity. Graphene has also been shown to maximize the activity of surface-assembled metal nanoparticle catalysts due to its unique characteristics of enhancing mass transport of reactants to catalysts. This paper specifically investigates the strategy of pre-formed nanoparticle self-assembly used for the formation of various metal nanoparticles supported on graphene families such as graphene, graphene oxide, and reduced graphene oxide and aims at understanding the interactions between ligand-capped metal nanoparticles and 2D nanomaterials. By varying the functional groups on the ligands between alkyl, aromatic, amine, and alcohol groups, different interactions such as van der Waals, ${\pi}-{\pi}$ stacking, dipole-dipole, and hydrogen bonding are formed as the 2D hybrids produced.

• Transactions of the Korean hydrogen and new energy society
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• v.28 no.5
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• pp.465-470
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• 2017

Sulfonated fluorinated block copolymers having diphenyl units were mixed with the sulfonated cationic conductive polymers at an optimum mixing ratio to form hybrid membranes for fuel cells and their characteristics were studied. 2D and 3D AFM topology analysis confirmed that the number of hydrophilic units in the hybrid membrane was improved. Through the FE-SEM, the microstructure of the hybrid membrane implied hydrogen bonding and pi-pi interactions, and EDAX confirmed carbon, oxygen, sulfur, and fluorine. The thermogravimetric analysis showed that the hybrid membrane was thermally stable and the hydrophilicity of the hybrid membrane was increased by the contact angle of water droplets. As a result, it was confirmed that the cation conductivity increased by a factor of 1.8 times as the number of acidic domains in the hybrid film increased.

• Bulletin of the Korean Chemical Society
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• v.30 no.3
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• pp.589-594
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• 2009

We have performed DFT B3LYP/6-31G(d,p) calculations to investigate the complexation behaviors of the ethyl ester derivative of p-tert-butylcalix[6]arene (1) toward a variety of alkylammonium ions. We have studied the binding sites of these host-guest complexes focusing on the p-tert-butylcalix[6]arene pocket (endo) of 1. The smaller alkylammonium cations have the better complexation efficiency than the bulkier alkylammonium ions with the p-tert-butylcalix[6]aryl ester. The hydrogen-bonding of N-H$\ldots$O is one of the important factors for the complexation behavior of the p-tert-butylcalix[6]aryl ester, in addition to the NH-aromatic π, CH-aromatic π and electrostatic interactions, and the steric hindrance of alkylammonium cation. The hydrogen-bonded distances and angles of N-H$\ldots$O are reported for the complexes of the p-tert-butylcalix[6]aryl ester with various alkylammonium ions.

• Bulletin of the Korean Chemical Society
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• v.13 no.1
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• pp.75-79
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• 1992

Differences in chromatographic properties in RPLC of four brands of cyano bonded silica stationary phases are rationalized in terms of the type and relative strength of the solute-stationary phase interactions, which can be readily inferred from multiple linear regression analyses of retention data for a set of standard compounds on the stationary phases under study based on the linear solvation energy relationships (LSERs). Although four brands of cyano bonded columns studied (CPS-Hypersil, Ultrasphere cyano, Spherisorb-CN and ${\mu}$-Bondapak-CN) have similar bonding density and have been prepared from monofunctional cyanopropylsilane reagents, they possess quite different, relative hydrogen bonding (HB) donor and acceptor strengths. Comparison of the retention behavior on a cyano-bonded silica column with that on an ODS column shows that there are significant differences in the strength of HB interactions between the solute and the stationary phase on the two columns with different functionalities. Information on the differences in the interaction characteristics among brands of the cyano-bonded silica columns and between the ODS and cyano-bonded columns can be utilized to optimize the selectivity for a given separation on these columns.

• Bulletin of the Korean Chemical Society
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• v.29 no.8
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• pp.1479-1484
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• 2008

Protein tyrosine phosphatase (PTP) 1B is the superfamily of PTPs and a negative regulator of multiple receptor tyrosine kinases (RTKs). Inhibition of protein tyrosine phosphatase 1B (PTP1B) has been proposed as a strategy for the treatment of type 2 diabetes and obesity. Recently, it has been reported that amentoflavone, a biflavonoid extracted from Selaginella tamariscina, inhibited PTP1B. In the present study, docking model between amentoflavone and PTP1B was determined using automated docking study. Based on this docking model and the interactions between the known inhibitors and PTP1B, we determined multiple pharmacophore maps which consisted of five features, two hydrogen bonding acceptors, two hydrogen bonding donors, and one lipophilic. Using receptor-oriented pharmacophore-based in silico screening, we searched the biflavonoid database including 40 naturally occurring biflavonoids. From these results, it can be proposed that two biflavonoids, sumaflavone and tetrahydroamentoflavone can be potent allosteric inhibitors, and the linkage at 5',8''-position of two flavones and a hydroxyl group at 4'-position are the critical factors for their allosteric inhibition. This study will be helpful to understand the mechanism of allosteric inhibition of PTP1B by biflavonoids and give insights to develop potent inhibitors of PTP1B.

• Korea-Australia Rheology Journal
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• v.15 no.1
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• pp.1-7
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• 2003

A new method is introduced to build up organic/organic multilayer films composed of cationic poly(allylamine hydrochloride) (PAH) and negatively charged poly (sodium 4-styrenesulfonate) (PSS) using the spinning process. The adsorption process is governed by both the viscous force induced by fast solvent elimination and the electrostatic interaction between oppositely charged species. On the other hand, the centrifugal and air shear forces applied by the spinning process significantly enhances desorption of weakly bound polyelectrolyte chains and also induce the planarization of the adsorbed polyelectrolyte layer. The film thickness per bilayer adsorbed by the conventional dipping process and the spinning process was found to be about 4 ${\AA}$ and 24 ${\AA}$, respectively. The surface of the multilayer films prepared with the spinning process is quite homogeneous and smooth. Also, a new approach to create multilayer ultrathin films with well-defined micropatterns in a short process time is Introduced. To achieve such micropatterns with high line resolution in organic multilayer films, microfluidic channels were combined with the convective self-assembly process employing both hydrogen bonding and electrostatic intermolecular interactions. The channels were initially filled with polymer solution by capillary pressure and the residual solution was then removed by the .spinning process.

• Journal of Photoscience
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• v.6 no.4
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• pp.165-170
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• 1999

Asymmetric recognition of chiral alcohol by fluorenone derivatives with chiral substituents through intermolecular hydrogen bonding interaction in the singlet excited state was attempted. 1-((1S, 2R, 5S)-(+)-Menthyloxycarbonyl)aminofluoren-9-one (1-MAF) and 1-((1S, 2R, 5S)-(+)-menthyloxycarbonyl)oxyfluoren-9-one (1-MOF) were synthesized and their photophysical behaviors were characterized by the measurement of absorption and fluorescence spectra, as well as the quantum yield and the lifetime of fluorescence. The excited singlet states of 1-MAF and 1-MOF were revealed to have characteristics similar to those of fluorenone, though the intramolecular CT nature was fairly suppressed as compared with 3- and 4-substituted aminofluorenones. Fluorescences of 1-MAF and 1-MOF in acetonitrile were quenched by the addition of alcohols. Differences in fluorescence quenching efficiency were hardly observe for rather small chiral alcohols such as (R)-(-)- or (S)-(+)-2-butanol, while bulky alcohols such as menthol and isopinocampheol showed chiral recognition effects in their fluorescence quenching of 1-MAF in either acetonitrile or butyronitrile.

• Korea-Australia Rheology Journal
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• v.17 no.2
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• pp.79-85
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• 2005

Aqueous mixtures of hyaluronic acid and poly(vinyl alcohol) system and hydrogels thereof were introduced to obtain new bioartificial materials that have excellent mechanical properties, biocompatibility and enhanced rheological properties. The interactions between hyaluronic acid and poly(vinyl alcohol) and/or borax were investigated by rheological measurements. Preparation parameters of the aqueous mixtures were mixture composition, the degree of hydrolysis of poly(vinyl alcohol) and borax concentration. From the rheological behavior, it could be deduced that the key factor of the interaction between hyaluronic acid and poly(vinyl alcohol) was the hydrogen bonding between them and the effect was pronounced with borax. Enhanced viscosity was observed at the composition of $20wt\%$ of hyaluronic acid solution and $80wt\%$ of poly(vinyl alcohol) and borax solution. Rheological properties were influenced by the degree of hydrolysis of poly(vinyl alcohol) and borax concentration. As the degree of hydrolysis and borax concentration increased, rheological properties increased due to the increased hydrogen bonding and networking of hyaluronate aggregates. Physical hydrogels from hyaluronic acid and poly(vinyl alcohol) were prepared and the composition dependence of the gels was rheologically investigated as well.

• Bulletin of the Korean Chemical Society
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• v.34 no.10
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• pp.3093-3097
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• 2013

The synthesis, X-ray crystallography, spectroscopic (IR, UV-vis), and electrochemical properties of the title compound, $[H_3O][Cr(dipic)_2][H_3O^+.Cl^-]$ (1), ($H_2dipic$ = 2,6-pyridinedicarboxylic acid), are reported. This complex crystallizes in the monoclinic space group Cc with a = 14.9006(10) ${\AA}$, b = 12.2114(8) ${\AA}$, c = 8.6337(6) ${\AA}$, ${\alpha}=90.00^{\circ}$, ${\beta}=92.7460(10)^{\circ}$, ${\gamma}=90.00^{\circ}$, and V = 1569.16(18) ${\AA}^3$ with Z = 4. The hydrogen bonding and noncovalent interactions play roles in the stabilization of the structure. In order to gain a better understanding of the most important geometrical parameters in the structure of the complex, atoms in molecules (AIM) method at B3LYP/6-31G level of theory has been employed.