• Bulletin of the Korean Chemical Society
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• v.23 no.6
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• pp.829-837
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• 2002

Recently it was reported that cycloaddition of 6,6-disubstituted cyclohexa-2,4-dienone, 1 with cyclopentadiene gave solely the adduct of type 1.while its reaction with 1,3-cyclohexadiene gave both Ⅱ and Ⅲ. Semiempirical MO calculations were done to elucidate the origin of the selectivity difference between the two dienes. Cycloaddition of 1 with cyclopentadiene is controlled thermodynamically to give only 1-diene adduct by ΔGvalues of 10.6-20.3 kcal/mol, while its reaction with 1,3-cyclohexadiene does not show 1-diene/1-dienophile selectivity due to similar stabilities of the two adducts. Thermodynamic parameters also show that 두애 adducts are more fabourably fromed in the cycloadditions of 1 with both cyclopentadiene and 1,3-cyclohexadiene, which coincides with experimental observations. Cope rearrangements of endo adducts are another avenue to convert between 1-diene and 1-dienophile.

• Bulletin of the Korean Chemical Society
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• v.12 no.3
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• pp.328-331
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• 1991

Fully optimized MNDO molecular orbital calculations are performed for N-nitroso-azirine (Ⅰ) and-diaziridine (Ⅱ). The ground state geometries show the nonplanar configuration around the imino nitrogen. The nitroso group rotational energy barriers and the ring inversion energy barriers are also discussed.

• Bulletin of the Korean Chemical Society
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• v.15 no.6
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• pp.453-455
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• 1994

Semiempirical MO calculations are applied to estimate the substituent effects on acylations of the nonfused N-vinyl-2-amino $\beta-lactams$ having frameworks analogous to 3-cephems. The stabilization energy for the reaction intermediate of the nucleophilic attack by the hydroxide ion is selected as the reactivity index and calculated by AM1 and PM3 methods for the model $\beta-lactams$ with substituents at the C1 and N-vinyl terminal positions. The reactivities are larger for -SH connected to the C1 and strong $\pi-acceptors$ at the N-vinyl terminal implying the large reactivity for known active cephalosporins. Quantum chemical calculation of stabilization energy could be useful in correlating antibiotic activities of many compounds obtained as derivatives of a lead compound.

• Bulletin of the Korean Chemical Society
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• v.11 no.5
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• pp.422-426
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• 1990

Fully optimized MNDO molecular orbital calculations are described for N-nitroso-aziridine (I), -oxaziridine (II), and -dioxaziridine (III). The ground state geometries show the nonplanar configuration around the imino nitrogen. The nitroso group rotational energy barriers are 3.25, 0.43 and 1.18 kcal/mol for I, II and III, respectively. Also the calculated aziridine ring inversion barriers are 3.98, 15.61 and 27.46 kcal/mol for I, II and III, respectively.

• Bulletin of the Korean Chemical Society
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• v.13 no.2
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• pp.155-157
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• 1992

Extensive search over the energy surface of bicyclo[4.2.2]decapentaene with MMP2 molecular mechanics method and AM1 semiempirical MO method revealed only one, deep energy minimum structure, which corresponds to 1. The alternative structure 2 could not be identified as a stationary point. Although the deviation of benzenoid ring from planarity is large in the energy minimum structure (${\phi} = 26^{\circ}$(MMP2), $37^{circ}$ (AM1)), the bond lengths show no severe alternation.

• Bulletin of the Korean Chemical Society
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• v.17 no.7
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• pp.604-607
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• 1996

Semiempirical PM3 MO calculations are applied to estimate both 1-atom (X=S,O,C) and 3-substituent (Y=R, CH2R, SR, CH2SR) effects on the reactions of some 1-atom-replaced and 3-substituted cephem-like β-lactam compounds of thiacephems, oxacephems, and carbacephems. Stabilization energy (SE) of the reaction intermediate for the reaction with a hydroxyl ion can be used to evaluate the facility of a reaction and selected as a chemical reactivity index. With the 1-atom effect only, the SE values obtained imply that thiacephems are generally more reactive than the other two cephem-like molecules and the reactivity order is thiacephems>oxacephems>carbacephems. When it comes to the 3-substituent (Y=R, CH2R, SR, CH2SR) effect, chemical reactivity can be best realized by using a 3-substituted thiacephem molecule capable of giving a resonance-stabilized and electron-rich leaving group after the reaction with a nucleophile. SE values, however, decrease in most cases when an additional intervening ethylene group is present (Y=CH2R, CH2SR). The overall 3-substituent reactivity tendency is SR>CH2SR>R>CH2R.

• Bulletin of the Korean Chemical Society
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• v.16 no.2
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• pp.112-120
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• 1995

The conformational study on malonic acid, hydrogen malonate, malonate, malonyl methyl sulfide, and malonyl methyl sulfide anion, as the model compounds of malonyl-CoA, was carried out using the semiempirical MO methods (MNDO, AM1, and PM3) and hydration shell model. On the whole, the feasible conformations of malonic acid, hydrogen malonate, and malonate seem to be similar to each other. In malonic acid and malonate, two carboxyl groups are nearly perpendicular to the plane of the carbon skeleton, despite of different orientation of two carboxyl groups themselves. In particular, two carboxyl groups of hydrogen malonate are on the plane formed by carbon atoms with an intramolecular hydrogen bond. The calculated results on the geometry and conformation of three compounds are reasonably consistent with those of X-ray and spectroscopic experiments as well as the previous calculations. The orientation of two carbonyl groups of malonyl methyl sulfide is quite similar to that of malonic acid, but different from that of its anion. Especially, the computed probable conformations of the sulfide anion by the three methods are different from each other. The role of hydration seems not to be crucial in stabilizing the overall conformations of malonic acid, hydrogen malonate, malonate, and malonyl methyl sulfide. However, the probable conformations of the unhydrated sulfide anion obtained by the MNDO and AM1 methods become less stabilized by including hydration. The AM1 method seems to be appropriate for conformational study of malonyl-CoA and its model compounds because it does not result in the formation of too strong hydrogen bonds and significant change in conformational energy from one compound to another.

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2000.11a
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• pp.32-34
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• 2000

Computational chemistry is a discipline using computational methods for the calculation of molecular structure, properties, and reaction or for the simulation of molecular behavior. Relating and turning the complexity of data from genomics, high-throughput screening, combinatorial chemical synthesis, gene-expression investigations, pharmacogenomics, and proteomics into useful information and knowledge is the primary goal of bioinformatics. In particular, the structure-based molecular design is one of essential fields in bioinformatics and it can be called as structural bioinformatics. Therefore, the conformational analysis for proteins and peptides using the techniques of computational chemistry is expected to play a role in structural bioinformatics. There are two major computational methods for conformational analysis of proteins and peptides; one is the molecular orbital (MO) method and the other is the force field (or empirical potential function) method. The MO method can be classified into ab initio and semiempirical methods, which have been applied to relatively small and large molecules, respectively. However, the improvement in computer hardwares and softwares enables us to use the ab initio MO method for relatively larger biomolecules with up to v100 atoms or ∼800 basis functions. In order to show how computational chemistry can be used in structural bioinformatics, 1 will present on (1) cis-trans isomerization of proline dipeptide and its derivatives, (2) positional preference of proline in ${\alpha}$-helices, and (3) conformations and activities of Arg-Gly-Asp-containing tetrapeptides.

• Bulletin of the Korean Chemical Society
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• v.19 no.12
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• pp.1314-1319
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• 1998

Electronic structures and properties of the organometallic precursors [Me2AlNHR]2 (R =Me, iPr, and tBu) have been calculated by the semiempirical (ASED-MO, MNDO, AM1 and PM3) methods. Optimized structures obtained from the MNDO, AM1, and PM3 calculations indicate that the N-C bond lengths are considerably affected by the change of the R groups bonded to nitrogen, but the bond lengths of the Al-N and Al-C bonds are little affected. This result is useful in explaining the experimental results for the elimination of the R groups bonded to nitrogen, and could serve as a guide in designing an optimum precursor for the AlN thin film formation.

• Bulletin of the Korean Chemical Society
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• v.16 no.3
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• pp.252-256
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• 1995

Semiempirical MO calculations using the PM3 method are performed on the reactions of acetate esters with substituted phenolate anions. The mechanistic change from rate-limiting formation to breakdown of the anionic intermediate is shown to occur in the gas-phase, especially for meta-nitrophenyl acetate. However the mechanistic change-over takes place at a lower basicity ($pK_0$) of the anion nucleophile than found for the corresponding formate. This lowering of $pK_0$ has been ascribed to the electron donating effect of the methyl group in the acetate. For the reactions involving rate-limiting breakdown of the intermediate, the large Bronsted coefficients, ${\beta}_X({\beta}_{nuc})$, are expected in general, but the magnitude increases to a larger value and the pK0 is lowered accordingly, when an electron-donating nonleaving group, like $CH_3$, is present. This type of nonleaving group effect provides a necessary condition for the carbonyl addition-elimination mechanism with rate-limiting breakdown of the intermediate.