• Bulletin of the Korean Chemical Society
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• v.20 no.10
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• pp.1129-1135
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• 1999

Free energy perturbation and molecular dynamics simulations were carried out to investigate the relative binding affinities of [17] ketonand (1) toward alkali metal cations in methanol. The binding affinities of 1 toward the alkali metal cations were calculated to be in the order Li+ > Na+ > K+ > Rb+ > Cs+, whereas our recent theoretically predicted and experimentally observed binding affinities for [18]starand (2) were in the order K+ > Rb+ > Cs+ > Na+ > Li+. The extremely different affinities of 1 and 2 toward smaller cations, Li + and Na+ , were explained in terms of the differences in their ability to change the conformation to accommodate cations of different sizes. The carbonyl groups constituting the central cavity of 1 can reorganize to form a cavity with the optimal M+ -O distance, even for the smallest Li+, without imposing serious strain on 1. The highest affinity of 1 for Li+ was predominantly due to the highest Coulombic attraction between the smallest Li+ and the carbonyl oxygens of 1.

• Bulletin of the Korean Chemical Society
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• v.16 no.2
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• pp.164-168
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• 1995

The band structure of nickel monoxide having a cation defect rock salt structure is calculated by means of the tight-binding extended Huckel method. The calculation is also made for the net charge, the DOS, the COOP, the electron density of the constituent atoms, and the O 1s binding energy shift when one of the adjacent nickel atoms is defected. It is found that the band gap near the Γ direction on the Brillouin zone is about 0.2 eV, and that all of the properties calculated including the electronic structure of the oxygen atom are more effectively affected by the surface defect than the inside one. The core O 1s binding energy shift is calculated by the use of valence potential method and the results are very satisfactory in comparison with the XPS experimental findings.

• Biotechnology and Bioprocess Engineering:BBE
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• v.6 no.2
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• pp.89-94
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• 2001

The binding of cellobiohydrolases to cullulose is a crucial initial step in cellulose hydrolysis. In the search for a detailed understanding of the function of cellobiohydrolases, much information concerning how the enzymes and their constituent catalytic and cellulose-binding changes during hydrolysis is still needed. The adsorption of purified two cellobiohydrolases (Ce17A and Ce16A) from Trichoderma reesei cellulase to microcrystalline cellulose has been studied. Cellobiohydrolase II (Ce16A) does not affect the adsorption of cellobiohydrolase I (Ce17A) significantly, and there are specific binding sites for both Ce17A and Ce16A. The adsorption affinity and tightness of the cullulase binding domain (CBD) for Ce17A are larger than those of the CBD for Ce16A. The CBD for Ce17A binds more rapidly and tightly to Avicel than the CBD for Ce16A. The decrease in adsorption observed when the two cellobihydrolases are studied together would appear to be the result of competition for binding sites on the cellulose. Ce17A competes more efficiently for binding sites than Ce16A. Competition for binding sites is the dominating factor when the two enzymes are acting together, furthermore adsorption to sites specific for Ce17A and Ce16A, also contributes to the total adsorption.

• Journal of the Korean Chemical Society
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• v.55 no.6
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• pp.905-911
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• 2011

The possible minimum structures of $C_{60}(CH_2)_nOH$ (n=0~2) and $C_{60}(OH)_2$have been optimized using density functional theory (DFT) with the 6-311G (d,f) basis set. 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 (ZPVE) have been considered to predict the binding energies. The predicted binding energy of $C_{60}CH_2OH$ is about 10 kcal/mol more stable than the binding energy of $C_{60}OH$.

• Journal of the Korean Institute of Telematics and Electronics
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• v.25 no.1
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• pp.27-32
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• 1988

Electron Spectroscopy for Chemical Analysis(ESCA) allowes the determination of the elemental composition and the bonding state of the surface atomes in the interface between two materials. In the binding energies of ESCA spectrum, there are zero error, voltage scaling error and random error. Accurate analysis of the intensity energy response functions and accurate calibration of the energy scale are essential to use X-ray photoelectron spectron meter. At the results of the calibration of the ESCA spectra in the copper and cordierite (Mg2Al4Si5kO18) interfaces, the errors relative to the copper are -3.03 eV for the zero error -z,-197 ppm for the voltage scaling error -V and 6.9 meV for the random error -R. The method of the calibration is able to apply for the binding energy calibration of the another ESCA spectra.

• Bulletin of the Korean Chemical Society
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• v.23 no.2
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• pp.262-266
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• 2002

Computations are presented for the ortho- and para-substituted benzyl alcohol-$H_2O$ 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 effects of substitution on the strength of the hydrogen bond in the clusters. F- and $NH_2-$ substituted clusters are studied to analyze the effects of electron-withdrawing and electron-pushing groups. In para-substituted clusters, the inductive effects are dominant, affecting the binding energies in opposite way depending on whether the hydroxyl group is proton-donating or -accepting. For ortho-substituted clusters, more direct involvement of the substituting group and the resulting geometry change of the hydrogen bond should be invoked to elucidate complicated pattern of the binding energy of the clusters.

• Bulletin of the Korean Chemical Society
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• v.35 no.7
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• pp.2114-2122
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• 2014

The association of silybin with ${\beta}$-cyclodextrin and its influence on silybin's binding with bovine serum albumin are reported. The stoichiometry, binding constant, and the structure of silybin-${\beta}$-cyclodextrin inclusion complex are reported. The titrations of silybin with bovine serum albumin in the absence and presence of ${\beta}$-cyclodextrin are carried out and the differences in binding strengths are discussed. Molecular modeling is used to optimize the sites and mode of binding of silybin with bovine serum albumin. F$\ddot{o}$rster resonance energy transfer is calculated and the proximity of interacting molecules is reported in the presence and absence of ${\beta}$-cyclodextrin.

• Journal of Photoscience
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• v.11 no.32
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• pp.65-69
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• 2004

The mechanism of interaction of four coumarin derivatives (CDS) with bovine serum albumin (BSA) was studied using spectrofluorometric technique. It was found that the coumarin ring common to all CDS makes major contribution to interaction. Binding affinities could be related to parachor values of CDS. Stem-Volmer plots indicated the presence of static component in the quenching mechanism. Results also showed that both tryptophan residues of protein are accessible to CDS. The high magnitude of rate constant of quenching indicated that the process of energy transfer occurs by intermolecular interaction forces and thus CDS binding site is in close proximity to tryptophan residues of BSA. Binding studies in the presence of the hydrophobic probe, 8-anilino-l-naphthalein-sulfonic acid showed that there is hydrophobic interaction between CDS and the probe and they do not share common sites in BSA. Thermodynamic parameters obtained from data at different temperatures showed that the binding of CDS to BSA involve hydrophobic bonds predominantly. The effects of various metal ions on the binding of CDS with BSA were also investigated.

• Journal of Microbiology and Biotechnology
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• v.23 no.12
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• pp.1699-1707
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• 2013

During the fermentative production of 1,3-propanediol under high substrate concentrations, accumulation of intracellular 3-hydroxypropionaldehyde will cause premature cessation of cell growth and glycerol consumption. Discovery of oxidoreductases that can convert 3-hydroxypropionaldehyde to 1,3-propanediol using NADPH as cofactor could serve as a solution to this problem. In this paper, the yqhD gene from Klebsiella pneumoniae DSM2026, which was found encoding an aldehyde reductase (KpAR), was cloned and characterized. KpAR showed broad substrate specificity under physiological direction, whereas no catalytic activity was detected in the oxidation direction, and both NADPH and NADH can be utilized as cofactors. The cofactor binding mechanism was then investigated employing homology modeling and molecular dynamics simulations. Hydrogen-bond analysis showed that the hydrogen-bond interactions between KpAR and NADPH are much stronger than that for NADH. Free-energy decomposition dedicated that residues Gly37 to Val41 contribute most to the cofactor preference through polar interactions. In conclusion, this work provides a novel aldehyde reductase that has potential applications in the development of novel genetically engineered strains in the 1,3-propanediol industry, and gives a better understanding of the mechanisms involved in cofactor binding.

• YAKHAK HOEJI
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• v.33 no.5
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• pp.308-311
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• 1989

Binding parameters of some edible dyes with bovine serum albumin were determined at pH 7.4 buffer solution. The edible dyes used were fast green, brilliant blue FCF, indigo carmine and allura red AC, and the final concentrations of each dyes were $3{\sim}9{\times}10^{-6}M$, $6{\times}10^{-6}M$, $3{\times}10^{-5}M$ and $3{\times}10^{-5}M$, respectively. The final concentrations of bovine serum albumin were $1{\sim}7{\times}10^{-5}M$. The values of binding free energy between edible dye and protein were ranged from -6,024 to -6,800 cal/mole.