• Journal of the Korean Magnetic Resonance Society
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• v.22 no.4
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• pp.139-143
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• 2018

Short antimicrobial peptide, A4W, have been studied by molecular dynamics (MD) simulation in an explicit dodecylphosphocholine (DPC) micelle. Peptide was aligned with DPC micelle and transferred new peptide-micelle coordinates within the same solvent box using specific micelle topology parameters. After initial energy minimization and equilibration, the conformation and orientation of the peptide were analyzed from trajectories obtained from the RMD (restrained molecular dynamics) or the subsequent free MD. Also, the information of solvation in the backbone and the side chain of the peptide, hydrogen bonding, and the properties of the dynamics were obtained. The results showed that the backbone residues of peptide are either solvated using water or in other case, they relate to hydrogen bonding. These properties could be a critical factor against the insertion mode of interaction. Most of the peptide-micelle interactions come from the hydrophobic interaction between the side chains of peptide and the structural interior of micelle system. The interaction of peptide-micelle, electrostatic potential and hydrogen bonding, between the terminal residues of peptide and the headgroups in micelle were observed. These interactions could be effect on the structure and flexibility of the peptide terminus.

• Bulletin of the Korean Chemical Society
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• v.30 no.11
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• pp.2595-2602
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• 2009

Hexamer cluster of N,N-dimethylformamide(DMF) based on the crystal structure was investigated for the equilibrium structure, the stabilization energies, and the vibrational properties in the density functional force field. The geometry (point group $C_i$) of fully optimized hexamer clustered DMF shows quite close similarity to the crystal structure weakly intermolecular hydrogen bonded each other. Stretching force constants for intermolecular hydrogen bonded methyl and formyl hydrogen atoms with nearby oxygen atom, methyl C–H${\cdots}$O and formyl C–H${\cdots}$O, were obtained in 0.055 $\sim$ 0.11 and $\sim$ 0.081 mdyn/$\AA$, respectively. In-plane bending force constants for hydrogen bonded methyl hydrogen atoms were in 0.25 $\sim$ 0.33, and for formyl hydrogen $\sim$ 0.55 mdynÅ. Torsion force constants through hydrogen bonding for methyl hydrogen atoms were in 0.038 $\sim$ 0.089, and for formyl hydrogen atom $\sim$ 0.095 mdynÅ. Calculated Raman and infrared spectral features of single and hexamer cluster represent well the experimental spectra of DMF obtained in the liquid state. Noncoincidence between IR and Raman frequency positions of stretching C=O, formyl C–H and other several modes was interpreted in terms of the intermolecular vibrational coupling in the condensed phase.

• Journal of Integrative Natural Science
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• v.5 no.3
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• pp.195-197
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• 2012

Halogen atoms in a molecule are traditionally considered as electron donors, since they have unshared electrons. Normally when they are bonded, there are three lone pair electrons. These lone pairs can function as Lewis bases. However, when they are bound to electron withdrawing groups, they can act as Lewis acids. Since the situation is similar hydrogen bonding (HB), this type of interaction is named as halogen bonding (XB). This mainly comes from the uneven distribution of electron density around the halogen atoms. Since the electron density around halogen atom opposite to ${\sigma}$-bond is depleted, its electropositive region is called ${\sigma}$-hole. This ${\sigma}$-hole can attract halogen bond acceptors, requiring more stringent directionality compared to HB. Since this interaction mainly comes from electrostatic origin, the geometry tends to be linear. Since the XB energy is comparable to corresponding HB. Still in its infancy, XB shows a broad range of applicability, with potentially more useful properties, compared to corresponding HB.

• The Transactions of the Korean Institute of Electrical Engineers C
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• v.49 no.7
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• pp.424-432
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• 2000

The plasma surface treatment, using hydrogen gas, of the silicon wafer was investigated as a pretreatment for the application to silicon-on-insulator (SOI) wafers using the silicon direct bonding technique. The chemical reactions of hydrogen plasma with surfaces were used for both the surface activation and the removal of surface contaminants. As a result of exposure of silicon wafer to the plasma, an active oxide layer was formed on the surface, which was rendered hydrophilic. The surface roughness and morphology were estimated as functions of plasma exposing time as well as of power. The surface became smoother with decreased incident hydrogen ion flux by reducing plasma exposing time and power. This process was very effective to reduce the carbon contaminants on the silicon surface, which was responsible for a high initial surface energy. The initial surface energy measured by the crack propagation method was 506 mJ/m2, which was up to about three times higher than that of a conventional RCA cleaning method.

• Journal of the Microelectronics and Packaging Society
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• v.28 no.4
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• pp.109-114
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• 2021

We investigated the effects of atmospheric hydrogen plasma treatment on Cu-Cu direct bonding. Hydrogen plasma was effective in reducing the surface oxide layer of Cu thin film, which was confirmed by GIXRD analysis. It was observed that larger plasma input power and longer treatment time were effective in terms of reduction and surface roughness. The interfacial adhesion energy was measured by DCB test and it was observed to decrease as the bonding temperature decreased, resulting in bonding failure at bonding temperature of 200℃. In case of wet treatment, strong Cu-Cu bonding was observed above bonding temperature of 250℃.

• Bulletin of the Korean Chemical Society
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• v.24 no.6
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• pp.695-702
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• 2003

Recent experimental and theoretical advances on the aromatic alcohol-water clusters are reviewed, focusing on the structure of the hydrogen bonding between the alcoholic OH group and the binding water molecules. The interplay of experimental observations and theoretical calculations for the elucidation of the structure is demonstrated for phenol-water, benzyl alcohol-water, substituted phenol-water, naphthol-water and tropolone -water clusters. Discussion is made on assigning the role (either proton-donating or -accepting) of the hydroxyl group by measuring the shifts of infrared frequency of the OH stretching mode in the cluster from that of bare aromatic alcohol for the experimental determination of the cluster structure.

• Bulletin of the Korean Chemical Society
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• v.35 no.6
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• pp.1590-1600
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• 2014

Cinchona-based bifunctional catalysts have been extensively employed in the field of organocatalysis due to the incorporation of both hydrogen-bonding acceptors (quinuclidine) and hydrogen-bonding donors (e.g., alcohol, amide, (thio)urea and squaramide) in the molecule, which can simultaneously activate nucleophiles and electrophiles, respectively. Among them, cinchona-derived (thio)urea and squaramide catalysts have shown remarkable application potential by using their bifurcated hydrogen bonding donors in activating electrophilic carbonyls and imines. However, due to their bifunctional nature, they tend to aggregate via inter- and intramolecular acid-base interactions under certain conditions, which can lead to a decrease in the enantioselectivity of the reaction. To overcome this self-aggregation problem of bifunctional organocatalysts, we have successfully developed a series of sulfonamide-based organocatalysts, which do not aggregate under conventional reaction conditions. Herein, we summarize the recent applications of our cinchona-derived sulfonamide organocatalysts in highly enantioselective methanolytic desymmetrization and decarboxylative aldol reactions. Immobilization of sulfonamide-based catalysts onto solid supports allowed for unprecedented practical applications in the synthesis of valuable bioactive synthons with excellent enantioselectivities.

• Journal of the Korean Chemical Society
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• v.36 no.5
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• pp.627-631
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• 1992

A simple one dimensional model was proposed to describe a hydrogen bonding in crystals, which was based on the Lippincott's empirical potential. The model was used to calculate internal stretching vibrational frequencies of $NH_4I$ crystal at high pressures. The calculated results were in agreement with Raman experimental results qualitatively. At relatively lower high pressures, as pressure increases internal stretching vibrational frequencies shift lower due to increase of the hydrogen bonding effect. At higher pressures, the frequencies shift higher due to the repulsive contribution of interatomic potential induced by the reduction of interatomic distance as pressure increases.

• Bulletin of the Korean Chemical Society
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• v.32 no.7
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• pp.2222-2226
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• 2011

Amylase is a digestive enzyme that catalyses the starch into sugar. It has been reported that the green tea flavonoid (or polyphenols) (-)-epigallocatechin 3-gallate (EGCG) inhibits human salivary ${\alpha}$-amylase (HSA) and induced anti-nutritional effects. In this study, we performed docking study for seven EGCG-like flavonoids and HSA to understand the interaction mechanism of HSA and EGCG and suggest new possible flavonoid inhibitors of HSA. As a result, EGCG and (-)-epicatechin gallate (ECG) bind to HSA with complex hydrogen bonding interactions. These hydrogen bonding interactions are important for inhibitory activity of EGCG against HSA. We suggested that ECG can be a potent inhibitor of HSA. This study will be helpful to understand the mechanism of inhibition of HSA by EGCG and give insights to develop therapeutic strategies against diabetes.

• Macromolecular Research
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• v.16 no.5
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• pp.399-403
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• 2008

Monodisperse, micron-sized, hybrid particles having a core-shell structure were prepared by coating the surface of poly(methyl methacrylate)(PMMA) microspheres with silica and by copolymerizing acrylamide (AAm) to supply the hydrogen bonding effect by means of the amide groups. Tetraethoxysilane (TEOS) was then slowly dropped onto the medium under certain conditions. Because of the hydrogen bonding between the amide of the PMMA particles and the hydroxyl group of the hydrolyzed silanol, a silica shell was generated on the PMMA core particles. The morphology of the hybrid particles was investigated with transmission (TEM) and scanning (SEM) electron microscopy as a function of the medium conditions and the amount of TEOS. Improved thermal properties were observed by TGA analysis.