• Journal of the Semiconductor & Display Technology
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• v.7 no.3
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• pp.35-39
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• 2008

We study the interaction of acetone molecule $[(CH_3)_2CO]$ on Si(001) surface using density functional theory. An acetone molecule is adsorbed on a Si atom of the Si dimer of the Si(001) surface. The adsorption of the acetone molecule on the Si atom at lower height between the two Si atoms of the dimer is more favorable than that on the Si atoms at upper height. Then we calculate an energy variation of dissociation and four-membered ring structures of the acetone molecule adsorbed on the Si surface. Total energy difference between the two structures is about 0.05 eV, indicating that the two structures are almost equally stable. Energy barrier exists when a hydrogen atom is dissociated and adsorbed on the other Si atom of the dimer, while energy barrier does not exist when the adsorbed acetone molecule changes to four-membered ring structure, except for the rotation of the acetone molecule along z-direction. Therefore, four-membered ring structure is kinetically more favorable than the dissociation structure when the acetone molecule is adsorbed on the Si(001) surface.

• Genomics & Informatics
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• v.11 no.3
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• pp.155-160
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• 2013

Structural information has been a major concern for biological and pharmaceutical studies for its intimate relationship to the function of a protein. Three-dimensional representation of the positions of protein atoms is utilized among many structural information repositories that have been published. The reliability of the torsional system, which represents the native processes of structural change in the structural analysis, was partially proven with previous structural alignment studies. Here, a web server providing structural information and analysis based on the backbone torsional representation of a protein structure is newly introduced. The web server offers functions of secondary structure database search, secondary structure calculation, and pair-wise protein structure comparison, based on a backbone torsion angle representation system. Application of the implementation in pair-wise structural alignment showed highly accurate results. The information derived from this web server might be further utilized in the field of ab initio protein structure modeling or protein homology-related analyses.

• Journal of the Korean Institute of Electrical and Electronic Material Engineers
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• v.18 no.7
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• pp.589-593
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• 2005

The electronic states of ZnO doped with Al, Ga and In, which belong to III family elements in periodic table, were calculated using the density functional theory. In this study, the calculation was performed by two Programs; the discrete variational Xa (DV-Xa) method, which is a sort of molecular orbital full potential method; Vienna Ab-initio Simulation Package (VASP), which is a sort of pseudo potential method. The fundamental mixed orbital structure in each energy level near the Fermi level was investigated with simple model using DV-Xa. The optimized crystal structures calculated by VASP were compared to the measured structures. The density of state and the energy levels of dopant elements were shown and discussed in association with properties.

• Journal of the Korean Chemical Society
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• v.27 no.6
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• pp.399-404
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• 1983

Raman spectra for the carbonyl stretching mode of the amides, and amide-solvent systems have been recorded to investigate the effect of alkyl substitutions at the carbonyl carbon and at the nitrogen on the amide hydrogen-bonding. The data have shown that the interaction affinities are in the order of amide-amide > amide-water > amide-alcohol in formamide system, and amide-water > amide-amide > amide-alcohol in acetamide and propionamide systems. The strength of the proton acceptor of the carbonyl oxygen is increased by the presence of alkyl group to the carbonyl carbon and the proton donorcity of the amide is decreased by the alkyl substitution at the nitrogen. The above results are in good agreement with the ab initio SCF MO calculation.

• Proceedings of the Korean Vacuum Society Conference
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• 2014.02a
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• pp.180.2-180.2
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• 2014

Opening a bandgap by forming graphene nanoribbons (GNRs) and tailoring their properties via doping is a promising direction to achieve graphene-based advanced electronic devices. Applying a first-principles computational approach combining density functional theory (DFT) and DFT-based non-equilibrium Green's function (NEGF) calculation, we herein study the structural, electronic, and charge transport properties of boron-nitrogen binary edge doped GNRs and show that it can achieve novel doping effects that are absent for the single B or N doping. For the armchair GNRs, we find that the B-N edge co-doping almost perfectly recovers the conductance of pristine GNRs. For the zigzag GNRs, it is found to support spatially and energetically spin-polarized currents in the absence of magnetic electrodes or external gate fields: The spin-up (spin-down) currents along the B-N undoped edge and in the valence (conduction) band edge region. This may lead to a novel scheme of graphene band engineering and benefit the design of graphene-based spintronic devices.

• Bulletin of the Korean Chemical Society
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• v.31 no.12
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• pp.3553-3560
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• 2010

A new hydrazone derivative compound has been synthesized and characterized by IR, $^1H$-NMR, $^{13}C$-NMR and UV-vis. spectroscopy techniques, elemental analysis and single-crystal X-ray diffraction (XRD). The new compound crystallizes in monoclinic space group C2/c. In addition to the crystal structure from X-ray experiment, the molecular geometry, vibrational frequencies and frontier molecular orbitals analysis of the title compound in the ground state have been calculated by using the HF/6-31G(d, p), B3LYP/6-311G(d, p) and B3LYP/6-31G(d, p) methods. The computed vibrational frequencies are used to determine the types of molecular motions associated with each of the observed experimental bands. To determine conformational flexibility, molecular energy profile of (1) was obtained by semi-empirical (AM1) calculation with respect to a selected degree of torsional freedom, which was varied from $-180^{\circ}$ to $+180^{\circ}$ in steps of $10^{\circ}$. Molecular electrostatic potential of the compound was also performed by the theoretical method.

• Journal of the Korean Chemical Society
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• v.57 no.3
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• pp.311-315
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• 2013

The geometry structures of hexa-coordinated [NiLX]X complexes ($X=Cl^-,\;Br^-,\;I^-$) {L = 8,9,18,19-tetrahydro-7H,17H-dibenzo[f,o] [1,5,9,13]dioxadiaza cyclohexadecine-8,18-diol} are optimized by density functional theory (DFT) using B3LYP/LANL2DZ. The calculated geometric parameters are in good agreement with the corresponding experimental values. Calculation results about these complexes show that dipole moment decreases, and the energy levels of HOMOs descend from iodo-complex to chloro-complex. The energy levels of HOMOs descend gently from iodo-complex to chloro-complex, while the energy levels of LUMOs in the present complexes are almost similar; therefore the energy gapes between HOMOs and LUMOs increased from iodo-complex to chloro-complex.

• Bulletin of the Korean Chemical Society
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• v.21 no.10
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• pp.953-954
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• 2000

The equilibrium geometrical structures of silver atom clusters at their electronic ground states have been theo-retically determined by using the nonrelativistic semiempirical INDO/1 method. The clusters investigated are Agn, Agn+, and Agn- (n = 7 , 8, 9). In order to find the most stable structure, i.e., the global minimum in energy hypersurface, geometry optimization and energy calculation processes have been repeatedly performed for all the possible graphical models by changing the bond parameters (resonance integral values). The heptamers are pentagonal bipyramidal-Ag7(D5h), Ag7+ (D5h), Ag7- (D5h); the octamers are pentagonal bipyramidal with one atom capped-Ag8(D2d), Ag8+ (Cs), Ag8- (D2d); the nonamers are pentagonal bipyramidal with two atoms capped -Ag9(C2v), Ag9+ (C2v), Ag9- (C2v). Our structures are in good agreement with those by ab initio calculations ex-cept for the anionic Ag9- cluster. And it is noted that the INDO/1 method can accurately predict the Ag cluster geometries when a proper set of bond parameters is used.

• 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.7 no.4
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• pp.262-266
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• 1986

A multi-reference many-body perturbation theory (MRMBPT) method is critically tested in second order by comparing with the corresponding configuration interaction (CI) calculations. Excitation energies of the four-valence-electron states of transition metal atoms and ions are used for the comparison. The agreement between the second order MRMBPT and CI calculations is very reasonable, confirming the reliability of the second order MRMBPT method. The reliability of calculations with the present second order MRMBPT method was only been inferred empirically in the past since most results have been gauged by the agreement with experiment and/or with other MRMBPT calculations based upon different sets of orbitals and configuration spaces. The present MRMBPT method appears to be an efficient ab initio multi-reference method for the calculation of electron correlation effects in atoms and molecules, and it is shown how MRMBPT can be used to estimate core-core and core-valence correlation effects which are often omitted in CI calculations because too many configurations and correlating electrons are involved.