• Proceedings of the Korean Vacuum Society Conference
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• 2010.02a
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• pp.61-61
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• 2010

In the present work, we present the optimized the hybrid structures of carbon nanotubes (CNTs) and metal nanocomposites including Cu, Al, Co and Ni using the first principle calculations based on the density functional theory. Introduction of CNTs into a metal matrix has been considered to improve the mechanical properties of the metal matrix. However, the binding energy between metals and pristine CNTs wall is known to be so small that the interfacial slip between CNTs and the matrix occurs at a relatively low external stress. The application of defective or functionalized CNTs has thus attracted great attention to enhance the interfacial strength of CNT/metal nanocomposites. Herein, we design the various hybrid structures of the single wall CNT/metal complexes and characterize the interaction between single wall CNTs and various metals such as Cu, Al, Co or Ni. First, differences in the binding energies or electronic structures of the CNT/metal complexes with the topological defects, such as the Stone-Wales and vacancy, are compared. Second, the characteristics of functionalized CNTs with various surface functional groups, such as -O, -COOH, -OH interacting with metals are investigated.We found that the binding energy can be enhanced by the surface functional group including oxygen since the oxygen atom can mediate and reinforce the interaction between carbon and metal. The binding energy is also greatly increased when it is absorbed on the defects of CNTs. These results strongly support the recent experimental work which suggested the oxygen on the interface playing an important role in the excellent mechanical properties of the CNT-Cu composite[1].

• Bulletin of the Korean Chemical Society
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• v.14 no.4
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• pp.491-496
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• 1993

A class A ${\beta}$-lactamase from Staphylococcus aureus PC1 complexed with 3R,5R-clavulanate is studied. The starting geometry for the computation is the crystal structure of the ${\beta}$-lactamase. Docking of the clavulanate to the enzyme is done exploiting the requirements of electrostatic and shape complementarity between the enzyme and clavulanate. This structure is then hydrated by water molecules and refined by energy minimization and short molecular dynamics simulation. In the energy refined structure of this complex, the carboxyl group of the clavulanate is hydrogen bonded to Lys-234, and the the carbonyl carbon atom of the clavulanate is adjacent to the $O_{\gamma}$ of Ser-70. It is found that a crystallographic water molecule initially located at the oxyanion hole, which is formed by the two -NH group of Ser-70 and Gln-237, is replaced by the carbonyl oxygen atom of the 3R,5R-clavulanate after docking and energy reginement. The crystallographic water molecules are proved to be important in ligand binding. Glu-166 residue is found to be repulsive to the binding of clavulanate, which is in agreement with experimental observation. Arg-244 residue is found to be important to the binding of clavulanate as well as to interaction with C2 side chain of the clavulanate. The electron density redistribution of the clavulanate on binding to the ${\beta}$-lactamase in studied by an ab initio quantum-mechanical calculation. A significant redistribution of electron density of the clavulanate is induced by the enzyme, toward the enzyme, toward the transition state of the enzymatic reaction.

• Bulletin of the Korean Chemical Society
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• v.22 no.1
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• pp.11-12
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• 2001

• Bulletin of the Korean Chemical Society
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• v.17 no.12
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• pp.1154-1157
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• 1996

The growth and electronic properties of ultrathin silver films deposited onto Pt(211) surface were studied using Auger electron spectroscopy (AES), low-energy electron diffraction (LEED), and x-ray photoelectron spectroscopy. The AES and LEED results indicate that the silver grows by a layer by layer growth followed by three dimensional islands growth. The XPS results show that the Ag 3d core-level binding energy of Ag overlayers on Pt(211) shifts toward lower binding energy relative to the bulk value at lower Ag coverage. This negative binding energy shift of the Ag 3d core level is explained by the reduced coordination number of the overlayer atoms and the resulting initial state band narrowing effect suggested by Wertheim and Citrin [Phys. Rev. Lett. 1978, 41, 1425].

• Journal of the Korean Chemical Society
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• v.31 no.2
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• pp.143-152
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• 1987

$\pi$-Binding energy of the 153 kinds of unsaturated acyclic polyenes and unsaturated cyclic polyenes has been calculated by the Kier's Molecular Connectivity Index. An excellent linear correlation is found between HMO $\pi$-binding energy and $\pi$-binding energy calculated by the Kier's Molecular Connectivity Index. In either class of unsaturated acyclic hydrocarbons and unsaturated cyclic hydrocarbon, the regression analysis reveals a highly significant linear correlation between $E_{\pi}$ and $^1{\chi}^v$ (the first order valence connectivity index).

• 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.

• Bulletin of the Korean Chemical Society
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• v.29 no.2
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• pp.363-371
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• 2008

As a computational method for the discovery of the effective agonists for PPARd, we address the usefulness of molecular dynamics free energy (MDFE) simulation with explicit solvent in terms of the accuracy and the computing cost. For this purpose, we establish an efficient computational protocol of thermodynamic integration (TI) that is superior to free energy perturbation (FEP) method in parallel computing environment. Using this protocol, the relative binding affinities of GW501516 and its derivatives for PPARd are calculated. The accuracy of our protocol was evaluated in two steps. First, we devise a thermodynamic cycle to calculate the absolute and relative hydration free energies of test molecules. This allows a self-consistent check for the accuracy of the calculation protocol. Second, the calculated relative binding affinities of the selected ligands are compared with experimental IC50 values. The average deviation of the calculated binding free energies from the experimental results amounts at the most to 1 kcal/mol. The computational efficiency of current protocol is also assessed by comparing its execution times with those of the sequential version of the TI protocol. The results show that the calculation can be accelerated by 4 times when compared to the sequential run. Based on the calculations with the parallel computational protocol, a new potential agonist of GW501516 derivative is proposed.

• Food Science and Biotechnology
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• v.14 no.3
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• pp.355-357
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• 2005

This study evaluated the binding abilities of rabbit anti-ovalbumin (OVA) immunoglobulin G (IgG) and egg-allergic patient IgE on gamma-irradiated OVA during proteolysis using pepsin and trypsin. The concentrations of both the intact and the irradiated OVAs decreased during proteolysis when detected with IgG However, when detected by patient IgE the concentration of the intact OVA decreased up to 30 min after the trypsin treatment and increased thereafter. Irradiated OVA detected by patient IgE showed a lower initial concentration (0.16%) than that of the intact OVA, and this reduced concentration was maintained stably. The results indicate that irradiation, rather than enzymatic treatment, could reduce the binding of the irradiated and enzyme-treated OVA. Therefore, gamma irradiation has potential as an effective method to reduce OVA-induced allergy and may enhance the safety of egg-allergic individuals.

• Bulletin of the Korean Chemical Society
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• v.23 no.8
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• pp.1073-1077
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• 2002

Binding of dodecyl trimethylammonium bromide (DTAB) to human and bovine hemoglobin and globin samples has been investigated in 50 mM glycine buffer pH = 10, I = 0.0318 and 300 K by equilibrium dialysis and temperature scanning spectrophotometry techniques and method for calculation of average hydrophobicity. The binding data has been analyzed, in terms of binding capacity concept $({\theta})$, Hill coefficient (nH) and intrinsic Gibbs free energy of binding $({\Delta}Gbv).$ The results of binding data, melting point (Tm) and average hydrophobicity show that human hemoglobin has more structural stability than bovine hemoglobin sample. Moreover the results of binding data analysis represent the systems with two and one sets of binding sites for hemoglobin and globin, respectively. It seems that the destabilization of hemoglobin structure due to removal of heme group, is responsible of such behavior. The results indicating the removal of heme group from hemoglobin caused the depletion of first binding set as an electrostatic site upon interaction with DTAB and exposing the hydrophobic patches for protein.

• Bulletin of the Korean Chemical Society
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• v.16 no.12
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• pp.1153-1162
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• 1995

The conformational details of β-lactose are investigated through molecular dynamics simulations in conjunction with the adiabatic potential energy map. The adiabatic energy map generated in vacuo contains five local minima. The lowest energy structure on the map does not correspond to the structure determined experimentally by NMR and the X-ray crystallography. When aqueous solvent effect is incorporated into the energy map calculation by increasing the dielectric constant, one of the local minima in the vacuum energy map becomes the global minimum in the resultant energy map. The lowest energy structure of the energy map generated in aquo is consistent with the one experimentally determined. Molecular dynamics simulations starting from those fivelocal minima on the vacuum energy map reveal that conformational transitions can take place among various conformations. Molecular dynamics simulations of the lactose and ricin B chain complex system in a stochastic boundary indicate that the most stable conformation in solution phase is bound to the binding site and that there are conformational changes in the exocyclic region of the lactose molecule upon binding.