• Bulletin of the Korean Chemical Society
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• v.22 no.8
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• pp.847-849
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• 2001

The OSS2(Ojame-Shavitt-Singer 2)[L. Ojame et al., J. Chem. Phys. 109, 5547 (1998)] model as a dissociable water model is examined in order to study the dynamics of H+ in water. MD simulations for 216 water system, 215 water + H+ ion system, and 215 water + OH- ion system using the OSS2 model at 298.15 K with the use of Ewald summation are carried out. The calculated O-H radial distribution functions for these systems are essentially the same and are in very good agreement with that obtained by Ojame.

• Bulletin of the Korean Chemical Society
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• v.29 no.8
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• pp.1505-1509
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• 2008

Comparative molecular simulations were performed to establish molecular interaction and inhibitory effect of flavonoid myricetin on formation of amyloid fibris. For computational comparison, the conformational stability of myricetin with amyloid $\beta$ -peptide (A$\beta$ ) and $\beta$ -amyloid fibrils (fA$\beta$) were traced with multiple molecular dynamics simulations (MD) using the CHARMM program from Monte Carlo docked structures. Simulations showed that the inhibition by myricetin involves binding of the flavonoid to fA$\beta$ rather than A$\beta$ . Even in MD simulations over 5 ns at 300 K, myricetin/fA$\beta$ complex remained stable in compact conformation for multiple trajectories. In contrast, myricetin/A$\beta$ complex mostly turned into the dissociated conformation during the MD simulations at 300 K. These multiple MD simulations provide a theoretical basis for the higher inhibitory effect of myricetin on fibrillogenesis of fA$\beta$ relative to A$\beta$ . Significant binding between myricetin and fA$\beta$ observed from the computational simulations clearly reflects the previous experimental results in which only fA$\beta$ had bound to the myricetin molecules.

• Macromolecular Research
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• v.10 no.6
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• pp.297-303
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• 2002

We have investigated the microstructural properties of a weakly charged polyelectrolyte modeled with both Hookean spring and Debye-Huckel potential, by employing a novel hybrid scheme of molecular dynamics (MD) and Monte Carlo (MC) simulations. Although the off-lattice pivot step facilitates the earlier computations stage, it gives rise to oscillations and hinders the stable equilibrium state. In order to overcome this problem, we adopt the MC off-lattice pivot step in early stage only, and then switch the computation to a pure MD step. The result shows that the computational speed-up compared to the previous method is entirely above 10 to 50, without loss of the accuracy. We examined the conformations of polyelectrolyte in solvents in terms of the end-to-end distance, radius of gyration, and structure factor with variations of the screening effects of solvent and the monomer charges. The emphasis can favorably be given on the elongation behavior of a polyelectrolyte chain, with observing the simultaneous snapshots.

• Bulletin of the Korean Chemical Society
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• v.14 no.2
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• pp.255-258
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• 1993

Molecular dynamics (MD) calculations were carried out in order to investigate the effect of MD cell size to predict the melting phenomena of A-type zeolite. We studied two model systems: a pseudocell of $(T_2O_4Na)_n$, (L= 12.264 $^{\AA}$, N= 84) and a true-cell of (SiAlO$_4Na)_n$. (L= 24.528 $^{\AA}$, N= 672), where T is Si or Al. The radial and bond angle distribution functions of T(Si, Al)-O-T(Si, Al) and diffusion coefficients of T and O were reported at various temperatures. For the true-cell model, the melting temperature is below 1500 K and probably around 1000 K, which is about 600-700 K lower than the pseudocell model. Although it took more time (about 30 times longer) to obtain the molecular trajectories of the true-cell model than those of the pseudocell model, the true-cell model gave more realistic structural transition for the A-type zeolite, which agrees with experiment.

• Macromolecular Research
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• v.12 no.2
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• pp.178-188
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• 2004

We performed molecular dynamics (MD) simulations at 300 K on a series of poly(benzyl ether) (PBE) dendrimers having a different core functionalities. We used the rotational isomeric state Metropolis Monte Carlo (RMMC) method to construct the initial configuration in a periodic boundary cell (PBC) before the MD simulations were undertaken. To elucidate the effects that the structural features have on the chain dimension, the overall internal structure, and the morphology, we monitored the radii of gyration, R$\sub$g/ and the conformational changes during the simulations. The PBE dendrimers in a glassy state adopted less-extended structures when compared with the conformations obtained from the RMMC calculations. We found that R$\sub$g/ of the PBE dendrimer depends on the molecular weight, M, according to the relation, R$\sub$g/∼M$\^$0.22/. The radial distributions of the dendrimers were developed identically in the PBC, irrespective of the core functionality. A gradual decrease in radial density resulted from the fact that the terminal branch ends are distributed all over the molecule, except for the core region.

• Bulletin of the Korean Chemical Society
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• v.35 no.7
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• pp.2097-2108
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• 2014

Chemical feature based quantitative pharmacophore models were generated using the HypoGen module implemented in DS2.5. The best hypothesis, Hypo1, which was characterized by the highest correlation coefficient (0.96), the highest cost difference (61.60) and the lowest RMSD (0.74), consisted of one hydrogen bond acceptor, one hydrogen bond donor, one hydrophobic and one ring aromatic. The reliability of Hypo1 was validated on the basis of cost analysis, test set, Fischer's randomization method and GH test method. The validated Hypo1 was used as a 3D search query to identify novel inhibitors. The screened molecules were further refined by employing ADMET, docking studies and visual inspection. Three compounds with novel scaffolds were selected as the most promising candidates for the designing of Mcl-1 antagonists. Finally, a 10 ns molecular dynamics simulation was carried out on the complex of receptor and the retrieved ligand to demonstrate that the binding mode was stable during the MD simulation.

• Bulletin of the Korean Chemical Society
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• v.34 no.3
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• pp.753-758
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• 2013

Molecular dynamics (MD) simulations have been used to study the diffusion behavior of small gas molecules ($CO_2$) in polyethylene terephthalate (PET)/polylactide (PLA) blends. The Flory-Huggins interaction parameters (${\chi}$) determined from the cohesive energy densities are smaller than the critical value of Flory-Huggins interaction parameters (${\chi}_{critical}$), and that indicates the good compatibility of PET/PLA blends. The diffusion coefficients of $CO_2$ are determined via MD simulations at 298 K. That the order of diffusion coefficients is correlated with the availably fractional free volume (FFV) of $CO_2$ in the PET/PLA blends means that the FFV plays a vital role in the diffusion behavior of $CO_2$ molecules in PET/PLA blends. The slopes of the log (MSD) as a function of log (t) are close to unity over the entire composition range of PET/PLA blends, which confirmes the feasibility of MD approach reaches the normal diffusion regime of $CO_2$ in PET/PLA blends.

• Bulletin of the Korean Chemical Society
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• v.24 no.11
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• pp.1590-1598
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• 2003

In this paper we have presented the results for viscosity and self-diffusion constants of model systems for four liquid n-alkanes ($C_{12}, C_{20}, C_{32}, and C_{44}$) in a canonical ensemble at several temperatures using molecular dynamics (MD) simulations. The small chains of these n-alkanes are clearly $<{R_{ee}}^2>/6<{R_g}^2>>1$, which leads to the conclusion that the liquid n-alkanes over the whole temperatures considered are far away from the Rouse regime. Calculated viscosity ${\eta}$ and self-diffusion constants D are comparable with experimental results and the temperature dependence of both ${\eta}$ and D is suitably described by the Arrhenius plot. The behavior of both activation energies, $E_{\eta}$ and $E_D$, with increasing chain length indicates that the activation energies approach asymptotic values as n increases to the higher value, which is experimentally observed. Two calculated monomeric friction constants ${\zeta}$ and ${\zeta}_D$ give a correct qualitative trend: decrease with increasing temperature and increase with increasing chain length n. Comparison of the time auto-correlation functions of the end-to-end vector calculated from the Rouse model for n-dodecane ($C_{12}$) at 273 K and for n-tetratetracontane ($C_{44}$) at 473 K with those extracted directly from our MD simulations confirms that the short chain n-alkanes considered in this study are far away from the Rouse regime.

• Journal of the Mineralogical Society of Korea
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• v.29 no.4
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• pp.209-220
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• 2016

Clay minerals are a major player to determine geochemical cycles of trace metals and carbon in the critical zone which covers the atmosphere down to groundwater aquifers. Molecular dynamics (MD) simulations can examine the Earth materials at an atomic level and, therefore, provide detailed fundamental-level insights related to physicochemical properties of clay minerals. In the current study, we have applied classical MD simulations with clayFF force field to dioctahedral clay minerals (i.e., gibbsite, kaolinite, and pyrophyllite) to analyze and compare structural parameters (lattice parameter, atomic pair distance) with experiments. We further calculated vibrational power spectra for the hydroxyls of the minerals by using the MD simulations results. The MD simulations predicted lattice parameters and interatomic distances respectively deviated less than 0.1~3.7% and 5% from the experimental results. The stretching vibrational wavenumber of the hydroxyl groups were calculated $200-300cm^{-1}$ higher than experiment. However, the trends in the frequencies among different surface hydroxyl groups of each mineral was consistent with experimental results. The angle formed by the surface hydroxyl group with the (001) plane and hydrogen bond distances of the surface hydroxyls were consistent with experimental result trends. The inner hydroxyls, however, showed results somewhat deviated from reported data in the literature. These results indicate that molecular dynamics simulations with clayFF can be a useful method in elucidating the roles of surface hydroxyl groups in the adsorption of metal ions to clay minerals.

• Membrane Journal
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• v.25 no.2
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• pp.162-170
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• 2015

In this study, gas permeability of polyimide materials having a various amine group was measured and molecular dynamics was used to analyze the dynamic characteristics of the gas molecules in the polyimide by calculating the position and velocity of the gas molecules with change of the time. The gas permeability of polyimide membrane having substitution site which increase free volume in the polymer was increased. However, polyimide with rigid structure showed decreased gas permeability. As a result of analyzing the change in the gas permeation behavior using molecular dynamics simulations, we confirmed that the results show the same tendency with actual measurements of the gas permeability.