• Bulletin of the Korean Chemical Society
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• v.32 no.12
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• pp.4341-4346
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• 2011

Impact sensitivity, one of the most important screening factors for novel high energy density materials (HEDMs), was predicted by use of quantitative structure-property relationship (QSPR) based on the electrostatic potential (ESP) values calculated on the van der Waals molecular surface (MSEP). Among various 3D descriptors derived from MSEP, we utilized total and positive variance of MSEP, and devised a new QSPR equation by combining three other parameters. We employed 37 HEDMs bearing a benzene scaffold and nitro substituents, which were also utilized by Rice and Hare. All the molecular structures were optimized at the B3LYP/6-31G(d) level of theory and confirmed as minima by the frequency calculations. Our new QSPR equation provided a good result to predict the impact sensitivities of the molecules in the training set including zwitterionic molecules.

• Bulletin of the Korean Chemical Society
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• v.34 no.4
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• pp.1043-1046
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• 2013

Prediction of physicochemical properties of organic molecules is an important process in chemistry and chemical engineering. The MSEP approach developed in our lab calculates the molecular surface electrostatic potential (ESP) on van der Waals (vdW) surfaces of molecules. This approach includes geometry optimization and frequency calculation using hybrid density functional theory, B3LYP, at the 6-31G(d) basis set to find minima on the potential energy surface, and is known to give satisfactory QSPR results for various properties of organic molecules. However, this MSEP method is not applicable to screen large database because geometry optimization and frequency calculation require considerable computing time. To develop a fast but yet reliable approach, we have re-examined our previous work on organic molecules using two semi-empirical methods, AM1 and PM3. This new approach can be an efficient protocol in designing new molecules with improved properties.

• Bulletin of the Korean Chemical Society
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• v.29 no.7
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• pp.1335-1343
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• 2008

Theoretical studies on the un-catalyzed and catalyzed aminations of ketene with $NH_3$ and $(NH_3)_2$, respectively, were studied using MP2 and hybrid density functional theory of B3LYP at the 6-31+G(d,p) and 6- 311+G(3df,2p) basis sets in the gas phase and in benzene and acetonitrile solvents. In the gas phase reaction, the un-catalyzed mechanism was the same as those previously reported by others. The catalyzed mechanism, however, was more complicated than expected requiring three transition states for the complete description of the C=O addition pathways. In the un-catalyzed amination, rate determining step was the breakdown of enol amide but in the catalyzed reaction, it was changed to the formation of enol amide, which was contradictory to the previous findings. Starting from the gas-phase structures, all structures were re-optimized using the CPCM method in solvent medium. In a high dielectric medium, acetonitrile, a zwitterions formed from the reaction of $CH_2$=C=O with $(NH_3)_2$, I(d), exists as a genuine minimum but other zwitterions, I(m) in acetonitrile and I(d) in benzene become unstable when ZPE corrected energies are used. Structural and energetic changes induced by solvation were considered in detail. Lowering of the activation energy by introducing additional $NH_3$ molecule amounted to ca. −20 $\sim$ −25 kcal/mol, which made catalyzed reaction more facile than un-catalyzed one.

• Bulletin of the Korean Chemical Society
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• v.30 no.3
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• pp.556-560
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• 2009

Aggregation behavior of three kinds of benzindocarbocyanine dyes in aqueous methanol solution was studied by UV-Vis absorption spectrum. The results indicated that the three dyes all existed monomer-dimer equilibrium in aqueous methanol solution (concentration range $10^{−5}\;to\;10^{−6}$ M) at 25.0$\sim$41.0 ${^{\circ}C}$ for Dye 1, 28.0$\sim$49.0 ${^{\circ}C}$ for Dye 2 and 26.0$\sim$47.0 ${^{\circ}C}$ for Dye 3. The fundamental property of the three dyes as the dimeric association constant KD, the dimeric free energy ${\Delta$}G_D, the dimeric entropy ${\Delta$}S_D, and the dimeric enthalpy ${\Delta$}H_D were determined. The ${\Delta$}H_D of three dyes: Dye 1, Dye 2 and Dye 3 was -42.5, -15.1 and -18.9 kJ/mol, respectively. The experimental observations were the subject of a theoretical study including the ground-state geometries which were fully optimized using DFT at B3LYP/6-31G level. The effect of dye molecule structure on ${\Delta$}H_D was discussed by theoretical calculations.

• Bulletin of the Korean Chemical Society
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• v.23 no.2
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• pp.201-204
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• 2002

The rates of the aminolysis of S-phenyl substituted-acetate series $(RC(=O)SC_6H_4Z$, with R=Me, Et, i-Pr, t-Bu and Bn) with benzylamines $(XC_6H_4CH_2NH_2)$ are not correlated simply with the Taft's polar $({\sigma}^{\ast})$ and/or steric effect constants $(E_s)$ of the substituents due to abnormally enhanced rate of the substrate with R=Et. Furthermore, the cross-interaction constant, ${\rho}x_z$ , is the largest with R=Et. These anomalous behaviors can only be explained by invoking the vicinal bond $({\sigma})$-antibond $({\sigma}^{\ast})$ charge transfer interaction between C-$C{\alpha}$ and C-S bonds. In the tetrahedral zwitterionic intermediate, $T^{\pm}$ , formed with R=Et the vicinal ${\sigma}_{c-c}-{\sigma}^{\ast}_{c-s}$ delocalization is the strongest with an optimum antiperiplanar arrangement and a narrow energy gap, ${\Delta}{\varepsilon}={\varepsilon}_{{\sigma}^{\ast}}-{\varepsilon}_{\sigma}$. Due to this charge transfer interaction, the stability of the intermediate increases (with the concomitant increase in the equilibrium constant K (= $k_a/k_{-a}$)) and also the leaving ability of the thiophenolate leaving group increases (and hence $k_b$ increases) so that the overall rate, $k_n\;=\;Kk_b$, is strongly enhanced. Theoretical support is provided by the natural bond orbital (NBO) analyses at the B3LYP/6-31+$G^{\ast}$ level. The anomaly exhibited by R=Et attests to the stepwise reaction mechanism in which the leaving group departure is rate limiting.

• Journal of the Korean Magnetic Resonance Society
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• v.21 no.4
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• pp.139-144
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• 2017

Ni(II) containing coenzyme F430 catalyzes the reduction of $CO_2$ in methanogen. Macrocyclic Ni(II) complexes with N,O shiff bases have been received a great attention since metal ions play an important role in the catalysis of reduction. The reducing power of metal complexes are supposed to be dependent on oxidoreduction state of metal ion and structural properties of macrocyclic ring moiety that can enhance electrochemical properties in catalytic process. Six different ${\alpha}$-oximinoketone compounds, precursor of macrocyclic ligands used in $CO_2$ reduction coenzyme F430 model complexes, were synthesized with yields over 90% and characterized by NMR. The molecular geometries of ${\alpha}$-oximinoketone analogues were fully optimized at Beck's-three-parameter hybrid (B3LYP) method in density functional theory (DFT) method with $6-31+G^*$ basis set using the ab initio program. In order to understand molecular planarity and substitutional effects that may enhance reducing power of metal ion are studied by computing the structure-dependent $^{13}C$-NMR chemical shift and comparing with experimental results.

• Proceeding of EDISON Challenge
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• 2014.03a
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• pp.1-13
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• 2014

Potential Energy Surface(PES)를 양자 계산을 통해 알아내는 것은 화학 반응을 이해하는 데에 큰 도움이 된다. 이를테면 Transition State(TS)의 configuration을 알 수 있고, 따라서 reaction path와 활성화 에너지 값을 예측하여, 진행시키고자 하는 화학반응의 이해를 도울 수 있다. 하지만 PES를 그리기 위해서는 해당 분자의 다양한 configuration에 대한 singlet point energy 계산이 필요하기 때문에, 계산적인 측면에서 많은 비용을 요구한다. 따라서 product와 reactant의 구조와 같은 critical point의 정보를 이용하여 최소한의 configuration을 sampling하여 전체 PES를 재구성하는 기계학습 알고리즘을 개발하여 다차원 PES 상에서의 화학반응의 예측을 가능하게 하고자 한다. 본 연구에서는 Barbaralane의 두 안정화 된 구조의 critical point로 하여 이 주변을 random normal distribution하여, B3LYP/6-31G(d) level의 DFT 계산을 통해 relaxed scanning하여 구조와 에너지를 구하였으며, 이 정보를 Support Vector Regression(SVR) 알고리즘을 적용하여 PES를 재구현하였으며, 반응경로와 TS의 구조 그리고 활성화 에너지를 구하였다. 또한 본 기계학습 알고리즘을 바닥상태에서 일어나는 반응이 아닌, 들뜬 상태와 전자 구조가 변하는 화학반응, avoid crossing, conical intersection과 같은 Non-adiabatic frame에서 일어나는 현상에 적용 가능성을 논하고자 한다.

• Proceeding of EDISON Challenge
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• 2015.03a
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• pp.151-155
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• 2015

The molecular interactions between the nucleic acid bases and water molecules are important in organism. Despite Adenine-Thymine Hoogsteen base pair and Guanine-Cytosine Watson-Crick base pair have been demonstrated to be most stable in a gas phase, the effect of water on the stability of these base pairs remains elusive. Here we report the structural and thermodynamic characteristics on possible Adenine-Thymine and Guanine-Cytosine base pairs in a gas phase as well as in an aqueous phase by using quantum mechanical method and statistical mechanical calculations. First, we optimized the direct base-pair interaction energies of four Adenine-Thymine base pairs (Hoogsteen base pair, reverse Hoogsteen base pair, Watson-Crick base pair, and reverse Watson-Crick base pair) and three Guanine-Cytosine base pairs (GC1 base pair, GC2 base pair, and Watson Crick base pair) in a gas phase at the $B3LYP/6-31+G^{**}$ level. Then, the effect of solvent was quantified by the electronic reorganization energy and the solvation free energy by statistical mechanical calculations. Thereby, we discuss the effect of water on the stability of Adenine-Thymine and Guanine-Cytosine base pairs, and argue why Adenine-Thymine Watson-Crick base pair and Guanine-Cytosine Watson-Crick base pair are most stable in an aqueous environment.

• Bulletin of the Korean Chemical Society
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• v.34 no.11
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• pp.3211-3217
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• 2013

Density functional theory (DFT) and time-dependent DFT (TD-DFT) calculations have been employed to investigate the molecular structures and absorption spectra of three D-${\pi}$-A-type organic dyes (C1-1, D5 and TH208) containing identical ${\pi}$-spacers and electron acceptors, but different aromatic amine electron-donating groups (tetrahydroquinoline, triphenylamine and phenothiazine). The coplanar geometries indicate that the strong conjugation is formed in the dyes. The electronic structures suggest that the intramolecular charge transfer from the donor to the acceptor occurs, and the electron-donating ability of tetrahydroquinoline is stronger than those of triphenylamine and phenothiazine. The computed orbital energy levels of these dyes confirm that the electrons could be injected from the excited dyes to the semiconductor conduction band and the oxidized dyes could be reduced effectively by electrolyte. The TD-DFT results show that the CAM-B3LYP/6-31+G(d, p) is suitable for calculating the absorption spectra. The first absorption band for these dyes is assigned to the HOMO${\rightarrow}$LUMO and HOMO-1${\rightarrow}$LUMO transitions.

• Journal of the Korean Chemical Society
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• v.57 no.5
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• pp.574-590
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• 2013

A new solid complexes of Ti(IV), Y(III) and Ce(IV) have been synthesized with ofloxacin. The formulae and structure of the complexes have been proposed in the light of analytical, spectral ($^1H$ NMR, IR and UV-Visible), magnetic, molar conductivities and thermal studies. The complexes are soluble in DMSO-$d_6$ and DMF. The measured molar conductance values indicate that, the three complexes are electrolyte in nature. The results support the formation of the complexes and indicated that ofloxacin reacts as a bidentate ligand chelate to the metal ion through the pyridone oxygen and one carboxylato oxygen. The kinetic parameters of thermogravimetric and its differential have been evaluated by using Coats Redfern (CR) and Horowitz-Metzeger (HM) methods. The thermodynamic data reflect the thermal stability for all complexes. The metal- ligand binding of the Ti(IV), Y(III) and Ce(IV) complexes is predicted using density funcational theory at the B3LYP-CEP-31G level of theory and total energy, dipole moment estimation of different Ti(IV), Y(III) and Ce(IV) ofloxacin structures. The biological activities of the ofloxacin, inorganic salts and their metal complexes were assayed against different bacterial species.