• Bulletin of the Korean Chemical Society
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• 제29권4호
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• pp.741-748
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• 2008

We have studied the folding mechanism of $\beta$ -hairpins in the proteins 1GB1, 3AIT and 1A2P by conducting unfolding simulations at moderately high temperatures. The analysis of trajectories obtained from molecular dynamics simulations in explicit aqueous solution suggests that the positions of the hydrophobic core residues lead to subtle differences in the details of folding dynamics. However, the folding of three different hairpins can be explained by a unified mechanism that is a blend of the hydrogen-bond-centric and the hydrophobiccentric models. The initial stage of $\beta$-hairpin folding involves various partially folded intermediate structures which are stabilized by both the van der Waals interactions of hydrophobic core residues and the electrostatic interactions of non-native hydrogen bonds. The native structure is obtained by forming native contacts in the final tune-up process. Depending on the relative positions of the hydrophobic residues, the actual mechanism of hairpi n folding may or may not exhibit well-defined intermediates.

• Archives of Pharmacal Research
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• 제10권4호
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• pp.232-238
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• 1987

The molecular structure of naproxen determined by X-ray diffraction technique was refine to the final R-value geing 0.042. The compound was recrystallized from ethanol solution in monoclinic crystal system, space group $P2_1$ , with Z = 2, a = 13.375(5) $\AA$, b = 5.793(2) $\AA$, c = 7.914 $\AA$, $\beta$=93.91(3)$\AA$ and $d_{obs}$ = 1.26, $d_{calc}$ = 1.25 g/cm$^{3}$. The structure was solved by direct method and refined by block diagonal least squares procedure for 747 relfections (F .leq. 6.sigma.(F)). The molecules are connected by two intermolecular OH--O type hydrogen bonds.

• 대한화학회지
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• 제10권1호
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• pp.15-17
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• 1966

Phenol과 각 종 Dimethylaniline(DMA)간의 수소결합을 Infrared Spectrophotometer로 연구하였다. 일반으로 DMA는 n-donor 및 ${\pi}$-donor의 2중 역활을 하나 주로 n-donor로 작용하며 phenol의 O-H stretching frequency의 shift(${\Delta}{\nu}$)는 DMA의 basicity에 비례하였고 (${\Delta}{\nu}$) 와 Hammett의 σcontant사이에는 linearity가 성립함을 알았다.

• Bulletin of the Korean Chemical Society
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• 제26권8호
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• pp.1229-1234
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• 2005

The conformational, configurtational behavior and the structure of N-2-(1,4-Dioxane)-N'-(4-methylbenzenesulfonyl)-O-(4-methylphenoxy) isourea 1 has been studied using DFT method. Calculations predict the imidoyl amino group of the dioxane ring prefers axial conformation and that the tosyl and tolyl groups about the C=N bond retain E configuration. The anomeric effect controls the population of dioxane ring conformers, and anomers. Intramolecular hydrogen bonds contribute to the stability of E isomers. The computational analysis of 1 complements the X-ray findings.

• Bulletin of the Korean Chemical Society
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• 제31권4호
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• pp.1004-1013
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• 2010

Three-dimensional superstructures of unique self-assemblies generated by exploring the conformational flexibility of various dipyrromethenes through creation of hydrogen-bonds with metal-halide anions are reported and the conformational diversity is thoroughly described in the solid and solution states by X-ray diffraction analysis and variable temperature NMR spectroscopy. The tetrahedral or octahedral structures of their precursors, various metal-dipyrromethene complexes, are also reported, based on the crystallographic data. STM images of the self-assemblies observed on graphite surfaces present interesting arrangements and appear as tubular bunches.

• Bulletin of the Korean Chemical Society
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• 제29권9호
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• pp.1769-1773
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• 2008

fThe kinetics and mechanism of the reactions of Y-O-aryl phenylphosphonochloridothioates with X-pyridines are investigated in acetonitrile at 35.0 ${^{\circ}C}$. The negative value of the cross-interaction constant, $\rho$XY = −0.46, indicates that the reaction proceeds by concerted $S_N2$ mechanism. The observed $k_H/k_D$ values involving d-5 pyridine ($C_5D_5N$) nucleophiles are greater than unity (1.05-1.11). The net primary deuterium kinetic isotope effects, $(k_H/k_D)_{net}$ = 1.28-1.35, excluding the increased $pK_a$ effect of d-5 pyridine are obtained. The transition state with a hydrogen bond between the leaving group Cl and the hydrogen (deuterium) atom in the C-H(D) is suggested for the studied reaction system.

• Archives of Pharmacal Research
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• 제19권1호
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• pp.71-73
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• 1996

The molecular structure of pirprofen, 3-chloro-4-(2,5-dihydro-1H-pyrrol-1-yl)-.alpha.-methyl-benzeneacetic acid, was determined by single crystal X-ray diffraction analysis. The compound was recrystallized from a mixture of chloroform and toluene in triclinic, space group P over $\bar1,\; with\; a=4.577(1),\; b=11.213(2),\; C=12.485(2){\AA},\alpa.=107.39(1),\;\beta=97.79(1),\;\gamma=92.03(2),\; and Z=2$ The calculated density is $1.384 g/cm^3$. The structure was solved by the direct method and refined by full matrix least-squares procedure to the final R value of 0.034 for 1681 independent reflections. The non-aromatic dihydropyrrol group is found to be coplanar to the central aromatic ring. The molecules are dimerized through the intermolecular hydrogen bonds at the carboxyl group in the crystal.

• Bulletin of the Korean Chemical Society
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• 제33권7호
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• pp.2439-2442
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• 2012

In order to explore the effects of the solvent on the formation rate of polyynes, we investigated the absorption spectra of polyynes obtained by laser ablation of a graphite target in different solvents at 1064 nm. Polyynes so produced were confirmed by the Raman band around $2200cm^{-1}$ which corresponds to the carbon triple bonds. The production of polyynes by laser ablation turned out to be significantly affected by the ratio of the hydrogen and carbon atoms in the solvent molecule. No clear correlations were observed in the formation of polyynes for other properties of the solvent such bond dissociation energy, thermal conductivity, and total mass of hydrogen atoms per volume of solvent.

• Bulletin of the Korean Chemical Society
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• 제28권6호
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• pp.936-940
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• 2007

The aminolyses of diphenyl phosphinic chloride (1) with substituted anilines in acetonitrile at 55.0 oC are investigated kinetically. Large Hammett ρ X (ρnuc = ?4.78) and Bronsted β X (βnuc = 1.69) values suggest extensive bond formation in the transition state. The primary normal kinetic isotope effects (kH/kD = 1.42-1.82) involving deuterated aniline (XC6H4ND2) nucleophiles indicate that hydrogen bonding results in partial deprotonation of the aniline nucleophile in the rate-limiting step. The faster rate of diphenyl phosphinic chloride (1) than diphenyl chlorophosphate (2) is rationalized by the large proportion of a frontside attack in the reaction of 1. These results are consistent with a concerted mechanism involving a partial frontside nucleophilic attack through a hydrogen-bonded, four-center type transition state.

• Bulletin of the Korean Chemical Society
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• 제18권1호
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• pp.18-23
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• 1997

Data from structure/activity studies in vir gene induction system have led to evaluate the working hypothesis of interaction between phenolic inducers and phenol binding proteins. The primary specificity in the association of a phenolic inducer with its receptor in our system is hypothesized to be the hydrogen bonding interactions through the ortho methoxy substituents as well as the proton transfer between the inducer and the binding protein. In this paper the proposed working model for phenol-mediating signal transduction was evaluated in several ways. The importance of the general acid-base catalysis was first addressed by the presence of an acidic residue and a basic residue in the phenol binding protein. Series of compounds were tested for vir gene expression activity to confirm the generation of a strong nucleophile by an acidic residue and an involvement of a basic residue as a proton acceptor. An attempt was made to correlate the pKa values of the phenolic compounds with vir gene induction activities as inducers to further support the proposed proton transfer mechanism. Finally, it was also observed that the regioselectively attached methoxy group on phenol compounds is required as the proper hydrogen bond acceptor.