• Proceedings of the Korean Biophysical Society Conference
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• 2003.06a
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• pp.74-74
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• 2003

We report here the results on N-acetyl-N'-methylamide of oxazolidine (Ac-Oxa-NHMe) calculated using the ab initio molecular orbital method with the self-consistent reaction field (SCRF) theory at the HF level of theory with the 6-3l+G(d) basis set. The displacement of the $\square$-CH$_2$ group in proline ring by oxygen atom has affected the structure of proline, cis$\^$∼/ trans equilibrium, and rotational barrier. The up-puckered structure is found to be prevalent for the trans conformers of the Oxa amide. The higher cis populations of the Oxa amide can be interpreted due to the longer distance between the acetyl methyl group and the 5-methylene group of the ring for the trans conformer of the Oxa amide than that of the Pro amide. The changes in charge of the prolyl nitrogen and the decrease in electron overlap of the C$\^$∼/ N bond for TS structures seem to play a role in lowering rotational barriers of the Oxa amide compared to that of the Pro amide. The calculated preferences for cis conformers in the order of Oxa > Pro amides and for trans-to-cis rotational barriers in the order of Pro > Oxa amide in water are consistent with experimental results on Oxa-containing peptides. The pertinent distance between the prolyl nitrogen and the N$\^$∼/ H amide group to form a hydrogen bond might indicate that this intramolecular hydrogen bond could contribute in stabilizing the TS structures of Oxa and Pro amides and play a role in prolyl isomerization.

• Bulletin of the Korean Chemical Society
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• v.32 no.3
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• pp.1017-1021
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• 2011

Two new benzimidazolyl-containing complexes have been synthesized by reactions of $Cu^{II}$ salts and 1,2-bis(benzimidazolyl) benzene ($H_2bbbz$) with two different dicarboxylate ligands. When phthalate acid ($H_2pt$) was employed as secondary ligand, a 0D molecular complex Cu$(H_2bbbz)(pt){\cdot}(H_2pt)$ (1)was furnished and when the secondary ligand was instead by a linear bridging ligand of terephthalic acid ($H_2tp$) a 1D zipper-like coordination polymer $[Cu(H_2bbbz)(tp){\cdot}2(C_2H_5OH){\cdot}H_2O]_n$ (2) was obtained, suggesting the structure-direction effect of the secondary dicarbxylate ligand. The preliminary investigation on the spectral properties of the complexes was also presented.

• Proceedings of the Microbiological Society of Korea Conference
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• 2006.05a
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• pp.66-68
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• 2006

SUF machinery in Echerichia coli, responsible for the biosynthesis of iron-sulfur clusters, is composed of six protein components (SufABCDSE), among which SufB, SufC, and SufD associate in a complex. We have determined the structures of SufA, SufC, and SufD by X-ray crystallography. SufA is a dimer, in which C-terminal segments containing essential cysteine residues (Cys-Gly-Cys) are positioned to allow coordination of an Fe-S cluster and/or an Fe atom. SufC has the overall structure similar to that of ABC-ATPase but takes an inactive form. SufD has a ${\beta}-helix$ flanked with a-helical domains. We also studied the functional roles of the residues in SufD by mutagenesis and determined the crystal structure of SufCD complex. Molecular mechanism of Fe-S cluster biosynthesis is discussed on the basis of the structural and functional evidence.

• Proceedings of the Korean Institute of Electrical and Electronic Material Engineers Conference
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• 2005.07a
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• pp.172-173
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• 2005

The electronic state of ZnO doped with Y was calculated using the density functional theory. In this study, the program used for the calculation on theoretical structures of ZnO and doped ZnO was Vienna Ab-initio Simulation Package (VASP), which is a sort of pseudo potential method. The detail of electronic structure was obtained by the descrite variational $X\alpha$ (DV-$X\alpha$) method, which is a sort of molecular orbital full potential method. The optimized crystal structures obtained by calculations were compared to the measured structure. The density of state and energy levels of dopant elements was shown and discussed in association with optical properties.

• Applied Chemistry for Engineering
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• v.27 no.2
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• pp.115-122
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• 2016

Melanin is a common name used for a certain type of natural dark pigments existing in living organisms, particularly in human hair, eyes, and skin. The unique free radical scavenging effect of melanine could help protecting cells and tissues from harmful UV light. While their exact molecular structures in nature are not still well defined, their multifunctional properties including electrical and ionic conductivities, antioxidation, wet adhesion, and metal ion chelation, are highlighted for the potential applications in bioorganic electronics including biomedical sensors and devices. In this mini-review, we will discuss sources, synthesis methods, structures and multifunctional properties of melanin materials in addition to current research directions on a wide range of applications.

• Bulletin of the Korean Chemical Society
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• v.19 no.1
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• pp.79-82
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• 1998

Novel coordination polymers of general form $[Co(NCS)_2(Py_2L)_2]_n\; (Py_2L=trans-1,2-bis(4-pyridyl)ethylene$ (bpee), 1; 1,2-bis(4-pyridyl)ethane (bpea), 2) have been synthesized by slow diffusion of aqueous solution of $Co(NCS)_2$ with ethanolic solution of appropriate spacer ligand, $Py_2L$, in a mole ratio of 1 : 2. X-ray analyses on both 1 and 2 have provided similar unit and infinite structures with space group Ibam. The local geometry around the cobalt(Ⅱ) atoms is an octahedral arrangement with two NCS groups in trans position (N-Co-N, 180.0° (1); 180.0°(2)) and four pyridine units in propeller fashion. Each spacer ligand connects two cobalt(Ⅱ) ions defining the edges of a $[Co(II)]_4$ rhombus. The most fascinating feature is the occurrence of perpendicular interwoven of independent square grid sheets: this is, one molecular network is perpendicularly interpenetrated through the centers of the $[Co(II)]_4$ rhombuses of another independent network with all of the cobalt(Ⅱ) atoms in a coplanar sheet. The physicochemical properties of the present unique structures were studied.

• Bulletin of the Korean Chemical Society
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• v.20 no.12
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• pp.1469-1474
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• 1999

New platinum(II) complexes with asymmetrically substituted chiral diamine ligands A₂PtX₂, (A₂ = NH₂CH(CH₃)CH₂NH($c-C_5H_9)$ (apcpa), NH₂CH(CH₃)CH₂NH($c-C_6H_11)$ (apcha); X₂ = 2Cl, isopropylidenmalonate (IPM), 1,1'-cyclobutandicarboxylate (CBDCA)) have been synthesized and characterized by means of elemental analyses, infrared and NMR spectroscopies, and X-ray crystallography. The crystal structures of (S-apcha)Pt[CBDCA] ·3H₂O (orthorhombic, P2₁2₁2(No. 18), a = 6.926(3), b = 15.243(3), c = 19.319(4)Å, V = 2039.5(10) ų, Z = 4, R = 0.072) and (S-apcha)Pt[IPM] ·2.5 H₂O (monoclinic, P2/C(No. 13), a = 9.882(1), b =18.502(1), c = 22.056(1)Å, V = 4032.8(5)ų, Z = 8, R=0.093) exhibit that the platinum atoms achieve a typical square planar arrangement with two nitrogen atoms in cis position and with the chiral center retained. The spectroscopic data disclose that these platinum complexes are stable and their molecular structures are retained in aqueous solution. Among these platinum complexes, the asymmetric diamine-Pt(II) complexes with chloride leaving group exhibit high in vivo activity comparable to cisplatin against leukemia L1210 cell line.

• Bulletin of the Korean Chemical Society
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• v.19 no.5
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• pp.569-575
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• 1998

Investigation of the structure of the gangliosides has proven to be very important in the understanding of their biological roles. We have determined the tertiary structure of asialoganglioside GM1 $(GA_1)$ using NMR spectroscopy and distance geometry calculations. All of the structures are very similar except the glycosidic torsion angles in the ring IV and ring III linkages. There are two low-energy structures for GA1, G1 and G2. G1 differs from G2 only in the IV-III glycosidic linkages and the orientation of acetamido group in ring III. There is a stable intramolecular hydrogen bond between the third hydroxyl group in ring I and the ring oxygen atom in ring II. Also, there may be a weak hydrogen bond between the second hydroxyl group in ring IV and the acetamido group in ring III. Small coupling constants of $^3J_{IH3,IOH3}\; and\; ^3J_{IVH2,IVOH2}$ support this result. Overall structural features of $(GA_1)$ are very similar to those of $(GM_1)$. It implicates that specificities of the sugar moieties in GM1 are caused not by their tertiary foldings, but mainly by the electrostatic interactions between the polar sialic acid and its receptors. Since it is evident that $(GA_1)$ is more hydrophobic than $(GA_1)$, a receptor with a hydrophobic binding site can recognize the $(GA_1)$ better than $(GA_1)$. Studies on the conformational properties of $(GA_1)$ may lead to a better understanding of the molecular basis of its functions.

• Mass Spectrometry Letters
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• v.10 no.3
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• pp.93-101
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• 2019

Algorithms and software for predicting tandem mass spectra have been developed in recent years. In this work, we explore how distinct in silico $MS^2$ spectra are predicted for isomers, i.e. compounds having the same formula and similar molecular structures, to differentiate between them. We used the CFM-ID 2.0/3.0 predictor with regard to (a) test compounds, whose experimental mass spectra had been randomly sampled from the MassBank of North America (MoNA) collection, and to (b) the most widespread isomers of test compounds searched in the PubChem database. In the first validation test, in silico mass spectra constitute a reference library, and library searches are performed for test experimental spectra of "unknowns". The searches led to the true positive rate (TPR) of ($46-48{\pm}10$)%. In the second test, in silico and experimental spectra were interchanged and this resulted in a TPR of ($58{\pm}10$)%. There were no significant differences between results obtained with different metrics of spectral similarity and predictor versions. In a comparison of test compounds vs. their isomers, a statistically significant correlation between mass spectral data and structural features was observed. The TPR values obtained should be regarded as reasonable results for predicting tandem mass spectra of related chemical structures.

• Journal of the Computational Structural Engineering Institute of Korea
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• v.20 no.3
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• pp.287-292
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• 2007

In general, the response of bulk material is independent of its size when it comes to considering classical elasticity theory. Because the surface to bulk ratio of the large solids is very small, the influence of surface can be negligible. But the surface effect plays important role as the surface to bulk ratio becomes larger, that is, the contribution of the surface effect must be considered in nano-size elements such as thin film or beam structure. Molecular dynamics computation has been a conventional way to analyze these ultra-thin structures but this method is limited to simulate on the order of $10^6{\sim}10^9$ atoms for a few nanoseconds, and besides, very time consuming. Analysis of structures in submicro to micro range(thin-film, wire etc.) is difficult with classical molecular dynamics due to the restriction of computing resources and time. Therefore, in this paper, the continuum-based method is considered to simulate the overall physical and mechanical properties of the structures in nano-scale, especially, for the thin-film.