• Proceeding of EDISON Challenge
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• 2015.03a
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• pp.6-13
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• 2015

이 연구는 초기 지구의 대기 환경에서 유기화합물(glycine)이 합성되는 실험(Urey-Miller 실험)에서의 반응 경로를 Deterministic한 방법의 중간체 sampling 방법으로 반응 네트워크를 구성하고 Yen's알고리즘으로 네트워크 내의 최단경로를 제시함으로써 반응물과 생성물이 결정되어 있을 때 최소한의 화학적 직관만을 이용하여 제시하는 것이 목표이다. 이 연구 결과는 2014년도 Nature Chemistry에 발표된 다른 방법론을 적용하여 제시된 Urey-Miller reaction path와 비교해 어떠한 반응이 상대적으로 더 타당한 경로를 제시했을지 알아보았다. 이 연구에서 나온 reaction path에서의 중간체들에 대해 GAMESS를 이용한 B3LYP/6-31g(d,p) DFT계산을 수행하였다. 결과를 분석해보면서 어떤 부분이 부족하며 이 연구에 적용한 방법론을 어떻게 발전시켜나가야 더 나은 결과를 얻을 수 있을지를 함께 고려해 보았다.

• 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.

• 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.

• Corrosion Science and Technology
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• v.21 no.1
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• pp.32-40
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• 2022

The o-Vanillin - Glutamine Schiff base [2-Hydroxy-3-Methoxy BenzylidineCarbomyl) -2-Butanoic Acid] was examined for low carbon steel corrosion inhibition in acid media. Weight loss studies were carried out at three different temperatures to determine the inhibition efficiency (IE). Electrochemical impedance spectroscopy revealed that the charge transfer resistance controlled the corrosion reaction and Tafel polarization indicated that the Schiff base acts as mixed mode of inhibitor. SEM images were recorded for the surface morphology of the low carbon steel surface. DFT studies revealed corrosion control mechanisms using quantum chemical parameters such as E_HOMO, E_LUMO, energy gap (∆E), chemical Hardness (η), chemical Softness (σ), Electronegativity (χ), and the fraction of electron transferred (∆N), which is calculated using Gaussian software 09. The gas-phase geometry was fully optimized in the Density Functional Theory (DFT/B3LYP-6-31G (d)).The DFT results are in good agreement with the experimental results. All the results proved that the Schiff Base (2-Hydroxy-3-Metoxy BenzylidineCarbomyl) -2-Butanoic is a suitable alternative for corrosion inhibition of low carbon steel in acid media.

• Bulletin of the Korean Chemical Society
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• v.33 no.2
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• pp.641-646
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• 2012

We used the hybrid density-functional (B3LYP/6-31G(d,p)) method to analyze the substitution patterns of $C_{20}H_{18}X_2$ derivatives (X = F, Cl, Br, or OH) obtained as disubstituted $C_{20}H_{20}$ cages. Our results suggest that the cis-1 regioisomers (1,2-dihalo derivatives) are less stable than the trans-1 regioisomers (1,20-dihalo derivatives), whereas in the case of the dihydroxy derivatives, the cis-1 regioisomer is more stable than the trans-1 regioisomer. This implies that in the dihalo-induced strain cages of $C_{20}H_{18}X_2$, the strain effect would affect the relative energies, while in the dihydroxide, the hydrogen bonds have a stronger effect on the relative energies in cis-1 regioisomer than the strain effect do. Thus this supports the experimental result in which the bisvicinal tetrol was of particular preparative-synthetic interest as a substitute for the lacking bisvicinal tetrabromide. Further, the topologies of the HOMO and LUMO characteristics of all $C_{20}H_{18}Cl_2$ and $C_{20}H_{18}Br_2$ regioisomers with the same symmetry are same, but they are different from those of $C_{20}H_{18}F_2$ and $C_{20}H_{18}(OH)_2$. This indicates that the five regioisomers of each $C_{20}H_{20}$ disubstituted derivative will have an entirely different set of characteristic chemical reactions.

• 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.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.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.

• 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.

• 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.