• Bulletin of the Korean Chemical Society
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• v.11 no.1
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• pp.34-41
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• 1990

The second order ab initio effective valence shell Hamiltonian is calculated for the valence state potential energy curves of NH and $NH^+$. From the potential energy curves various spectroscopic constants of valence states are determined. The results are in good agreement with experiments and configuration interaction calculations. They show the composite picture of potential energy curves and also indicate that the second order effective Hamiltonian theory is adequate for describing various valence states of a molecule and its ions simultaneously.

• Bulletin of the Korean Chemical Society
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• v.10 no.6
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• pp.488-491
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• 1989

Theoretical studies on the proton transfer reaction in a formamide dimer have been done by Ab initio SCF calculation. In this study, we have shown several effects on the potential energy profile of the proton transfer in a formamide dimer, such as the effect of a basis set, the effect of a geometry optimization, and the effect of a distance between proton-donor and proton-acceptor.

• Proceedings of the Korean Magnestics Society Conference
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• 2008.12a
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• pp.273.2-273.2
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• 2008

• Bulletin of the Korean Chemical Society
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• v.7 no.3
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• pp.218-224
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• 1986

The electronic structures of silane and chlorosilanes are studied by the SCF calculations using effective core potentials (ECP's). The results obtained with ECP's are in good agreement with corresponding all electron calculations demonstrating the reliability of ECP employed. The importance of polarization functions for the second row atoms is also evident in this study. The SCF calculations of silane and chlorosilanes are useful in qualitative understanding of many chemical properties since many trends are correctly obtained with the polarization functions included in basis sets of reasonable size.

• Proceedings of the PSK Conference
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• 2003.10b
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• pp.158.1-158.1
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• 2003

We report here the results on N-acetyl-N"-methylamide of oxazolidine (Ac-Oxa-NHMe) calculated using the ab initio molecular orbital method with the self-consistent reaction field (SCRF) theory at the HF level of theory with the 6-31 +G(d) basis set. The displacement of the $\gamma$-$CH_2$ group in proline ring by oxygen atom has affected the structure of proline, cis-trans equilibrium, and rotational barrier. The up-puckered structure is found to be prevalent for the trans conformers of the Oxa amide. (omitted)

• The Korean Journal of Pesticide Science
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• v.9 no.3
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• pp.191-198
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• 2005

Hippuryl-L-histidyl-L-leucine (Hip-L-His-L-Leu, HHL) is the known substrate of ACE, which used often in inhibition kinetic study to design new inhibitor. Here we use HHL molecule as a template to predict pharmacophore which can interact with residues in active site of AnCE, new potential insecticide target protein. To explain physicochemical properties related to molecular geometry and conformational change in reaction field as well as electron density of atoms associated to pharmacophores, geometry optimization, NMR chemical shifts and natural population analysis were performed by ab initio and DFT method. Calculated NMR chemical shifts showed good agreement with the experimental ones and obtained electron densities were used for analyzing pharmacophores of corresponding atoms. Finally, we could extract aye pharmacophores related to hydrophobic aliphatic and aromatic site, hydrogen bonding donor and acceptor site and Zn binding site from the HHL molecule.

• Proceeding of EDISON Challenge
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• 2014.03a
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• pp.63-74
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• 2014

Predicting protein loop structures is an important modeling problem since protein loops are often involved in diverse biological functions by participating in enzyme active sites, ligand binding sites, etc. However, loop structure prediction is difficult even when structures of homologous proteins are known due to large sequence and structure variability among loops of homologous proteins. Therefore, an ab initio approach is necessary to solve loop modeling problems. One of the difficulties in the development of ab initio loop modeling method is to derive an accurate scoring function that closely approximates the true free energy function. In particular, entropy as well as energy contribution have to be considered adequately for loops because loops tend to be flexible compared to other parts of protein. In this study, the contribution of conformational entropy is considered in scoring loop conformations by employing "colony energy" which was previously proposed to estimate the free energy for an ensemble of conformations. Loop conformations were generated by using two EDISON_Chem programs GalaxyFill and GalaxySC, and colony energy was designed for this sampling by tuning relevant parameters. On a test set of 40 loops, the accuracy of predicted loop structure improved on average by scoring with the colony energy compared to scoring by energy alone. In addition, high correlation between colony energy and deviation from the native structure suggested that more extensive sampling can further improve the prediction accuracy. In another test on 6 ligand-binding loops that show conformational changes by ligand binding, both ligand-free and ligand-bound states could be identified by using colony energy when no information on the ligand-bound conformation is used.

• Bulletin of the Korean Chemical Society
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• v.23 no.6
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• pp.837-845
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• 2002

Based on ab initio calculations at the MP2(FULL)/6-31+G**//RHF/6-31G** level, we compare the energetic and mechanistic features of a model reaction for catalytic action of Δ?-3-ketosteroid isomerase (KSL,E.C.5.3,3.1) with those of a corresponding nonenzymatic reaction in aqueous solution. The results show that the two catalytic acid residues,Tyr14 and Asp99, can lower the free energy of activation by 8.6kcal/mol, which is in good agreement with the experimentally predicted~9 kcal/mol,contribution of electrophilic catalyses to the whole enzymatic rate enhancement. The dienolate intermediate formed by proton transfer from the substrate carbon acid to the catalytic base residue (Asp38) ins predicted to be stabilized by 12.0 kcal/mol in the enzymatic reaction, making its formation thermodynamically favorable. It has been argued that enzymes catalyzing the reactions of carbon acids should resolve the thermodynamic problem of stabilizing the enolate intermediate as well as the kinetic porblem of lowering the free energy of activation for porton abstraction. We find that KSI can successfully overcome the thermodynamic difficulty ingerent in the nonenzymatic reaction through the electrophilic catalyses of the two acid residues. Owing to the stabilization of dienolate intermediate, the reketonization step could influence the overall reaction rate more significantly in the KSI- catalyzed reaction than in the nonenzymatic reaction, further supporting the previous experimental findings. However, the electrophilic catalyses alone cannot account for the whole catalygic capability (12-13 kcal/mol), confiming the earlier experimental implications for the invement of additional catalytic components. The present computational study indicates clearly how catalytic residues of KSI resolve the fundamental problems associated with the entropic penalty for forming the rate-limiting transition state and its destabilization in the bulk solvation environment.

• Journal of the Korean Chemical Society
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• v.39 no.5
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• pp.329-337
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• 1995

Energetic oxetane derivatives which undergo cationic polymerizations have been investigated theoretically by using ab initio HF/3-21G calculations. We have examined structures, charges, and molecular electrostatic potentials. The ring structure of oxetane has changed significantly due to (1) the introduction of large substituents in the ring or (2) the addition of either proton or BF3. This structural change is attributed to electrostatic interactions and/or steric repulsions. The nucleophilicity and basicity of oxetane derivatives can be explained by the negative charge and the minimum electrostatic potential value of O atom. The reactivity in the polymerization can be rationalized by (1) the basicity of O atom and (2) the difference between HOMO energy of oxetanes and LUMO energy of activated oxetane polymeric chains. Our calculations predict that 3-azidomethyl-3-methyl oxetane (AMMO) is more basic than 3-nitratomethyl-3-methyl oxetane (NMMO), and AMMO is more reactive toward both AMMO and NMMO polymeric chains. Our results are in good agreement with previous experimental data.

• Journal of the Korean Chemical Society
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• v.34 no.3
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• pp.232-238
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• 1990

To study the biological roles of Zn, we investigated simple model systems of $Zn^{++}, coordinated with OH_2 or NH_3,$ or with O=C- in peptide. The geometrical structures and net atomic charges were calculated by the ab initio HF-SCF theory using double zeta basis sets. The ligands of O-H, N-H, and O=C- are very polar due to $Zn^{++}$. Therefore, the carbon atom in peptide becomes so electrophilic that it can be easily attacked by other nucleophiles. In addition, to understand how $Zn^{++}$ is coordinated with ligands in enzyme, a molecular mechanics method is applied to the system of the enzyme of carboxypeptidase A (CPA) with the substrate of glycyltyrosine. From our results, it appears that the Zn ion is coordinated not only by four ligands in enzyme and substrate but also by one water molecule.