• 대한화학회지
• /
• 제57권5호
• /
• pp.554-559
• /
• 2013

본 연구에서는 ${\beta}$-D-glucopyranose 분자의 hydroxymethyl group의 두 torsion angle의 변화에 따른 포텐셜 에너지의 변화를 진공 상태와 implicit water 상태에서 연구하였으며 이를 통해 Solvation Energy가 구조에 미치는 영향에 대해서 알아보았다. 계산에 사용한 프로그램은 AMBER package였으며, force field는 GLYCAM_06을 사용하였다. Solvation model은 Hawkins, Cramer, Truhlar 등이 제안한 generalized Born model을 사용하였다. 계산 결과, methyl hydroxyl group 내의 hydroxyl group이 고리구조의 hydroxyl group과 강한 수소결합이 가능한 영역에서 많은 변화가 일어났다. 이를 통해 solvation effect로 인해서 수소 결합의 중요성이 감소했다는 결론을 내렸다.

• Nuclear Engineering and Technology
• /
• 제47권6호
• /
• pp.662-668
• /
• 2015

A suspension of titanium nanoparticles (Ti NPs) in liquid sodium (Na) has been proposed as a method to mitigate the violent sodium-water reaction (SWR). The interparticle potential between Ti NPs in liquid Na may play a significant role in the agglomeration of NPs on the reaction surface and in the bulk liquid Na, since the potential contributes to a reduction in the long-term dispersion stability. For the effective control of the SWR with NPs, a physical understanding of the molecular dynamics of NPs in liquid Na is key. Therefore in this study, the nonretarded Van der Waals model and the solvation potential model are employed to analyze the interparticle potential. The ab initio calculation reveals that a strong repulsive force driven by the solvation potential exceeds the interparticle attraction and predicts the agglomeration energy required for two 10-nm Ti NPs to be $4{\times}10^{-17}J$. The collision theory suggests that Ti NPs can be effective suppressors of the SWR due to the high energy barrier that prevents significant agglomeration of Ti NPs in quiescent liquid Na.

• EDISON SW 활용 경진대회 논문집
• /
• 제3회(2014년)
• /
• pp.237-249
• /
• 2014

Deposition of amyloid-${\beta}$ ($A{\beta}$) proteins is the conventional pathological hallmark of Alzheimer's disease (AD). The $A{\beta}$ protein formed from the amyloid precursor protein is predominated by the 40 residue protein ($A{\beta}40$) and by the 42 residue protein ($A{\beta}42$). While $A{\beta}40$ and $A{\beta}42$ differ in only two amino acid residues at the C-terminal end, $A{\beta}42$ is much more prone to aggregate and exhibits more neurotoxicity than $A{\beta}40$. Here, we investigate the molecular origin of the difference in the aggregation propensity of these two proteins by performing fully atomistic, explicit-water molecular dynamics simulations. Then, it is followed by the solvation thermodynamic analysis based on the integral-equation theory of liquids. We find that $A{\beta}42$ displays higher tendency to adopt ${\beta}$-sheet conformations than $A{\beta}40$, which would consequently facilitate the conversion to the ${\beta}$-sheet rich fibril structure. Furthermore, the solvation thermodynamic analysis on the simulated protein conformations indicates that $A{\beta}42$ is more hydrophobic than $A{\beta}40$, implying that the surrounding water imparts a larger thermodynamic driving force for the self-assembly of $A{\beta}42$. Taken together, our results provide structural and thermodynamic grounds on why $A{\beta}42$ is more aggregation-prone than $A{\beta}40$ in aqueous environments.

• Tribology and Lubricants
• /
• 제14권1호
• /
• pp.54-63
• /
• 1998

In many practical lubricated contacts such as a rough concentrated contact on the sliding of nominally flat surfaces, the fluid may be of molecular (nanometer) scale owing to the asperity interactions on the surfaces. Under this condition, there is insufficient lubricant on the concentrated contact spot to maintain a realistic continuum. Rheological behavior for this kind of concentrated contact has been studied extensively to know whether the application of viscous fluid model is appropriate. The interaction of two rough surfaces is simplified as perfectly flat-rough surfaces contact under certain conditions by "composite topography" and for a nanometer scale fluid film, three kinds of rheological fluid behavior are analyzed in elastohydrodynamic asperity point contact.t contact.

• 한국윤활학회:학술대회논문집
• /
• 한국윤활학회 1997년도 제26회 추계학술대회
• /
• pp.173-182
• /
• 1997

In many practical lubricated contacts such as a rough concentrated contact on the sliding of nominally flat surfaces, the fluid may be of molecular (nanometer) scale owing to the asperity interactions on the surfaces. Under this condition, there is insufficient lubricant on the concentrated contact spot to maintain a realistic continuum. Rheological behavior for this kind of concentrated contact was studied to know whether the application of viscous fluid model is appropriate. The interaction of two rough surfaces is simplified as perfectly flat-rough surfaces contact under certain conditions by "composite topography" and for a nanometer scale fluid film, three kinds of rheological fluid behavior are analyzed in elastohydrodynamic asperity point contact.t contact.

• Bulletin of the Korean Chemical Society
• /
• 제30권8호
• /
• pp.1845-1850
• /
• 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.

• 통합자연과학논문집
• /
• 제3권1호
• /
• pp.49-53
• /
• 2010

Molecular docking is a critical event which mostly forms Van der waals complex in molecular recognition. Since the majority of developed drugs are small molecules, docking them into proteins has been a prime concern in drug discovery community. Since the binding pose space is too vast to cover completely, many search algorithms such as genetic algorithm, Monte Carlo, simulated annealing, distance geometry have been developed. Proper evaluation of the quality of binding is an essential problem. Scoring functions derived from force fields handle the ligand binding prediction with the use of potential energies and sometimes in combination with solvation and entropy contributions. Knowledge-based scoring functions are based on atom pair potentials derived from structural databases. Forces and potentials are collected from known protein-ligand complexes to get a score for their binding affinities (e.g. PME). Empirical scoring functions are derived from training sets of protein-ligand complexes with determined affinity data. Because non of any single scoring function performs generally better than others, some other approaches have been tried. Although numerous scoring functions have been developed to locate the correct binding poses, it still remains a major hurdle to derive an accurate scoring function for general targets. Recently, consensus scoring functions and target specific scoring functions have been studied to overcome the current limitations.

• 대한화학회지
• /
• 제18권5호
• /
• pp.320-328
• /
• 1974

종래의 방법으로 고압하에서 전지의 표준기전력 $(E^{\circ})$를 산출하는 것은 불가능하다. 그러나 완전평형상수의 개념을 종래의 Nernst 방정식에 적용하므로서 고압하에서 표준기전력을 구할 수 있게 되었다(완전 Nernst방정식). 더욱이 다른 열역학적 성질 이를테면 수화수의 순변화(k), 용매의 압축을(${\beta}$), 전지반응에서 종래의 해리상수(K) 평형상태에서 표준자유에너지변화(${\Delta}G^{\circ}$) 표준엔탈피변화(${\Delta}H^{\circ}$) 및 표준엔트로피변화($S^{\circ}$) 등을 얻었다. 본 실험에서는 전지의 기전력(E)을 $20{\sim}35^{\circ}C$와 1∼2500 atms 범위에서 측정하였다. 일정한 온도에서 전지의 기전력은 압력이 증가함에 따라 증가하였으며, 일정한 압력에서 온도가 증가함에 따라 역시 증가하였다. 전지반응의 수화수의 순변화(k)는 $20^{\circ}C$에서 41.96으로서 압력에 따라 변하지 않고 일정한 값을 유지하였으나 한편 K와 ${\Delta}S^{\circ}C$는 압력에 따라 증가하였으나 ${\Delta}G^{\circ}$와 ${\Delta}H^{\circ}$는 감소하였다. 고압하에서도 완전 Nernst방정식으로부터 표준기전력을 계산할 수 있으므로 상압에서와 마찬가지로 화학평형론을 취급할 수 있게 되었다

• 대한화학회지
• /
• 제24권6호
• /
• pp.444-451
• /
• 1980

극성용매에서 전자의 용매화과정을 구체적으로 고찰하여 보기 위하여 테트라히드로퓨란(THF)-물 이성분계의 메디움효과를 측정하였다. 이 메디움효과는 Pt|$H_2Q$, Q, HCI, THF, $H_2O$|KC1 | $Hg_2Cl_2$|Hg(Pt) 셀로 수용액과 다른 용액(TGF-$H_2O$)에서 결정된 $H^+$ 이온에 대한 자유에너지 변화의 차(${\Delta}{\Delta}G_0$)를 이용하여 연구하였다. 여기서 $H_2Q$와 Q는 히드로퀴논과 퀴논을 각각 나타낸다. 자유에너지 변화의 차와 용매화된 전자의 최대흡수 에너지에 대한 용매의 유전상수 영향을 고찰하기 위하여 THF에서 $H_2O$의 회합정도를 관찰하였다. $H_2O$의 회합정도는 $H_2O$의 근적외선 스펙트럼을 이용하여 분석하였다. 이들 실험결과로부터 이성분 혼합용매에서 전자나 다른 이온의 용매화는 용매의 특정성분과 선택적으로 진행된다는 것을 알았다.