• Journal of the Korean Chemical Society
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• v.39 no.9
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• pp.741-748
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• 1995

Various catechol derivatives inhibiting 5-lipoxygenase were studied with theoretical calculations and QSAR study. It was hypothesized that receptor site model could accept the active site of the catechol derivatives. The molecular length, molecular surface area, C5 net charge, HOMO/LUMO energy, van der Waals surface area and volume were used as variables to find the relationships between activity and physicochemical parameters.

• Bulletin of the Korean Chemical Society
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• v.30 no.12
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• pp.3079-3081
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• 2009

• Journal of the Korean Chemical Society
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• v.68 no.3
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• pp.146-150
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• 2024

Precise molecular configuration elucidation of poly(3-hexylthiophene) (P3HT) through advanced spectroscopic techniques is pivotal for enhancing P3HT-based photovoltaic device efficiencies since its high charge-carrier mobility is directly correlated to its well-ordered structure. In this study, we examine Raman depolarization ratios of annealed and non-annealed P3HT films to elucidate their intermolecular π-π configurations. Our findings suggest that the backbone of the annealed film possesses stronger π-π conjugation overlaps than that of the non-annealed film owing to the greater depolarization ratio of the annealed film. In addition, the depolarization ratios are also supported by theoretical calculations, where parallel-stacked thiophene structures display a higher depolarization ratio compared with that of twisted-stacked structures, as calculated by the Møller-Plesset perturbation theory. This study highlights the utility of polarized Raman spectroscopy as a versatile tool for assessing the degree of molecular order in highly conjugated polymer films.

• Journal of Microbiology and Biotechnology
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• v.17 no.11
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• pp.1789-1796
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• 2007

A ${\beta}$-glucosidase with the molecular mass of 160,000 Da was purified to homogeneity from cell extract of a cellulolytic bacterium, Cellulomonas uda CS1-1. The kinetic parameters ($K_m$ and $V_{max}$) of the enzyme were determined with pNP-cellooligosccharides (DP 1-5) and cellobiose. The molecular orbital theoretical studies on the cellulolytic reactivity between the pNP-cellooligosaccharides as substrate (S) molecules and the purified ${\beta}$-glucosidase (E) were conducted by applying the frontier molecular orbital (FMO) interaction theory. The results of the FMO interaction between E and S molecules verified that the first stage of the reaction was induced by exocyclic cleavage, which occurred in an electrophilic reaction based on a strong charge-controlled reaction between the highest occupied molecular orbital (HOMO) energy of the S molecule and the lowest occupied molecular orbital (LUMO) energy of the hydronium ion ($H_3O^+$), more than endocyclic cleavage, whereas a nucleophilic substitution reaction was induced by an orbital-controlled reaction between the LUMO energy of the oxonium ion ($SH^+$) protonated to the S molecule and the HOMO energy of the $H_2O_2$ molecule. A hypothetic reaction route was proposed with the experimental results in which the enzymatic acid-catalyst hydrolysis reaction of E and S molecules would be progressed via $SN_1$ and $SN_2$ reactions. In addition, the quantitative structure-activity relationships (QSARs) between these kinetic parameters showed that $K_m$ has a significant correlation with hydrophobicity (logP), and specific activity has with dipole moment, respectively.

• Bulletin of the Korean Chemical Society
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• v.32 no.7
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• pp.2358-2368
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• 2011

Density functional theory (DFT) and time-dependent density functional theory (TDDFT) calculations, employing the B3LYP method and the LANL2DZ, 6-31G$^*$(LANL2DZ for Tc), 6-31G$^*$(cc-pVDZ-pp for Tc) and DGDZVP basis sets, have been performed to investigate the electronic structures and absorption spectra of the technetium-99m-labeled methylenediphosphonate ($^{99m}Tc$-MDP) complex of the simplest diphosphonate ligand. The bonding situations and natural bond orbital compositions were studied by the Mulliken population analysis (MPA) and natural bond orbital (NBO) analysis. The results indicate that the ${\sigma}$ and ${\pi}$ contributions to the Tc-O bonds are strongly polarized towards the oxygen atoms and the ionic contribution to the Tc-O bonding is larger than the covalent contribution. The electronic transitions investigated by TDDFT calculations and molecular orbital analyses show that the origin of all absorption bands is ascribed to the ligand-to-metal charge transfer (LMCT) character. The solvent effect on the electronic structures and absorption spectra has also been studied by performing DFT and TDDFT calculations at the B3LYP/6-31G$^*$(cc-pVDZ-pp for Tc) level with the integral equation formalism polarized continuum model (IEFPCM) in different media. It is found that the absorption spectra display blue shift in different extents with the increase of solvent polarity.

• Bulletin of the Korean Chemical Society
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• v.34 no.2
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• pp.475-481
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• 2013

By using ionic liquid 1-hexylpyridinium hexafluorophosphate ($HPPF_6$) based carbon ionic liquid electrode (CILE) as the substrate electrode, a $CoMoO_4$ nanorods and myoglobin (Mb) composite was casted on the surface of CILE with chitosan (CTS) as the film forming material to obtain the modified electrode (CTS/$CoMoO_4$-Mb/CILE). Spectroscopic results indicated that Mb retained its native structures without any conformational changes after mixed with $CoMoO_4$ nanorods and CTS. Electrochemical behaviors of Mb on the electrode were carefully investigated by cyclic voltammetry with a pair of well-defined redox peaks from the heme Fe(III)/Fe(II) redox center of Mb appeared, which indicated that direct electron transfer between Mb and CILE was realized. Electrochemical parameters such as the electron transfer number (n), charge transfer coefficient (${\alpha}$) and electron transfer rate constant ($k_s$) were estimated by cyclic voltammetry with the results as 1.09, 0.53 and 1.16 $s^{-1}$, respectively. The Mb modified electrode showed good electrocatalytic ability toward the reduction of trichloroacetic acid in the concentration range from 0.1 to 32.0 mmol $L^{-1}$ with the detection limit as 0.036 mmol $L^{-1}$ ($3{\sigma}$), and the reduction of $H_2O_2$ in the concentration range from 0.12 to 397.0 ${\mu}mol\;L^{-1}$ with the detection limit as 0.0426 ${\mu}mol\;L^{-1}$ ($3{\sigma}$).

• Bulletin of the Korean Chemical Society
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• v.35 no.3
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• pp.783-792
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• 2014

The binding interaction between a hemolytic peptide ${\delta}$-lysin and a zwitterionic lipid bilayer POPC was investigated through a series of molecular dynamics (MD) simulations. ${\delta}$-Lysin is a 26-residue, amphipathic, ${\alpha}$-helical peptide toxin secreted by Staphylococcus aureus. Unlike typical antimicrobial peptides, ${\delta}$-lysin has no net charge and it is often found in aggregated forms in solution even at low concentration. Our study showed that only the monomer, not dimer, inserts into the bilayer interior. The monomer is preferentially attracted toward the membrane with its hydrophilic side facing the bilayer surface. However, peptide insertion requires the opposite orientation where the hydrophobic side of peptide points toward the membrane interior. Such orientation allows the charged residues, Lys and Asp, to have stable salt bridges with the lipid head-group while the hydrophobic residues are buried deeper in the hydrophobic lipid interior. Our simulations suggest that breaking these salt bridges is the key step for the monomer to be fully inserted into the center of lipid bilayer and, possibly, to translocate across the membrane.

• Proceedings of the Korean Vacuum Society Conference
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• 2011.02a
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• pp.325-325
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• 2011

Very initial stage of oxidation process of Si (001) surface at room temperature (300 K) and high temperature (1200 K) was investigated using large scale molecular dynamics simulation. Reactive force field potential [1] was used for the simulation owing to its ability to handle charge variation as well as breaking and forming of bonds associated with the oxidation reaction. The results show that oxygen molecules adsorb dissociatively or otherwise leave the silicon surface. Initial position and orientation of oxygen molecule above the surface play important role in determining final state and time needed to dissociate. At 300 K, continuous transformation of ion $Si^+$ (or suboxide Si2O) to $Si2^+$ (SiO), $Si3^+$ (Si2O3) and finally to $Si4^+$ (SiO2) clearly observed. High temperature silicon surface provide heat energy that enable oxygen atom to penetrate into deeper silicon surface. The heat energy also retards adsorption process. As a result, transformation of ion $Si^+$ is impeded at 1200 K.

• Proceedings of the Korean Vacuum Society Conference
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• 2011.02a
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• pp.299-299
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• 2011

A dipolar interlayer can cause dramatic changes in the device characteristics of organic field-effect transistors (OFETs) or photovoltaics. A shift in the threshold voltage, for example, has been observed in an OFET where the organic semiconductor active layer is deposited on SiO2 modified with a dipolar monolayer. Dipolar molecules can similarly be used to change the current-voltage characteristics of organic-inorganic heterojunctions. We have conducted a series of experiments in which different molecular linkages are placed between a pentacene thin film and a silicon substrate. Interface modifications with different linkages allow us to predict and examine the nature of tunneling through pentacene on modified Si surfaces with different dipole moment. The molecular-scale structure and the tunneling properties of pentacene thin films on modified Si (001) with nitrobenzene and styrene were examined using scanning tunneling spectroscopy. Electronic interfaces using organic surface dipoles can be used to control the band lineups of a semiconductor at organic/inorganic interfaces. Our results can provide insights into the charge transport characteristics of organic thin films at electronic interfaces.

• Journal of the Korean Chemical Society
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• v.53 no.6
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• pp.671-676
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• 2009

Described here for the first time is an investigation on geometrical and electronic molecular structure of metol (N-methyl-p-aminophenol sulphate) as corrosion inhibitor of steel using density functional theory (DFT) calculations. Quantum chemical parameters such as highest occupied molecular orbital energy (EHOMO), lowest unoccupied molecular orbital energy (ELUMO), energy gap ((${\Delta}E$), Mulliken charges (($q_M$) and natural atomic (($q_n$) charge have been calculated both for gas and aqueous phases by using B3LYP/6-31G+(d,p) basis set. The relation between the inhibition efficiency and quantum chemical parameters have been discussed in order to elucidate the inhibition mechanism of the title compound.