• Journal of the Korean Chemical Society
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• v.31 no.2
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• pp.133-142
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• 1987

Stereoselectivities of (4+2) cycloaddition reactions of cyclopentadiene with the methyl-substituted allenic acids and esters were investigated by application of $\pi$-nonbonded interaction ($\pi$-NBI) theory. 2-FMO method has been found to be adequate for determination of endo selectivities of diene(LUMO)-dienophile (LUMO) interaction in the thermal reactions and diene (HOMO)-dienophile (LUMO) interaction in the Lewis acid catalyzed reactions. $\pi$-isoconjugate diene structure was formed by through-bond interaction of allene moiety with methyl group in the cumulated diene system; the methyl substituent acts as a conjugative chain and causes inter-level narrowing effect of the FMO's. In dienophiles which do not form $\pi$-isoconjugate diene system, methyl group acts merely as an electron donating group. In thermal reactions, the stereoselectivities are controlled by $\pi$-nonbonded secondary orbital interaction ($\pi$-NSOI) of methyl substituent, which behaves similarly as an ethylene molecule.

• 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.

• Applied Biological Chemistry
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• v.45 no.4
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• pp.223-227
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• 2002

Characteristic stereostructures of farnesyl protein transferase (FPTase) inhibition materials isolated from Artemisia sylvatica and regioselectivity of biogenic Diels-Alder reactions between dehydromatricarin molecules A and B were examined quantitatively. Results revealed that the major reaction of frontier molecular orbital (FMO) interaction proceeds through charge-control reaction between LUMO of A16, dienophile and HOMO of B1, diene, and the isolated 8-acetylarteminolide and artanomaloide were minor products. FPTase inhibition activity and hydrophobicity of 8-acetylarteminolide were $pI_{50}=3.75$ and logP=2.62, respectively. FPTase inhibition activity of 8-acetylarteminolide was higher than those of artanomaloide and dehydromatricarin.

• Analytical Science and Technology
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• v.20 no.4
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• pp.339-346
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• 2007

To search the ninhydrin derivatives that have high chromogenic and fluorogenic properties, molecular holographic quantitative structure property relationship (HQSPR) models on the reactivity between glycine and ninhydrin analogues as latent fingerprint detector were derived and investigated quantitatively. The ${\varepsilon}LUMO$ (e.v.) energy of ninhydrin molecule was an important factor to reactivity of ninhydrin. And, it is suggested that the nucleophilic reaction by orbital-controlled reaction from the frontier molecular orbital (FMO) interaction between glycine and ninhydrin derivatives was more superior than that of electrophilic reaction by charged controlled reaction. The analytical results in atomic contribution maps also shows that the reactivity of ninhydrin was increased by meta-substituents as strong electron withdrawing groups on the benzo ring. Therefore, it is sugested by HQSPR and QSPR model that the 5,6-dinitroninhydrin molecule would increase the reactivity as much as three times as compared to none substituted ninhydrin molecule.

• Bulletin of the Korean Chemical Society
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• v.4 no.5
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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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• v.17 no.11
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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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• v.5 no.2
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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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• v.1 no.1
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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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• v.17 no.9
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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.

• Journal of the Korean Chemical Society
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• v.23 no.5
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• pp.286-295
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• 1979

In order to predict the effect of Lewis acid catalysis on the regioselectivity of the Diels-Alder reactions between unsymmetrically substituted dienes and dienophiles, the frontier orbital theory applied to the theoretical model of the Lewis acid complexed dienophile was studied by means of CNDO/2 MO. In the majority of reactions, CNDO/2 calculations gave good results in accordance with experimental orientation. Also, it was shown that the secondary orbital interaction played an important role in the regioselectivity of the Diels-Alder reaction between unsymmetrically substituted dienes and dienophiles. Although ANH's treatment is mathematically simpler than other methods, ANH's method which laid emphasis on dissymmetrical transition state gave good results on decision of regioselectivity.