• Journal of the Korean Electrochemical Society
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• v.5 no.4
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• pp.183-188
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• 2002

The structure of species formed in $NbCI_5-I-ethyl-3-methylimidazolium$ chloride (EMIC) room-temperature molten salt (RTMS) was examined with the Raman spectroscopic measurement and ab initio molecular orbital calculation. The equilibrium structures of $NbCl_5,\;NbCl_6^-,\;Nb_2CI_{10},\;Nb_2CI_{11}^-,\;Nb_3CI_6^-,\;NbCI_6^--EMI^+\;(in\;which\;NbCI_6^-$ anion approaches $EMI^+$ cation with strong interaction) and $Nb_2CI_{11}^--EMI^+$ were obtained with the HF/LANL2DZ level of calculation. The harmonic frequencies at each equilibrium structure were compared with Raman spectra. The harmonic frequencies of $NbCI_6^--EMI^+,\; Nb_2CI_{11}^--EMI^+,\;and\;Nb_2CI_{10}$ were in good agreement with the Raman spectra of RTMS melts. In the $NbCI_5-EMIC RTMS$, the main species were $NbCI_6^-\;and\;EMI^+$. In the $NbCl_5-EMIC$ RTMS added $NbCl_5\;over\;50mol\%$, small amount of $Nb_2CI_{11}^-\;and\; Nb_2CI_{10}$ were also formed. The structures of anions and cation in the RTMS distorted from free ions with Coulomb force.

• Journal of the Korean Chemical Society
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• v.43 no.4
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• pp.378-383
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• 1999

Ab initio calculation is performed to estimate the substituent effects for Para-substituted pyridines. Electrostatic potentials are obtained from ab initio molecular orbital wavefunctions of optimized structures for substituted pyridines. Electrostatic potentials are computed to be minimum at nitrogen atom of pyridines. The potential minima are good correlated with the substituent constants, ${\sigma}_p$ and with the ${\Delta}pKa$. It is shown that the electrostatic potential minima can be used as a measure of substituent effects.

• Bulletin of the Korean Chemical Society
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• v.24 no.6
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• pp.728-730
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• 2003

Bond lengths, harmonic vibrational frequencies and dissociation energies of TlAt are calculated at ab initio molecular orbital and density functional theory using effective spin-orbit operator and relativistic effective core potentials. Spin-orbit effects estimated from density functional theory are in good agreement with those from ab initio calculations, implying that density functional theory with effective core potentials can be an efficient and reliable methods for spin-orbit interactions. The estimated $R_e$, $ω_e$ and $D_e$ values are 2.937 ${\AA}$, 120 $cm^{-1}$, 1.96 eV for TlAt. Spin-orbit effects generally cause the bond contraction in Group 13 elements and the bond elongation in the Group 17 elements, and spin-orbit effects on Re of TlAt are almost cancelled out. The spinorbit effects on $D_e$ of TlAt are roughly the sum of spin-orbit effects on $D_e$ of the corresponding element hydrides. Electron correlations and spin-orbit effects are almost additive in the TlAt molecule.

• 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.8 no.1
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• pp.10-15
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• 1987

The results of an ab initio (6-31G) molecular orbital calculation of the dipole moment derivatives and gas phase IR intensities of difluoromethane are reported. The results are compared with corresponding values obtained from a CNDO calculation. The directions of the dipole derivatives calculated by the two methods agree very well, whereas the intensities differ significantly. The results are also analyzed for the charge-charge flux-overlap electronic contributions to the dipole derivatives.

• Korean Journal of Crystallography
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• v.19 no.1
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• pp.1-6
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• 2008

The reaction of dilithio-o-carborane with dipenyl disulfide produces a phenyl thiolated o-carborane and it has been confirmed that there is conformational similarity between the structure of the compound elucidated by X-ray crystallography and that calculated by ab initio and density functional theory.

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2000.11a
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• pp.32-34
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• 2000

Computational chemistry is a discipline using computational methods for the calculation of molecular structure, properties, and reaction or for the simulation of molecular behavior. Relating and turning the complexity of data from genomics, high-throughput screening, combinatorial chemical synthesis, gene-expression investigations, pharmacogenomics, and proteomics into useful information and knowledge is the primary goal of bioinformatics. In particular, the structure-based molecular design is one of essential fields in bioinformatics and it can be called as structural bioinformatics. Therefore, the conformational analysis for proteins and peptides using the techniques of computational chemistry is expected to play a role in structural bioinformatics. There are two major computational methods for conformational analysis of proteins and peptides; one is the molecular orbital (MO) method and the other is the force field (or empirical potential function) method. The MO method can be classified into ab initio and semiempirical methods, which have been applied to relatively small and large molecules, respectively. However, the improvement in computer hardwares and softwares enables us to use the ab initio MO method for relatively larger biomolecules with up to v100 atoms or ∼800 basis functions. In order to show how computational chemistry can be used in structural bioinformatics, 1 will present on (1) cis-trans isomerization of proline dipeptide and its derivatives, (2) positional preference of proline in ${\alpha}$-helices, and (3) conformations and activities of Arg-Gly-Asp-containing tetrapeptides.

• Bulletin of the Korean Chemical Society
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• v.19 no.10
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• pp.1042-1047
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• 1998

The fluorescence excitation (FE) spectrum of the S1-S0 (1B2-1A1) transition of dimethyldiazirine cooled in supersonic jet expansions has been obtained. Dispersed fluorescence (DF) spectra have also been taken for some prominent features of the FE spectrum. Vibrational analyses of the FE and DF spectra with the help of an ab initio molecular orbital calculation lead to some new vibrational assignments and refined fundamental frequencies.

• Bulletin of the Korean Chemical Society
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• v.8 no.3
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• pp.174-179
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• 1987

The results of an ab initio (6-31G) molecular orbital calculations of the dipole moment derivatives and gas phase IR intensities in $CH_3F$ and $CF_4$ are reported. The results are compared with corresponding values obtained from a CNDO calculation. We have also analyzed the theoretical polar tensors into the charge, charge flux, and overlap contributions. The effective term charges of hydrogen atom appeared to be transferable among the fluoromethane molecules.

• 한국정보디스플레이학회:학술대회논문집
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• 2009.10a
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• pp.108-111
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• 2009

We have determined the electronic energy level alignment at the interface between 4,4'-bis-N-phenyl-1-naphthylamino biphenyl (NPB) and 1,4,5,8,9,11-hexaazatriphenylenehexacarbonitrile (HAT-CN) using ultraviolet photoelectron spectroscopy (UPS). The highest occupied molecular orbital (HOMO) of 20 nm thick HAT-CN film was located at 3.8 eV below the Fermi level. Thus the lowest unoccupied molecular orbital (LUMO) is very close to the Fermi level. The HOMO position of NPB was only about 0.3 eV below Fermi level at NPB/HAT-CN interface. This enables an easy excitation of electrons from the NPB HOMO to the HAT-CN LUMO, creating electron-hole pairs across this organic-organic interface. We also study the interaction of HAT-CN with a few metallic surfaces including Ca, Cu, and ITO using UPS and ab-inito electronic structure calculation techniques.