• Bulletin of the Korean Chemical Society
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• v.25 no.12
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• pp.1801-1806
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• 2004

Ligand-based quantitative structure-activity relationship (QSAR) studies were performed on indolinones derivatives as a potential inhibitor of the protein tyrosine kinase of fibroblast growth factor receptor (FGFR) by comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) implemented in the SYBYL packages. The initial X-ray structure of docked ligand (Su5402) to FGFR was used to minimize the 27 training set molecules using TRIPOS force field. Seven models were generated using CoMFA and CoMSIA with grid spacing 2 ${\AA}$. After the PLS analysis the best predicted CoMSIA model with hydrophobicity, hydrogen bond donor and acceptor property showed that a leave-one out(LOO) cross validated value $({r^2}_{cv})^$ and non-cross validated conventional value $({r^2}_{ncv})^$ are 0.543 and 0.938, respectively.

• Bioinformatics and Biosystems
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• v.1 no.2
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• pp.103-108
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• 2006

Computational prediction of protein-ligand binding has been widely used as a tool to discover lead compounds fur new drugs. Prediction accuracy is determined in part by the scoring function used in docking calculations. Diverse scoring functions are available, and these can be classified into force-field based, empirical, and knowledge-based functions depending upon the basic assumptions made in development. Among these, force-field based functions consider physical interactions the most in detail. However, the force-field based functions have the drawback of not including the entropic effect while considering only the energy contribution such as dispersion or electrostatic forces. In this article, a method to take into account of the entropic effect using the colony energy is suggested when force-field based scoring functions is used by extracting conformational information obtained from the pre-existing docking program. An improved result for decoy discrimination is illustrated when the method is applied to the DOCK scoring function, and this implies that more accurate docking calculation is possible.

• Proceedings of the Korean Society of Potoscience Conference
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• spring
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• pp.22-22
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• 2003

• Journal of the Korean Chemical Society
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• v.23 no.2
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• pp.65-74
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• 1979

An effect of the spin-orbit coupling interaction of ligand orbitals on the ground state for octahedral $[Ti(Ⅲ)A_3B_3]$, $ [V(Ⅲ)A_3B_3]$, $ [Fe(Ⅲ)A_3B_3]$ and $ [Ni(Ⅱ)A_3B_3]$ type complexes has been investigated in this work, applying the degenerate perturbation theory. The wave functions are not affected but the energy level splitting for the ground state of these complexes by the spin-orbit coupling interaction of ligand orbitals. The extent of effect on the energy level splitting for the ground state is decreased in order Ti(Ⅲ) > V(Ⅲ) > Fe(Ⅲ).

• Bulletin of the Korean Chemical Society
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• v.19 no.11
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• pp.1207-1210
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• 1998

The diamagnetic six-coordinate ruthenium polypyridyl complexes have been prepared and assigned. 1H NMR spectral studies were used to unravel the ligand field strength and the basicity on the chemical shift to the particular proton of ligand L in [(tpy)(L)RuⅡ(X)]+/2+ (L=bpy, bqi, dmbpy, phen; X=Cl, CN, N3, NCCD3, NO2, SCN) complexes.

• Interdisciplinary Bio Central
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• v.2 no.2
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• pp.6.1-6.5
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• 2010

Fragment molecular orbital (FMO) method provides a novel tool for ab initio calculations of large biomolecules. This method overcomes the size limitation difficulties in conventional molecular orbital methods and has several advantages compared to classical force field approaches. While there are many features in this method, we here focus on explaining the issues related to protein-ligand binding: FMO method provides useful interaction-analysis tools such as IFIE, CAFI and FILM. FMO calculations can provide not only binding energies, which are well correlated with experimental binding affinity, but also QSAR descriptors. In addition, FMO-derived charges improve the descriptions of electrostatic properties and the correlations between docking scores and experimental binding affinities. These calculations can be performed by the ABINIT-MPX program and the calculation results can be visualized by its proper BioStation Viewer. The acceleration of FMO calculations on various computer facilities is ongoing, and we are also developing methods to deal with cytochrome P450, which belongs to the family of drug metabolic enzymes.

• Bulletin of the Korean Chemical Society
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• v.15 no.2
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• pp.145-150
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• 1994

The low temperature luminescence and excitation, room-temperature UV-visible and infrared spectra of [Cr(${\pm})chxn_3]Cl_3$ (chxn=trans-1,2-cyclohexanediamine) have been measured. It is found that the zero-phonon line in the excitation spectrum splits into two components by $47\;cm^{-1}$. The eight electronic transitions due to spin-allowed and spin-forbidden are assigned. As expected, nitrogen atoms of chxn ligand have strong ${\sigma}-donor $properties toward chromium(Ⅲ). The positions and splittings of sharp-line transitions are analyzed as a function of the Cartesian bite (${\alpha}$) and twist (${\beta}$) angles to predict the metal-ligand geometry.

• Bulletin of the Korean Chemical Society
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• v.18 no.1
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• pp.23-27
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• 1997

The luminescence and excitation spectra of [Cr(trans-diammac)](ClO4)3 (trans-diammac=trans-6, 3-dimethyl-l, 4, 8, 11-tetraazacyclotetradecane-6, 13-diamine) taken at 77 K are reported. The mid and far-infrared spectra at room-temperature are also measured between 4000 cm-1and 50 cm-1. In the excitation spectrum the 2Eg components are splitted by 102 cm-1. Using the observed electronic transitions, a ligand field analysis was performed to determine more detailed bonding properties of the coordinated atoms toward chromium(Ⅲ). According to the results, we can confirm that the six nitrogen atoms have a strong σ-donor character, and the trans-diammac secondary amine has a greater value of eσ than does the primary amine.

• Bulletin of the Korean Chemical Society
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• v.14 no.3
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• pp.348-352
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• 1993

• Journal of Soil and Groundwater Environment
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• v.16 no.4
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• pp.23-30
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• 2011

Risk based pollution level of Pb and Cd in metal contaminated soils depending on physicochemical properties of soil in a target site was assessed using biotic ligand model. Heavy metal activity in soil solution defined as exposure activity (EA) was assumed to be toxic to Vibrio fischeri and soil organisms. Predicted effective activity (PEA) determined by biotic ligand model was compared to EA value to calculate risk quotient. Field contaminated soils (n = 10) were collected from a formes area and their risk based pollution levels were assessed in the present study using the calculated risk quotient. Concentrations of Pb determined by aqua regia were 295, 258, and 268 mg/kg in B, H and J points and concentrations of Cd were 4.73 and 6.36 mg/kg in G and I points, respectively. These points exceeded the current soil conservation standards. However, risk based pollution levels of the ten points were not able to be calculated because concentrations of Pb and Cd in soil solution were smaller than detection limits or one (i.e., non toxic). It was because heavy metal activity in soil solution was dominant toxicological form to organisms, not a total heavy metal concentration in soil. In addition, heavy metal toxicity was decreased by competition effect of major cations and formation of complex with dissolved organic carbon in soil solution. Therefore, it is essential to consider site-specific factors affecting bioavailability and toxicity for estimating reliable risk of Pb and Cd.