• Proceedings of the Korean Vacuum Society Conference
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• 2010.08a
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• pp.93-93
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• 2010

In this talk, I will introduce a reactive force field (ReaxFF) molecular dynamics (MD) simulation. In contrast to common MD simulations with empirical FFs, we can predict chemical reactions (bond breaking and formation) in large scale systems with the ReaxFF simulation where all of the ReaxFF parameters are from quantum mechanical calculations such as density functional theory to provide high accuracy. Accordingly, the ReaxFF simulation provides both accuracy of quantum mechanical calculations and description of large scale systems of atomistic simulations at the same time. Here, I will first discuss a theory in the ReaxFF including the differences from other empirical FFs, and then show several applications for studying chemical reactions of SiHx radicals on Si surfaces, which is an important issue in Si process.

• Proceeding of EDISON Challenge
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• 2014.03a
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• pp.287-299
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• 2014

Bicarbonate anion ($HCO_3{^-}$) takes the role of major buffer systems in our body by maintaining the pH at 7.4. Epithelial $HCO_3{^-}$ secretion also hydrolyzes the mucus which protects body from noxious infections. It has been widely known that such infections are closely related to $HCO_3{^-}$ permeability through membrane and, thus, increasing the $HCO_3{^-}$ permeability is essential. To evaluate the $HCO_3{^-}$ permeability through ion channels, the free energy changes relevant to ion pumping are calculated with the Integral Equation Formalism-PCM (IEF-PCM) theory. Molecular structures of various anions including $HCO_3{^-}$ were optimized with the density functional theory at the level of B3LYP/6-311++G(d,p) in gas and solution phase. In addition, the anion permeability is significantly influenced by the relative size of the anion and pore. We introduce a shifted volume factor model that describes the pore size effect when the charged solutes transfer through ion channels. We found excellent agreement between experimental and calculated permeability when our novel model of the size effect was taken into account to.

• Bulletin of the Korean Chemical Society
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• v.25 no.12
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• pp.1911-1916
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• 2004

The conformational preference of tetrahomodioxacalix[4]arenes with three different para substituents on the phenolic ring has been investigated by using ab initio molecular orbital theory (RHF/6-31$G^{\ast}$) and density functional theory (B3LYP/6-31$G^{\ast}$). The stability order is predicted to be cone > C-1,2-alternate > partial cone > 1,3-alternate > COC-1,2-alternate. The distorted cone conformation is found to be most stable in a gas phase and the calculated results are in agreement with the reported $^1$H NMR and X-ray experimental observations. The substitution of methylene with dimethyleneoxa bridges increases the size of the annulus of the molecule, its conformational mobility, and the number of hydrogen bonding patterns. The thermodynamic stability and the conformational characteristics of tetrahomodioxacalix[4]arenes are discussed in regards of the number of phenolic hydrogen bonding patterns and the polarity of a molecule. The substituent effects on the para position of the phenolic ring are also introduced.

• Bulletin of the Korean Chemical Society
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• v.31 no.4
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• pp.941-948
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• 2010

Ab initio and density functional theory methods have been employed to study all theoretically possible conformers of fluoroacetic acid. Molecular geometries and energetic of cis and trans monomers and cis dimers in gaseous phase have been obtained using HF, B3LYP and MP2 levels of theory, implementing 6-311++G(d,p) basis set. It was found that cis rotamers are more stable. In addition, it was found that in comparison with acetic acid the strength of hydrogen bonding in fluoroacetic acid decreased. The infrared spectrum frequencies and the vibrational frequency shifts are reported. Natural population and atom in molecule analysis performed to predict electrostatic interactions in the cyclic H-bonded complexes and charges. The proton transfer reaction is studied and activation energy is compared with acetic acid proton transfer reaction.

• Journal of the Korean Chemical Society
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• v.57 no.6
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• pp.684-690
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• 2013

Since a glycerol molecule has three active sites, two ${\alpha}$ and one ${\beta}$ hydroxyl groups; it undergoes condensation by releasing water molecules to produce linear, nonlinear and heterocyclic oligomers. The Gibbs free energy (G), enthalpy (H) and internal energy (E) of 7 diglycerol, 15 triglycerol and 23 tetraglycerol isomers were calculated at B3LYP level of theory using 6-311++G(d, p) basis set, in both gas and aqueous phases. Linear oligomers, ${\alpha}{\alpha}$-diglycerol, ${\alpha}{\alpha}$, ${\alpha}{\alpha}$-triglycerol and ${\alpha}{\alpha}$, ${\alpha}{\alpha}$, ${\alpha}{\alpha}$-tetraglycerol, were found to be the most stable oligomers in aqueous phase. It was found that the stability of cyclic oligomers decreases as the size of their rings increases. Cyclic oligomers are produced by dehydration of the acyclic ones which is an endothermic reaction while its ${\Delta}G$ is negative. The dehydration reaction is less endothermic in aqueous phase.

• Bulletin of the Korean Chemical Society
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• v.33 no.5
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• pp.1561-1565
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• 2012

The structures of the four lowest alanine conformers, along with their radical cations and the effect of ionization on the intramolecular proton transfer process, are studied using the density functional theory and MP2 method. The energy order of the radical cations of alanine differs from that of the corresponding neutral conformers due to changes in the basicity of the $NH_2$ group upon ionization. Ionization favors the intramolecular proton transfer process, leading to a proton-transferred radical-cation structure, [$NH_3{^+}-CHCH_3-COO{\bullet}$], which contrasts with the fact that a proton-transferred zwitterionic conformer is not stable for a neutral alanine in the gas phase. The energy barrier during the proton transfer process is calculated to be about 6 kcal/mol.

• Textile Coloration and Finishing
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• v.21 no.5
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• pp.35-40
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• 2009

Computational calculations of molecular orbital and electrochemical redox/oxidation potentials are of very importance to determine the compound properties. The energy levels of molecular orbital were calculated by the density function theory (DFT) with exchange correction functional of local density approximation (LSA) based on the Perdew-Wang (PWC) setting and cyclic voltammetry.

• Proceedings of the Korean Vacuum Society Conference
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• 2014.02a
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• pp.186.1-186.1
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• 2014

Graphene, which is a 2-dimensional carbon material, has been attracting much interest due to its unique properties and potential applications. So far, many interesting experimental and theoretical works have been done concerning the electronic properties of graphene on various substrates. Especially, there are many experimental reports about doping in graphene which is caused by interaction between graphene and its supporting substrates. Here, we report the study of charge transfer between graphene and oxide substrates using density functional theory (DFT) calculations. In this study, we have investigated the charge transfer related with graphene considering various oxide substrates such as SiO2(0001) and MgO(111). Details in charge transfer between graphene and oxides are analyzed in terms of charge density difference, band structure and work function.

• 한국정보디스플레이학회:학술대회논문집
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• 2000.01a
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• pp.35-36
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• 2000

The luminescence behaviors of Yttrium niobate and Bi doped Yttrium niobate were investigated under UV and low voltage electron excitations and interpreted with the first-principle calculations. In the UV excitation and emission spectra of $YNbO_4$ and $YNbO_4:Bi$, we were able to separate host contribution and Bi contribution and found that the shift in emission peak to longer wavelength is mainly due to Bi contribution. Using density functional theory, the cluster calculations were carried out for both $YNbO_4$ and $YNbO_4:Bi$. From the calculated density of states, we were also able to explain the charge transfer gap in the host and the effect of Bi in the excitation and emission spectra theoretically.

• Proceedings of the Korean Vacuum Society Conference
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• 2013.02a
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• pp.269-269
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• 2013

Usingvan der Waals (vdW) energy-corrected density-functional theory without or with self-consistent screening (SCS) effects, we calculate the adsorption energy of acetylene, ethylene and benzene on Si(100). We find that vdW interactions without SCS effects increase the adsorption energy by 0.23, 0.30, and 0.64 eV for adsorbed $C_2H_2$, $C_2H_4$, and $C_6H_6$ on Si(100), respectively. However, if SCS effects are included, this increase of the adsorption energy is reduced as 0.19, 0.24, and 0.54 eV for the three adsorption systems, respectively. The resulting adsorption energy for each system is between the values computed using the local-density approximation and the generalized-gradient approximation.