• Bulletin of the Korean Chemical Society
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• v.29 no.9
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• pp.1717-1722
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• 2008

The 70 kDa heat-shock protein (Hsp70) involved in various cellular functions, such as protein folding, translocation and degradation, regulates apoptosis in cancer cells. Recently, it has been reported that the green tea flavonoid (−)-epigallocatechin 3-gallate (EGCG) induces apoptosis in numerous cancer cell lines and could inhibit the anti-apoptotic effect of human Hsp70 ATPase domain (hATPase). In the present study, docking model between EGCG and hATPase was determined using automated docking study. Epi-gallo moiety in EGCG participated in hydrogen bonds with side chain of K71 and T204, and has metal chelating interaction with hATPase. Hydroxyl group of catechin moiety also participated in metal chelating hydrogen bond. Gallate moiety had two hydrogen bondings with side chains of E268 and K271, and hydrophobic interaction with Y15. Based on this docking model, we determined two pharmacophore maps consisted of six or seven features, including three or four hydrogen bonding acceptors, two hydrogen bonding donors, and one lipophilic. We searched a flavonoid database including 23 naturally occurring flavonoids and 10 polyphenolic flavonoids with two maps, and myricetin and GC were hit by map I. Three hydroxyl groups of B-ring in myricetin and gallo moiety of GC formed important hydrogen bonds with hATPase. 7-OH of A-ring in myricetin and OH group of catechin moiety in GC are hydrogen bond donors similar to gallate moiety in EGCG. From these results, it can be proposed that myricetin and GC can be potent inhibitors of hATPase. This study will be helpful to understand the mechanism of inhibition of hATPase by EGCG and give insights to develop potent inhibitors of hATPase.

• Bulletin of the Korean Chemical Society
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• v.35 no.6
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• pp.1769-1776
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• 2014

Binding modes of a series of catechol derivatives such as protein tyrosine phosphatase 1B (PTP1B) inhibitors were identified by molecular modeling techniques. Docking, molecular dynamics simulations and free energy calculations were employed to determine the modes of these new inhibitors. Binding free energies were calculated by involving different energy components using the Molecular Mechanics-Poisson-Boltzmann Surface Area and Generalized Born Surface Area methods. Relatively larger binding energies were obtained for the catechol derivatives compared to one of the PTP1B inhibitors already in use. The Molecular Mechanics/Generalized Born Surface Area (MM/GBSA) free energy decomposition analysis indicated that the hydroxyl functional groups and biphenyl ring system had favorable interactions with Met258, Tyr46, Gln262 and Phe182 residues of PTP1B. The results of hydrogen bound analysis indicated that catechol derivatives, in addition to hydrogen bonding interactions, Val49, Ile219, Gln266, Asp181 and amino acid residues of PTP1B are responsible for governing the inhibitor potency of the compounds. The information generated from the present study should be useful for the design of more potent PTP1B inhibitors as anti-diabetic agents.

• Bulletin of the Korean Chemical Society
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• v.35 no.1
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• pp.250-252
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• 2014

Lipoprotein-associated phospholipase A2 (Lp-$PLA_2$) is a crucial enzyme in atherosclerosis as a potential drug target. The most remarkable Lp-$PLA_2$ inhibitory drug is Darapladib. We determined the binding pose of Darapladib to Lp-$PLA_2$ through docking study. Darapladib formed two hydrogen bonding interactions with the side chain of Tyr160 and Gln352 and several pi-pi interactions with aromatic and aliphatic hydrophobic residues of Lp-$PLA_2$. It is known that the dietylpropan-amine moiety of Darapladib has influence on the improvement of its oral bioavailability and we supposed this in our docking results.

• Proceedings of the IEEK Conference
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• 1999.11a
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• pp.913-916
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• 1999

Recent developments of carbon nanotubes are reviewed［1,2,3,4］. We use Tersoff carbon potential for bonded interactions［5］ and Lennard-Jones 12-6 potential for non bonding interactions［6］to describe mechanical properties of the temperature-dependent armchair single wall carbon nanotube. At first we report that through defect number and bonding energy calculation, how single wall carbon nanutube is capped in the constant temperature. (300K, 2000K, 3000K, 4000K) At second, we perform MD simulation, which are performed on the energy optimized structure of carbon nanotube.

• Bulletin of the Korean Chemical Society
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• v.25 no.12
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• pp.1911-1916
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• 2004

The conformational preference of tetrahomodioxacalix[4]arenes with three different para substituents on the phenolic ring has been investigated by using ab initio molecular orbital theory (RHF/6-31$G^{\ast}$) and density functional theory (B3LYP/6-31$G^{\ast}$). The stability order is predicted to be cone > C-1,2-alternate > partial cone > 1,3-alternate > COC-1,2-alternate. The distorted cone conformation is found to be most stable in a gas phase and the calculated results are in agreement with the reported $^1$H NMR and X-ray experimental observations. The substitution of methylene with dimethyleneoxa bridges increases the size of the annulus of the molecule, its conformational mobility, and the number of hydrogen bonding patterns. The thermodynamic stability and the conformational characteristics of tetrahomodioxacalix[4]arenes are discussed in regards of the number of phenolic hydrogen bonding patterns and the polarity of a molecule. The substituent effects on the para position of the phenolic ring are also introduced.

• Bulletin of the Korean Chemical Society
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• v.31 no.4
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• pp.941-948
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• 2010

Ab initio and density functional theory methods have been employed to study all theoretically possible conformers of fluoroacetic acid. Molecular geometries and energetic of cis and trans monomers and cis dimers in gaseous phase have been obtained using HF, B3LYP and MP2 levels of theory, implementing 6-311++G(d,p) basis set. It was found that cis rotamers are more stable. In addition, it was found that in comparison with acetic acid the strength of hydrogen bonding in fluoroacetic acid decreased. The infrared spectrum frequencies and the vibrational frequency shifts are reported. Natural population and atom in molecule analysis performed to predict electrostatic interactions in the cyclic H-bonded complexes and charges. The proton transfer reaction is studied and activation energy is compared with acetic acid proton transfer reaction.

• Bulletin of the Korean Chemical Society
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• v.3 no.1
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• pp.9-13
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• 1982

Sulfametrole, $C_9H_{10}N_4O_3S_2$, crystallizes in the monoclinic system, space group $P2_1/n$ , with a = 8.145(2), b = 16.505(4), c = 9.637(1)${\AA},{\beta}=103.72(1)^{\circ},D_m=1.52gcm^{-3}$,Z=4.Intensities for 3594(2143 observed) unique reflections were measured on a four-circle diffractometer with Mo $K{\alpha}$ radiation $({\lambda}=0.71069{\AA})$. The structure was solved by direct method and refined by full-matrix least squares to a final R of 0.070. The geometrical features of the thiadiazole ring indicate some ${pi}$-electron delocalization inside the ring. The least squares planes defined by the benzene and thiadiazole rings are nearly perpendicular to each other(dihedral angle; $93.9^{\circ}$ ). All the potential hydrogen-bond donor atoms in the molecule, N(1) and N(2), are included in the hydrogen bonding. The molecules through hydrogen bonding form three dimensional network.

• Bulletin of the Korean Chemical Society
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• v.17 no.12
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• pp.1149-1153
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• 1996

Ab initio and extended Huckel calculations were carried out on the isomers of trans-RhCl(η2-C2H2)(PH3)2 (1). Due to π-back donation in 1 complex, the rotational energy barrier of alkyne ligand is computed to be in the range of 18.6-25.2 kcal/mol at MP4 levels. The optimized hydrido-alkynyl complex (2) at ab initio level has the distorted trigonal bipyramidal structure. Vinylidene complex (3) is computed to be more stable than 1 complex by 17.1 kcal/mol at MP4//MP2 level. The stabilities of isomers show similar trend at the various level calculations, that is, EHT, MP4//HF, and MP4//MP2 levels. The optimized geometries at ab initio level are in reasonable agreement with experimental data. A detailed account of the bonding in each isomers (1-3) have been carried out in terms of orbital analyses.

• Bulletin of the Korean Chemical Society
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• v.14 no.2
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• pp.191-195
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• 1993

Molecular orbital calculations at the extended Huckel level have been carried out for an electron deficient cluster, $Tl_3(FeL_3)_2{(FeL_4)_3}^{-3}$, where L=CO or $H^-$. The LUMO, $2a_2$", is destabilized by the secondary interaction of the LUMO with $1a_2$" on $(FeL_3)_2$ fragment. This is one of six skeletal bonding orbitals which are associated with $Tl-FeL_3$ bonds. Overlap population analysis has been applied to account for two kinds of Tl-Fe bonds. Replacement of the terminal $C_{3v}$, $FeL_4$, by the $C_{2v}$, $FeL_4$ units in cluster results in slight energy stabilization of the cluster.

• Bulletin of the Korean Chemical Society
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• v.21 no.3
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• pp.300-304
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• 2000

The B3LYP method based on the density functional theory(DFT) is shown to be much better than the ab initio MP2 method for structural determination of diphosphadithiatetrazocine systems having transannular S--S bonding. The presence of bonding between the two sulfur atoms across the cyclic ring is theoretically confirmed in the case of the neutral diphosphadithiatetrazocine. The S--S dobding disappears in the ionized species. The planarity of the dicationic heterocyclic ring system turns out to be closely associated with the $\pi-electron$ delocalization over the entire ring as well as the N-S-N bonds, which become stiffened upon ionizaiton. In the case of dianionic species, the chair-boat and chair conformers are nearly degenerate and far more stable than the crown conformer.