• Proceedings of the Korean Institute of Building Construction Conference
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• 2021.05a
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• pp.91-92
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• 2021

In the present work, we simulated and explained the bonding of three alkanethiols - hexanethiol (HT), decanethiol (DT), and 11-mercaptoundecanoic acid (MDA) - with Fe(110) surface and Fe2 clusters using Density Functional Theory (DFT) to probe the corrosion inhibition mechanisms. The interaction energies computed from periodic DFT calculations successfully predicted the experimental inhibition performance. We have found strong covalent bond formation between S(thiol) and Fe-atoms in both approaches, further confirmed by the projected density of states and electron density difference. Besides, natural bond orbital (NBO) charge distribution showed that DT had stronger electron-donation and back-donation synergic interactions with Fe-atoms.

• Journal of the Korean Chemical Society
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• v.40 no.4
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• pp.219-228
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• 1996

An ab initio molecular orbital method has been applied to investigation of molecular properties and equilibrium geometries for hexahydroxybenzene triscarbonate (C9O9) and its analogous cyclic compounds (C9S9, C9O6S3, C9O3S6). In these works, the optimized geometry of each compound has been obtained at HF and MP2 levels. These results have shown that the optimized geometries of these compounds prefer D3h planar structure to C3v bowl structure. Calculations of harmonic vibrational frequencies have been also carried out at HF/3-21G* level to analyze normal modes of these compounds. Bonding characters of these compounds are studied by Mulliken and natural populations obtained at HF/6-31G* level. We have also studied the structures and the populations of C6O6 and C6S6 at HF and MP2 levels which are obtained by pyrolyses of C9O9 and analogous compounds. In addition, the single point calculations have been performed to predict the approximate energy barrier for pyrolysis of each compound.

• 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.

• Nuclear Engineering and Technology
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• v.37 no.3
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• pp.293-298
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• 2005

We have performed the density functional theory calculations of $UO_2$ using the spin-polarized generalized gradient approximation (SP-GGA) and the SP-GGA+U approach. The SP-GGA+U approach correctly predicts the insulating electronic structure with antiferromagnetic ordering, but the SP-GGA calculations predict metallic behavior. The cohesive properties obtained from the SP-GGA+U calculations are in good agreement with the available experimental results and previous calculations. The spin-polarized local density of states shows that the antiferromagnetic ordering of $UO_2$ is governed by 5f orbitals of uranium ion. Our calculations demonstrate that the strong correlation of U 5f electrons should be taken into account for a reliable description of $UO_2$ physics.

• Bulletin of the Korean Chemical Society
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• v.34 no.7
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• pp.2051-2055
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• 2013

Existing theoretical calculations predict that infrared spectra of the two most fundamental reactive carbo-ions, methyl cation $CH{_3}^+$ with $D_{3h}$ symmetry and protonated methyl cation $CH{_5}^+$ with $C_s(I)$, $C_s(II)$, and $C_{2v}$ symmetries, appear together in the 7-${\mu}m$ region corresponding to the C-H bending modes. Vibrational band profiles of $CH{_3}^+$ and $CH{_5}^+$ have been compared by ab initio calculation methods that use the basis sets of MP2/aug-cc-pVTZ and CCSD(T)/cc-pVTZ. Our results indicate that the bands of rotation-vibration transitions of $CH{_3}^+$ and $CH{_5}^+$ should overlap not only in the 3-${\mu}m$ region corresponding to the C-H stretching modes but also in the 7-${\mu}m$ region corresponding to the C-H bending modes. Five band intensities of $CH{_5}^+$ among fifteen vibrational transitions between 6 and 8 ${\mu}m$ region are stronger than those of the ${\nu}_2$ and ${\nu}_4$ bands in $CH{_3}^+$. Ultimate near degeneracy of the two bending vibrations ${\nu}_2$ and ${\nu}_4$ of $CH{_3}^+$along with the stronger intensities of $CH{_5}^+$ in the three hydrogen scrambling structures may cause extreme complications in the analysis of the high-resolution carbo-ion spectra in the 7-${\mu}m$ region.

• Interdisciplinary Bio Central
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• v.2 no.2
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• pp.6.1-6.5
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• 2010

Fragment molecular orbital (FMO) method provides a novel tool for ab initio calculations of large biomolecules. This method overcomes the size limitation difficulties in conventional molecular orbital methods and has several advantages compared to classical force field approaches. While there are many features in this method, we here focus on explaining the issues related to protein-ligand binding: FMO method provides useful interaction-analysis tools such as IFIE, CAFI and FILM. FMO calculations can provide not only binding energies, which are well correlated with experimental binding affinity, but also QSAR descriptors. In addition, FMO-derived charges improve the descriptions of electrostatic properties and the correlations between docking scores and experimental binding affinities. These calculations can be performed by the ABINIT-MPX program and the calculation results can be visualized by its proper BioStation Viewer. The acceleration of FMO calculations on various computer facilities is ongoing, and we are also developing methods to deal with cytochrome P450, which belongs to the family of drug metabolic enzymes.

• Coupled systems mechanics
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• v.6 no.1
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• pp.75-96
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• 2017

As electron donor/acceptor materials for organic photovoltaic cells, small-molecules donors/acceptor are attracting more and more attention. In this work, we investigated the electronic structures, electrochemical properties, and charge carrier transport properties of four recently-synthesized small-molecule donors/acceptor, namely, DPDCPB (A), DPDCTB (B), DTDCPB (A1), and DTDCTB (B1), by a series of ab initio calculations. The calculations look into the electronic structure of singly oxidized and reduced molecules, the first anodic and cathodic potentials, and the electrochemical gaps. Results of our calculations were in accord with those from experiments. Using Marcus theory, we also computed the reorganization energies of hole/electron hoppings, as well as hole/electron transfer integrals of multiple possible molecular dimer configurations. Our calculations indicated that the electron/hole transport properties are very sensitive to the relative separations/orientations between neighboring molecules. Due to high reorganization energies for electron hopping, the hole mobilities in the molecular crystals are at least an order of magnitude higher than the electron mobilities.

• Bulletin of the Korean Chemical Society
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• v.27 no.9
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• pp.1297-1304
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• 2006

A systematic study of the structure, energetics and spectral characteristics of substituted aminoketenes $R(NH_2)$C=C=O (R = H, $CH_3$, $NH_2$, OH, $OCH_3$, CH=$CH_2$, C$\equiv$CH, CN, CHO, NO, $NO_2$) which are highly reactive and transient intermediates in synthesis has been conducted by ab initio calculations at the MP2/6- 31G*//MP2/6-31G* level. Twenty four stable isomers of the eleven substituted aminoketenes having dihedral angles $\phi NH_2\sim120{^{\circ}}$ and $60^{\circ}$ have been identified and their optimized geometries and energies obtained. Electrostatic and steric effects on the molecular geometries have been analyzed. While the $\pi$-acceptor groups lead to planar conformations, the electron-donor groups give rise to non-planar conformations. Isodesmic substituent stabilization energies relative to alkenes have been calculated and correlation with group electronegativities established. Role of induction effect by the substituent groups and resonance effects in charge distribution in the molecules has been analyzed. An analysis of the asymmetric stretching frequencies and intensities of the C=C=O group shows that affect of non-$\pi$ acceptor substituents on the frequency is determined by the field effect (F) and resonance effect (R) parameters, the calculated intensities I (km/mol.) are correlated to group electronegativities $x$ of the substituents by the relationship I = 640.2–100.1 $x$ (r = 0.92). The $\pi$-acceptor substituents increase the intensity which may be explained in terms of their delocalizing effect on the negative charge at the $C_{\beta}$ atom.

• Bulletin of the Korean Chemical Society
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• v.35 no.6
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• pp.1851-1854
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• 2014

• Bulletin of the Korean Chemical Society
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• v.31 no.9
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• pp.2527-2530
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• 2010

The stereoselectivity of the intramolecular Diels-Alder reactions of 1 and its derivatives were investigated by ab initio calculations. The stereoselectivity mainly originates from the steric repulsion and the orbital interactions. The additional s-cis and s-trans conformations by introducing the carbonyl group at the neighbor of diene or dienophile may change the stereoselectivity, hence this kind of substitution can be utilized for stereoselectivive asymmetric synthesis.