• Bulletin of the Korean Chemical Society
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• v.32 no.1
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• pp.162-168
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• 2011

Many ligands have been experimentally designed and tested for their activities as inhibitors against bacterial enoyl-ACP reductase (FabI), ENR. Here the binding energies of the reported ligands with the E. coli ENR-$NAD^+$ were calculated, analyzed and compared, and their molecular dynamics (MD) simulation study was performed. IDN, ZAM and AYM ligands were calculated to have larger binding energies than TCL and IDN has the largest binding energy among the considered ligands (TCL, S54, E26, ZAM, AYM and IDN). The contribution of residues to the ligand binding energy is larger in E. coli ENR-NAD+-IDN than in E. coli ENR-$NAD^+$-TCL, while the contribution of $NAD^+$ is smaller for IDN than for TCL. The large-size ligands having considerable interactions with residues and $NAD^+$ have many effective functional groups such as aromatic $\pi$ rings, acidic hydroxyl groups, and polarizable amide carbonyl groups in common. The cation-$\pi$ interactions have large binding energies, positively charged residues strongly interact with polarisable amide carbonyl group, and the acidic phenoxyl group has strong H-bond interactions. The residues which have strong interactions with the ligands in common are Y146, Y156, M159 and K163. This study of the reported inhibitor candidates is expected to assist the design of feasible ENR inhibitors.

• Journal of the Korean Chemical Society
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• v.54 no.4
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• pp.387-394
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• 2010

The theoretical calculations for $B_nH_n$, $B_nH_{n+1}$, $B_nH_{n+2}$ (n = 3-6) have been considered at the B3LYP level of theory with the 6-311G$^*$ basis set. The optimized geometries, harmonic vibrational frequencies, and binding energies are evaluated to elucidate the thermodynamic stability and spectroscopic properties. The harmonic vibrational frequencies for the molecules considered in this study show all real numbers implying true minima and the binding energies are corrected using zero-point vibrational energies (ZPVE). The binding energies and average energies due to increasing of BH monomer are predicted.

• Archives of Pharmacal Research
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• v.8 no.3
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• pp.169-175
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• 1985

The binding of bovine serum albumin (BSA)-edible dyes was studied by spectrophotometric method. The edible dyes used in this study were amaranth, erythrosine, tartrazine and sunset yellow. The binding free energies and binding sites were determined at pH 7.4. The ranges of edible dye concentration were from 0.3 to $7{\times}10^{-5}$M, and those of BSA were from 0.15 to $3{\times}10^{-5}$M. The binding free energies of BSA-edible dyes were from -6, 300 to -8, 100 cal/mole.

• Journal of the Korean Chemical Society
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• v.54 no.6
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• pp.671-679
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• 2010

The geometrical parameters and binding energies of the benzene ion-water complex [$C_6H_6^+-(H_2O)_n$(n=1-5)] have been investigated using ab initio (MP2) and density functional theory (DFT) with large basis sets. The harmonic vibrational frequencies and IR intensities are also determined to confirm that all the optimized geometries are true minima. Also zero-point vibrational energies have been considered to predict the binding energies. The predicted binding energy of 8.6 kcal/mol for $C_6H_6^+-(H_2O)$ at the MP2/aug-cc-pVTZ level of theory is in excellent agreement with recent experimental result of $8.5{\pm}1$ kcal/mol.

• Bulletin of the Korean Chemical Society
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• v.23 no.9
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• pp.1297-1303
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• 2002

Computations are presented for the catechol-$(H_2O)_n$ (n = 1-3) clusters. A variety of conformers are predicted,and their relative energies are compared. Binding energies of the clusters are computed, and detailed analysis is presented on the harmonic frequencies of stretching modes involving the hydrogen bonding in the clusters, comparing with the experimental observations.

• Journal of the Korean Chemical Society
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• v.50 no.3
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• pp.203-207
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• 2006

Ab initio calculations of the structure and the binding energies of K+(C2H5OH)n, (n=1~5) complexes were carried out with MP2/ full gen 6d and MP2/ 6-311G** methods. The stable structures of the complexes with n=2 to 5 were linear, trigonal, tetrahedral and trigonal bipyramid respectively. The binding energies of complexes were increased with the number of ligands, but the incremental binding energies were decreased. These results agreed well with the results of K+ complexes with other solvents.

• Bulletin of the Korean Chemical Society
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• v.28 no.3
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• pp.386-390
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• 2007

By use of a simple two-point extrapolation scheme estimating the correlation energies of the molecules along with the basis sets specifically targeted for extrapolation, we have shown that the MP2 basis set limit binding energies of large hydrogen-bonded complexes can be accurately predicted with relatively small amount of computational cost. The basis sets employed for computation and extrapolation consist of the smallest correlation consistent basis set cc-pVDZ and another basis set made of the cc-pVDZ set plus highest angular momentum polarization functions from the cc-pVTZ set, both of which were then augmented by diffuse functions centered on the heavy atoms except hydrogen in the complex. The correlation energy extrapolation formula takes the (X+1)-3 form with X corresponding to 2.0 for the cc-pVDZ set and 2.3 for the other basis set. The estimated MP2 basis set limit binding energies for water hexamer, hydrogen fluoride pentamer, alaninewater, phenol-water, and guanine-cytosine base pair complexes of nucleic acid by this method are 45.2(45.9), 36.1(37.5), 10.9(10.7), 7.1(6.9), and 27.6(27.7) kcal/mol, respectively, with the values in parentheses representing the reference basis set limit values. A comparison with the DFT results by B3LYP method clearly manifests the effectiveness and accuracy of this method in the study of large hydrogen-bonded complexes.

• Bulletin of the Korean Chemical Society
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• v.26 no.9
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• pp.1421-1426
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• 2005

The stationary point structures and relative energies between them as well as binding energies of $(CO)_2$ have been investigated at the CCSD(T) level using the correlation-consistent basis sets aug-cc-pVXZ(X=T,Q,5). It is found that while the equilibrium structure corresponds to the C-bonded T-shaped configuration with intermolecular distance of 4.4 $\AA$, there exists another minimum, slightly higher in energy ($\sim$10 $cm^{-1}$) than the global minimum, corresponding to the O-bonded T-shaped configuration with the intermolecular distance of 3.9 $\AA$. The CCSD(T) basis set limit binding energy of $(CO)_2$ is estimated to be 132 $cm^{-1}$.

• Proceedings of the Optical Society of Korea Conference
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• 2001.08a
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• pp.300-301
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• 2001

• Bulletin of the Korean Chemical Society
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• v.35 no.6
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• pp.1769-1776
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• 2014

Binding modes of a series of catechol derivatives such as protein tyrosine phosphatase 1B (PTP1B) inhibitors were identified by molecular modeling techniques. Docking, molecular dynamics simulations and free energy calculations were employed to determine the modes of these new inhibitors. Binding free energies were calculated by involving different energy components using the Molecular Mechanics-Poisson-Boltzmann Surface Area and Generalized Born Surface Area methods. Relatively larger binding energies were obtained for the catechol derivatives compared to one of the PTP1B inhibitors already in use. The Molecular Mechanics/Generalized Born Surface Area (MM/GBSA) free energy decomposition analysis indicated that the hydroxyl functional groups and biphenyl ring system had favorable interactions with Met258, Tyr46, Gln262 and Phe182 residues of PTP1B. The results of hydrogen bound analysis indicated that catechol derivatives, in addition to hydrogen bonding interactions, Val49, Ile219, Gln266, Asp181 and amino acid residues of PTP1B are responsible for governing the inhibitor potency of the compounds. The information generated from the present study should be useful for the design of more potent PTP1B inhibitors as anti-diabetic agents.