• 한국자기공명학회논문지
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• 제19권1호
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• pp.1-10
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• 2015

Refinements with atomistic molecular dynamics (MD) simulation have contributed to improving the qualities of NMR structures. In most cases, the calculations with atomistic MD simulation for NMR structures employ generalized-Born implicit solvent model (GBIS) to take into accounts solvation effects. Developments in algorithms and computational capacities have ameliorated GBIS to approximate solvation effects that explicit solvents bring about. However, the quantitative comparison of NMR structures in the latest GBIS and explicit solvents is lacking. In this study, we report the direct comparison of NMR structures that atomistic MD simulation coupled with GBIS and water molecules refined. Two model proteins, GB1 and ubiquitin, were recalculated with experimental distance and torsion angle restraints, under a series of simulated annealing time steps. Whereas the root mean square deviations of the resulting structures were apparently similar, AMBER energies, the most favored regions in Ramachandran plot, and MolProbity clash scores witnessed that GBIS-refined structures had the better geometries. The outperformance by GBIS was distinct in the structure calculations with sparse experimental restraints. We show that the superiority stemmed, at least in parts, from the inclusion of all the pairs of non-bonded interactions. The shorter computational times with GBIS than those for explicit solvents makes GBIS a powerful method for improving structural qualities particularly under the conditions that experimental restraints are insufficient. We also propose a method to separate the native-like folds from non-violating diverged structures.

• Bulletin of the Korean Chemical Society
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• 제11권4호
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• pp.309-313
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• 1990

The rates of solvolysis of trans-$[Co(N-eten)_2Cl_2)$+ (N-eten; N-ethylethylenediamine) have been investigated using spectrophotometric method in binary aqueous mixtures containing methyl alcohol, isopropyl alcohol, t-butyl alcohol, ethylene glycol and glycerol. The values of ${\Delta}H^{\neq}$ and ${\Delta}S^{\neq}$ obtained from temperature effect on the rate constants were $80{\sim}84 kJmol^{-1}$ and $- 28{\sim} - 45 JK^{-1}mol^{-1}.$ Extrema found in the variation of the enthalpy and entropy of activation with solvent composition correlated very well with extrema in the variation of the physical properties of mixture which relate to sharp change in the solvent structure. The reaction mechanism was discussed in terms of correlation diagrams involving the exess molar Gibbs function of mixing for the binary mixtures. The behavior of this cobalt(Ⅲ) complex was compared with that of t-butyl chloride. The application of free energy cycle to the process initial state to transition state in water and in the mixture showed that the solvation of transition state had dominant effect on the rates in the mixtures. It was found that $S_N1$ character was increased with increasing the content of co-solvent in the mixture.

• Bulletin of the Korean Chemical Society
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• 제32권7호
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• pp.2167-2168
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• 2011

• Bulletin of the Korean Chemical Society
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• 제29권11호
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• pp.2295-2298
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• 2008

• 대한화학회지
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• 제65권3호
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• pp.179-184
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• 2021

본 연구에서는 용매 특성에 따른 인지질 내 글리세롤 골격 구조 변화를 알아보기 위해서 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) 단분자에 대한 분자동역학 시뮬레이션을 용매 특성을 변화시켜가며 진행하였다. DOPC 골격구조는 인지질 내 글리세롤 C1-C2 결합의 비틀림각에 따라 A(θ3 = trans, θ4 = gauche), B(θ3 = gauche, θ4 = gauche-), C(θ3 = gauche-, θ4 = trans) 세가지 형태로 구분된다. 용매의 유전상수와 표면장력을 변수로 하여 DOPC의 골격 구조 변화를 살펴본 결과, 유전상수가 증가할수록, 표면장력이 클수록 B 구조의 빈도가 증가하였으며 그 이유는 B 구조의 solvation 에너지가 A에 비해서 더 크고, 표면적이 A에 비해서 작기 때문이다. 이러한 연구 결과는 추후 인지질 구조 연구에 활용될 것으로 기대된다.

• Genomics & Informatics
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• 제5권1호
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• pp.24-29
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• 2007

Computational virtual screening has become an essential platform of drug discovery for the efficient identification of active candidates. Moleculardocking, a key technology of receptor-centric virtual screening, is commonly used to predict the binding affinities of chemical compounds on target receptors. Despite the advancement and extensive application of these methods, substantial improvement is still required to increase their accuracy and time-efficiency. Here, we evaluate several advanced structure-based virtual screening approaches for elucidating the rank-order activity of chemical libraries, and the quantitative structureactivity relationship (QSAR). Our results show that the ensemble-average free energy estimation, including implicit solvation energy terms, significantly improves the hit enrichment of the virtual screening. We also demonstrate that the assignment of quantum mechanical-polarized (QM-polarized) partial charges to docked ligands contributes to the reproduction of the crystal pose of ligands in the docking and scoring procedure.

• 대한화학회지
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• 제28권4호
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• pp.210-216
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• 1984

MeOH-MeCN 혼합용매의 Taft용매 파라미터인 ${\pi}^{\ast}$(용매의 polarity-polarizability), ${\alpha}$(용매의 수소결합 주게 산도) 그리고 ${\beta}$(용매의 수소결합 받게 염기도)를 여러 지시약을 사용하여 분광용매화 비교법으로 구하였다. 또한 Swain의 용매 파라미터인 A(음이온을 용매화 시키는 척도)와 B(양이온을 용매화 시키는 척도)를 반응속도 자료를 이용하여 최소 자승법으로 구하였다. 용매 상수 ${\beta}$는 용매의 염기도에 의존하며 혼합용매의 MeOH 함량이 증가할 수록 $(MeOH)_n$의 기여에 의해 증가하는 것을 알 수 있었다. ${\pi}^*$는 용매의 쌍극자 모멘트에 의존하며 혼합용매의 MeCN 함량이 증가할 수록 ${\pi}^{\ast}$값도 커지며 ${\alpha}$는 MeOH의 수소결합주게 효과에 의해 혼합용매의 MeOH함량이 증가할 수록 크게 증가하는 것을 나타냈다. 앞서 보고된 반응들에 용매 파라미터를 적용하여 반응상수를 구하였으며 Taft의 반응상수 a, s와 Swain의 반응상수 a, b사이에는 용매 척도의 차이 때문에 서로 연관성이 없었다. 그러나 그들의 비인 a/s와 a/b는 서로 좋은 직선관계를 보여 주었으며 이들 반응상수 비를 이용하여 반응 메카니즘이나 치환기 변화 및 이탈기 변화에 미치는 용매효과를 논의 하였다.

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

• International Journal of Industrial Entomology and Biomaterials
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• 제27권2호
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• pp.326-328
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• 2013

Sericin undergoes gelation by the structural transition from random coil to b-sheet transition. In the present study, the gelation time of sericin solution was investigated in the presence of NaCl, KCl and $CaCl_2$. The addition of salts delayed the gelation time, and $CaCl_2$ had the most pronounced effect, which delayed about 8 h at maximum. The gelation time increased with the concentration of salt. The transition of secondary structure of sericin was retarded in the presence of salt. The effect of salts on the gelation time of sericin might be due to the solvation effect of relevant cation.

• 한국해양공학회:학술대회논문집
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• 한국해양공학회 2003년도 춘계학술대회 논문집
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• pp.262-268
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• 2003

Organic coatings are widely used to control the corrosion of steel structure. The water in coatings may cause swelling or solvation of coatings, leading to the degradation of coatings. In addition, water affects the permeation of oxygen and other corrosive agents, and consequently the presence of such substances at coating-metal interface promotes corrosion of metal substrate. In this study, the anticorrosive properties of 4 types of coating, such as epoxy-epoxy, epoxy-urethane, urethane-epoxy, urethane-urethane, were evaluated. The evaluation tests were carried out under cyclic water-absorption/desorption conditions, consisting of alternative exposure to diluted 0.001M-LiCl($a_{1120}{\fallingdotseq}1$) and concentrated l0M-LiCl($a_{1120}{\fallingdotseq}0.05$). The anticorrosive performances of coatings were found to decrease in the order of urethane-urethane> urethane-epoxy> epoxy-epoxy coating.