• Bulletin of the Korean Chemical Society
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• v.21 no.8
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• pp.779-784
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• 2000

Comparing the adsorption properties and dissociation on a Pt(111) iththat ona Fe(111) surface, we have con-sidered seven coordination modes of the adsorbed binding site: $di-${\sigma}$${\Delta}$\mu\pi/\mu$, 1-fbld,2-fold, and 3-fbld sites. On the Pt(111) surface, t he adsorbed binding site of carbon dioxide was strongestat the1-fold site and weakest at the $\pi/\mu-site.$ The adsorbed binding site on the Fe(111) surface was strongest at the di-бsite and weakest at the 3-fold site. We have found that the binding energy at each site that excepted 3-fold on the Fe(111) surface was stronger than the binding energy on the Pt(111) surface and that chemisorbed $CO_2bends$ because of metal mixing with $2\piu${\rightarrow}$6a_1CO_2orbital.$, The dissociation reaction occured in two steps, with an intermediate com-plex composed of atomic oxygen and ${\pi}bonding$ CO forming. The OCO angles of reaction intermediate com-plex structure for the dissociation reaction $were115^{\circ}Con$ the Pt(111), and $117^{\circ}C$ on the Fe(111) surface. We have found that the $CO_2dissociation$ rea11) surface proceeds easily,with an activationenergy about 0.2 eV lower than that on the Pt(111) surface.

• Bulletin of the Korean Chemical Society
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• v.24 no.6
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• pp.817-823
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• 2003

We have performed ab initio calculation on the active site of HIV-1 protease. The FEP method was used to determine the binding free energy of four different of protonated states of HIV-1 protease with inhibitor. The structure of the active site and hole structure was taken from the X-ray crystallographic coordinates of the C₂ symmetric inhibitor A74704 protease bound. The active site was modeled with the fragment molecules of binding pocket, acetic acid/ acetate anion (Asp25, Asp125), formamide (amide bond of Thr26/Gly27, Thr126/ Gly127), and methanol as inhibitor fragment. All possibly protonated states of the active site were considered, which were diprotonated state (0, 0), monoprotonated (-1, 0),(0, -1) and diunprotonated state (-1, -1). Once the binding energy Debind, of each model was calculated, more probabilistic protonated states can be proposed from binding energy. From ab-initio results, the FEP simulations were performed for the three following mutations: Ⅰ) Asp25 … Asp125 → AspH25 … Asp125, ⅱ) Asp25 … Asp125 → Asp25 … AspH125, ⅲ) AspH25 … Asp125 → AspH25 … AspH125. The free energy difference between the four states gives the information of the more realistic protonated state of active site aspartic acid. These results provide a theoretical prediction of the protonation state of the catalytic aspartic residues for A74707 complex, and may be useful for the evaluation of potential therapeutic targets.

• Bulletin of the Korean Chemical Society
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• v.32 no.3
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• pp.921-926
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• 2011

This study investigates a root cause of the improved rate performance of $LiFePO_4$ after metal doping to Fesites. This is because the metal doped $LiFePO_4$/C maintains its initial capacity at higher C-rates than undoped one. Using $LiFePO_4$/C and doped $LiFe_{0.97}M_{0.03}PO_4$/C (M=$Al^{3+}$, $Cr^{3+}$, $Zr^{4+}$), which are synthesized by a mechanochemical process followed by one-step heat treatment, the Li content before and after chemical delithiation in the $LiFePO_4$/C and the binding energy are compared using atomic absorption spectroscopy (AAS) and X-ray photoelectron spectroscopy (XPS). The results from AAS and XPS indicate that the low Li content of the metal doped $LiFePO_4$/C after chemical delithiation is attributed to the low binding energy induced by weak Li-O interactions. The improved capacity retention of the doped $LiFePO_4$/C at high discharge rates is, therefore, achieved by relatively low binding energy between Li and O ions, which leads to fast Li diffusivity.

• Bulletin of the Korean Chemical Society
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• v.35 no.1
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• pp.253-256
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• 2014

Functionalization of zigzag graphene nanoribbon (ZGNR) segment containing 120 C atoms with pyridine (3NV-ZGNR) defects was investigated on the basis of density-functional theory (DFT) calculations, results show that edge-modified ZGNRs by Sc can adsorb multiple hydrogen molecules in a quasi-molecular fashion, thereby can be a potential candidate for hydrogen storage. The stability of Sc functionalization is dictated by a strong binding energy, suggesting a reduction of clustering of metal atoms over the metal-decorated ZGNR.

• Journal of Photoscience
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• v.12 no.1
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• pp.25-32
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• 2005

Binding of N-Alkyl phenothiazines (NAP) to bovine serum albumin (BSA) was studied by spectroscopic methods.It was found that the phenothiazine ring common to all drugs makes major contribution to interaction. However, the nature of alkylamino group at position 10 influences the protein binding significantly. Stern-Volmer plots indicated the presence of static component in the quenching mechanism. The high magnitude of rate constant of quenching indicated that the process of energy transfer occurs by intermolecular interaction and thus the drug-binding site is in close proximity to tryptophan residues of BSA. Binding studies in presence of hydrophobic probe, 8-anilino-1-naphthalein-sulphonic acid showed that there is hydrophobic interaction between drug and the probe and they do not share common sites in BSA. Thermodynamic parameters obtained from data at different temperatures showed that the binding of NAP to BSA predominantly involve hydrophobic forces. The effects of some cations and anions common ions were investigated on NAP-BSA interactions. The CD spectrum of BSA in presence of drug showedthat binding of drug leads to change in the helicity of the protein.

• Journal of the Korean Chemical Society
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• v.54 no.6
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• pp.671-679
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• 2010

The geometrical parameters and binding energies of the benzene ion-water complex [$C_6H_6^+-(H_2O)_n$(n=1-5)] have been investigated using ab initio (MP2) and density functional theory (DFT) with large basis sets. The harmonic vibrational frequencies and IR intensities are also determined to confirm that all the optimized geometries are true minima. Also zero-point vibrational energies have been considered to predict the binding energies. The predicted binding energy of 8.6 kcal/mol for $C_6H_6^+-(H_2O)$ at the MP2/aug-cc-pVTZ level of theory is in excellent agreement with recent experimental result of $8.5{\pm}1$ kcal/mol.

• BMB Reports
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• v.33 no.1
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• pp.43-48
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• 2000

4-Aminobutyrate aminotransferase is a key enzyme of the 4-aminobutyric acid shunt. It converts the neurotransmitter 4-aminobutyric acid to succinic semialdehyde. In order to study the structural and functional aspects of catalytically active Cys residues of pig brain 4-aminobutyrate aminotransferase, we purified the active form in E. coli by coproduction of thioredoxin. The structural arrangement for functional requirements of a dimeric protein using a bifunctional sultbydryl reagent was then characterized, and the spatial proximity between the essential SH groups and a cofactor (pyridoxal-5'-phosphate) binding site was determined. The bifunctional sultbydryl reagent DMDS reacted with the enzyme at the ratio of one molecule per enzyme dimer. This resulted in an approximately 50% loss of enzymatic activity. The spatial proximity of the distance between the essential SH groups and the cofactor-binding site was determined by the energy transfer measurement technique. The result (approximate 20 ${\AA}$) suggested that cross-linking of two sulfhydryl groups with DMDS is not near a PLP binding site.

• Journal of the Korean Vacuum Society
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• v.1 no.1
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• pp.83-87
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• 1992

Rencently, angle-resolved ultraviolet photoemission measurements of the Fermi surface contours for Mo(011) and W(011) are reported. The electron contour of W(011) is expanded upon hydrogen adsorption, which implies that the surface states consisting of electron pockets are shifted to higher binding energy. This phenomena can be explained by the band flattening. We explained here the reconstruction of W(011) surface induced by adsorption of hydrogen in terms of band flattening of surface states with a combination of S. E. Trullinger long range dipole-dipole interaction force and Kohn anomaly.

• Proceeding of EDISON Challenge
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• 2013.04a
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• pp.77-88
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• 2013

The computational study on the fluoride ion binding with bis(bora)calix[4]arene has been performed using density functional theory and ONIOM model. The computed structure and fluorescent behavior of bis(bora)calix[4]arene was corresponded to experiment value. The binding energy for fluoride anion is computed to be 28.05kJ/mol in the chloroform solution. We also predicted that this sensing mechanism is only valid for fluoride ion in halogens. By analyzing molecular orbitals, binding with fluoride ion reduces energy differences between HOMO and LUMO, which leads to fluorescent sensing.

• Journal of Photoscience
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• v.12 no.1
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• pp.11-15
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• 2005

The mechanism of interaction of two drugs viz., amoxicillin and cloxacillin with bovine serum albumin has been investigated using fluorescence absorption and circular dichroism spectroscopy. The quenching mechanism of fluorescence of bovine serum albumin by amoxicillin and cloxacillin was discussed. The binding sites number n and apparent binding constant Kwere measured by fluorescence quenching method. The thermodynamic parameters obtained from data at different temperatures were calculated. The distance r between donor (bovine serum albumin) and acceptor (amoxicillin and cloxacillin) was obtained according to Forster theory of non-radiative energy transfer. The effect of common ions on binding constant was also investigated. The results of synchronous fluorescence spectra, UV-vis absorption spectra and circular dichroism of BSA in presence of amoxicillin and cloxacillin show that the conformation of bovine serum albumin changed