• Bulletin of the Korean Chemical Society
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• v.35 no.8
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• pp.2311-2316
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• 2014

Conformations and vibrational frequencies of the racemic (2RS,3RS)-5-amino-3-(4-phenylpiperazin-1-yl)-1,2,3,4-tetrahydronaphthalen-2-ol-(I) [(2RS,3RS)-(I)], a precursor of benzovesamicol analogues, have been carried out using various DFT methods (M06-2X, B3LYP, B3PW91, PBEPBE, LSDA, and B3P86) with basis sets of 6-31G(d), 6-31+G(d,p), 6-311+G(d,p), 6-311++G(d,p), cc-pVTZ, and TZVP. The LSDA/6-31G(d) level of theory shows the best performance in reproducing the X-ray powder structure. However, the PBEPBE/cc-pVTZ level of theory is the best method to predict the vibrational frequencies of (2RS,3RS)-(I). The potential energy surfaces of racemic pairs (2RS,3RS)-(I) and -(II) are obtained at the LSDA/6-31G(d) level of theory in the gas phase and in water. The results indicate that (2RS,3RS)-(I) are more stable by ~0.75 kcal/mol in energy than (2RS,3RS)-(II) in water, whereas conformer AIIg and BIIg are more stable by ~0.04 kcal/mol than AIg in gas phase. In particular, the hydrogen bond distances between the N of piperazine and the OH of tetrahydronaphthalen become longer in gas, compared with those in the water phase. Vibrational frequencies calculated at the PBEPBE/cc-pVTZ level of theory in the gas phase are larger than those in water, whereas their intensities in the gas phase are weaker than those in water.

• Bulletin of the Korean Chemical Society
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• v.35 no.8
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• pp.2494-2504
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• 2014

P38 mitogen activated protein (MAP) kinase is an important anti-inflammatory drug target, which can be activated by responding to various stimuli such as stress and immune response. Based on the conformation of the conserved DFG loop (in or out), binding inhibitors are termed as type-I and II. Type-I inhibitors are ATP competitive, whereas type-II inhibitors bind in DFG-out conformation of allosteric pocket. It remains unclear that how these allosteric inhibitors stabilize the DFG-out conformation and interact. Organosilicon compounds provide unusual opportunity to enhance potency and diversity of drug molecules due to their low toxicity. However, very few examples have been reported to utilize this property. In this regard, we performed docking of an inhibitor (BIRB) and its silicon analog (Si-BIRB) in an allosteric binding pocket of p38. Further, molecular dynamics (MD) simulations were performed to study the dynamic behavior of the simulated complexes. The difference in the biological activity and mechanism of action of the simulated inhibitors could be explained based on the molecular mechanics/generalized Born surface area (MM/GBSA) binding free energy per residue decomposition. MM/GBSA showed that biological activities were related with calculated binding free energy of inhibitors. Analyses of the per-residue decomposed energy indicated that van der Waals and non-polar interactions were predominant in the ligand-protein interactions. Further, crucial residues identified for hydrogen bond, salt bridge and hydrophobic interactions were Tyr35, Lys53, Glu71, Leu74, Leu75, Ile84, Met109, Leu167, Asp168 and Phe169. Our results indicate that stronger hydrophobic interaction of Si-BIRB with the binding site residues could be responsible for its greater binding affinity compared with BIRB.

• Korean Chemical Engineering Research
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• v.58 no.2
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• pp.176-183
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• 2020

In this study, synthesis of a hydrogel consisted of a coordination bond network between small organic molecules and transition metals had been carried out. By adding a tackifying material to the gel, the potential of the gel to be used as an adhesive material had been also confirmed. Synthesis of the adhesive had been done with simple mixing of 3 components: tannic acid, transition metal, and polymer. The tannic acid molecule possesses multiple hydroxyl groups that can form coordination bonds with the transition metals and hydrogen bonds with the hydrophilic polymers. Due to the morphology of the metal-organic complex and polymer dispersed in water, the fabricated material exhibited high adhesiveness and cohesiveness. Optimizing the rheological property had been conducted for use in adhesive by the synthesis with varying the transition metal (Fe³⁺, Ti⁴⁺), polymer, and treatment conditions. Rheological measurement results demonstrate the promising potential of the material as a bio-compatible and versatile pressure-sensitive adhesive with both high adhesiveness and cohesiveness.

• Journal of Pharmaceutical Investigation
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• v.40 no.4
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• pp.237-244
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• 2010

This study investigated basic material properties and compressibility of commonly used pharmaceutical excipients. Five classes of excipients are selected including starch, lactose, calcium phosphate, microcrystalline cellulose (MCC), and povidone. The compressibility was evaluated using compression parameters derived from Heckel and Kawakita equation. The Heckel plot for lactose and dicalcium phosphate showed almost linear relationship. However, for MCC and povidone, curves in the initial phase of compression were observed followed by linear regions. The initial curve was considered as particle rearrangement and fragmentation and then plastic deformation at the later stages of the compression cycle. The Kawakita equation showed MCC exhibited higher compressibility, followed by povidone, lactose, and calcium phosphate. MCC undergoes significant plastic deformation during compression bringing an extremely large surface area into close contact and facilitating hydrogen bond formation between the plastically deformed, adjacent cellulose particles. Lactose compacts are consolidated by both plastic deformation and fragmentation, but to a larger extent by fragmentation. Calcium phosphate has poor binding properties because of its brittle nature. When formulating tablets, selection of suitable pharmaceutical excipients is very important and they need to have good compression properties with decent powder flowability. Material properties tested in this study might give a good guide how to select excipients for tablet formulations and help the formulation scientists design the optimum ones.

• Proceedings of the Korean Vacuum Society Conference
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• 2011.08a
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• pp.312-312
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• 2011

In SiH4/H2 discharge for growth process of hydrogenated amorphous silicon (a-Si:H), silane polymers, produced by SiH2 + Sin-1H2n ${\rightarrow}$ SinH2n+2, have no reactivity on the film-growing surface. However, under the SiH2 rich condition, high silane reactive species (HSRS) can be produced by electron collision to silane polymers. HSRS, having relatively strong reactivity on the surface, can react with dangling bond and form Si-H2 networks which have a close correlation with photo-induced degradation of a-Si:H thin film solar cell [1]. To find contributions of suggested several external plasma conditions (pressure, frequency and ratio of mixture gas) [2,3] to suppressing productions of HSRS, some plasma characteristics are studied by numerical methods. For this study, a zero-dimensional global model for SiH4/H2 discharge and a one-dimensional particle-in-cell Monte-Carlo-collision model (PIC-MCC) for pure SiH4 discharge have been developed. Densities of important reactive species of SiH4/H2 discharge are observed by means of the global model, dealing 30 species and 136 reactions, and electron energy probability functions (EEPFs) of pure SiH4 discharge are obtained from the PIC-MCC model, containing 5 charged species and 15 reactions. Using global model, SiH2/SiH3 values were calculated when pressure and driving frequency vary from 0.1 Torr to 10 Torr, from 13.56 MHz to 60 MHz respectively and when the portion of hydrogen changes. Due to the limitation of global model, frequency effects can be explained by PIC-MCC model. Through PIC-MCC model for pure SiH4, EEPFs are obtained in the specific range responsible for forming SiH2 and SiH3: from 8.75 eV to 9.47 eV [4]. Through densities of reactive species and EEPFs, polymerization reactions and production of HSRS are discussed.

• Korean Journal of Materials Research
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• v.28 no.2
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• pp.118-123
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• 2018

5 nm-thick $SiO_2$ layers formed by plasma-enhanced chemical vapor deposition (PECVD) are densified to improve the electrical and interface properties by using nitric acid oxidation of Si (NAOS) method at a low temperature of $121^{\circ}C$. The physical and electrical properties are clearly investigated according to NAOS times and post-metallization annealing (PMA) at $250^{\circ}C$ for 10 min in 5 vol% hydrogen atmosphere. The leakage current density is significantly decreased about three orders of magnitude from $3.110{\times}10^{-5}A/cm^2$ after NAOS 5 hours with PMA treatment, although the $SiO_2$ layers are not changed. These dramatically decreases of leakage current density are resulted from improvement of the interface properties. Concentration of suboxide species ($Si^{1+}$, $Si^{2+}$ and $Si^{3+}$) in $SiO_x$ transition layers as well as the interface state density ($D_{it}$) in $SiO_2/Si$ interface region are critically decreased about 1/3 and one order of magnitude, respectively. The decrease in leakage current density is attributed to improvement of interface properties though chemical method of NAOS with PMA treatment which can perform the oxidation and remove the OH species and dangling bond.

• Polymer(Korea)
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• v.30 no.5
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• pp.412-416
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• 2006

The superparamagnetic nanoparticles were prepared by coprecipitation of $FeCl_3$ and $Na_2SO_3$ with $NH_4OH$ and the surface charge on hydroxyl group by chemisorption was changed depending on pH. We studied correlation between surface charge of magnetite and pH. Using this correlation the properties of poly (acrylic acid) (PAAc) hydrogel embedded with magnetite was studied. The magnetite was characterized by XRD, AFM. and FTIR. The zeta-potential of magnetite was influenced by pH: great positive charge was shown high under the pH 4 and isoelectric point was found at pH 7. The hydrogen bond formed by combining oi PAAc hydrogel and magnetic colloid under pH 4 caused tensile strength to increase, while swelling and elongation at break to decrease. The result confirmed that the magnetic moment was increased proportionally to the content of magnetite.

• Elastomers and Composites
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• v.50 no.2
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• pp.110-118
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• 2015

In this study, diethylaminoethyl methacrylate-styrene-butadiene terpolymer (DEAEMA-SBR), in which diethylaminoethyl methacrylate (DEAEMA) was introduced to the SBR molecule as a third monomer, was synthesized by cold emulsion polymerization. It is expected that amine group introduced to a rubber molecule would improve dispersion of silica by the formation of hydrogen bond (or ionic coupling) between the amine group and silanol groups of silica surface. The chemical structure of DEAEMA-SBR was analyzed using proton nuclear magnetic resonance spectroscopy (H-NMR), Fourier transform infrared spectroscopy (FTIR), gel permeation chromatography (GPC) and differential scanning calorimetry (DSC). Then, various properties of DEAEMA-SBR/silica composite such as crosslink density, bound rubber content, abrasion resistance, and mechanical properties were evaluated. As a result, bound rubber content and crosslink density of DEAEMA-SBR/silica compound were higher than those of the SBR 1721 composite. Abrasion resistance and moduli at 300% elongation of the DEAEMA-SBR/silica composite were better than those of SBR 1721 composite due to the high bound rubber content and crosslink density. These results are attributed to high affinity between DEAEMA-SBR and silica. The proposed study suggests that DEAEMA-SBR can help to improve mechanical properties and abrasion resistance of the tire tread part.

• Bulletin of the Korean Chemical Society
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• v.31 no.11
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• pp.3333-3340
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• 2010

A three dimensional pharmacophore model was generated for the molecules which are responsible for anti-inflammatory activities targeting Interleukin-2 inducible tyrosine kinase (Itk). 16 structurally diverse molecules were selected as training set to generate the hypotheses using Discovery Studio v2.1. The best hypothesis, Hypo1, comprises two hydrogen bond acceptor (HBA), one hydrophobic aromatic (HA), one ring aromatic (RA) and shows high cost difference (63.71), high correlation coefficient (0.97) as well as low RMS deviation (0.81). Hypo1 has been further validated toward a test set, decoy set and Fischer's randomization method. Furthermore, Hypo1 was used to screen NCI and Maybridge databases. Finally, 2 hit molecules were identified as potential leads against Itk, which may be useful for future drug development.

• Bulletin of the Korean Chemical Society
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• v.28 no.8
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• pp.1335-1340
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• 2007

β-Ketoacyl acyl carrier protein synthase (KAS) III is a particularly attractive target in the type II fatty acid synthetic pathway, since it is central to the initiation of fatty acid synthesis. Enterococcus faecalis, a Grampositive bacterium, is one of the major causes of hospital acquired infections. The rise of multidrug-resistant of most bacteria requires the development of new antibiotics, such as inhibition of the KAS III. In order to block the fatty acid synthesis by inhibition of KAS III, at first, three dimensional structure of Enterococcus faecalis KAS III (efKAS III) was determined by comparative homology modeling using MODELLER based on x-ray structure of Staphylococcus aureus KAS III (saKAS III) which is a gram-positive bacteria and is 36.1% identical in amino acid sequences with efKAS III. Since His-Asn-Cys catalytic triad is conserved in efKAS III and saKAS III, substrate specificity of efKAS III and saKAS III and the size of primer binding pocket of these two proteins are expected to be similar. Ligand docking study of efKAS III with naringenin and apigenin showed that naringenin docked more strongly with efKAS III than apigenin, resulting in the intensive hydrogen bond network between naringenin and efKAS III. Also, only naringenin showed antibacterial activity against E. faecalis at 256 μg/mL. This study may give practical implications of flavonoids for antimicrobial effects against E. faecalis.