• Title/Summary/Keyword: chemical structure analysis

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Molecular Docking, 3D QSAR and Designing of New Quinazolinone Analogues as DHFR Inhibitors

  • Yamini, L.;Kumari, K. Meena;Vijjulatha, M.
    • Bulletin of the Korean Chemical Society
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    • v.32 no.7
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    • pp.2433-2442
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    • 2011
  • The three dimensional quantitative structure activity relationship (3D QSAR) models were developed using Comparative molecular field analysis (CoMFA), comparative molecular similarity indices analysis (CoMSIA) and docking studies. The fit of Quinazolinone antifolates inside the active site of modeled bovine dihydrofolate reductase (DHFR) was assessed. Both ligand based (LB) and receptor based (RB) QSAR models were generated, these models showed good internal and external statistical reliability that is evident from the $q^2_{loo}$, $r^2_{ncv}$ and $r^2_{pred}$. The identified key features enabled us to design new Quinazolinone analogues as DHFR inhibitors. This study is a building bridge between docking studies of homology modeled bovine DHFR protein as well as ligand and target based 3D QSAR techniques of CoMFA and CoMSIA approaches.

Density Functional Theory Demonstration of Anomeric Effect and Structure: Conformational and Configurational Analysis of N-2-(1,4-Dioxane)-N'-(4-methylbenzenesulfonyl)-O-(4-methylphenoxy) Isourea

  • Dabbagh, Hossein A.;Najafi Chermahini, Ali Reza;Modarresi-Alam, Ali Reza
    • Bulletin of the Korean Chemical Society
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    • v.26 no.8
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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.

Rietveld Analysis of Nano-crystalline MnFe2O4 with Electron Powder Diffraction

  • Kim, Jin-Gyu;Seo, Jung-Wook;Cheon, Jin-Woo;Kim, Youn-Joong
    • Bulletin of the Korean Chemical Society
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    • v.30 no.1
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    • pp.183-187
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    • 2009
  • The structure of nano-crystalline $MnFe_2O_4$ was determined and refined with electron powder diffraction data employing the Rietveld refinement technique. A nano-crystalline sample (with average crystal size of about 10.9 nm) was characterized by selected area electron diffraction in an energy-filtering transmission electron microscope operated at 120 kV. All reflection intensities were extracted from a digitized image plate using the program ELD and then used in the course of structure refinements employing the program FULLPROF for the Rietveld analysis. The final structure was refined in space group Fd-3m (# 227) with lattice parameters a=8.3413(7) $\AA$. The reliability factors of the refinement are $R_F$=7.98% and $R_B$=3.55%. Comparison of crystallographic data between electron powder diffraction data and reference data resulted in better agreement with ICSD-56121 rather than with ICSD-28517 which assumes an initial structure model.

Nondestructive Characterization of Degradation of EPDM Rubber for Automotive Radiator Hoses (자동차 냉각기 호스용 EPDM고무의 노화에 대한 비파괴 특성평가)

  • Kwak, Seung-Bum;Choi, Nak-Sam;Choi, Youn-Joung;Shin, Sei-Moon
    • Journal of the Korean Society for Nondestructive Testing
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    • v.25 no.5
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    • pp.368-376
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    • 2005
  • Coolant rubber hoses for automobile radiators can be degraded and thus failed due to the influence of contacting stresses of air and coolant liquid under thermal and mechanical loadings. In this study, for EPDM(ethylene-propylene diene monomer) rubber conventionally used as a radiator hose material the aging behaviors of the skin part due to thermo-oxidative and electro-chemical stresses were nondestructively evaluated. Through the thermo-oxidative aging test, it was shown that the surface hardness IRHD(International Rubber Hardness Degrees) of the rubber increased with a considerable reduction of failure strain. On account of the penetration of coolant liquid into the skin part the weight of rubber specimens degraded by electro-chemical degradation(ECD) test increased, whereas their. failure strain and IRHD hardness decreased largely. The penetration of coolant liquid seemed to induce some changes in inner structure and micro hardness distribution of the rubbers. Consequently, EPDM rubbers degraded by thermo-oxidative aging and ECD could be characterized nondestructively by micro-hardness and chemical structure analysis methods.

Hydro/solvothermal synthesis, crystal structure, and thermal behaviour of piperazine-templated nickel(II) and cobalt(II) sulfates

  • Kim, Chong-Hyeak;Park, Chan-Jo;Lee, Sueg-Geun
    • Analytical Science and Technology
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    • v.19 no.4
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    • pp.309-315
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    • 2006
  • Two piperazine-templated metal sulfate complexes, $(C_4N_2H_{12})[Ni(H_2O)_6](SO_4)_2$, I and ($C_4N_2H_{12}$) $[Co(H_2O)_6](SO_4)_2$, II, have been synthesized by hydro/solvothermal reactions and their crystal structures analyzed by single crystal X-ray diffraction methods. Complex I crystallizes in the monoclinic system, $P2_1/n$ space group, a=12.920(3), b=10.616(2), $c=13.303(2){\AA}$, ${\beta}=114.09(1)^{\circ}$, Z=4, $R_1=0.030$ for 3683 reflections; II: monoclinic $P2_1/n$, a=12.906(3), b=10.711(2), $c=13.303(2){\AA}$, ${\beta}=114.10(2)^{\circ}$, Z=4, $R_1=0.032$ for 4010 reflections. The crystal structures of the piperazine-templated metal(II) sulfates demonstrate zero-dimensional compound constituted by diprotonated piperazine cations, metal(II) cations and sulfate anions. The structures of complex I and II are substantially isostructural to that of the previously reported our piperazine-templated copper(II) sulfate complex $(C_4N_2H_{12})[Cu(H_2O)_6](SO_4)_2$. The central metal(II) atoms are coordinated by six water molecules in the octahedral geometry. The crystal structures are stabilized by three-dimensional networks of the $O_{water}-H{\cdots}O_{sulfate}$ and $N_{pip}-H{\cdots}O_{sulfate}$ hydrogen bonds between the water molecules and sulfate anions and protonated piperazine cations. Based on the results of thermal analysis, the thermal decomposition reactions of the complex I was analyzed to have three distinctive stages whereas the complex II proceed through several stages.

Enhancement of Analyte Ionization in Desoprtion/Ionization on Porous Silicon (DIOS)-Mass Spectrometry(MS)

  • Lee Chang-Soo;Kim Eun-Mi;Lee Sang-Ho;KIm Min-Soo;Kim Yong-Kweon;Kim Byug-Gee
    • Biotechnology and Bioprocess Engineering:BBE
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    • v.10 no.3
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    • pp.212-217
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    • 2005
  • Desorption/ionization on silicon mass spectrometry (DIOS-MS) is a relatively new laser desorption/ionization technique for mass spectrometry without employing an organic matrix. This present study was carried to survey the experimental factors to improve the efficiency of DIOS-MS through electrochemical etching condition in structure and morphological properties of the porous silicon. The porous structure of silicon structure and its properties are crucial for the better performance of DIOS-MS and they can be controlled by the suitable selection of electrochemical conditions. The fabrication of porous silicon and ion signals on DIOS-MS were examined as a function of silicon orientation, etching time, etchant, current flux, irradiation, pore size, and pore depth. We have also examined the effect of pre- and post-etching conditions for their effect on DIOS-MS. Finally, we could optimize the electrochemical conditions for the efficient performance of DIOS-MS in the analysis of small molecule such as amino acid, drug and peptides without any unknown noise or fragmentation.

Chemical Structure Analysis on the ONO Superthin Film by Second Derivative AES Spectra (2차 미분 AES 스펙트럼에 의한 ONO 초박막의 화학구조 분석)

  • 이상은;윤성필;김선주;서광열
    • Proceedings of the Korean Institute of Electrical and Electronic Material Engineers Conference
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    • 1998.06a
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    • pp.79-82
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    • 1998
  • Film characteristics of thin ONO dielectric layers for MONOS(metal-oxide-nitride-oxide-semiconductor) EEPRM was investigated by AES and AFM. Second derivative spectra of AES Si LVV overlapping peak provided useful information for chemical state analysis of superthin film. The ONO films with dimension of tunneling oxide 24${\AA}$, nitride 33${\AA}$, and blocking oxide 40${\AA}$ were fabricated. During deposition of the LPCVD nitride films on tunneling oxide, this thin oxide was nitrized. When the blocking oxide were deposited on the nitride film, the oxygen not only oxidized the nitride surface, but diffused through the nitride. The results of ONO film analysis exhibits that it is made up of SiO$_2$(blocking oxide)/O-rich SiON(interface/N-rich SiON(nitride)/-rich SiON(interface)/N-rich SiON(nitride)/O-rich SiON(tunneling oxide).

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Density Functional Analysis of the Spin Exchange Interactions in VOSb2O4

  • Koo, Hyun-Joo
    • Bulletin of the Korean Chemical Society
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    • v.33 no.7
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    • pp.2338-2340
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    • 2012
  • The spin exchange parameters of $VOSb_2O_4$ were evaluated by performing energy-mapping analysis based on density functional calculations. The spin exchange interaction between the nearest-neighbor $V^{4+}$ ions is strongly antiferromagnetic while other interactions are negligible. Thus, the magnetic structure of $VOSb_2O_4$ is best described by a spin-1/2 Heisenberg antiferromagnetic chain with no spin frustration.

A Chemical Component of the Marine Alga Ishige Okamurae

  • Kim, Eun-Sook;Choi, Byoung-Wook;Lee, Bong-Ho
    • Proceedings of the PSK Conference
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    • 2003.04a
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    • pp.255.3-256
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    • 2003
  • Marine Algae of order Chordariales are rich resources of bioactive metabolites. Methanolic extracts of the brown alga /shige Okamurae exhibited potent antioxidative and butyrylcholinesterase(BChE) inhibitory effects. Bio-guided purification [solvent partition, ODS flash, silica flash, gel-filtration on Sephadex LH 20, ODS HPLC] of them gave a compound 1. Its structure was elucidated by detailed analysis of spectroscopic data of 1 and comparison of literature data. A variety of bioassay for 1 is in progress.

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