• 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.

• Bulletin of the Korean Chemical Society
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• 제33권3호
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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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• 제26권4호
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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.

• 대한화학회지
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• 제35권5호
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• pp.443-451
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• 1991

전도도법을 이용하여 물과 물-유기용매계에서 몇 가지 이온들의 용매화수를 측정하였다. 용매화된 이온의 Stokes 반지름을 Nightingale 법으로 보정하였으며, 혼합용매계에서의 각 용매의 용매화수는 몇 가지 가정을 세워 산정하였다. 이와 같이 정한 용매화수는 이온의 선택적 용매화를 나타내었고 등용매화점을 이용하여 이온의 선택적 용매화 정도를 알아보았다.

• Bulletin of the Korean Chemical Society
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• 제24권12호
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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.

• 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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• 제6권1호
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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.

• 대한화학회지
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• 제39권8호
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• pp.589-597
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• 1995

물과 에탄올 혼합 용매에서 전도도법으로 염의 한계 당량 전도도를 구한 후, TATB법으로 이온의 당량전도도를 구하고 Nightingale법으로 이온의 보정 유효반지름을 얻고, 이온에 용매화된 용매의 부피를 계산하여 몇가지 용매화수를 제안하고 이들중에서 해당 이온에 가장 타당한 용매화수$(h_{H_2O}/+h_o)$를 구하고, 해당 이온에 대한 등용매화점을 얻었다. 물과 에탄올 혼합 용매에서의 해당 이온에 대한 등용매화점이 물과 메탄올 혼합 용매에서의 해당 이온에 대한 등용매화점보다 높은 곳에서 나타남을 알 수 있었다. 이는 용매의 $E_T$의 경향과 잘 일치했으며, 이 경향으로 결과 해석이 가능했다. 그리고 해당 이온에 가장 타당한 용매화수로부터 물과 에탄올 혼합 용매의 조성이 바뀜에 따라 해당 이온에 선택적으로 용매화하는 용매를 알았다.

• 대한화학회지
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• 제37권3호
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• pp.309-316
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• 1993

전도도법을 이용하여 물과 에탄올 혼합 용매에서 LiCl, NaCl, KCl 및 KBr의 한계 당량전도도를 측정한 후, TATB법을 이용하여 염을 구성하는 이온들의 한계 당량전도도를 구했다. 이온의 한계 당량전도도와 혼합 용매의 점성도의 항으로 이루어진 식을 사용하여 이온의 Stokes 반지름을 얻었으며, Nightgale법을 사용하여 이온의 보정반지름을얻었다. 또한 이온의 보정 반지름과 결정 반지름으로 부터 이온에 용매화된 용매의 부피를 구하고, 간단한 가정을 이용하여 이온의 여러가지 용매화수를 얻었다. 이들 중에서 가장 타당한 용매화수 (h$_{H_2O}$ ＋ h$_0$)를 구하고, 등용매화점으로부터 물과 메탄올 혼합 중에서 메탄올의 조성이 바뀜에 따라 이온에 선택적 용매화를 하는 용매를 알았다.

• Bulletin of the Korean Chemical Society
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• 제29권4호
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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 $mol^{-1}$.