• Journal of the Korean Magnetic Resonance Society
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• v.19 no.1
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• pp.1-10
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• 2015

Refinements with atomistic molecular dynamics (MD) simulation have contributed to improving the qualities of NMR structures. In most cases, the calculations with atomistic MD simulation for NMR structures employ generalized-Born implicit solvent model (GBIS) to take into accounts solvation effects. Developments in algorithms and computational capacities have ameliorated GBIS to approximate solvation effects that explicit solvents bring about. However, the quantitative comparison of NMR structures in the latest GBIS and explicit solvents is lacking. In this study, we report the direct comparison of NMR structures that atomistic MD simulation coupled with GBIS and water molecules refined. Two model proteins, GB1 and ubiquitin, were recalculated with experimental distance and torsion angle restraints, under a series of simulated annealing time steps. Whereas the root mean square deviations of the resulting structures were apparently similar, AMBER energies, the most favored regions in Ramachandran plot, and MolProbity clash scores witnessed that GBIS-refined structures had the better geometries. The outperformance by GBIS was distinct in the structure calculations with sparse experimental restraints. We show that the superiority stemmed, at least in parts, from the inclusion of all the pairs of non-bonded interactions. The shorter computational times with GBIS than those for explicit solvents makes GBIS a powerful method for improving structural qualities particularly under the conditions that experimental restraints are insufficient. We also propose a method to separate the native-like folds from non-violating diverged structures.

• 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.

• Bulletin of the Korean Chemical Society
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• v.31 no.1
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• pp.168-170
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• 2010

• Bulletin of the Korean Chemical Society
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• v.31 no.10
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• pp.3013-3016
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• 2010

• 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.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.

• Tribology and Lubricants
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• v.14 no.1
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• pp.54-63
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• 1998

In many practical lubricated contacts such as a rough concentrated contact on the sliding of nominally flat surfaces, the fluid may be of molecular (nanometer) scale owing to the asperity interactions on the surfaces. Under this condition, there is insufficient lubricant on the concentrated contact spot to maintain a realistic continuum. Rheological behavior for this kind of concentrated contact has been studied extensively to know whether the application of viscous fluid model is appropriate. The interaction of two rough surfaces is simplified as perfectly flat-rough surfaces contact under certain conditions by "composite topography" and for a nanometer scale fluid film, three kinds of rheological fluid behavior are analyzed in elastohydrodynamic asperity point contact.t contact.

• Proceedings of the Korean Society of Tribologists and Lubrication Engineers Conference
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• 1997.10a
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• pp.173-182
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• 1997

In many practical lubricated contacts such as a rough concentrated contact on the sliding of nominally flat surfaces, the fluid may be of molecular (nanometer) scale owing to the asperity interactions on the surfaces. Under this condition, there is insufficient lubricant on the concentrated contact spot to maintain a realistic continuum. Rheological behavior for this kind of concentrated contact was studied to know whether the application of viscous fluid model is appropriate. The interaction of two rough surfaces is simplified as perfectly flat-rough surfaces contact under certain conditions by "composite topography" and for a nanometer scale fluid film, three kinds of rheological fluid behavior are analyzed in elastohydrodynamic asperity point contact.t contact.

• Bulletin of the Korean Chemical Society
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• v.35 no.2
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• pp.610-616
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• 2014

The influence of solvent polarity on the absorption spectra of some synthesized azo dye with heterocyclic moieties and ${\beta}$-naphthol (1-3) have been investigated using a UV-Visible spectrophotometer. The spectral characteristics of the azo dyes (1-3) in different solvents at room temperature were analyzed. The solvatochromic empirical variables like ${\pi}^*$, ${\alpha}$, and ${\beta}$ have been used to discuss the solvatochromic behaviour of the dyes and to evaluate their contributions to the solute-solvent interactions. A multi-parameter regression model for quantitative assessment of the solute/solvent interaction and the absorption has been used to explain the solvent effect on azo dyes (1-3).

• Bulletin of the Korean Chemical Society
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• v.30 no.12
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• pp.3006-3010
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• 2009

We have performed long time REMD simulation on 15-19 residues of human calcitonin hormone (DFNKF) which is known to form highly ordered amyloid fibril. The simulation started from randomly oriented multiple DFNKF strand. Using all-atom level simulations with the generalized Born solvation (GB) model (param99MOD3), we observed spontaneous formation of ${\beta}$-sheet for tetramer. Interestingly, the current simulation gives anti-parallel sheet as a major conformation, consistent with experiments. The major interaction stabilizing the anti-parallel sheet seems to be the inter-strand hydrogen bond.