• 대한화학회지
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• 제31권2호
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• pp.133-142
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• 1987

시클로로펜타디엔과 메틸기로 치환된 알렌의 산 및 에스테르간의 (4+2)고리화반응에서 입체 선택성을 $\pi$-비결합상호작용($\pi$-NBI)을 적용하여 고찰하였다. 열반응에서는 diene(LUMO)-dienophile (HOMO)만을 고려한 2-FMO방법이, 산촉매반응에서는 diene (HOMO)-dienophile (LUMO)상호작용만을 고려한 2-FMO방법이 이들의 입체선택성의 결정에 중요하였다. cumulated diene계의 친디엔체에서 메틸 치환기는 알렌구조와 through-bond 상호작용에 의해 $\pi$-isoconjugate diene 구조를 형성하여 컨쥬게이션기로 작용하며 FMO의 에너지에 narrowing effect를 주고 있으나 이같은 $\pi$-isoconjugated diene 구조를 만들 수 없는 친디엔체에서는 메틸기가 단순히 전자주는기로 작용한다. 열반응에서 입체선택성은 에틸렌 분자와 마찬가지로 메틸 치환기의 $\pi$-비결합 2차궤도 상호작용($\pi$-NSOI)에 의해서 좌우되었다.

• Interdisciplinary Bio Central
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• 제2권2호
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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.

• Applied Biological Chemistry
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• 제45권4호
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• pp.223-227
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• 2002

그늘쑥(Artemisia sylvatica Max.)으로부터 분리된 sesquiterpene lactone계 화합물들의 구조적인 특성과 FPTase 저해활성을 나타내는 dehydromatricarin A, B 분자들 사이 biogenic Diels-Alder 반응의 경계분자 궤도함수 (FMO)상호작용에 대한 배향성을 검토하였다. 그 결과, 주 생성물이 얻어지는 반응은 B1(diene)의 HOMO와 A16(dienophile)의 LUMO간 hard-hard한 charge-control 반응이었다. 그리고 AO계수 분극간의 상호작용에 따른 배향성은 분리된 8-acetylarteminolide와 artanomaloide들이 모두 biogenic Diels-Alder 반응의 부 생성물들임을 시사하였다. 또한, 8-acetyl-arteminolide의 FPTase 저해활성($pI_{50}=3.75$ 및 logP=2.62)은 큰 반면에 artanomaloide 및 dehydromatricarin은 작았다.

• 분석과학
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• 제20권4호
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• pp.339-346
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• 2007

높은 염색성과 형광성을 나타내는 ninhydrin 유도체를 탐색하기 위하여 잠재지문 검출제로서 ninhydrin 유도체들과 glycine 분자와의 반응성에 관한 분자 홀로그래피적인 HQSPR 모델을 유도하고 정량적으로 검토하였다. Ninhydrin의 반응성은 ${\varepsilon}LUMO$ 에너지가 중요한 요인이었으며, ninhydrin 유도체들과 glycine 분자 사이의 경계분자궤도(FMO) 상호작용으로부터 궤도조절반응에 의한 친핵성 반응이 전하조절반응에 의한 친전자성 반응보다 우세하였다. 기여도 분석결과, benzo 고리상 강한 전자끌게로서 meta-치환체가 ninhydrin의 반응성을 증가시켰으며 HQSPR 및 QSPR 모델에 의하여 5,6-dinitroninhydrin 분자는 비 치환체보다 3배 이상의 반응성을 향상시킬것으로 예측되었다.

• Bulletin of the Korean Chemical Society
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• 제4권5호
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• pp.197-200
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• 1983

The Diels-Alder cycloaddition reactions between dienes and allenic ketones were studied theoretically using CNDO/2 method. It was found that the reaction is a neutral electron demand type with matrix element control and the reactivity, the regio- and stereo-selectivities can be correctly predicted based on interaction energies calculated with the 4-center FMO formalism.

• Journal of Microbiology and Biotechnology
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• 제17권11호
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• pp.1789-1796
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• 2007

A ${\beta}$-glucosidase with the molecular mass of 160,000 Da was purified to homogeneity from cell extract of a cellulolytic bacterium, Cellulomonas uda CS1-1. The kinetic parameters ($K_m$ and $V_{max}$) of the enzyme were determined with pNP-cellooligosccharides (DP 1-5) and cellobiose. The molecular orbital theoretical studies on the cellulolytic reactivity between the pNP-cellooligosaccharides as substrate (S) molecules and the purified ${\beta}$-glucosidase (E) were conducted by applying the frontier molecular orbital (FMO) interaction theory. The results of the FMO interaction between E and S molecules verified that the first stage of the reaction was induced by exocyclic cleavage, which occurred in an electrophilic reaction based on a strong charge-controlled reaction between the highest occupied molecular orbital (HOMO) energy of the S molecule and the lowest occupied molecular orbital (LUMO) energy of the hydronium ion ($H_3O^+$), more than endocyclic cleavage, whereas a nucleophilic substitution reaction was induced by an orbital-controlled reaction between the LUMO energy of the oxonium ion ($SH^+$) protonated to the S molecule and the HOMO energy of the $H_2O_2$ molecule. A hypothetic reaction route was proposed with the experimental results in which the enzymatic acid-catalyst hydrolysis reaction of E and S molecules would be progressed via $SN_1$ and $SN_2$ reactions. In addition, the quantitative structure-activity relationships (QSARs) between these kinetic parameters showed that $K_m$ has a significant correlation with hydrophobicity (logP), and specific activity has with dipole moment, respectively.

• Bulletin of the Korean Chemical Society
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• 제5권2호
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• pp.68-73
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• 1984

An enhancement of through-bond interaction by bond angle distortion in pyrazine was examined using various MO methods. Results of MINDO/3 geometry optimization with an angle (${\alpha}$) at $C_2$ atom fixed to 120∼90$^{\circ}$ lead to distorted structures in which the distorted bond is brought closer toward lone pair orbital n of N atom. It was also found that the bond angle distortion increased the P character at the atom $C_2$, resulting in an increased vicinal overlap between n and the $C_2-C_3$ bond. The FMO patterns of ${\sigma}$ framework showed three-fold degeneracy, one of which was of different symmetry which mixes in the symmetry adapted pair, $n_+\;and\;n_-;\;both\;n_+\;and\;n_-$ orbitals thus can interact with both FMOs of the ${\sigma}$ framework. The LCBO-MO analysis with partial elimination of bonds, antibonds or both, however, revealed that the main interaction of $n_+$ was with the HO-${\sigma}$ and that of $n_-$ was with the LU-${\sigma}^{\ast}$ orbital of the ${\sigma}$ framework.

• Bulletin of the Korean Chemical Society
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• 제1권1호
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• pp.4-10
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• 1980

Simple rules for predicting nonbonded interactions have been proposed. It was found that an end-to-end nonbonded interaction is either attractive or repulsive depending on the sign of the product of AO coefficients of two end atoms in the HOMO of a closed shell conjugated system with a crowded structure. The nonbonded attraction becomes the greatest in a 4N + 2 electron conjugated system, while it is repulsive in a 4N electron system. For 4N + 1 and 4N - 1 electron systems, it is attractive but the effect is less than that in 4N + 2 system. As a result of the attractive interaction, the overlap population of an atom pair increases (decreases) if the HOMO is antibonding (bonding) for the atom pair. The rules were illustrated with some examples.

• Bulletin of the Korean Chemical Society
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• 제17권9호
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• pp.849-853
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• 1996

Hetero Dieis-Alder reactions containing phosphorus atom at various positions of diene and dienophile as well as standard Dieis-Alder reaction between ethylene and cis-l,3-butadiene have been studied using ab initio method. Activation energy showed a good linear relationship with the FMO energy gap between diene and dienophile, which can be normally used to explain Dieis-Alder reactivity. Since π-bond cleavage and σ-bonds formation occur concertedly at the TS, geometrical distortion of diene and dienophile from the reactant to the transition state is the source of barrier. Based on the linear correlations between activation barrier and deformation energy, and between deformation energy and π-bond order change, it was concluded that the activation barrier arises mainly from the breakage of π-bonds in diene and dienophile. Stabilization due to favorable orbital interaction is relatively small. The geometrical distortions raise MO levels of the TS, which is the origin of the activation energy. The lower barrier for the reactions of phosphorus containing dienophile (reactions C, D, and E) can be explained by the electronegativity effect of the phosphorus atom.

• 대한화학회지
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• 제23권5호
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• pp.286-295
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• 1979

非對稱으로 置環된 diene과 dienophile 間의 反應에서 配向性에 미치는 산촉매의 효과를 豫期하기 위해서 루이스酸과 錯物을 形成한 dienophile의 理論的모델에 FMO 理論을 적용하여CNDO/2 방법으로 고찰하였다. 電子的性質이 類似한 치환기로 치환된 diene, dienophile의 반응(즉, 電子不足 diene과 電子不足 dienophile의 반응)에서 일어나는 半極性 고리化반응을 제외한 주어진 대부분의 반응에 대해서, CNDO/2방법이 실험적인 配向性과 一致하는 좋은 결과를 주었다. 또한 二次軌道相互作用이 非對稱으로 치환된 diene과 dienophile의 Diels-Alder 반응의 배향성에 중요한 역할을 했다는 사실을 보여주었다. Anh의 방법이 다른 방법보다 수식적으로 간단할지라도, 非對稱전이상태를 강조한 Anh의 방법이 配向性 결정에 좋은 결과를 주었다.