• Bulletin of the Korean Chemical Society
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• 제32권9호
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• pp.3261-3266
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• 2011

The interaction of bilobalide (BB) and ginkgolides B (GB) with bovine serum albumin (BSA) was investigated by fluorescent technique and UV/vis absorption spectroscopy. The results showed that BB and GB could intensively quench the fluorescence of BSA through a static quenching procedure. The binding constants (Ka) and the average binding distance between the donor (BSA) and the acceptor (ginkgolides) were obtained ($r_{BB}$ = 5.33 nm and $r_{GB}$ = 4.20 nm) by the theory of non-radiation energy transfer, and then the thermodynamic parameters such as ${\Delta}S^0$ (0.17-0.32 kJ/mol), ${\Delta}G^0$ (-20.76 ~ -17.79 kJ/mol) and ${\Delta}H^0$ (32.47-76.52 kJ/mol) could be calculated, respectively. All these results revealed that the interaction of BB and GB with BSA were driven mainly by hydrophobie force. The synchronous fluorescence spectroscopy was applied to examine the effect of two ginkgolides on the configuration of BSA. The configuration alteration of BSA could be induced by the hydrophobicitv environment of tyrosine with the increase of the drug concentration.

• 산업기술연구
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• 제26권B호
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• pp.163-171
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• 2006

Human immunodeficiency virus type 1 (HIV-1) integrase plays a critical role in the life cycle of the HIV virus. An ability to accurately map its electrostatic potential, and then use this information to predict the manner in which DNA will bind to the active site of the catalytic domain could provide a foundation for inhibitory design. Attempts to discern the crystal structure of HIV-1 integrase have proven problematic, especially in the region of enzymatic activity, that being those residues involved in the catalysis of the integration of viral DNA into the host cell. However, there is a structural correlation in to the region of interest with avian sarcoma virus (ASV), so a homology model utilizing this similarity was constructed to approximate the behavior/structure of the undetermined portions of the HIV-1 integrase crystal. After this model was constructed and its energy minimized, electrostatic calculations were carried out on the substance, so that an electrostatic potential map was constructed. Using this information, it was determined that DNA binding was oriented so as to exploit the regions of positive potential nearby the active site, as well as the positive potential of the magnesium cofactors.

• Steel and Composite Structures
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• 제16권3호
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• pp.325-337
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• 2014

The strength and buckling problem of a five layer sandwich beam under axial compression or bending is presented. Two faces of the beam are thin aluminium sheets and the core is made of aluminium foam. Between the faces and the core there are two thin binding glue layers. In the paper a mathematical model of the field of displacements, which includes a share effect and a bending moment, is presented. The system of partial differential equations of equilibrium for the five layer sandwich beam is derived on the basis of the principle of stationary total potential energy. The equations are analytically solved and the critical load is obtained. For comparison reasons a finite element model of the beam is formulated. For the case of bended beam the static analysis has been performed to obtain the stress distribution across the height of the beam. For the axially compressed beam the buckling analysis was carried out to determine the buckling load and buckling shape. Moreover, experimental investigations are carried out for two beams. The comparison of the results obtained in the analytical and numerical (FEM) analysis is shown in graphs and figures. The main aim of the paper is to present an analytical model of the five layer beam and to compare the results of the theoretical, numerical and experimental analyses.

• Bulletin of the Korean Chemical Society
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• 제31권12호
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• pp.3644-3652
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• 2010

The metallo-$\beta$-lactamases ($M{\beta}Ls$) are clinically significant enzymes which readily hydrolyze most $\beta$-lactam antibiotics. Discovering potential inhibitors for the $M{\beta}Ls$ is an expensive, time consuming endeavor. Virtual screening can sieve out inhibitor candidates with incompatible features prior to synthesis, decreasing these costs. Using Autodock 4.0, the binding locations and energies of four previously-studied potential inhibitors and four additional compounds obtained from the National Cancer Institute (NCI) database were computationally calculated. Based on the docking models of these eight compounds, we then designed several hypothetical inhibitor structures, compounds A through F, and performed their respective docking experiments. The docking results for compound F showed that it binds to the zinc containing active sites with a lowest predicted binding energy of -6.70 kcal/mol, suggesting F is the most likely potential $M{\beta}L$ inhibitor.

• Bulletin of the Korean Chemical Society
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• 제30권11호
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• pp.2523-2531
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• 2009

Effects of some diacid, diamine and dinitro aromatic compounds on the structure and activity of adenosine deaminase (ADA) were investigated by UV-Vis spectrophotometry in 50 mM phosphate buffer at pH = 7.5 and 27 ${^{\circ}C}$ and molecular docking studies. The results showed that all tested ligands are showing inhibition; five ligands are uncompetitive and other two ligands are mixed of competitive and noncompetetive inhibitors with majority of competitive behavior. For the later case analysis was done based on competitive inhibition. Diacids have larger size and higher inhibition constant ($K_I$) relative to others. A logical correlation between calculated free energy of binding and experimental values was obtained for un-competitive. Experimental and calculated data showed that competitive inhibitors are distributed near the active site of enzyme and form several cluster of ranks, whereas uncompetitive inhibitors bind to the enzyme-substrate complex and distributed far from the active site. Results of structure-activity relationship showed that, larger, more hydrophobe, less spherical and more aromatic ligands have higher inhibition constants.

• Bulletin of the Korean Chemical Society
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• 제27권11호
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• pp.1851-1853
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• 2006

We herein report a new analytical application of XPS to the identification of organic molecules in room temperature ionic liquid for the first time. An organic compound, propargylamine (1), produced in 1-butyl-3-methylimidazolium hexafluorophosphate ([bmim][$PF_6$]), which is one of the room temperature ionic liquids (RTILs), via $A^3$ coupling reaction, is characterized by means of x-ray photoelectron spectroscopy (XPS) rather than using conventional organic compound analysis techniques. There are four non-equivalent carbons in RTILs and 1 each. The ratios of normalized integrated areas of the deconvoluted binding energy of core electron of carbon (C1s) peaks are well matched to the number of carbons in those compounds. The binding energies of C1s of the featured carbons in 1, C4 (sp carbons in acetylene group) and C5 ($sp^2$ carbons in benzene ring), are assigned 286.2 and 285.4 eV, respectively. These results will be able to provide an important tool and a new strategy for the analysis of organic molecules

• Bulletin of the Korean Chemical Society
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• 제24권5호
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• pp.547-551
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• 2003

In the present work, the interaction of three water soluble porphyrins, tetra(p-trimethyle) ammonium phenyl porphyrin iodide (TAPP) as a cationic porphyrin, tetra sodium meso-tetrakis (p-sulphonato phenyle) porphyrin (TSPP) as an anionic porphyrin and manganese tetrakis (p-sulphonato phenyl) porphinato acetate (MnTSPP) as a metal porphyrin, with histone H₂B have been studied by isothermal titration microcalorimetry at 8 mM phosphate buffer, pH 6.8 and 27 °C. The values of binding constant, entropy, enthalpy and Gibbs free energy changes for binding of the first MnTSPP, and first and second TSPP and TAPP molecules were estimated from microcalorimetric data analysis. The results represent that the process is both entropy and enthalpy driven and histone induces self-aggregation of the porphyrins. The results indicate that both columbic and hydrophobic interactions act as self-aggregation driving forces for the formation of aggregates around histone.

• Archives of Pharmacal Research
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• 제29권11호
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• pp.1006-1017
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• 2006

A series of 3-(substituted-benylidene)-1, 3-dihydro- indolin-2-one, 3-(substituted-benylidene)-1, 3-dihydro- indolin-2-thione and 2, 2'-dithiobis 3-(substituted-benylidene)-1, 3-dihydro-indole derivatives was investigated as inhibitor of $p60^{c-Src}$tyrosine kinase by performing receptor docking studies and inhibitory activity toward tyrosine phosphorylation. Some compounds were shown to be docked at the site, where the selective inhibitor PP1 [1-tert-Butyl-3-p-tolyl-1H-pyrazolo[3,4-d]pyrimidine-4-yl-amine] was embedded at the enzyme active site. Evaluation of all compounds for the interactions with the parameters of lowest binding energy levels, capability of hydrogen bond formations and superimposibility on enzyme active site by docking studies, it can be assumed that 3-(substituted-benzylidene)-1, 3-dihydro-indolin-2-one and thione derivatives have better interaction with enzyme active site then 2, 2'-dithiobis 3-(substituted-benzylidene)-1, 3-dihydro indole derivatives. The test results for the inhibitory activity against tyrosine kinase by Elisa method revealed that 3-(substituted-benylidene)-1, 3-dihydro- indolin-2-thione derivatives have more activity then 3-(substituted-benylidene)-1, 3-dihydro- indolin-2-one derivatives.

• 한국진공학회:학술대회논문집
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• 한국진공학회 2009년도 제38회 동계학술대회 초록집
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• pp.340-340
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• 2010

Various structures of vacancy defects in graphene layers and carbon nanotubes have been reported by high resolution transmission electron microscope (HR-TEM) and those arouse an interest of reconstruction processes of vacancy defects. In this talk, we present reconstruction processes of vacancy defects in a graphene and a carbon nanotube by tight-binding molecular dynamics (TBMD) simulations and by first principles total energy calculations. We found that a structure of a dislocation defect with two pentagon-heptagon (5-7) pairs in graphene becomes more stable than other structures when the number of vacancy units is ten and over. The simulation study of scanning tunneling microscopy reveals that the pentagon-heptagon pair defects perturb the wavefunction of electrons near Fermi level to produce the $\sqrt{3}\;{\times}\;\sqrt{3}$ superlattice pattern, which is in excellent agreement with experiment. It is also observed in our tight-binding molecular dynamics simulation that 5-7 pair defects play a very important role in vacancy reconstruction in a graphene layer and carbon nanotubes.

• 대한환경공학회지
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• 제27권3호
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• pp.253-261
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• 2005

불균일 $CoO_x/TiO_2$ 촉매가 충진된 연속 흐름식 고정층 반응기 내에서 ppm 수준으로 수중에 존재하는 trichloroethylene (TCE) 제거반응을 수행하였으며, 가장 우수한 반응활성을 갖는 촉매의 결정구조와 표면화학적 특성을 분석함으로써 반응시간에 따라 분해활성이 전이영역을 보이는 원인을 규명하고자 하였다. $36^{\circ}C$의 반응온도에서 모델반응의 내부확산저항은 없었으며, $TiO_2$ 표면에 흡착에 의한 액상 TCE 제거정도는 무시할 수 있었다. 5% $CoO_x/TiO_2$ 촉매는 본 대상반응에 대하여 가장 우수한 활성을 갖는 것으로 나타났으며, 반응시간의 경과정도에 따라 TCE 분해효율이 점진적으로 증가하여 안정화되는 전이영역의 존재를 확인할 수 있었다. 반응 전 5% $CoO_x$ 촉매에 대한 XRD 패턴에서 담지체로 사용된 $TiO_2$에 의한 피크들 외에 새로운 피크가 관찰되었고, 5시간 이상 동안 반응한 후에 건조된 촉매의 경우에도 반응 전 촉매의 XRD 피크와 매우 유사하였다. $Co_3O_4$의 XRD 패턴들과 대조한 결과, 5% $CoO_x$ 촉매상에서 Co 화합물에 의해 야기되는 XRD 피크들은 $Co_3O_4$에 의한 것임을 알 수 있었다. 반응물에 노출되지 않은 5% $CoO_x/TiO_2$ 촉매에 대한 XPS 측정은 797.1 eV에서 Co $2p_{1/2}$에 대한 주피크와 함께 781.3 eV에서 Co $2p_{3/2}$에 대한 주피크가 관찰되어졌다. 반응 후 촉매의 경우에는 Co $2p_{3/2}$ 및 Co $2p_{1/2}$의 binding energy들은 각각 780.3과 795.8 eV에서 나타났다. 반응 전 후 촉매상에서 Co $2p_{3/2}$의 binding energy 차이는 1.0 eV이고, Co $2p_{1/2}$의 binding energy 차이는 1.3 eV이다. 표준 $Co_3O_4$에 대한 XPS 측정결과, 반응 후 촉매상에 존재하는 $CoO_x$는 $Co_3O_4$로 존재하고, 반응 전의 경우에는 이와는 다른 chemical state를 보여주었다. XRD 및 XPS 결과를 바탕으로, 촉매표면에 존재하는 $Co_3O_4$의 외부표면이 $Co_2TiO_4$와 $CoTiO_3$ 같은 $CoTiO_x$로 encapsulation되어 있는 모델구조를 제안할 수 있고, 이는 반응시간의 함수로 나타나는 촉매활성에 있어서 전이영역의 존재를 잘 설명할 수 있을 뿐만 아니라, XRD와 XPS에서 얻어진 촉매의 물리화학적인 특성을 잘 반영할 수 있다.