• Bulletin of the Korean Chemical Society
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• 제25권6호
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• pp.924-926
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• 2004

• Bulletin of the Korean Chemical Society
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• 제26권5호
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• pp.769-775
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• 2005

An efficiency of Monte Carlo (MC) docking simulations was examined for the prediction of chiral discrimination by cyclodextrins. Docking simulations were performed with various computational parameters for the chiral discrimination of a series of 17 enantiomers by $\beta$-cyclodextrin ($\beta$-CD) or by 6-amino-6-deoxy-$\beta$-cyclodextrin (am-$\beta$-CD). A total of 30 sets of enantiomeric complexes were tested to find the optimal simulation parameters for accurate predictions. Rigid-body MC docking simulations gave more accurate predictions than flexible docking simulations. The accuracy was also affected by both the simulation temperature and the kind of force field. The prediction rate of chiral preference was improved by as much as 76.7% when rigid-body MC docking simulations were performed at low-temperatures (100 K) with a sugar22 parameter set in the CHARMM force field. Our approach for MC docking simulations suggested that the conformational rigidity of both the host and guest molecule, due to either the low-temperature or rigid-body docking condition, contributed greatly to the prediction of chiral discrimination.

• Bulletin of the Korean Chemical Society
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• 제34권2호
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• pp.677-679
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• 2013

• Bulletin of the Korean Chemical Society
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• 제24권3호
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• pp.377-383
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• 2003

Physicochemical properties of a series of PC monolayers with different alkyl chains (C24, C20, C16, and C8), at the air/water interface were investigated. The surface pressure is influenced mainly by the hydrophobicity of the PCs, which is confirmed by the curve shape and the on-set value of π-A isotherms at the air/water interface by increasing the number of alkyl chain. The on-set values of surface pressure were 125 Ų/molecule for DOPC(C8), 87 Ų/molecule for DPPC(C16), 75 Ų/molecule for DAPC(C20), and 55 Ų/molecule for DLPC(C24), respectively. The orientations of alkyl chains at the air/water interface are closely connected with the rigidity of the monolayers, and it was confirmed by the tendency of monolayer thickness in ellipsometry data. The temperature dependence of a series of PCs shows that the surface pressure decreases by increasing temperature, because the longer the alkyl chain length, the larger the hydrophobic interaction in surface pressure. The temperature effects and the conformational changes of unsaturated and saturated PCs were confirmed by the computer simulation study of the cis-trans transition with POPC and DPPC(C16). The cistrans conformational energy difference of POPC is 62.06 kcal/mol and that of DPPC(C16) is 6.75 kcal/mol. Due to the high conformational energy barrier of POPC, phase transition of POPC is limited in comparison with DPPC(C16).

• Bulletin of the Korean Chemical Society
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• 제22권4호
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• pp.401-404
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• 2001

A new chiral stationary phase (CSP) based on (1R,2S)-2-amino-1-indanol, which is expected to be conformationally rigid because of its cyclic nature, was prepared. The new CSP was applied in resolving various $N-acyl-\alpha-arylalkylamines$. The chromatographic resolution results on the new CSP were compared with those on the other CSP based on (1S,2R)-norephedrine, which is believed to be conformationally flexible. Comparison of the chromatographic resolution results on the two CSPs demonstrated that conformationally flexible analytes are resolved better on the conformationally rigid CSP while conformationally rigid analytes are resolved better on the conformationally flexible CSP. From these results it was concluded that conformational rigidity or flexibility of CSPs is the important factor for the chiral recognition.

• 통합자연과학논문집
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• 제2권2호
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• pp.55-58
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• 2009

A ligand-receptor docking program is an indispensible tool in modern pharmaceutical design. An accurate prediction of small molecular docking pose to a receptor is essential in drug design as well as molecular recognition. An effective docking program requires the ability to locate a correct binding pose in a surprisingly complex conformational space. However, there is an inherent difficulty to predict correct binding pose. The odds are more demanding than finding a needle in a haystack. This mainly comes from the flexibility of both ligand and receptor. Because the searching space to consider is so vast, receptor rigidity has been often applied in docking programs. Even nowadays the receptor may not be considered to be fully flexible although there have been some progress in search algorithm. Improving the efficiency of searching algorithm is still in great demand to explore other applications areas with inherently flexible ligand and/or receptor. In addition to classical search algorithms such as molecular dynamics, Monte Carlo, genetic algorithm and simulated annealing, rather recent algorithms such as tabu search, stochastic tunneling, particle swarm optimizations were also found to be effective. A good search algorithm would require a good balance between exploration and exploitation. It would be a good strategy to combine algorithms already developed. This composite algorithms can be more effective than an individual search algorithms.

• Bulletin of the Korean Chemical Society
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• 제30권4호
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• pp.849-852
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• 2009

The work describes EPR and 17O NMR measurements followed by theoretical calculation of the rotational correlation time $({\tau}_R)$, the water residence time $({\tau}_m)$, and the longitudinal electronic spin relaxation time $(T_{le})$(T_1e) for two new gadolinium complexes 1 and 2 of the type [$Gd(L)(H_2O)$] (L = tranexamic esters) in order to investigate their efficiency as a paramagnetic contrast agent (PCA). Of three correlation times, τR plays a major and predominant role to the unusually high relaxivity of 1 and 2 as compared with that of clinically approved MR CAs such as [$Gd(DTPA)(H_2O)]2‐ (Magnevist${\circledR}$), [Gd(DTPA-BMA)(H2O)] (Omniscan${\circledR}$), and $[Gd(DOTA)(H_2O)]^-$ (Dotarem${\circledR}$). The presence of bulky tranexamic ester in the ligand seems to be responsible for the conformational rigidity, which in turn causes such great an increase in ${\tau}_R$.