• Bulletin of the Korean Chemical Society
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• v.31 no.6
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• pp.1479-1484
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• 2010

Photosynthesis uses light energy to drive the oxidation of water at an oxygen-evolving catalytic site within photosystem II (PSII). Chlorophyll binding by the photosystem II subunit S protein, PsbS, was found to be necessary for energy-dependent quenching (qE), the major energy-dependent component of non-photochemical quenching (NPQ) in Arabidopsis thaliana. It is proposed that PsbS acts as a trigger of the conformational change that leads to the establishment of nonphotochemical quenching. However, the exact structure and function of PsbS in PSII are still unknown. Here, we clone and express the recombinant PsbS gene from Arabidopsis thaliana in E. coli and purify the resulting homogeneous protein. We used various biochemical and biophysical techniques to elucidate PsbS structure and function, including circular dichroism (CD), fluorescence, and DSC. The protein shows optimal stability at $4^{\circ}C$ and pH 7.5. The CD spectra of PsbS show that the conformational changes of the protein were strongly dependent on pH conditions. The CD curve for PsbS at pH 10.5 curve had the deepest negative peak and the peak of PsbS at pH 4.5 was the least negative. The fluorescence emission spectrum of the purified PsbS protein was also measured, and the ${\lambda}_{max}$ was found to be at 328 nm. PsbS revealed some structural changes under varying temperature and oxygen gas condition.

• Macromolecular Research
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• v.8 no.2
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• pp.53-58
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• 2000

Stabilities and structures of resorcinol formaldehyde resins (RF resins) and their dependence on solvent were studied by molecular mechanics and molecular dynamics. Dimers to decamers of the RF resins in the conditions of dielectric constant = 1.00, 21.01, 36.64, and 80.10 were calculated. The average distance between oxygen atoms in 1-hydroxyl groups of adjacent resorcinols of the resins became longer with increased dielectric constant of the environment. The number of intramolecular hydrogen bonds of the resins decreased by increasing the dielectric constant of the environment. The RF resin structure on the surface of fabric or steel cord was explained based on the present calculation.

• Bulletin of the Korean Chemical Society
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• v.34 no.12
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• pp.3800-3804
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• 2013

In this study, molecular dynamics simulations of SPC/E (extended simple point charge) model have been carried out in the canonical NVT ensemble over the range of temperatures 300 to 550 K with and without Ewald summation. The quaternion method was used for the rotational motion of the rigid water molecule. Radial distribution functions $g_{OO}(r)$, $g_{OH}(r)$, and $g_{HH}(r)$ and self-diffusion coefficients D for SPC/E water were determined at 300-550 K and compared to experimental data. The temperature dependence on the structural and diffusion properties of SPC/E water was discussed.

• Bulletin of the Korean Chemical Society
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• v.25 no.2
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• pp.198-202
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• 2004

Hydrogen bond is an important factor in the structures of carbohydrates. Because of great strength, short range, and strong angular dependence, hydrogen bonding is an important factor stabilizing the structure of carbohydrate. In this study, conformational properties and the hydrogen bonds in GlcNAc( ${\beta}$1,3)Gal(${\beta}$)OMe in DMSO are investigated through NMR spectroscopy and molecular dynamics simulation. Lowest energy structure in the adiabatic energy map was utilized as an initial structure for the molecular dynamics simulations in DMSO. NOEs, temperature coefficients, SIMPLE NMR data, and molecular dynamics simulations proved that there is a strong intramolecular hydrogen bond between O7' and HO3' in GlcNAc( ${\beta}$1,3)Gal(${\beta}$)OMe in DMSO. In aqueous solution, water molecule makes intermolecular hydrogen bonds with the disaccharides and there was no intramolecular hydrogen bonds in water. Since DMSO molecule is too big to be inserted deep into GlcNAc(${\beta}$1,3)Gal(${\beta}$)OMe, DMSO can not make strong intermolecular hydrogen bonding with carbohydrate and increases the ability of O7' in GlcNAc(${\beta}$1,3)Gal(${\beta}$)OMe to participate in intramolecular hydrogen bonding. Molecular dynamics simulation in conjunction with NMR experiments proves to be efficient way to investigate the intramolecular hydrogen bonding existed in carbohydrate.

• Journal of the Korean Ceramic Society
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• v.34 no.7
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• pp.713-721
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• 1997

Molecular dynamic (MD) simulations with new interatomic potential function including the covalent bond were performed on the phase transition of $\alpha$-quartz-type GeO2 under high pressure. The optimized crystal structure and the pressure dependence of the lattice constant showed higher reproducibility than the previous models and were in very good agreement with the experimental data. A phase transition of $\alpha$-quartz and $\alpha$-quartz-type GeO2 by simulation was found approximately 24 GPa and 6-7 GPa, respectively. This phase transition involved an abrupt volume shrinkage and showed 4-6 coordination mixed structure with the increasing in the coordination number of cation.

• ETRI Journal
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• v.24 no.3
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• pp.221-225
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• 2002

We performed nonlinear transmission measurements and quantum-chemical calculations on dithienothiophene(DTT)-based molecules to gain insight into the effect of acceptor and donor groups on two-photon absorption(TPA) properties. The TPA intensity showed dispersion characteristics of the single-photon absorption spectrum. When the molecules included an asymmetric donor-acceptor pair, the single- and two-photon absorption maximum wavelengths were red-shifted more than when the molecules had a symmetric donor-donor structure. We interpreted this result as indicating that the $S_2$ state plays the dominating role in the absorption process of molecules with a symmetric structure. The experimental TPA ${\delta}$ values at the absorption peak wavelength showed a dependence on the structural variations. We found the self-consistent force-field theory and Hartree-Fock Hamiltonian with single configuration interaction formalism to be valid for evaluating TPA ${\delta}$. Although the quantum-chemical calculations slightly underestimated the experimental ${\delta}$ values obtained from nonlinear trans -mission measurements, they reasonably predicted the dependence of the ${\delta}$ value on the structural variations. We confirmed the role of molecular symmetry by observing that donor-donor substituted structure gave the highest experimental and theoretical TPA ${\delta}$ values and that the donor-acceptor substituted structure showed a greater red-shift in the TPA absorption maximum wavelength. Overall, the theoretical ${\delta}$ values of DTT-based molecules were in the order of $10^{-46}\;cm^4{\cdot}s{\cdot}photon^{-1}$ and are higher than that of AF-50 by nearly two orders of magnitude.

• Bulletin of the Korean Chemical Society
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• v.28 no.9
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• pp.1472-1476
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• 2007

Artificial neural networks (ANNs) are successfully developed for the modeling and prediction of normalized polarity parameter (ETN) of 216 various solvents with diverse chemical structures using a quantitative-structure property relationship. ANN with architecture 5-9-1 is generated using five molecular descriptors appearing in the multi-parameter linear regression (MLR) model. The most positive charge of a hydrogen atom (q+), total charge in molecule (qt), molecular volume of solvent (Vm), dipole moment (μ) and polarizability term (πI) are input descriptors and its output is ETN. It is found that properly selected and trained neural network with 192 solvents could fairly represent the dependence of normalized polarity parameter on molecular descriptors. For evaluation of the predictive power of the generated ANN, an optimized network is applied for prediction of the ETN values of 24 solvents in the prediction set, which are not used in the optimization procedure. Correlation coefficient (R) and root mean square error (RMSE) of 0.903 and 0.0887 for prediction set by MLR model should be compared with the values of 0.985 and 0.0375 by ANN model. These improvements are due to the fact that the ETN of solvents shows non-linear correlations with the molecular descriptors.

• Journal of Korean Ophthalmic Optics Society
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• v.1 no.1
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• pp.65-72
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• 1996

The general property of plastic ophthalmic lens has been reviewed by the optical property and polymer structure. A PMMA which is synthesized by the polymerization of monomers of two or more kinds is termed a copolymer, and the main chain composes a skeleton of molecular structure in the polymer. Refraction index of polymer was governed mainly by the polarization of molecular and was followed to increase it conspicuously as Cl, Br, and Iodine was substitude to hydrogen. Thermal dependence of refraction index of polymer show that the higher distinctive characteristic than glass material.

• Bulletin of the Korean Chemical Society
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• v.21 no.4
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• pp.434-440
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• 2000

We present the results of computer simulation for the steady shear flows of rodlike molecules using nonequi-librium molecular dynamics simulation (NEMD) method. The model particle is a rigid rod composed of lin-early connected 6-sites and the Lennard-Jones 12-6 potential governs interactions between sites in different molecules. The system of rodlike molecules exhibits the change of orientational structure, that is, isotropic-nematic transition at high shear rates. We elucidate the nature of the ordered system developed from an isotro-pic phase by steady shear through an analysis of various quantities: orientational order parameters, orientational pair correlation functions, orientational distribution function, and snapshots of configurations. The effects of temperature and density on the shear rate dependence of orientational structure are described.

• Bulletin of the Korean Chemical Society
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• v.7 no.4
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• pp.275-279
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• 1986

Concentration dependences of the isotropic Raman band width and the peak position for the ${\nu}_1$ (C-H stretching) mode of nitromethane in chloroform-d, pyridine-$d_5$, 1,3,5-trifluorobenzene, and hexafluorobenzene have been investigated. For all solutions, the experimental concentration dependences have been well described by the concentration fluctuation model of Knapp and Fischer when appropriate values for the effective numbers (N) of nearest neighbors were used. For the $CH_3NO_2/C_6F_6$ solution, an abnormally small value (2) of N indicates strong intermolecular interaction.