• 한국생물공학회:학술대회논문집
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• 2001.11a
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• pp.886-889
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• 2001

C-terminus specific immobilization often results in a increased structural stability resistant to various denaturation factors. In order to elucidate the immobilization effect on the c-terminus in molecular level, we made over 200 protein data set from Protein Data Bank(PDB), analyzed c-terminus structure of each protein, and investigated the structural relationship with the stabilizing factors such as hydrogen bond, ion pairs, cation pi, disulfide bond, solvation free energy, surface area, flexibility and so on.

• 한국신재생에너지학회:학술대회논문집
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• 2006.11a
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• pp.438-442
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• 2006

The degradation of Nafion membrane by hydrogen peroxide was investigated in polymer electrolyte membrane fuel cell (PEMFC). Degradation tests were carried out in a solution of $10{\sim}30%$ hydrogen peroxide containing 4ppm $Fe^{2+}$ ion which is well known as Fenton's reagent at $80^{\circ}C$ for 48hr. Characterization of degraded membranes were examined through the IR, Water-uptake, Ion exchange capacity, mechanical strength and $H_2$ permeability. After degradation, C-F, S-O and C-O chemical bonds of membrane were broken by radical formed by $H_2O_2$ decomposition. Breaking of C-F bond which is the membrane backbone reduced the mechanical strength of Nafion membrane and hence induced pinholes, resulting in increase of $H_2$ crossover through the membrane. Also the decomposition of C-O and S-O, side chain and terminal bond of membrane, decreased the ion exchange capacity of the membrane.

• Bulletin of the Korean Chemical Society
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• v.23 no.9
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• pp.1297-1303
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• 2002

Computations are presented for the catechol-$(H_2O)_n$ (n = 1-3) clusters. A variety of conformers are predicted,and their relative energies are compared. Binding energies of the clusters are computed, and detailed analysis is presented on the harmonic frequencies of stretching modes involving the hydrogen bonding in the clusters, comparing with the experimental observations.

• Molecules and Cells
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• v.38 no.5
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• pp.409-415
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• 2015

Low-barrier hydrogen bonds (LBHBs) have been proposed to have important influences on the enormous reaction rate increases achieved by many enzymes. ${\Delta}^5$-3-ketosteroi isomerase (KSI) catalyzes the allylic isomerization of ${\Delta}^5$-3-ketosteroid to its conjugated ${\Delta}^4$-isomers at a rate that approache the diffusion limit. Tyr14, a catalytic residue of KSI, has been hypothesized to form an LBHB with the oxyanion of a dienolate steroid intermediate generated during the catalysis. The unusual chemical shift of a proton at 16.8 ppm in the nuclear magnetic resonance spectrum has been attributed to an LBHB between Tyr14 $O{\eta}$ and C3-O of equilenin an intermediate analogue, in the active site of D38N KSI. This shift in the spectrum was not observed in Y30F/Y55F/D38N and Y30F/Y55F/Y115F/D38N mutant KSIs when each mutant was complexed with equilenin, suggesting that Tyr14 could not form LBHB with the intermediate analogue in these mutant KSIs. The crystal structure of Y30F/Y55F/Y115F/D38N-equilenin complex revealed that the distance between Tyr14 $O{\eta}$ and C3-O of the bound steroi was within a direct hydrogen bond. The conversion of LBHB to an ordinary hydrogen bond in the mutant KSI reduced the binding affinity for the steroid inhibitors by a factor of 8.1-11. In addition, the absence of LBHB reduced the catalytic activity by only a factor of 1.7-2. These results suggest that the amount of stabilization energy of the reaction intermediate provided by LBHB is small compared with that provided by an ordinary hydrogen bond in KSI.

• Proceedings of the Korean Vacuum Society Conference
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• 2012.08a
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• pp.211-211
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• 2012

Using spin-polarized density-functional theory calculations, we find that the existence of either Peierls instability or antiferromagnetic spin ordering is sensitive to hydrogen passivation near the step. As hydrogens are covered on the terrace, the dangling bond electrons are localized at the step, leading to step-induced states. We investigate the competition between charge and spin orderings in dangling-bond (DB) wires of increasing lengths fabricated on an H-terminated vicinal Si(001) surface. We find antiferromagnetic (AF) ordering to be energetically much more favorable than charge ordering. The energy preference of AF ordering shrinks in an oscillatory way as the wire length increases. This oscillatory behavior can be interpreted in terms of quantum size effects as the DB electrons fill discrete quantum levels.

• Bulletin of the Korean Chemical Society
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• v.23 no.2
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• pp.262-266
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• 2002

Computations are presented for the ortho- and para-substituted benzyl alcohol-$H_2O$ clusters. A variety of conformers are predicted, and their relative energies are compared. Binding energies of the clusters are computed, and detailed analysis is presented on the effects of substitution on the strength of the hydrogen bond in the clusters. F- and $NH_2-$ substituted clusters are studied to analyze the effects of electron-withdrawing and electron-pushing groups. In para-substituted clusters, the inductive effects are dominant, affecting the binding energies in opposite way depending on whether the hydroxyl group is proton-donating or -accepting. For ortho-substituted clusters, more direct involvement of the substituting group and the resulting geometry change of the hydrogen bond should be invoked to elucidate complicated pattern of the binding energy of the clusters.

• Journal of Integrative Natural Science
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• v.5 no.3
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• pp.195-197
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• 2012

Halogen atoms in a molecule are traditionally considered as electron donors, since they have unshared electrons. Normally when they are bonded, there are three lone pair electrons. These lone pairs can function as Lewis bases. However, when they are bound to electron withdrawing groups, they can act as Lewis acids. Since the situation is similar hydrogen bonding (HB), this type of interaction is named as halogen bonding (XB). This mainly comes from the uneven distribution of electron density around the halogen atoms. Since the electron density around halogen atom opposite to ${\sigma}$-bond is depleted, its electropositive region is called ${\sigma}$-hole. This ${\sigma}$-hole can attract halogen bond acceptors, requiring more stringent directionality compared to HB. Since this interaction mainly comes from electrostatic origin, the geometry tends to be linear. Since the XB energy is comparable to corresponding HB. Still in its infancy, XB shows a broad range of applicability, with potentially more useful properties, compared to corresponding HB.

• Bulletin of the Korean Chemical Society
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• v.17 no.2
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• pp.201-205
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• 1996

The crystal and molecular structure of thiourea dioxide, (NH2)2CSO2, was determined by x-ray single crystal diffraction techniques. Lattice constants are a=10.669(2), b=10.119(2), and c=3.9151(5) Å with the space group Pnma and Z=4. The thiourea portion of the molecule has a planar conformation. When the two oxygen atoms are included, the sulfur atom is at the apex of a trigonal pyramid formed with the two oxygen atoms and the carbon atom as the base. The crystal structure is stabilized by strong intermolecular hydrogen bonds. Ab initio calculations were performed to investigate the bonding features and reactivity of thiourea dioxide. The calculated bond order of S-C is only 0.481. The hydrogen bond energy was computed to be 22.3 kcal/mol for dimer. MEP analysis reveals that the sites on nucleophilic reactions are S and C atoms.

• International Journal of Advanced Culture Technology
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• v.11 no.2
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• pp.323-329
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• 2023

In this study, Proline pentamer model was used to investigate change in the dihedral angle, intramolecular hydrogen bonding and formation energies during structural optimization. L-Proline (LP, as an imino acid residue) pentamers having four conformation types [β: φ/ψ=t−/t+, α: φ/ψ=g−/g−, PP_II: φ/ψ=g−/t+ and Plike: φ/ψ= g−/g+] were carried out by QCC [B3LYP/6-31G(d,p)]. The optimized structure and formation energy were examined for designated structure. In LP, P-like and PP_II types did not change by optimization, and β types were transformed into PP_II having no H-bond independently of the designated ψ values. PP_II was more stable than P-like by about 2.2 kcal/mol/mu. The hydrogen bond distances of d2(4-6) type H-bonds were 1.94 - 2.00Å. In order to understand the processes of the transformations, the changes of φ/ψ, distances of NH-OC (d_NH/CO) and formation energies (ΔE, kcal/mol/mu) were examined.

• Bulletin of the Korean Chemical Society
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• v.24 no.6
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• pp.763-770
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• 2003

The $BH_5$ molecule, which is suggested as an intermediate of the acidolysis of $BH_4^-$, contains a weak two-electron-three-center bond and it requires extremely high-level of theories to calculate the energy and structure correctly. The structures and energies of $BH_5$ and the transition state for the hydrogen scrambling have been studied using recently developed multi-coefficient correlated quantum mechanical methods (MCCMs). The dissociation energies and the barrier heights agree very well with the previous results at the CCSD(T)/ TZ(3d1f1g, 2p1d) level. We have also calculated the potential energy curves for the dissociation of $BH_5$ to $BH_3$ and $H_2$. The lower levels of theory were unable to plot correct potential curves, whereas the MCCM methods give very good potential energy curves and requires much less computing resources than the CCSD(T)/ TZ(3d1f1g,2p1d) level. The potential energy of the $BH_5$ scrambling has been obtained by the multiconfiguration molecular mechanics algorithm (MCMM), and the rates are calculated using the variational transition state theory including multidimensional tunneling approximation. The rate constant at 300 K is 2.1 × $10^9s^{-1}$, and tunneling is very important.