• Bulletin of the Korean Chemical Society
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• 제22권8호
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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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• 제29권8호
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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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• 제10권6호
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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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• 제14권2호
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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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• 제12권2호
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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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• 제35권7호
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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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• 제34권3호
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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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• 제24권11호
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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.

• 한국광물학회지
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• 제29권4호
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• pp.209-220
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• 2016

점토광물은 대기부터 지하수에 이르는 크리티컬존(critical zone) 영역에서 금속과 탄소 순환을 결정짓는 역할을 한다. 계산광물학 연구방법 중에 하나인 분자동역학(molecular dynamics) 시뮬레이션은 지구물질을 원자단위로 계산하기 때문에, 점토광물의 물리화학적 현상들에 대해 원자수준의 자세한 정보를 제공할 수 있다. 이번 연구에서는 clayFF 힘 장(force field)을 사용한 분자동역학 시뮬레이션을 이팔면체 점토광물인 깁사이트(gibbsite, $Al(OH)_3$), 카올리나이트(kaolinite, $Al_2Si_2O_5(OH)_4$), 파이로필라이트(pyrophyllite, $Al_2Si_4O_{10}(OH)_2$)에 적용하여 300 K, 1기압조건에서 각 광물이 가지는 격자상수와 원자간 거리를 계산하고 실험결과와 비교하였다. 더불어 수산기의 방향성 및 수소결합의 양상 그리고 파워스펙트럼(power spectrum)을 추가적으로 계산하였다. 계산 결과, 격자상수는 기존의 실험결과와 약 0.1~3.7% 미만의 오차율을 보였으며, 원자간 거리는 실험결과와 약 5% 미만의 차이를 가졌다. 깁사이트나 카올리나이트의 팔면체층 표면에 존재하는 수산기가 가지는 신축진동파수(stretching vibrational wavenumber)는 실험값 보다 약 $200-300cm^{-1}$ 높게 계산되었지만, 팔면체층 표면에 존재하는 수산기들의 상대적 크기의 경향은 기존 실험 결과와 일치하였다. 팔면체층 표면의 수산기가 (001)면과 이루는 각도도 기존 실험결과와 상당부분 일치한 반면에 내부 수산기의 경우는 다소 차이를 보였다. ClayFF를 사용한 분자동역학 시뮬레이션 연구 방법은 이팔면체 점토광물 표면 내(층간) 금속이온 흡착에 대한 수산기의 역할을 규명하는데 유용한 연구방법이 될 수 있음을 시사한다.

• 멤브레인
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• 제25권2호
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• pp.162-170
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• 2015

본 연구에서는 다양한 아민기를 가지는 폴리이미드 소재 및 분리막을 제조하여 그들의 구조의 변화에 따른 기체 투과도를 측정하였으며 동력학(Molecular dynamics; MD) 기술을 이용하여 해당 기체의 시간의 변화에 따른 위치와 속도를 계산하여, 기체분자의 동적 특성을 분석하는데 활용하였다. 투과도 측정결과 합성된 고분자 소재의 경우 고분자 내의 free volume을 증가시키는 치환기를 도입시켰을 경우 기체투과도가 증가되었으나 rigid한 구조가 도입된 폴리이미드는 투과도가 감소되는 경향을 확인하였다. 또한 분자동력학 시뮬레이션을 이용하여 기체투과거동 변화를 분석한 결과 실제 기체투과도 측정결과와 유사한 결과를 나타냄을 확인할 수 있었다.