• Journal of the Korean Society of Industry Convergence
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• v.15 no.4
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• pp.95-101
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• 2012

In order to explain observed catalytic reactivity of aminophosphine complexes (seven-membered chelate), total energy, net charge, atomic orbital electron population, HOMO and LUMO energy of free ligands are calculated by PM3 methods of HyperChem 6.0. Free ligands are 1,2-bis{(diphosphino)amino}propane{$H_2PNHCH_2CH(CH_3)NHPH_2$;ligand 1},1,2-bis{(dimenylphosphino)amino}propane{$(CH_3)_2PNHCH_2CH(CH_3)NHP(CH_3)_2$;ligand 2},1,2-bis{(diphenylphosphino)amino}propane{$(C_6H_5)_2PNHCH_2CH(CH_3)NHP(C_6H_5)_2$;ligand 3}. The result showed that ligand 3 is stable than ligand 2 and ligand 1 and ligand 2 is stable than ligand 1 in total energy. Net charge of P atom is changed by H atom, methyl groups and phenyl groups in P atoms. Net charge of N atoms in ligands is nagative. The results of atomic orbital electron population are similar net charge data..

• Bulletin of the Korean Chemical Society
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• v.32 no.12
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• pp.4167-4170
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• 2011

An inexpensive and efficient catalyst system has been developed for the N-arylation of phenylurea including a variety of aryl halides. This simple protocol uses $Cu_2O$ as the catalyst, microwave assisted, solvent- and ligand-free, $K_3PO_4{\cdot}H_2O$ as the base.

• Journal of the Korean Magnetic Resonance Society
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• v.2 no.1
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• pp.33-40
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• 1998

The cross peak intensities versus mixing times of 2D NOESY spectrum for a corepressor L-trp were simulated for the case of a ligand exchanging between free (AX) and bound (A'X') forms in protein/DNA complex. The direct NOE (I(AX)) of the free ligand exhibited a small positive intensity indicative of the strong dominant influence of the bound ligand. The exchange-mediated NOE peak (I(AX')) was very sensitive to corepressor exchange. However, both diagonal (I(A'A')) and direct NOE (I(A'X')) intensities of the bound ligand were not affected much at initial stage. Both peaks were severely influenced by exchange at mixing times of greater than 100 ms. In conclusion, since the NOE intensity is a function of exchange rate, the exchange effect should be considered to properly extract accurate distance information for bound ligand in the presence of conformational exchange.

• 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.

• Journal of the Korean Magnetic Resonance Society
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• v.5 no.2
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• pp.130-137
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• 2001

Backbone dynamics of the catalytic residues in free and steroid-bound $\Delta$$^{5}$ -3- ketosteroid isomerase from Pseudomonas testosteroni has been examined by $^{15}$ N relaxation measurements. The relaxation data were analyzed using the model-free formalism to extract the model-free parameters (S$^2$, $\tau$$_{e}$, and R$_{ex}$). Tyr-34 and Asp-99 exhibit enhanced high-frequency (pico- to nanosecond) internal motions in the free enzyme, which are restricted upon ligand binding, while Asp-38 experiences severe restriction of the internal motions in the fee enzyme, suggesting that Tyr-14 and Asp-99 are more actively involved in the ligand binding than Asp-38. The results also indicate that the H-bond network in the catalytic cavity might be slightly strengthened upon ligand binding, which may have some implications on the enzyme mechanism.he enzyme mechanism.m.

• Bulletin of the Korean Chemical Society
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• v.33 no.6
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• pp.2067-2070
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• 2012

• Analytical Science and Technology
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• v.10 no.6
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• pp.453-458
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• 1997

Many polymeric poly(vinyl chloride) membrane electrodes have been developed for the determination of basic drugs. But relatively little has been roported concerning the behavior of ligand free PVC memebranes. In connection with the evaluation of various ionophores, we bave evaluated a near-Nernstian response and selectivity of these ligand-free PVC electrodes towards basic drugs such as alverine, chlorpromazine and promazine. The electrode membranes were constructed with only several plasticizer and poly (vinyl chloride) matrix. The plasticizer studied were dioctyl phenylphosphonate, 2-nitrophenyl octyl ether, isododecyl phenylphosphate and dioctyl maleate.

• Biomolecules & Therapeutics
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• v.7 no.2
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• pp.164-169
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• 1999

The synthesis and antimicrobial activity of N-substituted glycol derivatives of Norfloxacin were described. Norfloxacin was treated with chloroacetyl chloride to yield chloroacetyl norfloxacin (1). This compounds was reacted with alkyldiamines to afford bivalent ligand quinolone carboxylic acids (2-6), which was added to pivaloyloxymethyl chloride to give bivalent ligand pivaloyloxymethyl quinolone carboxylates (7-11). Chloroacetyl norfloxacin (1) treated with alkylamines to obtain monovalent ligand quinolone carboxylic acids (12-15), which was reacted with pivaloyloxymethyl chloride to get monovalent ligand pivaloyloxymethyl quinolone carboxylates (16-19). Free carboxylic quinolones (2-6, 12-15) showed little stronger activities to their pivaloyloxymethyl esters (7-11, 16-19). In monovalent ligand quinolone analogues, longer a1kyl chain com-pounds showed stronger activities than shorter one.

• Bulletin of the Korean Chemical Society
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• v.33 no.3
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• pp.770-774
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• 2012

Protein loops are often involved in diverse biological functions, and some functional loops show conformational changes upon ligand binding. Since this conformational change is directly related to ligand binding pose and protein function, there have been numerous attempts to predict this change accurately. In this study, we show that it is plausible to obtain meaningful ensembles of loop conformations for flexible, ligand-binding protein loops efficiently by applying a loop modeling method. The loop modeling method employs triaxial loop closure algorithm for trial conformation generation and conformational space annealing for global energy optimization. When loop modeling was performed on the framework of ligand-free structure, loop structures within $3\AA$ RMSD from the crystal loop structure for the ligand-bound state were sampled in 4 out of 6 cases. This result is encouraging considering that no information on the ligand-bound state was used during the loop modeling process. We therefore expect that the present loop modeling method will be useful for future developments of flexible protein-ligand docking methods.

• Bulletin of the Korean Chemical Society
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• v.13 no.2
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• pp.119-122
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• 1992

The affinity chromatographic technique was applied to the isolation of Thromboxane Synthase, with a variety of imidazolyl alkanoic acids coupled Sepharose 2B including a gel (G in Table 4) which has one free COOH group in the bound affinity ligand. The effect of ligand structure on the "affinity" and "selectivity" for thromboxane synthase isolation is described.