• 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.

• Bulletin of the Korean Chemical Society
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• v.24 no.12
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• pp.1742-1750
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• 2003

In order to characterize the hydrophobic parameters of N-acetyl amino acid amides in 1-octanol/water, a theoretical calculation was carried out using a solvation free energy density model. The hydrophobicity parameters of the molecules are obtained with the consideration of the solvation free energy over the solvent volume surrounding the solute, using a grid model. Our method can account for the solvent accessible surface area of the molecules according to conformational variations. Through a comparison of the hydrophobicity of our calculation and that of other experimental/theoretical works, the solvation free energy density model is proven to be a useful tool for the evaluation of the hydrophobicity of amino acids and peptides. In order to evaluate the solvation free energy density model as a method of calculating the activity of drugs using the hydrophobicity of its building blocks, the contracture of Bradykinin potentiating pentapeptide was also predicted from the hydrophobicity of each residue. The solvation free energy density model can be used to employ descriptors for the prediction of peptide activities in drug discovery, as well as to calculate the hydrophobicity of amino acids.

• Bulletin of the Korean Chemical Society
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• v.29 no.4
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• pp.736-740
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• 2008

The interaction of myelin basic protein (MBP) from bovine central nervous system with divalent calcium ion was studied by isothermal titration calorimetry at 27 ${^{\circ}C}$ in aqueous solution. The extended solvation model was used to reproduce the enthalpies of $Co^{2+}$-MBP interaction over the whole $Co^{2+}$ concentrations. The solvation parameters recovered from the solvation model were attributed to the structural change of MBP due to the metal ion interaction. It was found that there is a set of three identical and noninteracting binding sites for $Co^{2+}$ ions. The association equilibrium constant is 0.015 ${\mu}M^{-1}$. The molar enthalpy of binding is $\Delta$H = −14.60 kJ $mol^{-1}$.

• Bulletin of the Korean Chemical Society
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• v.13 no.6
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• pp.636-642
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• 1992

Preferential solvation (PS) phenomena of solutes based on solvent polarity, $E_T$ and AN, were studied by UV/vis. and NMR spectra in MeOH binary mixtures. According to the extent of solvent-solvent interaction, different solvation phenomena were found. PS concept was applied to explain the reactivity of tert-butyl halides solvolysis. The findings of solvation phenomena have been related to the rate of solvolysis and PS suggested as a reason for the solvent dependence of the rates of reaction. Moreover, we found that the results of principal components analysis using six parameters are in good accordance with the results of PS phenomena in mixed methanol systems.

• Bulletin of the Korean Chemical Society
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• v.11 no.4
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• pp.297-302
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• 1990

Retention of mono-substituted phenols in reversed-phase liquid chromatography has been studied based on the linear solvation energy relationships using the solvatochromic mobile phase parameters, ${\pi}_m^{\ast}, {\alpha}_m$ and ${\beta}_m$. It has been observed that retention behavior of phenols in RPLC were well represented by regression equations vs. solvatochromic mobile phase parameters even though the equations may be incomplete due to lack of an explicit cavity term. Dependence of retention of monosubstituted phenols on the mobile phase properties were varied depending on the type of the organic cosolvent in the mobile phase, e.g., ${\beta}_m$ and {\alpha}_m$ in methanol-water system, but ${\pi}_m^{\ast} and ${\beta}_m$ in THF-water system. It has been suggested that retention of phenols in methanol-water system is controlled by the solvophobicity of the mobile phase.

• Bulletin of the Korean Chemical Society
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• v.15 no.10
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• pp.868-873
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• 1994

We have re-examined the linear solvation energy relationships in reversed phase liquid chromatography by considering various solutes including quite a number of compounds of strong hydrogen bond capability. We observed that solutes of strong hydrogen bond ability should be excluded in order to obtain resonable correlations between In k' and solute polarity parameters and that inclusion of one or two such solutes causes severe distortions of correlation results. This anomaly may be due to existence of residual silanol groups in the stationary phase, that is, their specific interactions with solutes.

• Bulletin of the Korean Chemical Society
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• v.26 no.2
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• pp.238-240
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• 2005

The enthalpies of transfer, ${\Delta}H_t{\Theta}$, of NaI from water to aqueous methanol, ethanol and isopropanol, iPrOH, systems are reported. These data have been analysed in terms of the new solvation theory. These data are considered in terms of the new developed solvation theory including variable ($\alpha$n + $\beta$N), the net effect of the solute on the solvent-solvent bonding, is positive if there is a net breaking or weakening of solvent-solvent bonds. The solvation parameters recovered from the analyses indicate that the net affect of NaI on solvent structure is a breaking of solvent-solvent bonds and that NaI is preferentially solvated by water in all aqueous alcohol systems considered. ($\alpha$n + $\beta$N) values increase with increasing in the size of the alcohol alkyl residue from methanol to iPrOH.

• BMB Reports
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• v.36 no.3
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• pp.243-250
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• 2003

In this paper we investigate (using AM1 semi-empirical as well as HF methods at the STO-3G, 3-21G, 6-31G, 6-$31G^*$ and 6-31+$G^{**}$ level) the conformations, geometrical parameters, Mulliken charges, and solvation effects of the triphosphate form of AZT (AZTTP), as well as the thymidine nucleotide (dTTP) structure. Our calculated geometrical parameters and Mulliken charges, with and without solvation effects, are correlated with recent experimental results.

• Bulletin of the Korean Chemical Society
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• v.26 no.11
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• pp.1761-1766
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• 2005

Solvolysis rates of isopropenyl chloroformate (3) in water, $D_2O$, $CH_3OD$ and in aqueous methanol, ethanol, 2,2,2-trifluoroethanol (TFE), acetone, 1,4-dioxane as well as TFE-ethanol at 10 ${^{\circ}C}$ are reported. Additional kinetic data for pure water, pure ethanol and 80%(w/w) 2,2,2-trifuoroethanol (T)-water (W) at various temperatures are also reported. These rates show the phenomena of maximum rates in specific solvents (30% (v/v) methanol-water and 20% (v/v) ethanol-water) and, variations in relative rates are small in aqueous alcohols. The kinetic data are analyzed in terms of GW correlations, steric effect, kinetic solvent isotope effects (KSIE), and a third order model based on general base catalysis (GBC). Solvolyses based on predominately stoichiometric solvation effect relative to medium solvation are proceeding in 3 and the results are remarkably similar to those for p-nitrobenzoyl chloride (4) in mechanism and reactivity.

• Bulletin of the Korean Chemical Society
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• v.30 no.6
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• pp.1262-1266
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• 2009

Thermodynamics of the interaction between Cerium (III) chloride, $Ce^{3+}$, with Human Serum Albumin, HSA, was investigated at pH 7.0 and $27\;{^{\circ}C}$ in phosphate buffer by isothermal titration calorimetry. Our recently solvation model was used to reproduce the enthalpies of HSA interaction by $Ce^{3+}$. The solvation parameters recovered from our new model, attributed to the structural change of HSA and its biological activity. The interaction of HSA with $Ce^{3+}$ showed a set of two binding sites with negative cooperativity. $Ce^{3+}$ interacts with multiple sites on HSA affecting its biochemical and biophysical properties.