• Bulletin of the Korean Chemical Society
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• v.31 no.5
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• pp.1247-1251
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• 2010

We propose an improved solvent contact model to estimate the solvation free energies of amino acids from individual atomic contributions. The modification of the solvation model involves the optimization of three kinds of parameters in the solvation free energy function: atomic fragmental volume, maximum atomic occupancy, and atomic solvation parameters. All of these atomic parameters for 17 atom types are developed by the operation of a standard genetic algorithm in such a way to minimize the difference between experimental and calculated solvation free energies. The present solvation model is able to predict the experimental solvation free energies of amino acids with the squared correlation coefficients of 0.94 and 0.93 for the parameterization with Gaussian and screened Coulomb potential as the envelope functions, respectively. This result indicates that the improved solvent contact model with the newly developed atomic parameters would be a useful tool for the estimation of the molecular solvation free energy of a protein in aqueous solution.

• Nuclear Engineering and Technology
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• v.47 no.6
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• pp.662-668
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• 2015

A suspension of titanium nanoparticles (Ti NPs) in liquid sodium (Na) has been proposed as a method to mitigate the violent sodium-water reaction (SWR). The interparticle potential between Ti NPs in liquid Na may play a significant role in the agglomeration of NPs on the reaction surface and in the bulk liquid Na, since the potential contributes to a reduction in the long-term dispersion stability. For the effective control of the SWR with NPs, a physical understanding of the molecular dynamics of NPs in liquid Na is key. Therefore in this study, the nonretarded Van der Waals model and the solvation potential model are employed to analyze the interparticle potential. The ab initio calculation reveals that a strong repulsive force driven by the solvation potential exceeds the interparticle attraction and predicts the agglomeration energy required for two 10-nm Ti NPs to be $4{\times}10^{-17}J$. The collision theory suggests that Ti NPs can be effective suppressors of the SWR due to the high energy barrier that prevents significant agglomeration of Ti NPs in quiescent liquid Na.

• Journal of the Korean Chemical Society
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• v.57 no.5
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• pp.554-559
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• 2013

In this study, we have investigated potential energy of ${\beta}$-D-glucopyranose in vacuum and implicit water condition. By Comparing two conditions we find that how solvation energy influence ${\beta}$-D-glucopyranose structure. We use AMBER package program and GLYCAM_06 force field. Solvation model was used for the generalized Born model with Hawkins, Cramer, Truhlar has been proposed. We conclude that difference of contour map of two conditions is caused by solvation effect by reducing hydrogen bonding interaction.

• Bulletin of the Korean Chemical Society
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• v.29 no.5
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• pp.979-984
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• 2008

In this study, 8 solutes (aniline, caffeine, p-cresol, ethyl benzene, methylparaben, phenol, pyridine, and toluene) have been tested in terms of linear solvation energy relationships (LSER). Several micellar liquid chromatography (MLC) systems using cationic surfactant cetyltrimethylammonium bromide (CTAB) and a mixture of water with (methanol, n-propanol, and n-butanol) modifiers were characterized using the LSER solvation parameter model. The effects of the surfactant and modifier concentration on the retention in MLC were discussed. LSER model had demonstrated high potential to predict retention factors with high squared correlation coefficients ($r^2$ > 0.99). A comparison of predicted and experimental retention factors suggests that LSER formalism is able to reproduce adequately the experimental retention factors of the solutes studied in the different experimental conditions investigated. This model is a helpful tool to understand the solute-surfactant interactions and evaluate the retention characteristic of micellar liquid chromatography.

• Bulletin of the Korean Chemical Society
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• v.33 no.3
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• pp.917-924
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• 2012

The conformational study of glycerol has been carried out using the M06-2X/cc-pVTZ level of theory in the gas phase and the SMD M06-2X/cc-pVTZ level of theory in water in order to understand its conformational preferences and solvation effects. Most of the preferred conformers of glycerol have two $C_5$ hydrogen bonds in the gas phase, as found by the analysis of calorimetric data. It has been known that the solvation drove the hydrogen bonds of glycerol to be weaker and its potential surface to be fatter and that glycerol exists as an ensemble of many feasible local minima in water. The calculated populations of glycerol in the gas phase and in water are consistent with the observed values, which are better than the previously calculated ones at the G2(MP2), CBS-QB3, and SM5.42 HF/6-31G(d) levels of theory.

• Proceeding of EDISON Challenge
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• 2015.03a
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• pp.70-75
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• 2015

Fasciclin 1 (FAS1) is an extracellular protein whose aggregation in cornea leads to visual impairment. While a number of FAS1 mutants have been studied that exhibit enhanced/decreased aggregation propensity, no structural information has been provided so far that is associated with distinct aggregation potential. In this study, we have investigated the structural and thermodynamic characteristics of the wild-type FAS1 and its two mutants, R555Q and R555W, by using molecular dynamics simulations and three-dimensional reference interaction site model (3D-RISM) theory. We find that the hydrophobic solvent accessible surface area increases due to hydrophobic core repacking in the C-terminus caused by the mutation. We also find that the solvation free energy of the mutants increases due to the enhanced non-native H-bonding. These structural and thermodynamic changes upon mutation contribute to understand the aggregation of these mutants.

• Journal of Integrative Natural Science
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• v.3 no.4
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• pp.231-236
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• 2010

Partial charge is an important and fundamental concept which can explain many aspects of chemistry. Since a molecule can be regarded as neclei surrounded by electron cloud, there is no way to define a partial charge accurately. Nevertheless, there have been many attempts to define these seemingly impossible parameters, since they would facilitate the understanding of molecular properties such as molecular dipole moment, solvation, hydrogen bonding, molecular spectroscopy, chemical reaction, etc. Common methods are based on the charge equalization, orbital occupancy, charge density, and electric multipole moments, and electrostatic potential fitting. Methods based on the charge equalization using electronegativity are very fast, and therefore they have been used to study many compounds. Methods to subdivide orbital occupancy using basis set conversion, relies on the notion that molecular orbitals are composed of atomic orbitals. The main idea is to reduce overlap integral between two nuclei using converted orthogonal basis sets. Using some quantum mechanical observables like electrostatic potential or charge multipole moments. Using potential grids obtained from wavefunction, partial charges can be fitted. these charges are most useful to describe intermolecular electrostatic interactions. Methods to using dipole moment and its derivatives, seems to be sensitive the level of theory, Dividing electron density using density gradient being the most rigorous theoretically among various schemes, bears best potential to describe the charge the most adequately in the future.

• Bulletin of the Korean Chemical Society
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• v.11 no.3
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• pp.224-227
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• 1990

The excitation mechanism of polycyclic aromatic amines (amino-PAHs) and polycyclic aromatic hydrocarbons(PAHs) for the chemiluminescence arising from the reaction between oxalate ester, bis(2,4,6-trichlorophenyl)oxalate (TCPO) or bis(2,4-dinitrophenyl)oxalate (DNPO) and hydrogen peroxide has been studied in terms of the excitation efficiencies to singlet excitation energies and the oxidative half-wave potentials. As a results of the study, the excitations of both amino-PAHs and PAHs appear to involve the charge transfer type of energy transfer. However the chemiluminescence efficiency corrected for fluorescence quantum yield of the amino-PAHs are varied more sensitively to the oxidative half-wave potential than that of PAHs possibly due to the large difference in solvation energy between the compounds and their ions.

• Applied Chemistry for Engineering
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• v.16 no.5
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• pp.684-688
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• 2005

Aniline was polymerized in various protonic acid (HF, HC1, HBr, HI, $H_2SO_4$) aqueous solutions with different acidity. During the reaction, the dimer formation and the reaction rate were examined as functions of acidity (pH) and the size of counter ions. Open-circuit potential measurements were carried out to investigate the effect of protonic acid on the reaction rate. The results showed that polymerization rate in HF aqueous solution was very slow and polymerization did not occur in HI aqueous solution. These results were explained in terms of acidity and power of oxidation. The ratio of formation of dimers varied with the kind of protonic acid, and the results were explained with the nucleophilicity, solvation effect, and mobility of counter ions.

• Journal of the Korean Chemical Society
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• v.31 no.2
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• pp.123-132
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• 1987

Nucleophilic substitution reactions of methylthiocyanate(MTC) with anion nucleophiles,$SH^-,\;CN^-$ and $OH^-$, have been investigated using MNDO method. For the three reaction centers of MTC, gas-phase and solution-phase selectivities are discussed for each nucleophile by considering potential energy profiles calculated(intrinsic term) and magnitudes of negative charge on the nucleophile at the transition state(solvation term). It was found that both components of the selectivity for $SH^-$agreed with the experimental results obtained for 4-methylbenzylthiocyanate (4-MBTC), but the selectivity order for TEX>$CN^-$ was found to agree only with that of the intrinsic term and that of $OH^-$disagreed with any theoretical selectivity order. The MNDO optimized geometries for all species at the stationary points are reported.