• Journal of the Korean Chemical Society
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• v.47 no.4
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• pp.325-333
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• 2003

The geometrical parameters, vibrational frequencies, and relative energies for 1,2-, 1,3-dioxetanes, and 1,3-cyclodisiloxane have been investigated using high level ab initio quantum mechanical techniques with large basis sets. The geometries have been optimized at the self-consistent field(SCF), the single and double excitation configuration interaction(CISD), the coupled cluster with single and double excitation(CCSD), and the CCSD with connected triple excitations[CCSD(T)] levels of theory. The highest level of theory employed in this study is TZ2P CCSD(T). Harmonic vibrational frequencies and IR intensities are also determined at the SCF level of theory with various basis sets and confirm that all the optimized geometries are true minima. Also zero-point vibrational energies have been considered to predict the dimerization energies for 1,2- and 1,3-isomers.

• 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.35 no.3
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• pp.839-844
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• 2014

The gas-phase radical-radical reaction $O(^3P)$ + $C_2H_5$ (ethyl) ${\rightarrow}$ $H(^2S)$ + $CH_3CHO$(acetaldehyde) was investigated by applying a combination of vacuum-ultraviolet laser-induced fluorescence spectroscopy in a crossed beam configuration and ab initio calculations. The two radical reactants $O(^3P)$ and $C_2H_5$ were respectively produced by photolysis of $NO_2$ and supersonic flash pyrolysis of the synthesized precursor azoethane. Doppler profile analysis of the nascent H-atom products in the Lyman-${\alpha}$ region revealed that the average translational energy of the products and the average fraction of the total available energy released as translational energy were $5.01{\pm}0.72kcalmol^{-1}$ and 6.1%, respectively. The empirical data combined with CBS-QB3 level ab initio theory and statistical calculations demonstrated that the title exchange reaction is a major channel and proceeds via an addition-elimination mechanism through the formation of a short-lived, dynamical addition complex on the doublet potential energy surface. On the basis of systematic comparison with several exchange reactions of hydrocarbon radicals, the observed small kinetic energy release can be explained in terms of the loose transition state with a product-like geometry and a small reverse activation barrier along the reaction coordinate.

• Journal of the Korean Chemical Society
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• v.45 no.5
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• pp.401-412
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• 2001

The geometrical parameters, vibrational frequencies, and dissociation energies for $H_{2n+1}^+$ (n=1~6) clusters have been investigated using high level ab initio quantum mechanical techniques with large basis sets. The equilibrium geometries have been optimized at the self-consistent field (SCF), the single and double excitation configuration interaction (CISD), the coupled cluster with single and double excitation (CCSD), and the CCSD with connected triple excitations [CCSD(T)] levels of theory. The highest levels of theory employed in this study are TZ2P+d CCSD(T) up to $H^+_g$ and TZ2P CCSD(T) for $H_{11}^+$ and $H_{13}^+$. Harmonic vibrational frequencies are also determined at the SCF level of theory with various basis sets and confirm that all the optimized geometries are true minima. The dissociation energies, $D_e$, for $H_{2n+1}^+$ (n=26) have been predicted using energy differences at each optimized geometry and zero-point vibrational energies(ZPVEs) have been considered to compare with experimental dissociation energies, $D_0$.

• Proceedings of the Korean Vacuum Society Conference
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• 2011.02a
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• pp.428-429
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• 2011

Recently, we performed ab initio total energy calculation and tight-binding molecular dynamics (TBMD) simulation to study structures and the reconstruction of native defects in graphene. In the previous study, we predicted by TBMD simulation that a double vacancy in graphene is reconstructed into a 555-777 composed of triple pentagons and triple heptagons [1]. The structural change from pentagon-octagon-pentagon (5-8-5) to 555-777 has been confirmed by recent experiments [2,3] and the detail of the reconstruction process is carefully studied by ab initio calculation. Pentagon-heptagon (5-7) pairs are also found to play an important role in the reconstruction of vacancy in graphene and single wall carbon nanotube [4]. In the TBMD simulation of graphene nanoribbon (GNR), we found the evaporation of carbon atoms from both the zigzag and armchair edges is preceded by the formation of heptagon rings, which serve as a gateway for carbon atoms to escape. In the simulation for a GNR armchair-zigzag-armchair junction, carbon atoms are evaporated row-by-row from the outermost row of the zigzag edge [5], which is in excellent agreement with recent experiments [2, 6]. We also present the recent results on the formation and development of dislocation in graphene. It is found that the coalescence of 5-7 pairs with vacancy defects develops dislocation in graphene and induces the separation of two 5-7 pairs. Our TBMD simulations also show that adatoms are ejected and evaporated from graphene surface due to large strain around 5-7 pairs. It is observed that an adatom wanders on the graphene surface and helps non-hexagonal rings change into stable hexagonal rings before its evaporation.

• Journal of the Korean Electrochemical Society
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• v.5 no.4
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• pp.183-188
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• 2002

The structure of species formed in $NbCI_5-I-ethyl-3-methylimidazolium$ chloride (EMIC) room-temperature molten salt (RTMS) was examined with the Raman spectroscopic measurement and ab initio molecular orbital calculation. The equilibrium structures of $NbCl_5,\;NbCl_6^-,\;Nb_2CI_{10},\;Nb_2CI_{11}^-,\;Nb_3CI_6^-,\;NbCI_6^--EMI^+\;(in\;which\;NbCI_6^-$ anion approaches $EMI^+$ cation with strong interaction) and $Nb_2CI_{11}^--EMI^+$ were obtained with the HF/LANL2DZ level of calculation. The harmonic frequencies at each equilibrium structure were compared with Raman spectra. The harmonic frequencies of $NbCI_6^--EMI^+,\; Nb_2CI_{11}^--EMI^+,\;and\;Nb_2CI_{10}$ were in good agreement with the Raman spectra of RTMS melts. In the $NbCI_5-EMIC RTMS$, the main species were $NbCI_6^-\;and\;EMI^+$. In the $NbCl_5-EMIC$ RTMS added $NbCl_5\;over\;50mol\%$, small amount of $Nb_2CI_{11}^-\;and\; Nb_2CI_{10}$ were also formed. The structures of anions and cation in the RTMS distorted from free ions with Coulomb force.

• 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.

• Journal of the Korean Chemical Society
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• v.49 no.1
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• pp.16-28
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• 2005

• Bulletin of the Korean Chemical Society
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• v.29 no.6
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• pp.1269-1272
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• 2008