• Bulletin of the Korean Chemical Society
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• 제25권4호
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• pp.553-556
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• 2004

In this study we have performed ab initio computer simulations to investigate the conformational characteristics of the tetraethyl (1) and triethyl ester (2) of p-tert-butylcalix[4]arene. The structures of different conformational isomers for each compound have been optimized using ab initio RHF/6-31G methods. After optimization, B3LYP/6-31+G(d,p) single point calculations of the final structures are done to include the effect of electron correlation and the basis set with diffuse function and polarization function. Relative stability of tetraethyl ester (1) of p-tert-butylcalix[4]arene is in following order: cone (most stable) > partial cone > 1,3- alternate > 1,2-alternate isomer. Relative stability of triethyl ester (2) of p-tert-butylcalix[4]arene is in following order: cone (most stable) > 2-partial cone > 1-partial cone > 3-partial cone ~ 1,3-alternate ~ 1,2- alternate isomer.

• Bulletin of the Korean Chemical Society
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• 제25권1호
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• pp.55-58
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• 2004

In this study we have performed ab initio computer simulations to investigate the conformational characteristics of the tetramethoxycalix[4]arenes (1 and 2). The structures of four types (cone, partial cone, 1,2-alternate, and 1,3-alternate) of conformers for each compound have been optimized using ab initio RHF/6-31G and 6-31$G^{**}$ methods. General trends in relative stabilities of tetramethyl ether derivatives of calix[4]arene 1 and p-tert-butylcalix[4]arene 2 are similar and decrease in following order: partial cone (most stable) > cone > 1,3-alternate > 1,2-alternate. The calculated results of the most stable conformation of partial cone structure agree with the reported NMR experimental observations.

• 한국재료학회지
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• 제20권9호
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• pp.478-482
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• 2010

A series of molecular dynamic (MD), finite element (FE) and ab initio simulations are carried out to establish suitable modeling schemes for the continuum-based analysis of aluminum matrix nanocomposites reinforced with carbon nanotubes (CNTs). From a comparison of the MD with FE models and inferences based on bond structures and electron distributions, we propose that the effective thickness of a CNT wall for its continuum representation should be related to the graphitic inter-planar spacing of 3.4${\AA}$. We also show that shell element representation of a CNT structure in the FE models properly simulated the carbon-carbon covalent bonding and long-range interactions in terms of the load-displacement behaviors. Estimation of the effective interfacial elastic properties by ab initio simulations showed that the in-plane interfacial bond strength is negligibly weaker than the normal counterpart due to the nature of the weak secondary bonding at the CNT-Al interface. Therefore, we suggest that a third-phase solid element representation of the CNT-Al interface in nanocomposites is not physically meaningful and that spring or bar element representation of the weak interfacial bonding would be more appropriate as in the cases of polymer matrix counterparts. The possibility of treating the interface as a simply contacted phase boundary is also discussed.

• 한국표면공학회지
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• 제39권2호
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• pp.76-81
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• 2006

Molecular dynamics simulations were carried out to investigate physical sputtering of Fe(100) substrate due to energetic ion bombardments. Repulsive interatomic potentials at short internuclear distances were determined with ab initio calculations using the density functional theory. Bohr potentials were fitted to the ab initio results on diatomic pairs (Ar-Fe, Fe-Fe) and used as repulsive screened Coulombic potentials in sputtering simulations. The fitted-Bohr potentials improve the accuracy of the sputtering yields predicted by molecular dynamics for sputtering of Fe(100), whereas Moliere and ZBL potentials were found to be too repulsive and gave relatively high sputtering yields. In spite of assumptions and limitations in this simulation work, the sputtering yields predicted by the molecular dynamics method were in fairly good accordance with the obtainable experimental data in absolute values as well as in manner of the variation according to the Incident energy. Threshold energy for sputtering of Fe(100) substrate was found to be about 40 eV. Additionally, distributions of kinetic energies of sputtered atoms and their original depths could be obtained.

• Bulletin of the Korean Chemical Society
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• 제27권4호
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• pp.508-514
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• 2006

In this study, we have performed ab initio computer simulations to investigate the conformational and complexation characteristics of the trimethyl ether of p-tert-butylmonodeoxycalix[4]arene (6) with a potassium ion. The structures of different conformers of 6 and their potassium complexes were optimized by using ab initio RHF/6-31G and B3LYP/6-31G(d,p) methods. The relative stability of the various conformers of the uncomplexed 6 is in following order: cone (most stable) > 1-partial-cone ~ 2i-partial-cone > 2-partial-cone ~ 1,3-alternate > 3i-partial-cone. However, the relative stability of the conformational complexes of 6 with $K^+$ is in the following order: 2-partial cone ~ 1,3-alternate > cone > 3-partial cone > 1-partial cone (least stable). The highest binding strengths of 2-partial-cone and 1,3-alternate complexes originate from two strong cation-$\pi$ interactions and two strong cation-oxygen interactions in the complex of 6+$K^+$. Due to the cation-$\pi$ interactions, the calculated C-C bond distances in the arenes of the $K^+$-complexes are about 0.0048 $\AA$ longer than the values of their isolated hosts.

• EDISON SW 활용 경진대회 논문집
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• 제4회(2015년)
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• pp.91-98
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• 2015

Formamide의 중성가수분해 mechanism은 QM/MM (quantum mecahnics/molecular mechanics) molecular dynamics simulations 및 CPMD과 같은 방법으로 연구되어왔다. 본 연구에서는. Umbrella sampling을 이용한 QM/MM-MD simulation을 사용하여 4가지 반응의 free energy surface를 도출해냈다. 전체적으로, 가장 선호되는 메커니즘은 two step으로 구성된 water assisted stepwise mechanism이었으며 모든 mechanism은 ab-initio calculation과 QM/MM-MD simulation이 수행되었다. water assisted stepwise mechanism을 살펴보면, 첫 번째 step에서 formamide의 carbonyl group이 hydrate되면서 gem-diol intermediate를 형성한다. 다음 step에서, intermediate의 hydroxyl group으로부터 amino group으로 water-assisted proton transfer이 일어난다. 두 반응 모두에서 물이 proton transfer를 직접적으로 도와주는 것을 관찰할 수 있었다. 특히, ab-initio calculation과는 다르게 QM/MM-MD에서는 gem-diol intermediate가 안정화되는 것으로 solvent effect를 잘 보여준다.

• 한국신재생에너지학회:학술대회논문집
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• 한국신재생에너지학회 2010년도 추계학술대회 초록집
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• pp.113.2-113.2
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• 2010

We report that the novel covalent organic frameworks (COFs) are capable of reversibly providing an extremely high uptake capacity of carbon dioxide and hydrogen at room temperature. These COFs are designed based on the multiscale simulations approach via the combination of ab initio calculations and force-field calculations. For this goal, we explore the adsorption sites of carbon dioxide and hydrogen on COFs, their porosity, as well as carbon dioxide adsorption isotherms. We identify the binding sites and energies of $CO_2$ on COFs using ab initio calculations and obtain the carbon dioxide adsorption isotherms using grand canonical ensemble Monte Carlo calculations. Moreover, the calculated adsorption isotherms are compared with the experimental values in order to build the reference model in describing the interactions between the $CO_2/H_2$ and the COFs and in predicting the $CO_2$ and $H_2$ adsorption isotherms of COFs. Finally, we design three new COFs, 2D COF-05, 3D COF-05 (ctn), and 3D COF-05 (bor), for the high capacity $CO_2/H_2$ and $H_2$ storage.

• Bulletin of the Korean Chemical Society
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• 제24권6호
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• pp.817-823
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• 2003

We have performed ab initio calculation on the active site of HIV-1 protease. The FEP method was used to determine the binding free energy of four different of protonated states of HIV-1 protease with inhibitor. The structure of the active site and hole structure was taken from the X-ray crystallographic coordinates of the C₂ symmetric inhibitor A74704 protease bound. The active site was modeled with the fragment molecules of binding pocket, acetic acid/ acetate anion (Asp25, Asp125), formamide (amide bond of Thr26/Gly27, Thr126/ Gly127), and methanol as inhibitor fragment. All possibly protonated states of the active site were considered, which were diprotonated state (0, 0), monoprotonated (-1, 0),(0, -1) and diunprotonated state (-1, -1). Once the binding energy Debind, of each model was calculated, more probabilistic protonated states can be proposed from binding energy. From ab-initio results, the FEP simulations were performed for the three following mutations: Ⅰ) Asp25 … Asp125 → AspH25 … Asp125, ⅱ) Asp25 … Asp125 → Asp25 … AspH125, ⅲ) AspH25 … Asp125 → AspH25 … AspH125. The free energy difference between the four states gives the information of the more realistic protonated state of active site aspartic acid. These results provide a theoretical prediction of the protonation state of the catalytic aspartic residues for A74707 complex, and may be useful for the evaluation of potential therapeutic targets.

• 한국진공학회:학술대회논문집
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• 한국진공학회 2011년도 제40회 동계학술대회 초록집
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• pp.428-429
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• 2011

Recently, we performed ab initio total energy calculation and tight-binding molecular dynamics (TBMD) simulation to study structures and the reconstruction of native defects in graphene. In the previous study, we predicted by TBMD simulation that a double vacancy in graphene is reconstructed into a 555-777 composed of triple pentagons and triple heptagons [1]. The structural change from pentagon-octagon-pentagon (5-8-5) to 555-777 has been confirmed by recent experiments [2,3] and the detail of the reconstruction process is carefully studied by ab initio calculation. Pentagon-heptagon (5-7) pairs are also found to play an important role in the reconstruction of vacancy in graphene and single wall carbon nanotube [4]. In the TBMD simulation of graphene nanoribbon (GNR), we found the evaporation of carbon atoms from both the zigzag and armchair edges is preceded by the formation of heptagon rings, which serve as a gateway for carbon atoms to escape. In the simulation for a GNR armchair-zigzag-armchair junction, carbon atoms are evaporated row-by-row from the outermost row of the zigzag edge [5], which is in excellent agreement with recent experiments [2, 6]. We also present the recent results on the formation and development of dislocation in graphene. It is found that the coalescence of 5-7 pairs with vacancy defects develops dislocation in graphene and induces the separation of two 5-7 pairs. Our TBMD simulations also show that adatoms are ejected and evaporated from graphene surface due to large strain around 5-7 pairs. It is observed that an adatom wanders on the graphene surface and helps non-hexagonal rings change into stable hexagonal rings before its evaporation.

• 대한기계학회:학술대회논문집
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• 대한기계학회 2003년도 춘계학술대회
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• pp.1083-1088
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• 2003

Molecular dynamics simulations on the deformation behavior of single-walled carbon nanotube are performed. Formation energies of CNT's by interatomic potentials are computed and compared with ab initio results. Bending and axial compression are applied under lattice statics and NVT ensemble conditions. Specifically, we focus on the mechanism of kink formation in bending. The simulation results are comprehensively explained in the framework of atomistic energetics. The effects of temperature and chirality on the deformation of carbon nanotube are also studied.