• Bulletin of the Korean Chemical Society
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• 제33권8호
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• pp.2669-2674
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• 2012

Crown ether is one of well-known host molecules and able to selectively sequester metal cation. We employed M06-2X density functional theory with IEFPCM and SMD continuum solvation models to study selectivity of dibenzo-18-crown-6-ether (DB18C6) for alkaline earth dications, $Ba^{2+}$, $Sr^{2+}$, $Ca^{2+}$, and $Mg^{2+}$ in the gas phase and in aqueous solution. $Mg^{2+}$ showed predominantly strong binding affinity in the gas phase because of strong polarization of CO bonds by cation. In aqueous solution, binding free energy differences became smaller among these dications. However, $Mg^{2+}$ had the best binding, being incompatible with experimental observations in aqueous solution. The enthalpies of the dication exchange reaction between DB18C6 and water cluster molecules were computed as another estimation of selectivity in aqueous solution. These results also demonstrated that $Mg^{2+}$ bound to DB18C6 better than $Ba^{2+}$. We speculated that the species determining selectivity in water could be 2:1 complexes of two DB18C6s and one dication.

• 한국수소및신에너지학회논문집
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• 제24권2호
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• pp.172-178
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• 2013

This study examined the electrochemical deposition and dissolution of lithium on nickel electrodes in 1 mol $dm^{-3}$ (M) $LiPF_6$ dissolved in propylene carbonate (PC) containing different 1,2-dimethoxyethane (DME) concentrations as a co-solvent. The DME concentration was found to have a significant effect on the reactions occurring at the electrode. The poor cycleability of the electrodes in the pure PC solution was improved considerably by adding small amounts of DME. This results suggested that the dendritic lithium growth could be suppressed by using co-solvents. After hundredth cycling in the 1 M $LiPF_6$/PC:DME (67:33) solution, almost no dead lithium has been found from the disassembled cell, resulting from suppression of dendritic lithium growth. Scanning electron microscopy revealed that dendritic lithium formation was greatly affected by the ratio of DME. Raman spectroscopy results suggested that the structure of solvated lithium ions is a crucial important factor in suppressing dendritic lithium formation.

• EDISON SW 활용 경진대회 논문집
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• 제4회(2015년)
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• pp.151-155
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• 2015

The molecular interactions between the nucleic acid bases and water molecules are important in organism. Despite Adenine-Thymine Hoogsteen base pair and Guanine-Cytosine Watson-Crick base pair have been demonstrated to be most stable in a gas phase, the effect of water on the stability of these base pairs remains elusive. Here we report the structural and thermodynamic characteristics on possible Adenine-Thymine and Guanine-Cytosine base pairs in a gas phase as well as in an aqueous phase by using quantum mechanical method and statistical mechanical calculations. First, we optimized the direct base-pair interaction energies of four Adenine-Thymine base pairs (Hoogsteen base pair, reverse Hoogsteen base pair, Watson-Crick base pair, and reverse Watson-Crick base pair) and three Guanine-Cytosine base pairs (GC1 base pair, GC2 base pair, and Watson Crick base pair) in a gas phase at the $B3LYP/6-31+G^{**}$ level. Then, the effect of solvent was quantified by the electronic reorganization energy and the solvation free energy by statistical mechanical calculations. Thereby, we discuss the effect of water on the stability of Adenine-Thymine and Guanine-Cytosine base pairs, and argue why Adenine-Thymine Watson-Crick base pair and Guanine-Cytosine Watson-Crick base pair are most stable in an aqueous environment.

• 대한화학회지
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• 제53권2호
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• pp.133-136
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• 2009

4-아미노피리딘 (4AP)–HCl와 –HBr 복합체에 대한 양자화학적 계산을 수행하였다. 전하분리된 (즈비 터이온) 형태의 [4AP$H^+-Cl^-$]는 안정하지 않으나, [4AP$H^+-Br^-$]은 안정하여 저온기체상에서 관찰될 것으로 예측되었다. 이것은 HCl에 비하여 HBr의 해리에너지가 작다는 사실과, 4AP의 아미노기가 HBr의 “용매”로 작용 한 결과로 해석되었다.

• 대한화학회지
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• 제36권3호
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• pp.345-350
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• 1992

Ln$(NO_3)_3$/DMF 상자성 용액의 양성자 선-나비와 화학적이동을 240 K부터 380 K 사이에서 측정하였다. 이들 데이터로부터 DMF 분자의 CHO기에 대한 배위구 교환속도와 열역학 교환파라미터를 추출하였다. 1/$T_2$ 와 ${\Dellta}{\omega}$ 데이터의 온도의존성을 자세하게 분석하고 고찰하여 결과를 정리하였다. 분석의 결과를 살펴보면 짝짓지 않은 전자 스핀이 몇몇 $Ln^{3+}$이온에서 첫 배위구를 넘어 퍼지면서 bulk 용매의 DMF 분자로 스칼라이완의 기여를 제공하는 것 같다.

• 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.

• 한국자기공명학회논문지
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• 제8권2호
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• pp.127-138
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• 2004

We obtained the chemical shifts of amide protons (NHs) in helical peptides at various temperatures and trifluoroethanol (TFE) concentrations using 2-dimensional NMR spectroscopy. These NH chemical shifts and their temperature dependence exhibited characteristic periodicity of 3-4 residues per cycle along the helix, where downfield shifted NHs showed larger temperature dependence. In an attempt to understand these observations, we focused on hydrogen bonding changes in the peptides and examined the validity of two possible explanations: (1) changes in intermolecular hydrogen bonding caused by differential solvation of backbone carbonyl groups by TFE, and (2) changes in intramolecular hydrogen bonding due to disproportionate variations in the hydrogen bonding within the peptide helix. Interestingly, the slowly exchanging NHs, which were on the hydrophobic side of the helix, showed consistently larger temperature dependences. This could not be explained by the differential solvation assumption, because the slowly exchanging NHs would become more labile if the preceding carbonyl groups were preferentially solvated by TFE. We suggest that the disproportionate changes in intramolecular hydrogen bonding better explain both the temperature dependence and the exchange behavior observed in this study.

• Bulletin of the Korean Chemical Society
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• 제13권1호
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• pp.75-79
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• 1992

Differences in chromatographic properties in RPLC of four brands of cyano bonded silica stationary phases are rationalized in terms of the type and relative strength of the solute-stationary phase interactions, which can be readily inferred from multiple linear regression analyses of retention data for a set of standard compounds on the stationary phases under study based on the linear solvation energy relationships (LSERs). Although four brands of cyano bonded columns studied (CPS-Hypersil, Ultrasphere cyano, Spherisorb-CN and ${\mu}$-Bondapak-CN) have similar bonding density and have been prepared from monofunctional cyanopropylsilane reagents, they possess quite different, relative hydrogen bonding (HB) donor and acceptor strengths. Comparison of the retention behavior on a cyano-bonded silica column with that on an ODS column shows that there are significant differences in the strength of HB interactions between the solute and the stationary phase on the two columns with different functionalities. Information on the differences in the interaction characteristics among brands of the cyano-bonded silica columns and between the ODS and cyano-bonded columns can be utilized to optimize the selectivity for a given separation on these columns.

• 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.

• 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.