• Korean Journal of Mineralogy and Petrology
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• v.36 no.4
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• pp.355-363
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• 2023

In this study, we explore the nature of clumped isotopes of H₂O molecule using quantum chemical calculations. Particularly, we estimated the relative clumping strength between diverse isotopologues, consisting of oxygen (¹⁶O, ¹⁷O, and ¹⁸O) and hydrogen (hydrogen, deuterium, and tritium) isotopes and quantify the effect of temperature on the extent of isotope clumping. The optimized equilibrium bond lengths and the bond angles of the molecules are 0.9631-0.9633 Å and 104.59-104.62°, respectively, and show a negligible variation among the isotopologues. The calculated frequencies of the modes of H₂O molecules decrease as isotope mass number increases, and show a more prominent change with varying hydrogen isotopes over those with oxygen isotopes. The equilibrium constants of isotope substitution reactions involving these isotopologues reveal a greater effect of hydrogen mass number than oxygen mass number. The calculated equilibrium constants of clumping reaction for four heavy isotopologues showed a strong correlation; particularly, the relative clumping strength of three isotopologues was 1.86 times (HT¹⁸O), 1.16 times (HT¹⁷O), and 0.703 times (HD¹⁷O) relative to HD¹⁸O, respectively. The relative clumping strength decreases with increasing temperature, and therefore, has potential for a novel paleo-temperature proxy. The current calculation results highlight the first theoretical study to establish the nature of clumped isotope fractions in H₂O including ¹⁷O and tritium. The current results help to account for diverse geochemical processes in earth's surface environments. Future efforts include the calculations of isotope fractionations among various phases of H₂O isotopologues with a full consideration of the effect of anharmonicity in molecular vibration.

• Korean Journal of Crystallography
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• v.2 no.2
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• pp.22-27
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• 1991

4-Amino-n-(2,6-dimethyk4-pyrimidnyl) benzenesulfonamide, C12H14N402. Unit cell parameters are a =12.626, b=11.262, c=9.375, a:b:r=90°, V =1333.07h3, D,at=1.390 g /cm3, and λ(Cu-Ka)=1.5418, The space group is Pca21, Orthorhombic. The final R factor of 1068 unique observed reflections is R=0.040. Two pair of molecules which related by symmetry operation has strong hydrogen bond. One is between H(N2) and N(3), and the other is H(NIA) and 0(1).

• Journal of the Korean Chemical Society
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• v.27 no.2
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• pp.150-156
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• 1983

Solvent shift effect on absorption spectra of oxodipyrromethenes and bilirubin IX-${\alpha}$ were studied. In methanol or acetic acid the oxodipyrromethenes exist as flat conjugated conformations and in strong acid medium as enol forms of oxodipyrromethenes and bilirubin. The visible absorption bands of bilirubin IX-${\alpha}$ and the model compounds, oxodipyrrinethenes, are assigned as ${\pi}{\rightarrow}{\pi}^{\ast}$transition due to their large molar absorption coefficients and to the fact that the more alkyl-substituted one absorbs at rather longer wavelengths than less alkyl-substituted one. A weak blue shift of bilirubin IX-${\alpha}$ in polar solvent is probably attribute to disruption of intramolecular hydrogen bond.

• Journal of the Korean Chemical Society
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• v.23 no.1
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• pp.20-29
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• 1979

The origin of barriers to internal rotation of hydrogen peroxide and ethane is investigated by using the concept of Bonding and Antibonding Regions. The strong bond formations between the axial and end atoms on the same side make the real charge densities in these molecules less dependent on conformations than those in the hypothetical molecules having no axial atoms. Thus, the existence of the axial atoms should induce the migration of the transition density from the Bonding region to the Antibonding region. Barrier to internal rotation can be understood in terms of this migration of the transition density to such an extent that the change in nuclear-nuclear repulsion energy becomes the dominating part of the total perturbation energy.

• Bulletin of the Korean Chemical Society
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• v.5 no.1
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• pp.27-32
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• 1984

To investigate the hydration effects on the conformational changes of N-pivaloly-L-prolyl-N-methyl-N'-isopropyl-L-alanin amide (PPMIA), the conformational free energy changes have been calculated by using an empirical potential function varying all the independent degrees of freedom of PPMIA backbones. It is found that cis conformers are folded by a strong intramolecular hydrogen bond involving both terminal CO and NH groups whereas trans conformers accommodate the open conformation. Conformers in the free state are proved to be less stable than in the hydrated state. The free energy changes of cis and trans PPMIA due to the hydration are -50.5 and -39.8 kcal/mole, their conformational energy changes are -52.3 and -41.0 kcal/mole, and their conformational entropy changes are -5.9 and -4.0 e.u., respectively. The free energy changes of cis PPMIA to trans PPMIA in the free and hydrated states are 5.3 and 16.0 kcal/mole, their conformational energy changes are 7.6 and 18.8 kcal/mole, and the entropy changes due to the conformational transitions correspond to 7.5 and 9.4 e.u., respectively. From these results, it is found that the bound water molecules play an important role in stabilizing the conformation of PPMIA.

• Bulletin of the Korean Chemical Society
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• v.29 no.7
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• pp.1311-1314
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• 2008

Bacillus halodurans O-methyltransferase (BhOMT) is an S-adenosylmethionine dependent methyltransferase. In our previous study, three dimensional structure of the BhOMT has been determined by comparative homology modeling and automated docking study showed that two hydroxyl groups at 3'- and 4'-position in Bring and structural rigidity of C-ring resulting from the double bond characters between C2 and C3 of flavonoid, were key factors for interaction with BhOMT. In the present study, BhOMT was cloned and expressed. Binding assay was performed on purified BhOMT using fluorescence experiments and binding affinity of luteolin, quercetin, fisetin, and myricetin were measured in the range of $10^7$. Fluorescence quenching experiments indicated that divalent cation plays a critical role on the metal-mediated electrostatic interactions between flavonoid and substrate binding site of BhOMT. Fluorescence study confirmed successfully the data obtained from the docking study and these results imply that hydroxyl group at 7-position of luteolin, quercetin, fisetin, and myricetin forms a stable hydrogen bonding with K211 and carboxyl oxygen of C-ring forms a stable hydrogen bonding with R170. Hydroxyl group at 3'-and 4'-position in the B-ring also has strong $Ca^{2+}$ mediated electrostatic interactions with BhOMT.

• Polymer(Korea)
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• v.30 no.3
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• pp.271-278
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• 2006

In order to investigate the structure and dynamics of atatic poly (vinyl alcohol) (PVA)/water system, laser light scattering experiment has been done in the semi-dilute concentration regime at $25^{\circ}C$. The scattering intensity I(q) can be analyzed with the fractal equation of $I(q){\sim}q^{-m}$ instead of Onstein-Zernike type equation. The fractal dimensionality m was found to be constant after reaching the plateau value of $m=2.6{\pm}0.3$ above C=3wt%. The time correlation function of dynamic light scattering has always two different modes such as fast mode and slow one. The cooperative diffusion of fast mode showed concentration independence contrary 4o the reptation theory's concentration dependent exponent of 3/4. The slow mode can be interpreted as the motion of large scale heterogeneities and its strong concentration dependence is apparent with a large negative exponent of -3.0. It is considered that the stereo-regular arrangement with four successive meso units of -OH plays as a key role in forming such heterogeneity.

• Applied Chemistry for Engineering
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• v.30 no.6
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• pp.673-680
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• 2019

GAP or GAP-co-BO based energetic thermoplastic elastomers (ETPEs) were synthesized by changing the hard segment content percent in the range of 30~45% by 5% difference. Thermal and mechanical properties of GAP-co-BO based ETPEs were compared to those of GAP based ETPEs. FT-IR results showed that the capability of forming hydrogen bond increases with increasing the hard segment content in GAP/GAP-co-BO based ETPE, and also the GAP-co-BO based ETPEs are stronger than GAP based ETPEs in the hydrogen bond formation. DSC and DMA results showed that the glass transition temperature (T_g) of GAP based ETPEs increased with the increment of the hard segment content, while the T_g of GAP-co-BO based ETPEs was maintained even the hard segment content increased. The storage modulus at room temperature of the GAP-co-BO based ETPEs was higher than that of the GAP based ETPEs. This was due to the strong phase separation behavior of the hard and soft segment of GAP-co-BO based ETPEs, which further resulted in the stronger breaking strength and lower tensile elongation at break point for GAP-co-BO based ETPE than the GAP based one.

• Journal of the Korean Chemical Society
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• v.9 no.3
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• pp.128-133
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• 1965

Hydrazonium diphosphate crystallizes with the space-group symmetry $P2_1/C.$ There are two formular units of $N_2H_6H_4(PO_4)_2$ in the unit cell, for which $a = 4.52{\pm}0.02, b = 8.06{\pm}0.03, c = 10.74{\pm}0.03{\AA}\;and\; {\beta} = 100{\pm}0.5^{\circ}.$ The determination of the crystal structure was carried out by means of Patterson, Fourier and difference syntheses. The phosphate group has configuration of nearly regular tetrahedron with the mean P-O distance of $1.55{\AA}.$ The N-N distance found is $1.40{\AA},$ which corresponds to previously reported values for the $N_2H_6^{++} \;ion \;in\; N_2H_6SO_4.$ A molecule has a transform with a center of symmetry in it. Each nitrogen atom forms three hydrogen bonds with the N…O distances 2.62, 2.79 and $2.89{\AA}.$ And a O…O hydrogen bond between different phosphate groups is found with the distance $2.63{\AA}.$ The structure is held together by three-dimensional network of the strong hydrogen bonds.

• Bulletin of the Korean Chemical Society
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• v.33 no.3
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• pp.869-880
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• 2012

Identification of the selective chemical features for Aurora-B inhibitors gained much attraction in drug discovery for the treatment of cancer. Hence to identify the Aurora-B critical features various techniques were utilized such as pharmacophore generation, virtual screening, homology modeling, molecular dynamics, and docking. Top ten hypotheses were generated for Aurora-B and Aurora-A. Among ten hypotheses, HypoB1 and HypoA1 were selected as a best hypothesis for Aurora-B and Aurora-A based on cluster analysis and ranking score, respectively. Test set result revealed that ring aromatic (RA) group in HypoB1 plays an essential role in differentiates Aurora-B from Aurora-A inhibitors. Hence, HypoB1 used as 3D query in virtual screening of databases and the hits were sorted out by applying drug-like properties and molecular docking. The molecular docking result revealed that 15 hits have shown strong hydrogen bond interactions with Ala157, Glu155, and Lys106. Hence, we proposed that HypoB1 might be a reasonable hypothesis to retrieve the structurally diverse and selective leads from various databases to inhibit Aurora-B.