• Bulletin of the Korean Chemical Society
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• v.35 no.12
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• pp.3495-3501
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• 2014

A novel crystal, the mono-protonated metformin acetate (1), was obtained and characterized by elemental analysis, IR spectroscopy and X-ray crystallography. It was found that one of the imino group in the metformin cation was protonated along with the proton transfer from the secondary amino group to the other imino group. Its crystal structure was then compared with the previously reported diprotonated metformin oxalate (2). The difference between them is that the mono-protonated metformin cations can be linked by hydrogen bonding to form dimers while the diprotonated metformin cations cannot. Both of them are stabilized by intermolecular hydrogen bonds to assemble a 3-D supermolecular structure. The four potential tautomer of the mono-protonated metformin cation (tautomers 1a, 1b, 1c and 1d) were optimized and their single point energies were calculated by Density Functional Theory (DFT) B3LYP method based on the Polarized Continuum Model (PCM) in water, which shows that the most likely existed tautomer in human cells is the same in the crystal structure. Based on the optimized structure, their Wiberg bond orders, Natural Population Analysis (NPA) atomic charges, molecular electrostatic potential (MEP) maps were calculated to analyze their electronic structures, which were then compared with the corresponding values of the diprotonated metformin cation (cation 2) and the neutral metformin (compound 3). Finally, the possible tautomeric mechanism of the mono-protonated metformin cation was discussed based on the observed phenomena.

• Journal of Korean Tunnelling and Underground Space Association
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• v.7 no.4
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• pp.305-311
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• 2005

Shotcrete adhesive strength in large section tunnels in jointed rock masses plays an important role in preventing rock block from falling and shotcrete debonding due to blasting vibration. Nevertheless, it has not been considered as a major factor such as shotcrete compressive strength in design and construction. For this reason, the purpose of this study is to analyze the effect on shotcrete adhesive strength for large-sectioned tunnels. First, the parametric study using numerical model similar to Holmgren's punch-loaded test was executed for various range of adhesive strength. It shows that the shotcrete bearing capacity is linearly proportioned to the adhesive strength between shotcrete layer and blocks. And then, distinct element analysis of a jointed rock tunnel for an adhesive strength of 1 MPa and a conventional fully-bonded condition between the shotcrete layer and the excavation face was compared in order to evaluate the effect of the shotcrete adhesive strength.

• Korean Journal of Fisheries and Aquatic Sciences
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• v.19 no.1
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• pp.45-51
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• 1986

Equimolar aqueous solutions of D-glucose and glycine were heated at $50^{\circ}C\;and\;95^{\circ}C$ at pH 6.7. The headspace volatiles and the ether extracts from the reaction mixture were analyzed by gas chromatography and gas chromatography-mass spectrometry using a fused silica capillary column. The major components formed were identified as diacetyl, three furfurals, two pyrroles, one furanone, two pyranones and two amides. In order to elucidate the formation mechanisms of the amides formed front amino-carbonyl reaction, two model systems were adopted. N-butylacetamide were formed as major components from diacetyl-butylamine ana glyoxal-butylamine systems, respectively. The results obtained suggest that such ${\alpha}-dicarbonyls$ as 3-deoxy-D-erythro-2,3-hexodiulose and diacetyl generated in the amino-carbonyl reaction react with amino compounds, amides then being formed by cleavage of the C-C bond in the ${\alpha}-dicarbonyls$.

• Proceedings of the Korea Technical Association of the Pulp and Paper Industry Conference
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• 1999.11b
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• pp.204-208
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• 1999

Friction was measured on filter paper sheets impregnated with model compounds representing wood extractives using an apparatus based on the horizontal plane principle. The best lubrication of paper surfaces was achieved when they were completely separated by a densely packed film of saturated long-chain amphophilic molecules, such as fatty acids. The fatty acids adsorbed with their polar ends on the paper surface, causing their hydrocarbon chaine to be orientated perpendicularly to the paper surface. The saturated C18-acid, stearic acid, was an efficient lubricator for paper surfaces. The introduction of a double bond in stearic acid eliminated its lubricating ability. The spatial length of the lubricating fatty acid thereby decreases from 24${\AA}$ to 11${\AA}$. However the transisomer of oleic acid, elidic acid, had the ability to lower friction due to an increased spatial length of the fatty acid. Both the spatial length of the hydrocarbon chain and the number of lubricating chains may be of importance for the paper-to-paper friction caused by wood extractives. A hydrophilic head-graup in the wood extractive and an ordered molecular layer of lubricating molecules seems also to be prerequisites for efficient lubrication. A chemical weak boundary layer between the paper sheets was suggested to cause the low friction when long chain saturated fatty acids were deposited on paper.

• Analytical Science and Technology
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• v.6 no.1
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• pp.39-45
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• 1993

We have examined Raman spectra of cis-peptide model complex, diketopiperazine in water and $D_2O$ with 320 nm through 218 nm excitation. Our study examines assignment of the resonance enhanced amide vibrations and characterizes their enhancement mechanism. Three resonance enhaned cis-peptide marker bands were observed in aqueous solution at 1676, 1533 and $806cm^{-1}$, which were assigned to the cis-amide I, II and S band, respectively. The $1533cm^{-1}$ amide II band, which is almost pure C-N stretching, was most dominant in water and shifted to $1520cm^{-1}$ upon N-deuteration. This band will be probably a potential probe band for cis-peptide moieties in proteins. The excitation profile data and an Albrecht A-term fit indicated that the cis-peptide vibrations derive their intensities from the 188 nm cis-peptide ${\pi}-{\pi}^*$ electronic transition. We Propose that the geometry of cis-peptide ${\pi}^*$ excited state is C-N bond displacement relative to that of electronic ground state.

• Bulletin of the Korean Chemical Society
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• v.31 no.11
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• pp.3333-3340
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• 2010

A three dimensional pharmacophore model was generated for the molecules which are responsible for anti-inflammatory activities targeting Interleukin-2 inducible tyrosine kinase (Itk). 16 structurally diverse molecules were selected as training set to generate the hypotheses using Discovery Studio v2.1. The best hypothesis, Hypo1, comprises two hydrogen bond acceptor (HBA), one hydrophobic aromatic (HA), one ring aromatic (RA) and shows high cost difference (63.71), high correlation coefficient (0.97) as well as low RMS deviation (0.81). Hypo1 has been further validated toward a test set, decoy set and Fischer's randomization method. Furthermore, Hypo1 was used to screen NCI and Maybridge databases. Finally, 2 hit molecules were identified as potential leads against Itk, which may be useful for future drug development.

• Asian Journal of Atmospheric Environment
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• v.2 no.1
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• pp.34-46
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• 2008

Emissions inputs for use in air quality modeling of Korea were generated with the emissions inventory data from the National Institute of Environmental Research (NIER), maintained under the Clean Air Policy Support System (CAPSS) database. Source Classification Codes (SCC) in the Korea emissions inventory were adapted to use with the U.S. EPA's Sparse Matrix Operator Kernel Emissions (SMOKE) by finding the best-matching SMOKE default SCCs for the chemical speciation and temporal allocation. A set of 19 surrogate spatial allocation factors for South Korea were developed utilizing the Multi-scale Integrated Modeling System (MIMS) Spatial Allocator and Korean GIS databases. The mobile and area source emissions data, after temporal allocation, show typical sinusoidal diurnal variations with high peaks during daytime, while point source emissions show weak diurnal variations. The model-ready emissions are speciated for the carbon bond version 4 (CB-4) chemical mechanism. Volatile organic carbon (VOC) emissions from painting related industries in area source category significantly contribute to TOL (Toluene) and XYL (Xylene) emissions. ETH (Ethylene) emissions are largely contributed from point industrial incineration facilities and various mobile sources. On the other hand, a large portion of OLE (Olefin) emissions are speciated from mobile sources in addition to those contributed by the polypropylene industry in point source. It was found that FORM (Formaldehyde) is mostly emitted from petroleum industry and heavy duty diesel vehicles. Chemical speciation of PM2.5 emissions shows that PEC (primary fine elemental carbon) and POA (primary fine organic aerosol) are the most abundant species from diesel and gasoline vehicles. To reduce uncertainties in processing the Korea emission inventory due to the mapping of Korean SCCs to those of U.S., it would be practical to develop and use domestic source profiles for the top 10 SCCs for area and point sources and top 5 SCCs for on-road mobile sources when VOC emissions from the sources are more than 90% of the total.

• Proceedings of the Korean Biophysical Society Conference
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• 2003.06a
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• pp.75-75
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• 2003

We report here the results on N-acetyl-N'-dimethylamide of proline (Ac-Pro-NM $e_2$) calculated using the ab initio molecular orbital method with the self-consistent reaction field (SCRF) theory at the HF level with the 6-31+G(d) basis set to investigate the conformational preference of polyproline depending on the cis/trans peptide bonds and down/up puckerings along the backbone torsion angle $\square$ in the gas phase, chloroform, and water. In the gas phase, Ac-Pro-NM $e_2$ has seven local minima of tFd, tFu, cFd, cFu, cAu, tAu, and cAd conformations. In particular, polyproline conformations tFd, tFu, cFd, and cFu are found to be more stable than $\square$-helical conformations cAu, tAu, and cAd. In contrast, Ac-Pro-NHMe has seven local minima of tCd, tCu, cBd, cAu, tAu, cFd, and cFu conformations. Conformations tCd and tCu are found to be most stable, which is ascribed to the intramolecular hydrogen bond between C=O of acetyl group and $N^{~}$ H of N'-methyl amide group. The stability of the cFd conformation (i.e., the polyproline I structure) in chloroform is somewhat increased, relative to that in water, although tFd and tFu conformations (i.e., the polyproline II structure) are dominate both in chloroform and water. The population of backbone conformations feasible in chloroform and water is consistent with the experiments. This work is supported by a Korea Research Foundation Grant (KRF-2002-041-C00129).

• Archives of Pharmacal Research
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• v.29 no.1
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• pp.50-58
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• 2006

Translationally controlled tumor protein (TCTP), also known as histamine releasing factor (HRF), is found abundantly in different eukaryotic cell types. The sequence homology of TCTP between different species is very high, belonging to the MSS4/DSS4 superfamily of proteins. TCTP is involved in both cell growth and human late allergy reaction, as well as having a calcium binding property; however, its primary biological functions remain to be clearly elucidated. In regard to many possible functions, the TCTP of Plasmodium falciparum (Pf) is known to bind with an antimalarial agent, artemisinin, which is activated by heme. It is assumed that the endoperoxide-bridge of artemisinin is opened up by heme to form a free radical, which then eventually alkylates, probably to the Cys14 of PfTCTP. Study of the docking of artemisinin with heme, and subsequently with PfTCTP, was carried out to verify the above hypothesis on the basis of structural interactions. The three dimensional (3D) structure of PfTCTP was built by homology modeling, using the NMR structure of the TCTP of Schizosaccharomyces pombe as a template. The quality of the model was examined based on its secondary structure and biological function, as well as with the use of structure evaluating programs. The interactions between artemisinin, heme and PfTCTP were then studied using the docking program, FlexiDock. The center of the peroxide bond of artemisinin and the Fe of heme were docked within a short distance of $2.6{\AA}$, implying the strong possibility of an interaction between the two molecules, as proposed. When the activated form of artemisinin was docked on the PfTCTP, the C4-radical of the drug faced towards the sulfur of Cys14 within a distance of $2.48{\AA}$, again suggesting the possibility of alkylation having occurred. These results confirm the proposed mechanism of the antimalarial effect of artemisinin, which will provide a reliable method for establishing the mechanism of its biological activity using a molecular modeling study.

• Bulletin of the Korean Chemical Society
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• v.31 no.6
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• pp.1704-1710
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• 2010

The structure of a 2D grid-like copper(II) complex [Cu$(NCO)_2$(pyz)](pyz=pyrazine) (1) consists of 1D chains of Cu-pyz units connected by double end-on (EO) cyanato bridges. Each Cu(II) ion has a distorted octahedral coordination, completed by the four EO cyanato and two pyrazine ligands. Magnetic interactions through EO cyanato and pyrazine bridges in 1 are discussed on the basis of DFT broken-symmetry calculations at the B3LYP level. For model dicopper(II) complexes I (bridged by cyanato) and II (bridged by pyrazine), electronic structure calculations reproduce very well the experimental couplings for the S = 1/2 ferromagnetic and antiferromagnetic exchange-coupled 2D system: the calculated exchange parameters J are +1.25 $cm^{-1}$ and -3.07 $cm^{-1}$ for I and II, respectively. The $\sigma$ orbital interactions between the Cu $x^2-y^2$ magnetic orbitals and the nitrogen lone-pair orbitals of pyrazine are analyzed from the viewpoint of through-bond interaction. The energy splitting of 0.106 eV between two SOMOs indicates that the superexchange interaction should be antiferromagnetic in II. On the other hand, there are no bridging orbitals that efficiently connect the two copper(II) magnetic orbitals in I because the HOMOs of the basal-apical NCO bridge do not play a role in the formation of overlap interaction pathway. The energy separation in the pair of SOMOs of I is calculated to be very small (0.054 eV). This result is consistent with the occurrence of weakly ferromagnetic properties in I.