• 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.11 no.4
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• pp.309-313
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• 1990

The rates of solvolysis of trans-$[Co(N-eten)_2Cl_2)$+ (N-eten; N-ethylethylenediamine) have been investigated using spectrophotometric method in binary aqueous mixtures containing methyl alcohol, isopropyl alcohol, t-butyl alcohol, ethylene glycol and glycerol. The values of ${\Delta}H^{\neq}$ and ${\Delta}S^{\neq}$ obtained from temperature effect on the rate constants were $80{\sim}84 kJmol^{-1}$ and $- 28{\sim} - 45 JK^{-1}mol^{-1}.$ Extrema found in the variation of the enthalpy and entropy of activation with solvent composition correlated very well with extrema in the variation of the physical properties of mixture which relate to sharp change in the solvent structure. The reaction mechanism was discussed in terms of correlation diagrams involving the exess molar Gibbs function of mixing for the binary mixtures. The behavior of this cobalt(Ⅲ) complex was compared with that of t-butyl chloride. The application of free energy cycle to the process initial state to transition state in water and in the mixture showed that the solvation of transition state had dominant effect on the rates in the mixtures. It was found that $S_N1$ character was increased with increasing the content of co-solvent in the mixture.

• Bulletin of the Korean Chemical Society
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• v.32 no.7
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• pp.2167-2168
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• 2011

• Bulletin of the Korean Chemical Society
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• v.29 no.11
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• pp.2295-2298
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• 2008

• Journal of the Korean Chemical Society
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• v.65 no.3
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• pp.179-184
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• 2021

In this study, the molecular dynamics simulation of 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) single molecule was conducted by changing the solvent properties in order to investigate the change in the glycerol backbone structure in phospholipids according to the solvent properties. DOPC has three different conformations according to glycerol C1-C2 bond: A(θ3 = trans, θ4 = gauche), B(θ3 = gauche, θ4 = gauche-), C(θ3 = gauche-, θ4 = trans). Changes in the glycerol backbone structure of the DOPC were examined using the solvent's dielectric constant and surface tension constant as variables. As a result, the population of the B structure increased as the dielectric constant increased. The reason is that the solvation energy of the B structure is larger than that of A. In addition, as the surface tension constant increased, the population of the B structure increased because the surface area of B was smaller than that of A. The results of these studies are expected to be used in the study of phospholipid structure in the future.

• 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.

• Journal of the Korean Chemical Society
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• v.28 no.4
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• pp.210-216
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• 1984

Solvatochromic comparison methods were applied to determine Taft's solvent parameters, ${\pi}^{\ast}$(solvent polarity-polarizability), ${\alpha}$(solvent hydrogen bond donor acidity) and ${\beta}$ (solvent hydrogen bond acceptor basicity) for MeOH-MeCN solvent mixtures. Swain's solvent parameters A(anion solvation scale) and B(cation solvation scale) were also determined by least square fitting of kinetic data in the same binary solvent mixtures. It was found that: (i)${\beta}$ depends on the basicity of the solvent and increases with the MeOH content owing to the increase in polymeric structure of methanol; (ii) ${\pi}^{\ast}$depends on the dipole moment of the solvent and increases with the MeCN content of the solvent; (iii) ${\alpha}$ increases rapidly with the MeOH content as the hydrogen bond donor acidity of the solvent mixtures increases. Taft's reaction constants a and s and Swain's reaction constants a and b were determined for the reactions reported from our laboratory previously using solvent parameters determined in this work. No meaningful inter-relationship was found between the two set of reaction parameters, but a good linear correlation was found between the ratios a/s and a/b. Solvent effect on the reaction mechanism, substituent effect and leaving group ability were examined in the light of these reaction constants ratios.

• Bulletin of the Korean Chemical Society
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• v.30 no.8
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• pp.1845-1850
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• 2009

We have performed replica-exchange molecular dynamics (REMD) simulations on the dimer formation of fibrilforming segments of $\alpha$-Synuclein (residues 71 - 82) using implicit solvation models with two kinds of force fields- AMBER parm99SB and parm96. We observed spontaneous formation of dimers from the extensive simulations, demonstrating the self-aggregating and fibril forming properties of the peptides. Secondary structure profile and clustering analysis showed that dimers with antiparallel $\beta$-sheet conformations, stabilized by well-defined hydrogen boding, are major species corresponding to global free energy minimum. Parallel dimers with partial $\beta$-sheets are found to be off-pathway intermediates. The relative instability of the parallel arrangements is due to the repulsive interactions between bulky and polar side chains as well as weaker backbone hydrogen bonds.

• International Journal of Industrial Entomology and Biomaterials
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• v.27 no.2
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• pp.326-328
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• 2013

Sericin undergoes gelation by the structural transition from random coil to b-sheet transition. In the present study, the gelation time of sericin solution was investigated in the presence of NaCl, KCl and $CaCl_2$. The addition of salts delayed the gelation time, and $CaCl_2$ had the most pronounced effect, which delayed about 8 h at maximum. The gelation time increased with the concentration of salt. The transition of secondary structure of sericin was retarded in the presence of salt. The effect of salts on the gelation time of sericin might be due to the solvation effect of relevant cation.

• Proceedings of the Korea Committee for Ocean Resources and Engineering Conference
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• 2003.05a
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• pp.262-268
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• 2003

Organic coatings are widely used to control the corrosion of steel structure. The water in coatings may cause swelling or solvation of coatings, leading to the degradation of coatings. In addition, water affects the permeation of oxygen and other corrosive agents, and consequently the presence of such substances at coating-metal interface promotes corrosion of metal substrate. In this study, the anticorrosive properties of 4 types of coating, such as epoxy-epoxy, epoxy-urethane, urethane-epoxy, urethane-urethane, were evaluated. The evaluation tests were carried out under cyclic water-absorption/desorption conditions, consisting of alternative exposure to diluted 0.001M-LiCl($a_{1120}{\fallingdotseq}1$) and concentrated l0M-LiCl($a_{1120}{\fallingdotseq}0.05$). The anticorrosive performances of coatings were found to decrease in the order of urethane-urethane> urethane-epoxy> epoxy-epoxy coating.