• Bulletin of the Korean Chemical Society
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• v.25 no.11
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• pp.1657-1660
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• 2004

Several critical geometries associated with the rearrangement of $CH_3SNO_2\;to\;CH_3SONO$ are calculated with the density functional theory (DFT) method and compared with those of the ab initio molecular orbital methods. There are two probable pathways for this rearrangement, one involving the transition state of an oxygen migration and the other through the homolytic decomposition to radicals. The reaction barrier via the transition state is about 60 kcal/mol and the decomposition energy into radicals about 35 kcal/mol, suggesting that the reaction pathway via the homolytic cleavage to radical species is energetically favorable. Since even the homolytic cleavage requires large energies, the rearrangement reaction is unlikely without the aid of catalysts.

• Proceedings of the Korean Vacuum Society Conference
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• 2013.08a
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• pp.127.1-127.1
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• 2013

Recent experimental evidence that fluorinated graphene creates local magnetic moments around F adatoms has not been supported by semilocal density-functional theory (DFT) calculations where the adsorption of an F adatom induces no magnetic moment in graphene. Here, we show that such an incorrect prediction of the nonmagnetic ground state is due to the self-interaction error inherent in semilocal exchange-correlation functionals. The present hybrid DFT calculation for an F adatom on graphene predicts not only a spin-polarized ground state with a spin moment of ${\sim}1{\mu}_B$, but also a long-range spin polarization caused by the bipartite nature of the graphene lattice as well as the induced spin polarization of the graphene states. The results provide support for the experimental observations of local magnetic moments in fluorinated graphene.

• Korean Journal of Mineralogy and Petrology
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• v.34 no.2
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• pp.121-131
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• 2021

Magnesium (Mg) present in carbonate minerals as impurities has been used as a geochemical proxy to infer the environmental conditions where the minerals precipitated. The reliability of Mg geochemical proxies requires fundamental understanding of Mg incorporation into minerals based on accurate speciation of Mg ²⁺ in the crystal structure, which is determined mainly by application of X-ray absorption spectroscopy (XAS). However, high uncertainties are involved in interpreting the XAS spectra of minerals containing trace amount of Mg ²⁺. Because density function theory (DFT) can predict an XAS spectrum for a crystal structure, DFT calculations can reduce the uncertainties in the interpretation of the XAS spectrum. In this study, we calculated ab initio Mg K-edge absorption spectra of Mg silicates and (hydr)oxides based on DFT and analyzed the correlation between the calculated spectra and Mg structural parameters. Our ab initio Mg K-edge absorption spectra well reproduced the key features of the experimental spectra. The absorption-edge positions of the calculated spectra showed the weak positive correlation with the average Mg-O bond distance or Mg effective coordination number. The current study shows that DFT-based core-level spectroscopy method is a powerful tool in providing standard Mg K-edge spectra of diverse Mg minerals and determining the Mg chemical species within carbonate minerals.

• Journal of Integrative Natural Science
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• v.15 no.4
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• pp.179-186
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• 2022

The c-Jun N-terminal kinase (JNK3) play major role in neurodegenerative diseases like Alzheimer's disease, Parkinson's disease, cerebral ischemia and other Central Nervous System disorders. Since JNK3 is primarily stated in the brain and stimulated by stress-stimuli, this situation is conceivable that inhibiting JNK3 could be a possible treatment for the mechanisms underlying neurodegenerative diseases. In this study drugs from Zinc15 database were screened to identify the JNK3 inhibitors by Molecular docking and Density functional theory approach. Molecular docking was done by Autodock vina and the ligands were selected based on the binding affinity. Our results identified top ten novel ligands as potential inhibitors against JNK3. Molecular docking revealed that Venetoclax, Fosaprepitant and Avapritinib exhibited better binding affinity and interacting with proposed binding site residues of JNK3. Density functional theory was used to compute the values for energy gap, lowest unoccupied molecular orbital (LUMO), and highest occupied molecular orbital (HOMO). The results of Density functional theory study showed that Venetoclax, Fosaprepitant and Avapritinib serves as a lead compound for the development of JNK3 small molecule inhibitors.

• Journal of Korean Society of Environmental Engineers
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• v.35 no.7
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• pp.457-463
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• 2013

The removal of sulfonamide antibiotics (SAs) by activated carbon was investigated by using granular activated carbon (GAC) tests and density functional theory (DFT) simulations. The GAC absorption tests show the removal efficiency of 68.4~90.7% and 99.0~99.9% in 1 and 24 hours, respectively. In both GAC tests, the removal efficiency of sulfamethazine (SMZ) was the highest followed by those of sulfathiazole (STZ) and sulfamethoxazole (SMTZ): SMZ > STZ > SMTZ. In DFT adsorption simulations, we found that the 4-aminobenzenesulfonamide parts of SMZ and STZ and the 3-methyl-1,2-oxazol-5-amine part of SMTZ are preferentially adsorbed on the edges of graphene model, provided that the adsorbates keep their structures without dissociation upon adsorption process. The adsorption energies of SMZ, STZ, and SMTZ are -4.91, -4.64, and -4.62 eV, respectively. This adsorption strength (SMZ > STZ > STMZ) agrees with the trend of the removal efficiency of SAs by GAC. In addition, dissociative adsorption configurations of SAs are discussed.

• Proceedings of the Korean Vacuum Society Conference
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• 2013.02a
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• pp.193-193
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• 2013

Perfluorocarbons (PFCs) have been suggested as possible replacements for $SF_6$ and the fluorocarbons used in and emitted during technological plasma treatments because PFCs have significantly low greenhouse warming potentials. Of many PFCs, c-$C_4F_8$ and 2-$C_4F_8$ attract special attention because of their high CF2 radicallevels in commercial plasma treatments. Accordingly, several experimental and theoretical studies of these $C_4F_8$ species have been conducted, although only the geometries at their stationary states and their adiabatic electron affinities (EAs) have been determined. However, this information is not sufficient for a deep understanding of all the possible fates and roles of $C_4F_8$ species and their fragments in plasma phases. Although the performance and reliability ofeach DFT functional have been examined carefully by the development team of each functional form with respect to the training and test data sets of well-known molecular systems, no PFC was included in the data sets. So a careful additional assessment of the reliability of DFT functionals for the study of PFC systems is highly required. In order to find a DFT method appropriate to PFCs, the geometry, energy, and chemical reaction properties of $C_4F_8$ were calculated and compared with reference data.

• Journal of the Korean Magnetic Resonance Society
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• v.16 no.1
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• pp.78-90
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• 2012

To understand the electronic structure of $[NiS_4]^-$ complex ions, two complexes with such $[NiS_4]^-$ core, $FcCH=CHPymCH_3[Ni(dmit)_2]$ (Pym = pyridinium, $dmit^{2-}$ = 2-thioxo-1,3-dithiole-4,5-dithiolate) and $FcCH=CHPymCH_3[Ni(dddt)_2]{\cdot}{\frac{1}{2}}H_2O$ ($dddt^{2-}=5,6-dihydro-1,4-dithiin-2,3-dithiolato$), were synthesized to be characterized by X-ray crystallography, single crystal electron paramagnetic resonance (EPR) and density functional theory (DFT) calculation. Powder EPR spectra show narrow g-anisotropy but the anisotropy is bigger in $[Ni(dmit)_2]^-$ than in $[Ni(dddt)_2]^-$, indicating bigger spin density in Ni(III) d-orbital of $[Ni(dmit)_2]^-$ than in $[Ni(dddt)_2]^-$, which is consistent to DFT results. EPR studies of the crystals of the complexes surprisingly suggest that the $g_y$-axis of $[Ni(dddt)_2]^-$ is approximately on or perpendicular to the $[NiS_4]^-$ plane while the $g_y$-axis of $[Ni(dmit)_2]^-$ is on the plane, though DFT study of the complexes of this study and previously reported $[NiS_4]^-$ complexes indicate that the $g_y$-axis is on the $[NiS_4]^-$ plane.

• Journal of the Korean Electrochemical Society
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• v.14 no.3
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• pp.145-151
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• 2011

ZnSe, as a II-VI compound semiconductor which has a wide band gap in the visible region is applicable to the various fields such as laser diode, display and solar cell. By using the electrochemical deposition method, ZnSe thin film was synthesized on the ITO glass substrate. The synthesis of ZnSe grains and their structure having zinc blende shape were verified through the analysis of XRD and SEM. UV spectrophotometric method determined the band gap as the value of 2.76 eV. Applying the DFT (Density Functional Theory) in the molecular dynamics, the band structure of ZnSe grains was analyzed. For ZnSe grains with zinc blende structure, the band structure and its density of state were simulated using LDA (Local Density Approximation), PBE (Perdew Burke Ernzerhof), and B3LYP (Becke, 3-parameter, Lee-Yang-Parr) functionals. Among the calculations of energy band gap upon each functional, the simulated one of 2.65 eV based on the B3LYP functional was mostly near by the experimental measurement.

• Proceeding of EDISON Challenge
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• 2015.03a
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• pp.400-404
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• 2015

2차원 물질인 metal mono chalcogenides(MMC) 중 GaS와 GaSe를 대상으로 하여 층과 층 사이의 van der Waals(vdW) 상호작용을 density functional theory(DFT) 계산을 이용해 연구하였다. Local density approximation(LDA)와 generalized gradient approximation (GGA)의 두 가지 다른 exchange correlation functional을 이용하고, 또한 두 개의 층 사이에 작용하는 van der Waals 상호작용을 고려한 LDA-D2, GGA-D2 계산을 수행하였다. 이와 같은 네 가지 방법으로 층간거리를 바꾸어 binding energy curve를 계산하였다. 그 결과 GGA-D2계산이 MMC의 층간 상호 작용을 가장 잘 기술하였다.

• Journal of the Korean Chemical Society
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• v.61 no.6
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• pp.311-319
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• 2017

By using Density Functional Theory (DFT), we have performed alkali metal and alkaline earth metal inside fullerene-like BeO cluster (FLBeOC) in terms of energetic, geometric, charge transfer, work function and electronic properties. It has been found that encapsulated processes of the alkali metal are exothermic and thermodynamically more favorable than alkaline earth metal encapsulation, so that interaction energy ($E_{int}$) of the alkali metal encapsulation FLBeOC is in the range of -0.02 to -1.15 eV at level of theory. It is found that, the electronic properties of the pristine fullerene-like BeO cluster are much more sensitive to the alkali metal encapsulation in comparison to alkaline earth metal encapsulation. The alkali and alkaline earth metal encapsulated fullerene-like BeO cluster systems exhibit good sensitivity, promising electronic properties which may be useful for a wide variety of next-generation nano-sensor device components. The encapsulation of alkali and alkali earth metal may increase the electron emission current from the FLBeOC surface by reducing of the work function.