• Bulletin of the Korean Chemical Society
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• 제31권5호
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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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• 제47권6호
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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.

• 대한화학회지
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• 제57권5호
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• pp.554-559
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• 2013

본 연구에서는 ${\beta}$-D-glucopyranose 분자의 hydroxymethyl group의 두 torsion angle의 변화에 따른 포텐셜 에너지의 변화를 진공 상태와 implicit water 상태에서 연구하였으며 이를 통해 Solvation Energy가 구조에 미치는 영향에 대해서 알아보았다. 계산에 사용한 프로그램은 AMBER package였으며, force field는 GLYCAM_06을 사용하였다. Solvation model은 Hawkins, Cramer, Truhlar 등이 제안한 generalized Born model을 사용하였다. 계산 결과, methyl hydroxyl group 내의 hydroxyl group이 고리구조의 hydroxyl group과 강한 수소결합이 가능한 영역에서 많은 변화가 일어났다. 이를 통해 solvation effect로 인해서 수소 결합의 중요성이 감소했다는 결론을 내렸다.

• Bulletin of the Korean Chemical Society
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• 제29권5호
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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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• 제33권3호
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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.

• EDISON SW 활용 경진대회 논문집
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• 제4회(2015년)
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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.

• 통합자연과학논문집
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• 제3권4호
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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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• 제11권3호
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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.

• 공업화학
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• 제16권5호
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• pp.684-688
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• 2005

산도가 각기 다른 양성자산(HF, HCI, HBr, HI, $H_2SO_4$)의 수용액내에서 아닐린을 중합하였다. 이때 산도(pH)와 상대이온(counter ion)의 반응성에 따른 반응속도에 관하여 조사하였다. 반응속도에 대한 양성자산의 영향을 조사하기 위하여, open-circuit potential을 측정하였다. 그 결과 HF 수용액내에서 중합속도가 가장 느리게 나타났고, HI 수용액내에서는 중합반응이 진행되지 않았으며, 이러한 결과들을 산도(pH)와 산화력과의 관계로 설명하였다. 양성자산의 종류에 따라 dimer들의 생성비율도 각기 다르게 나타났으며, 이러한 결과들을 상대이온(음이온)의 친핵성도 (nucleophilicity), 용매화효과 및 이동도의 영향으로 설명하였다.

• 대한화학회지
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• 제31권2호
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• pp.123-132
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• 1987

반경험적 분자궤도함수법인 MNDO방법을 사용하여 $SH^-,\;CN^-$ 그리고 $OH^-$와 메틸티오시아네이트(MTC)의 친핵성치환반응을 연구하였다. 각 친핵체에 대해 MTC세반응중심의 계산된 포텐샬에너지곡면(Intrinsic term)과 전이상태에서의 친핵체의 음전하크기(Solvent term)을 고려하여 가스상과 용액상에 대한 선택성을 논의하였다. 결과로써$SH^-$에 대해서는 선택성의 두 성분 모두 4-methylbenzylthiocyanate (4-MBTC)에 대해 얻어진 실험결과와 일치한반면 $CN^-$의 경우에는 고유항(Intrinsic term)의 선택성만이 일치하였고 $OH^-$의 경우에는 두 항중 어느것도 실험결과로 얻은 선택성과 일치하지 않았다. 정류점에서 모든 종에 대한 MNDO최적화된 구조들을 밝혔다.