• Proceeding of EDISON Challenge
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• 2017.03a
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• pp.95-99
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• 2017

Protein contact map은 단백질 삼차구조에 대한 정보를 이차원의 이미지로 표현하는 방법의 하나로, 비교적 간략하지만 단백질 구조에 대한 핵심적 정보를 함축하고 있다. 이러한 단백질 구조를 바탕으로 단백질의 internal energy, solvation free energy, free energy 와 같은 열역학 함수를 도출할 수 있다. 본 연구에서는 이미지 인식에 대한 머신러닝 기법을 사용하여 단백질 구조를 함축하는 단백질의 contact map으로부터 단백질의 열역학적 함수를 예측하는 연구를 진행하였다. 단백질의 main-chain 간의 contact map, side-chain 간의 contact map, main-chain과 side-chain 간의 contact map 들로부터 단백질의 여러 가지 열역학적 함수를 예측하고자 했으며 최종적으로 Convolution Neural Network (CNN) 기법을 사용하여 단백질의 free energy를 ~18 kcal/mol의 범위에서 예측 가능함을 보였다. 본 연구를 바탕으로 단백질의 contact map과 열역학 함수 사이의 상관관계가 있으며, 머신러닝 기법을 사용하여 단백질 contact map으로부터 열역학적 함수를 예측하는 것이 가능함을 보였다.

• 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.26 no.4
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• pp.585-588
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• 2005

Bipyridine and its derivatives have been widely used as the ligands in transition metal complexes. The proton affinities of pyridine derivatives were calculated using an ab initio quantum mechanical method (B3LYP with various double zeta and triple zeta basis sets) in combination with the Poisson-Boltzmann continuum solvation model. Van der Waals radii of the atoms in the heterocyclic rings for the solvation energy calculation were set to values determined to reproduce the $pK_a$ values of guanine and oxoguanine derivatives and that of chlorine was optimized to reproduce the experimental values of relating compounds. The $pK_a$ values for the heterocyclic ring compounds were in agreement with the experimental values with a mean unsigned error of 0.45 $pK_a$ units.

• Bulletin of the Korean Chemical Society
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• v.33 no.8
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• pp.2711-2718
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• 2012

The alkylation of the ambident enolates of a methyl glycinate Schiff base with ethyl chloride was studied at B3LYP and MP2 levels with $6-31+G^*$ basis set. The free (E)-enolates and (Z)-enolate are similar in energy and geometry. The transition states for the alkylation of the free (E)/(Z)-enolate with ethyl chloride have similar energy barriers of ~13 kcal/mol. However, with a lithium ion, the (E)-enolate behaves as an ambident enolate and makes a cyclic lithium-complex in bidentate pattern which is more stable by 11-23 kcal/mol than the (Z)-enolate-lithium complexes. And the TS for the alkylation of (E)-enolate-lithium complex coordinated with one methyl ether is lower in energy than those from (Z)-enolate-lithium complexes by 4.3-7.3 kcal/mol. Further solvation model (SCRF-CPCM) and reaction coordinate (IRC) were studied. This theoretical study suggests that the alkylation of ambident enolates proceeds with stable cyclic bidentate complexes in the presence of metal ion and solvent.

• 한국생물공학회:학술대회논문집
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• 2001.11a
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• pp.886-889
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• 2001

C-terminus specific immobilization often results in a increased structural stability resistant to various denaturation factors. In order to elucidate the immobilization effect on the c-terminus in molecular level, we made over 200 protein data set from Protein Data Bank(PDB), analyzed c-terminus structure of each protein, and investigated the structural relationship with the stabilizing factors such as hydrogen bond, ion pairs, cation pi, disulfide bond, solvation free energy, surface area, flexibility and so on.

• Bulletin of the Korean Chemical Society
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• v.19 no.12
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• pp.1347-1350
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• 1998

The equivalent conductances for tetraethylammonium perchlorate (TEAP), tetrabutylammonium perchlorate (TBAP), tetrahexylammonium perchlorate (THAP), and tetradodecylammonium perchlorate (TDDAP) were measured in pyridine (Py) at 25 ℃. The measured data have been analyzed by Onsager conductance theory. From Kohirausch's law of independent migration of ion, the limiting ionic conductances of tetraalkylammonium ions were determined using the limiting ionic conductance of perchlorate cited from reference. Using those and viscosity of pyridine, the Stokes and hydrodynamic radii of tetraethylammonium, tetrabutylammonium, tetrahexylammonium, and tetradodechylammonium ions were calculated. And, the salvation numbers of corresponding ions were also calculated using the hydrodynamic and crystallographic radii and the volume of one pyridine molecule. From those results, the model of salvation for those ions was extracted by comparison with the model for ion salvation. And the electrostatic Gibbs free energy (ΔGel) fitted for our salvation model was calculated. Those of corresponding ions in pyridine at 25 ℃ also increased with increasing radii of tetraalkylammonium ions. This trend of ΔGel was explained by the different ion-solvent interaction between tetraalkylammonium ion and pyridine.

• Bulletin of the Korean Chemical Society
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• v.33 no.8
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• pp.2669-2674
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• 2012

Crown ether is one of well-known host molecules and able to selectively sequester metal cation. We employed M06-2X density functional theory with IEFPCM and SMD continuum solvation models to study selectivity of dibenzo-18-crown-6-ether (DB18C6) for alkaline earth dications, $Ba^{2+}$, $Sr^{2+}$, $Ca^{2+}$, and $Mg^{2+}$ in the gas phase and in aqueous solution. $Mg^{2+}$ showed predominantly strong binding affinity in the gas phase because of strong polarization of CO bonds by cation. In aqueous solution, binding free energy differences became smaller among these dications. However, $Mg^{2+}$ had the best binding, being incompatible with experimental observations in aqueous solution. The enthalpies of the dication exchange reaction between DB18C6 and water cluster molecules were computed as another estimation of selectivity in aqueous solution. These results also demonstrated that $Mg^{2+}$ bound to DB18C6 better than $Ba^{2+}$. We speculated that the species determining selectivity in water could be 2:1 complexes of two DB18C6s and one dication.

• Proceeding of EDISON Challenge
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• 2014.03a
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• pp.237-249
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• 2014

Deposition of amyloid-${\beta}$ ($A{\beta}$) proteins is the conventional pathological hallmark of Alzheimer's disease (AD). The $A{\beta}$ protein formed from the amyloid precursor protein is predominated by the 40 residue protein ($A{\beta}40$) and by the 42 residue protein ($A{\beta}42$). While $A{\beta}40$ and $A{\beta}42$ differ in only two amino acid residues at the C-terminal end, $A{\beta}42$ is much more prone to aggregate and exhibits more neurotoxicity than $A{\beta}40$. Here, we investigate the molecular origin of the difference in the aggregation propensity of these two proteins by performing fully atomistic, explicit-water molecular dynamics simulations. Then, it is followed by the solvation thermodynamic analysis based on the integral-equation theory of liquids. We find that $A{\beta}42$ displays higher tendency to adopt ${\beta}$-sheet conformations than $A{\beta}40$, which would consequently facilitate the conversion to the ${\beta}$-sheet rich fibril structure. Furthermore, the solvation thermodynamic analysis on the simulated protein conformations indicates that $A{\beta}42$ is more hydrophobic than $A{\beta}40$, implying that the surrounding water imparts a larger thermodynamic driving force for the self-assembly of $A{\beta}42$. Taken together, our results provide structural and thermodynamic grounds on why $A{\beta}42$ is more aggregation-prone than $A{\beta}40$ in aqueous environments.

• Bulletin of the Korean Chemical Society
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• v.35 no.4
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• pp.1029-1035
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• 2014

The protolytic dissociation process of hydrochloric acid (HCl) and hydrofluoric acid (HF) is studied using the B3LYP and MP2 methods with the 6-311+G(d,p) basis set in the gas phase and in aqueous solution. To study the phenomena in detail, discrete and discrete/continuum models were applied by placing water molecules in various positions around the acid. The dissociation process was studied using the thermodynamic cycle involving the structures optimized both in the gas phase and in aqueous solution and was analyzed with two key energy factors, relaxation free energy (${\Delta}G_{Rex(g)}$) and solvation free energy (${\Delta}G_s$). Based on the results, we could understand the dissociation mechanism and wish to propose the best way to study acid dissociation process using the CPCM methodology in aqueous solution.

• Genomics & Informatics
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• v.5 no.1
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• pp.24-29
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• 2007

Computational virtual screening has become an essential platform of drug discovery for the efficient identification of active candidates. Moleculardocking, a key technology of receptor-centric virtual screening, is commonly used to predict the binding affinities of chemical compounds on target receptors. Despite the advancement and extensive application of these methods, substantial improvement is still required to increase their accuracy and time-efficiency. Here, we evaluate several advanced structure-based virtual screening approaches for elucidating the rank-order activity of chemical libraries, and the quantitative structureactivity relationship (QSAR). Our results show that the ensemble-average free energy estimation, including implicit solvation energy terms, significantly improves the hit enrichment of the virtual screening. We also demonstrate that the assignment of quantum mechanical-polarized (QM-polarized) partial charges to docked ligands contributes to the reproduction of the crystal pose of ligands in the docking and scoring procedure.