• 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.33 no.3
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• pp.828-832
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• 2012

We performed replica exchange molecular dynamics (REMD) simulations of the tripzip2 peptide (betahairpin) using the GB implicit and TI3P explicit solvation models. By comparing the resulting free energy surfaces of these two solvation model, we found that the GB solvation model produced a distorted free energy map, but the explicit solvation model yielded a reasonable free energy landscape with a precise location of the native structure in its global free energy minimum state. Our result showed that in particular, the GB solvation model failed to describe the tryptophan packing of trpzip2, leading to a distorted free energy landscape. When the GB solvation model is replaced with the explicit solvation model, the distortion of free energy shape disappears with the native-like structure in the lowest free energy minimum state and the experimentally observed tryptophan packing is precisely recovered. This finding indicates that the main source of this problem is due to artifact of the GB solvation model. Therefore, further efforts to refine this model are needed for better predictions of various aromatic side chain packing forms in proteins.

• Bulletin of the Korean Chemical Society
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• v.26 no.4
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• pp.589-593
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• 2005

The solvation free energy of proton in methanol was calculated by B3LYP flavor of density functional calculations in combination with the Poisson-Boltzmann continuum solvation model. In order to check the adequacy of the computation level, the free energies of clustering in the gas phase were compared with the experimental data. The solvents were taken into account in a hybrid manner, i.e. one to five molecules of methanol were explicitly considered while other solvent molecules were represented with an implicit solvation model.

• Journal of the Korean Chemical Society
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• v.35 no.5
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• pp.443-451
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• 1991

The solvation numbers of some ions in water and of KCl in mixed solvent systems were measured using the conductometric method. Stoke's radii of ions in solution were calibrated by the Nightingale method and the solvation numbers of ions in mixed solvents were deduced by simple assumptions. The deduced solvation numbers of each solvent reasonably go with its selective properties of solvation. From the isosolvation point of ions, the selective properties of ionic solvation were discussed.

• 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.

• 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.6 no.1
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• pp.19-23
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• 1985

Solvolysis of 1-adamantyl chloride, -bromide and -tosylate have been studied in methanol-acetonitrile mixtures. Rate maxima were found for 1-adamantyl bromide and tosylate at 80-90 % methanol mixtures. The rate maximum observed was interpreted as a result of cooperative enhancement of cation and anion solvation. 1-Adamantyl tosylate had small cation solvation but had extensive anion solvation. It was concluded that the Y scale based on adamantyl tosylate is superior to others since it varies in a wide range especially for weakly ionizing medium.

• Journal of the Korean Chemical Society
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• v.39 no.8
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• pp.589-597
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• 1995

In water-ethanol systems, the limiting equivalent conductances of electrolytes were obtained using conductometric method. Using TATB method, the limiting equivalent ionic conductances of Li+, Na+, K+, Cl-, and Br- ions were also obtained. The effective radii of corresponding ions were determined using Nightingale method. From the volume of the solvation shell, the four solvation numbers were suggested. The reasonable solvation numbers (hH2O+hO) were estimated by comparing the values obtained by from the various suggested methods. The isosolvation point of ion in water-ethanol estimated was found to be larger than that of in water-methanol. This result agree with ET (solvent polarity) values of solvents. From the reasonable solvation numbers of ions in water-ethanol, the selective solvents of corresponding ions in water-ethanol were obtained.

• Journal of the Korean Chemical Society
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• v.37 no.3
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• pp.309-316
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• 1993

The limiting equivalent ionic conductances of Li$^+$, Na$^+$, K$^+$, Cl$^-$, and Br$^-$ ions were obtained with TATB[Tetraphenyl Arsonium Tetraphenyl Borate] method from limiting equivalent conductances of LiCl, NaCl, KCl and KBr measured in water-methanol systems by conductometric method. With those values and viscosity of water-methanol systems, the Stokes radii of corresponding ions have been extracted. The latter values corrected by calibration method of Nightingale and supplemented by the crystallographic radii were utilized to calculate the volume of solvation-shell that surrounds ions. The reasonable solvation numbers (h$_{H_2O}$ ＋ h$_0$) were estimated by comparing the values obtained by the various suggested methods. The selective properties of ion solvation were also discussed.

• 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 $mol^{-1}$.