• Bulletin of the Korean Chemical Society
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• 제29권2호
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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.

• 한국세라믹학회지
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• 제28권12호
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• pp.961-968
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• 1991

The nature and composition of the surfaces of silicon nitride and β-Sialon powders were investigated using high voltage and high resolution transmission electron microscopy (TEM) and X-ray photoelectron spectroscopy (XPS). β-Sialon powder was produced from Hadong kaolin by the carbothermic reduction and simultaneous nitridation. XPS showed that Al was contained in the surface of β-Sialon powder besides Si, N and O components, which is different from that of silicon nitride. It was supposed that Al in the surface of β-Sialon was bonded with oxygen from the oxygen-nitrogen ratio and the measurement of Al 2p binding energies. After both silicon nitride and β-Sialon powders were oxidized at 800℃ for 24h in air, nitrogen didn't exist in the surfaces and the depth of the oxide layer increased. The measurement of Si 2p binding energies showed that the chemical shifts occurred from Si3N2O and/or Si2N2O to SiO2 phase.

• 한국재료학회지
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• 제15권9호
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• pp.566-576
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• 2005

This paper describes an ab Initio study on interface energies, misfit strain energies, and electron structures at coherent interfaces Fe(bcc structure)/MCs(NaCl structure M=Ti, Zr, Hf). The interface energies at relaxed interfaces Fe/TiC, Fe/ZrC and Fe/HfC were 0.263, 0.153 and $0.271 J/m^2$, respectively. It was understood that the dependence of interface energy on the type of carbide was closely related to changes of the binding energies between Fe, M and C atoms before and after formation of the interfaces Fe/MCs with the help of the DLP/NNBB (Discrete Lattice Plane/ Nearest Neighbour Broken Bond) model and data of the electron structures. The misfit strain energies in Fe/TiC, Fe/ZrC and Fe/HfC systems were 0.390, 1.692 and 1.408 eV per 16 atoms(Fe: 8 atoms and MC; 8 atoms). More misfit energy was generated as difference of lattice parameters between the bulk Fe and the bulk MCs increased.

• Interdisciplinary Bio Central
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• 제2권2호
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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.

• 대한화학회지
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• 제56권1호
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• pp.34-46
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• 2012

Dopants and defects can be introduced as well as the intercalation of metals into single wall carbon nanotubes (SWCNTs) to modify their electronic and magnetic properties, thus significantly widening their application areas. Through spinpolarized density functional theory (DFT) calculations, we have systemically studied the following: (i) (10,0) and (5,5) SWCNT doped with nitrogen ($CN_xNT$), (ii) (10,0) and (5,5) SWCNT with pyridine-like defects (3NV-$CN_xNT$), and (iii) chemical functionalization of (10,0) and (5,5) 3NV-$CN_xNT$ with 12 different transition metals (TMs) (Sc, Ti, V, Cr, Mn, Fe, Co, Ni, Cu, Zn, Pd, and Pt). Attention was done in searching for the most stable configurations, deformation, calculating the formation energies, and exploring the effects of the doping concentration of nitrogen and pyridine-like nitrogenated defects on the electronic properties of the nanotubes. Also, calculating the corresponding binding energies and effects of chemical functionalization of TMs on the electronic and magnetic properties of the nanotubes has been made. We found out that the electronic properties of SWCNT can be effectively modified in various ways, which are strongly dependent not only on the concentration of the adsorbed nitrogen but also to the configuration of the adsorbed nitrogen impurities, the pyridine-like nitrogenated defects, and the TMs absorbed; due to the strong interaction between the d orbitals of TMs and the p orbitals of N atoms, the binding strengths of TMs with the two 3NV-$CN_xNT$ are significantly enhanced when compared to the pure SWCNTs.

• Bulletin of the Korean Chemical Society
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• 제35권4호
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• pp.1005-1010
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• 2014

We have performed DFT calculations to devise some possible fullerene dimers (from $C_{60}$ and $C_{80}$) connected through $C_{24}$ and $C_{36}$ bridge cages with the face-to-face linking model. The fullerene dimers with $C_{36}$ bridges have lower binding energies and greater HOMO-LUMO gaps than those of the fullerene dimers with $C_{24}$ bridges. Also, the replacement of $C_{60}$ cages with $C_{80}$ ones always leads to an increase in binding energies and HOMO-LUMO gaps in these systems. Dimerization of $C_{60}$ and $C_{80}$ fullerenes with $C_{24}$ and $C_{36}$ results in a significant decrease in antiaromaticity of the antiaromatic cages $C_{24}$ and $C_{80}$, and an increase in the aromaticity of the aromatic cages $C_{36}$ and $C_{60}$. Therefore, DFT results indicate that those fullerene dimers involving the initially harshly antiaromatic $C_{24}$ or $C_{80}$ cages are more energetically favorable configuration than the fullerene dimers involving the aromatic $C_{36}$ and $C_{60}$ cages.

• 한국전기전자재료학회논문지
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• 제18권9호
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• pp.781-786
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• 2005

The binding energy in the n-type $GaAs/Al_xGa_{1-x}As$ quantum well is calculated. The shooting method, modified from the finite difference method, is used for the calculation of the subband energy level and its wave function. In order to account tot the change of the potential energy due to the charged particles, impurities and electrons, the self consistent method is employed. The wave function used for the calculation of the binding energy is assumed to be composed of the envelope function and hydrogenic 1s function. Then, the binding energies calculated by taking into account lot two different types of the hydrogenic 1s function are compared.

• Bulletin of the Korean Chemical Society
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• 제31권11호
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• pp.3291-3296
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• 2010

A gelastatins (1), natural MMP inhibitors, and their hydroxamate analogues (2) in TACE enzyme evaluated for discovery of potent TACE inhibitors. We have employed molecular dynamics simulations to compute the relative free energy of hydration and binding to TACE for gelastatin (1) and its hydroxamate analogue (2). The relative free energy difference is directly described in this article using the free energy perturbation approach as a means to accurately predict the TACE inhibitor of gelastatin analogues. The results show that the good agreement between the experimental and theoretical relative free energies of binding, gelastatin hydroxamate (2) binds stronger to TACE by -3.37 kcal/mol. The desolvation energy costs significantly reduced binding affinity, hydroxamate group associated with high desolvation energy formed strong favorable interactions with TACE with more than compensated for the solvation costs and therefore led to an improvement in relative binding affinity.

• Bulletin of the Korean Chemical Society
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• 제23권1호
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• pp.48-52
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• 2002

Using several molecular modeling programs we have performed computer simulations to investigate the complexation behaviors of an ester derivative of p-tert-butylcalix[5]arene (1e) toward a variety of butylammonium ions. Semi-empirical AM1 method was used for calculating the binding energies and the formation enthalpies. MM and CVFF forcefields for molecular mechanics calculations were adapted to express the complexation energies of the host. Molecular dynamics were performed to the calculated complex systems to simulate the ionophoric behavior of the host-guest complexes. The absolute Gibbs free energies of the host (1e) complexed with four kinds of butylammonium ions have been calculated using the Finite Difference Thermodynamic Integration (FDTI) method in Discover. Calculation results show that the trend in complex formation is n-$BuNH_3^+$ > iso-$BuNH_3^+$ >> sec-$BuNH_3^+$ > tert-$BuNH_3^+$, which is in good agreement with the experimental results.

• Advances in nano research
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• 제3권1호
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• pp.13-27
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• 2015

Size dependent emission properties and the interband optical transition energies in group-III nitride based quantum dots are investigated taking into account the geometrical confinement. Exciton binding energy and the optical transition energy in $Ga_{0.9}In_{0.1}N$/GaN and $Al_{0.395}In_{0.605}N$/AlN quantum dots are studied. The largest intersubband transition energies of electron and heavy hole with the consideration of geometrical confinement are brought out. The interband optical transition energies in the quantum dots are studied. The exciton oscillator strength as a function of dot radius in the quantum dots is computed. The interband optical absorption coefficients in GaInN/GaN and AlInN/AlN quantum dots, for the constant radius, are investigated. The result shows that the largest intersubband energy of 41% (10%) enhancement has been observed when the size of the dot radius is reduced from $50{\AA}$ to $25{\AA}$ of $Ga_{0.9}In_{0.1}N$/GaN ($Al_{0.395}In_{0.605}N$/AlN) quantum dot.