• Bulletin of the Korean Chemical Society
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• 제17권1호
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• pp.7-11
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• 1996

The interconversion barriers between two twisted conformers of four oxygen-containing cyclohexene analogues have been investigated utilizing a periodic hindered pseudorotational model, molecular mechanics (MM3) calculations, and previously reported far-infrared spectra. The six-fold pseudorotational potential energy function satisfactorily fits the observed bending transitions. The interconversion barrier heights calculated from the pseudorotational model show excellent agreement with those determined from two-dimensional potential energy surfaces for the ring-bending and ring-twisting vibrations. The barriers to interconversion range from 3350 $cm^{-1}$ (9.6 kcal/mol) to 3890 $cm^{-1}$ (11.1 kcal/mol) for four oxygen-containing cyclohexene analogues.

• Bulletin of the Korean Chemical Society
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• 제17권1호
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• pp.19-24
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• 1996

The potential energies of HIV-1 protease, inhibitor, and their complex have been calculated by molecular mechanics and the "binding energy", defined as the difference between the potential energy of complex and the sum of potential energies of HIV-1 protease and its inhibitor, has been compared to the free energy in inhibition reaction. The trend in these binding energies seems to agree with that in free energies.

• 통합자연과학논문집
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• 제5권4호
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• pp.216-219
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• 2012

Structure-based drug design possibly benefit from in silico methods that precisely predict the binding affinity of small molecules to target macromolecules. There are many limitations arise from the difficulty of predicting the binding affinity of a small molecule to a biological target with the current scoring functions. There is thus a strong interest in novel methodologies based on MD simulations that claim predictions of greater accuracy than current scoring functions, helpful for a regular use designed for drug discovery in the pharmaceutical industry. Herein, we report a short review on free energy calculations using MMPBSA method a useful method in structure based drug discovery.

• Interaction and multiscale mechanics
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• 제6권3호
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• pp.301-316
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• 2013

The influence of indenter geometry on nanoindentation was studied using a static molecular dynamics simulation. Dislocation nucleation, dislocation locks, and dislocation movements during nanoindentation into Al (001) were studied. Spherical, rectangular, and Berkovich indenters were modeled to study the material behaviors and dislocation activities induced by their different shapes. We found that the elastic responses for the three cases agreed well with those predicted from elastic contact theory. Complicated stress fields were generated by the rectangular and Berkovich indenters, leading to a few uncommon nucleation and dislocation processes. The calculated mean critical resolved shear stresses for the Berkovich and rectangular indenters were lower than the theoretical strength. In the Berkovich indenter case, an amorphous region was observed directly below the indenter tip. In the rectangular indenter case, we observed that some dislocation loops nucleated on the plane. Furthermore, a prismatic loop originating from inside the material glided upward to create a mesa on the indenting surface. We observed an unusual softening phenomenon in the rectangular indenter case and proposed that heterogeneously nucleating dislocations are responsible for this.

• Interaction and multiscale mechanics
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• 제4권2호
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• pp.139-153
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• 2011

In this paper we develop a fully anisotropic pressure and temperature dependent model to investigate the effect of the microstructure on the shock response of ${\beta}$-HMX molecular single and polycrystals. This micromechanics-based model can account for crystal orientation as well as crystallographic twinning and slip during deformation and has been calibrated using existing gas gun data. We observe that due to the high degree of anisotropy of these polycrystals, certain orientations are more favorable for plastic deformation - and therefore defect and dislocation generation - than others. Loading along these directions results in highly localized deformation and temperature fields. This observation confirms that most of the temperature rise during high rates of loading is due to plastic deformation or dislocation pile up at microscale and not due to volumetric changes.

• 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.

• 약학회지
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• 제41권6호
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• pp.765-772
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• 1997

Conformational analyses on thromboxane $A_2$ (Tx$A_2$) and thromboxane $A_2$ receptor antagonists (TxRA) were carried out by molecular mechanics method. Based on the assumption that active conformer is the nonintrahydrogen bonding and more stable former of Tx$A_2$ and TxRA, the molecular structural requirements for potent TxA2 receptor antagonists are like below: 1) The distance is 5.0-5.6${\AA}$ between C atom of carboxyl group and S atom of sulfonyl group or C atom which is bonded to hydroxyl group in the active conformers. 2) The putative active conformers of Tx$A_2$and TxRAs are hairpin-like forms.

• 한국환경보건학회지
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• 제31권4호
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• pp.241-245
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• 2005

Laccase catalyzes the oxidation and polymerization of aromatic compounds in the presence of molecular oxygen. Studies were conducted to characterize the use of polyethylene glycol (PEG) as an additive to keep up the enzymatic stability. The enzymatic activities highly remained and bisphenol A (BPA) was rapidly converted in the presence of 5 mg/l of PEC. These effects were accomplished with PEG of molecular weight 3,350. A linear relationship was found between the quantity of BPA to be converted $(10-120\;{\mu}M)$ and the optimum dose of PEC required for greater than $95\%$ conversion. This result suggests that it is the interaction between the PEG and the reaction products. In the optimum dose of PEG, the aeration of reaction mixture neither enhanced the conversion of BPA nor retarded the inactivation of the enzyme.

• Coupled systems mechanics
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• 제6권1호
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• pp.75-96
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• 2017

As electron donor/acceptor materials for organic photovoltaic cells, small-molecules donors/acceptor are attracting more and more attention. In this work, we investigated the electronic structures, electrochemical properties, and charge carrier transport properties of four recently-synthesized small-molecule donors/acceptor, namely, DPDCPB (A), DPDCTB (B), DTDCPB (A1), and DTDCTB (B1), by a series of ab initio calculations. The calculations look into the electronic structure of singly oxidized and reduced molecules, the first anodic and cathodic potentials, and the electrochemical gaps. Results of our calculations were in accord with those from experiments. Using Marcus theory, we also computed the reorganization energies of hole/electron hoppings, as well as hole/electron transfer integrals of multiple possible molecular dimer configurations. Our calculations indicated that the electron/hole transport properties are very sensitive to the relative separations/orientations between neighboring molecules. Due to high reorganization energies for electron hopping, the hole mobilities in the molecular crystals are at least an order of magnitude higher than the electron mobilities.

• Interaction and multiscale mechanics
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• 제5권2호
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• pp.115-129
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• 2012

Nanowires (NWs) have attracted intensive researches owing to the broad applications that arise from their remarkable properties. Over the last decade, immense numerical studies have been conducted for the numerical investigation of mechanical properties of NWs. Among these numerical simulations, the molecular dynamics (MD) plays a key role. Herein we present a brief review on the current state of the MD investigation of nanowires. Emphasis will be placed on the FCC metal NWs, especially the Cu NWs. MD investigations of perfect NWs' mechanical properties under different deformation conditions including tension, compression, torsion and bending are firstly revisited. Following in succession, the studies for defected NWs including the defects of twin boundaries (TBs) and pre-existing defects are discussed. The different deformation mechanism incurred by the presentation of defects is explored and discussed. This review reveals that the numerical simulation is an important tool to investigate the properties of NWs. However, the substantial gaps between the experimental measurements and MD results suggest the urgent need of multi-scale simulation technique.