• 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.21 no.5
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• pp.503-509
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• 2000

The solvent effects on the relative free energies of solvation and the difference in partition coefficients (log P) for $Rb^+$ to $K^+$ mutation in several solvents have been investigated using Monte Carlo simulation (MCS) of statistical perturbation theory(SPT). In comparing the relative free energies for interconversion of one ion pair, $Rb^+$ to $K^+$, in $H_2O$(TIP4P) in this study with the relative free energies of the computer simulations and the experimental, we found that the figure in this study with the relative free energies of the computert simulations and the experimental, we found that the figure in this study is $-5.00\pm0.11$ kcal/mol and those of the computer simulations are $-5.40\pm1.9$, -5.5, and -5.4 kcal/mol. The experimental is -5.1 kcal/mol. There is good agreement among various studies, taking into account both methods used to obtain the hydration free energies and standard deviations. There is also good agreement between the calculated structural properties of this study and the simulations, ab initio and the experimental results. We have explained the deviation of the relationship between the free energy difference and the Onsager dielectric function of solvents by the electron pair donor properties of the solvents. For the $Rb^+$ and $K^+$ ion pair, the Onsager dielectric function of solvents (or solvent permittivity), donor number of solvent and the differences in solvation dominate the differences in the relative free energies of solvation and partition coefficients.

• 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.

• Bulletin of the Korean Chemical Society
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• v.32 no.6
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• pp.1985-1992
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• 2011

The stable conformers of glycine and the inter-conversions between them were studied theoretically at various levels of theory, B3LYP, MP2, CCSD and CCSD(T), in the gas phase and in aqueous solution. In aqueous solution, the structures examined by use of the conductor-like polarizable continuum model (CPCM) with various cavity models, UA0, UAHF, UAKS, UFF, BONDI and PAULING, and by use of a discrete/continuum solvation model with eight water clusters. The Gibbs free energy differences between the neutral (NE) and zwitterionic conformers (ZW), ${\Delta}G_{Z-N}[=G_{ZW}-G_{NE}]$, in aqueous solution were well reproduced by using the BONDI and PAULING cavity models. However the ${\Delta}G_{Z-N}$ values were underestimated in other cavity models, although the ZW conformers existed as stable species in aqueous solution. In the studies of a discrete/continuum solvation model with eight water clusters, gas phase results are still insufficient to reproduce the experimental findings. However the ${\Delta}G_{Z-N}$ values calculated by use of CPCM method in aqueous solution agreed well with the experimental ones.

• Bulletin of the Korean Chemical Society
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• v.29 no.2
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• pp.431-437
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• 2008

The solvent effects on the relative free energies of binding of K+ and Na+ ions to 12-crown-4 and Dlog Ks (the difference of stability constant of binding) have been investigated by a Monte Carlo simulation of statistical perturbation theory (SPT) in several solvents. Comparing the relative free energies of binding of K+ and Na+ ions to 12-crown-4, in CH3OH of this study with experimental works, there is a good agreement among the studies. We have reported here the quantitative solvent-polarity relationships (QSPR) studied on the solvent effects the relative free energies of binding of K+ and Na+ ions to 12-crown-4. We noted that DN(donor number) dominates the differences in relative solvation Gibbs free energies of K+ and Na+ ions and DN dominates the negative values in differences in the stability constant (Dlog Ks) as well as the relative free energies of binding of K+ and Na+ ions to 12-crown-4 and p* (Kamlet-Tafts solvatochromic parameters) dominates the positive values in differences in the stability constant (Dlog Ks) as well as the relative free energies of binding of K+ and Na+ ions to 12-crown-4.

• Bulletin of the Korean Chemical Society
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• v.22 no.8
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• pp.877-882
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• 2001

The solvent effects on the relative free energies of Eu3+ to Yb3+ ion mutation in solution have been investigated using a Monte Carlo simulation of statistical perturbation theory (SPT). Our results agree well with available data that were obtained by others. Particularly, the results of water (SPC/E) solvent are almost identical with experimental data. For the present Eu3+ and Yb3+ ions, the relative free energies of solvation vs. Born’s function of bulk solvents decrease with increasing Born’s function of bulk solvents. There is also good agreement between the calculated structural properties in this study and the published works obtained by computer simulation and experimental work.

• Bulletin of the Korean Chemical Society
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• v.27 no.12
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• pp.2011-2018
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• 2006

We have investigated the solvent effects on $\Delta log\;K_s $(the difference of stability constant of binding) and the different free energies of binding of $Nd^{3+}$ and $Eu^{3+}$ ions to 18-crown-6, i.e., the selectivity of $Nd^{3+}$ and $Eu^{3+}$ ions to 18-crown-6 using a Monte Carlo simulation of statistical perturbation theory (SPT) in diverse solvents. The stability constant ($\Delta log\;K_s $) of binding of $Nd^{3+}$ and $Eu^{3+}$ ions to 18-crown-6, in $CH_3OH$ was calculated in this study as -1.06 agrees well with the different experimental results of -0.44~-0.6, respectively. We have reported here the quantitative solvent-polarity relationships (QSPR) studied on the solvent effects the relative free energies of binding of $Nd^{3+}$ and $Eu^{3+}$ ions to 18-crown-6. From the calculated coefficients of QSPR, we have noted that solvent polarity (ET) and Kamlet -Tafts solvatochromic parameters (b ) dominate the differences in relative solvation Gibbs free energies of $Nd^{3+}$ and $Eu^{3+}$ ions but basicity (Bj) dominates the negative values in differences in the stability constant ($\Delta log\;K_s $) as well as the relative free energies of binding of $Nd^{3+}$ and $Eu^{3+}$ ions to 18-crown-6 and acidity (Aj) dominates the positive values in differences in the stability constant ($\Delta log\;K_s $) as well as the relative free energies of binding of $Nd^{3+}$ and $Eu^{3+}$ ions to 18-crown-6.

• Bulletin of the Korean Chemical Society
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• v.24 no.6
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• pp.751-756
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• 2003

We have investigated the solvent effects on Δlog $K_s$ (the difference of stability constant of binding) and the relative free energies of binding of $La^{3+} and Nd^{3+}$ ions to 18-crown-6 by a Monte Carlo simulation of statistical perturbation theory (SPT) in diverse solvents. We compared relative binding Gibbs free energies and the differences in stability constant (Δlog $K_s$) of binding of $La^{3+} and Nd^{3+}$ ions to 18-crown-6 in $CH_3OH$ in this study with the experimental. There is a good agreement between our study and the experimental. We noted that Borns function of the solvents, the electron pair donor properties of the solvent, the radii of host and guest and the differences in solvation dominate the differences in the stability constant (Δlog $K_s$) as well as the relative free energies of binding of TEX>$La^{3+} to Nd^{3+}$ ions to 18-crown-6. The results of this study appear promising for providing the association properties of crown ethers with alkaline earth metals among polar solvents and the less polar or non-polar solvents.

• Bulletin of the Korean Chemical Society
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• v.31 no.11
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• pp.3291-3296
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• 2010

A gelastatins (1), natural MMP inhibitors, and their hydroxamate analogues (2) in TACE enzyme evaluated for discovery of potent TACE inhibitors. We have employed molecular dynamics simulations to compute the relative free energy of hydration and binding to TACE for gelastatin (1) and its hydroxamate analogue (2). The relative free energy difference is directly described in this article using the free energy perturbation approach as a means to accurately predict the TACE inhibitor of gelastatin analogues. The results show that the good agreement between the experimental and theoretical relative free energies of binding, gelastatin hydroxamate (2) binds stronger to TACE by -3.37 kcal/mol. The desolvation energy costs significantly reduced binding affinity, hydroxamate group associated with high desolvation energy formed strong favorable interactions with TACE with more than compensated for the solvation costs and therefore led to an improvement in relative binding affinity.

• Proceeding of EDISON Challenge
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• 2015.03a
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• pp.151-155
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• 2015

The molecular interactions between the nucleic acid bases and water molecules are important in organism. Despite Adenine-Thymine Hoogsteen base pair and Guanine-Cytosine Watson-Crick base pair have been demonstrated to be most stable in a gas phase, the effect of water on the stability of these base pairs remains elusive. Here we report the structural and thermodynamic characteristics on possible Adenine-Thymine and Guanine-Cytosine base pairs in a gas phase as well as in an aqueous phase by using quantum mechanical method and statistical mechanical calculations. First, we optimized the direct base-pair interaction energies of four Adenine-Thymine base pairs (Hoogsteen base pair, reverse Hoogsteen base pair, Watson-Crick base pair, and reverse Watson-Crick base pair) and three Guanine-Cytosine base pairs (GC1 base pair, GC2 base pair, and Watson Crick base pair) in a gas phase at the $B3LYP/6-31+G^{**}$ level. Then, the effect of solvent was quantified by the electronic reorganization energy and the solvation free energy by statistical mechanical calculations. Thereby, we discuss the effect of water on the stability of Adenine-Thymine and Guanine-Cytosine base pairs, and argue why Adenine-Thymine Watson-Crick base pair and Guanine-Cytosine Watson-Crick base pair are most stable in an aqueous environment.