• 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.31 no.3
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• pp.595-598
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• 2010

Ab initio and DFT molecular orbital calculations predict that acetyl radical reacts with acetylene through interactions primarily involving the SOMO of the radical and the in-plane ${\pi}$-bond of acetylene. An energy barrier (${\Delta}E_1$) of 39.6 kJ $mol^{-1}$ is predicted for the preferred anti arrangement of reactants at the CCSD(T)/cc-pVDZ//BHandHLYP/cc-pVDZ level of theory. NBO analysis reveals additional interactions between the radical SOMO and the nearby C-H ${\sigma}$-bond in acetylene worth about 10% of the total transition state interaction energy. This type of orbital interaction has not previously been observed in radical addition reactions involving C-C ${\pi}$-bonds.

• Bulletin of the Korean Chemical Society
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• v.33 no.7
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• pp.2341-2344
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• 2012

A molecular orbital study is presented of the magnetic coupling in the one-dimensional vanadium oxide $Ba_2V_3O_9$ with a bridge formed by two different types of $VO_4$ tetrahedra. The concept of complementary versus counter-complementary effect has been used to explain the structural origin of the magnetic behavior of the compound. Namely, the observed antiferromagnetic coupling is dominated by the orbital complementarity of the V(1) tetrahedra sharing only one oxygen corner with two adjacent $VO_6$ octahedra. The second type of V(2) tetrahedra does not provide a noticeable contribution to the magnetic coupling due to the orbital counter-complementarity of the bridging ligand.

• Proceedings of the Korean Vacuum Society Conference
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• 2016.02a
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• pp.142.2-142.2
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• 2016

The metal intercalation to an organic semiconductor is of importance since the charge transfer between a metal and an organic semiconductor can induce the highly enhanced conductivity for achieving efficient organic electronic devices. In this regard, the changes of the electronic structure of copper phthalocyanine (CuPc) caused by the intercalation of potassium are studied by ultraviolet photoemission spectroscopy (UPS) and density functional theory (DFT) calculations. Potassium intercalation leads to the appearance of an intercalation-induced peak between the highest molecular occupied orbital (HOMO) and the lowest molecular unoccupied orbital (LUMO) in the valence-band spectra obtained using UPS. The DFT calculations show that the new gap state is attributed to filling the LUMO+1, unlike a common belief of filling the LUMO. However, the LUMO+1 is not conductive because the ${\pi}$-conjugated macrocyclic isoindole rings on the molecule do not make a contribution to the LUMO+1. This is the origin of a metal-insulator transition through heavily potassium doped CuPc.

• Bulletin of the Korean Chemical Society
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• v.15 no.8
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• pp.658-662
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• 1994

Ab initio and extended Huckel calculations have been applied to discuss the electronic structure, ring inversion barrier, and geometry of the $Cp_2TiS_3$ compound. The deformation of four membered ring in the planar geometry is originated from a second-order Jahn-Teller distortion due to the small energy gap between HOMO and LUMO on the basis of extended Huckel calculations. The puckered $C_s$ geometry is stabilized by the interaction of the $x^2-y^2$ metal orbital with the hybrid orbital in sulfur. Ab initio calculations have been carried out to explore the ring inversion process for the model $Cl_2TiS_3$ compound. We have optimized $C_s$ and $C_{2v}$ structures of the model compound at the RHF level. The energy barriers for the ring inversion are sensitive to the used basis set. With 4-31$G^*$ for the Cl and S ligands, the barriers are computed to be 8.41 kcal/mol at MP2 and 8.02 kcal/mol at MP4 level.

• Bulletin of the Korean Chemical Society
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• v.32 no.7
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• pp.2358-2368
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• 2011

Density functional theory (DFT) and time-dependent density functional theory (TDDFT) calculations, employing the B3LYP method and the LANL2DZ, 6-31G$^*$(LANL2DZ for Tc), 6-31G$^*$(cc-pVDZ-pp for Tc) and DGDZVP basis sets, have been performed to investigate the electronic structures and absorption spectra of the technetium-99m-labeled methylenediphosphonate ($^{99m}Tc$-MDP) complex of the simplest diphosphonate ligand. The bonding situations and natural bond orbital compositions were studied by the Mulliken population analysis (MPA) and natural bond orbital (NBO) analysis. The results indicate that the ${\sigma}$ and ${\pi}$ contributions to the Tc-O bonds are strongly polarized towards the oxygen atoms and the ionic contribution to the Tc-O bonding is larger than the covalent contribution. The electronic transitions investigated by TDDFT calculations and molecular orbital analyses show that the origin of all absorption bands is ascribed to the ligand-to-metal charge transfer (LMCT) character. The solvent effect on the electronic structures and absorption spectra has also been studied by performing DFT and TDDFT calculations at the B3LYP/6-31G$^*$(cc-pVDZ-pp for Tc) level with the integral equation formalism polarized continuum model (IEFPCM) in different media. It is found that the absorption spectra display blue shift in different extents with the increase of solvent polarity.

• Bulletin of the Korean Chemical Society
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• v.5 no.2
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• pp.61-64
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• 1984

The molecular orbital calculations for solid HF are performed by using the pseudolattice method considering the coulomb lattice sum. In order to obtain the reliable net atomic charges and lattice energy of one dimensional chains, the limited counting of interactions terms up to second neighbours for zig-zag chain and third neighbours for linear chain are sufficient in this calculation. In three dimensional solid HF, the contribution of interaction energy between non-hydrogen bonded neighbours to lattice energy is about 3.5% and the lattice energy of nonpolar structure is stablized by 2.05 kcal/mole compared with that of polar structure. And, this method is further tested and compared with the other methods.

• Proceeding of EDISON Challenge
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• 2017.03a
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• pp.128-131
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• 2017

We explore the inverse electron demand Diels-Alder reactions of tetrazines with various functional groups employing quantum calculations. In general, the rate of inverse electron demand Diels-Alder reaction depends on molecular orbital levels of electron donor and electron acceptor. Likewise, ${\pi}$ orbital of the dienophile and ${\pi}^*$ orbital of the diene is a key factor. In this work, we discuss the case where the energy of diene's ${\pi}^*$ molecular orbital is not the sole governing factor to determine the reaction rate, rather the rate shows strong correlation with the charge density of dienes.

• Journal of the Korean Chemical Society
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• v.57 no.4
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• pp.461-471
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• 2013

Optimized geometrical structure, atomic charges, molecular electrostatic potential, nonlinear optical (NLO) effects and thermodynamic properties of the title compound N-(2,5-methylphenyl)salicylaldimine (I) have been investigated by using ab initio quantum chemical computational studies. Calculated results showed that the enol form of (I) is more stable than keto form. The solvent effect was investigated for obtained molecular energies, hardneses and the atomic charge distributions of (I). Natural bond orbital and frontier molecular orbital analysis of the title compound were also performed. The total molecular dipole moment (${\mu}$), linear polarizability (${\alpha}$), and first-order hyperpolarizability (${\beta}$) were calculated by B3LYP method with 6-31G(d), 6-31+G(d,p), 6-31++G(d,p), 6-311+G(d) and 6-311++G(d,p) basis sets to investigate the NLO properties of the compound (I). The standard thermodynamic functions were obtained for the title compound with the temperature ranging from 200 to 450 K.

• Journal of the Korean Chemical Society
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• v.53 no.6
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• pp.671-676
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• 2009

Described here for the first time is an investigation on geometrical and electronic molecular structure of metol (N-methyl-p-aminophenol sulphate) as corrosion inhibitor of steel using density functional theory (DFT) calculations. Quantum chemical parameters such as highest occupied molecular orbital energy (EHOMO), lowest unoccupied molecular orbital energy (ELUMO), energy gap ((${\Delta}E$), Mulliken charges (($q_M$) and natural atomic (($q_n$) charge have been calculated both for gas and aqueous phases by using B3LYP/6-31G+(d,p) basis set. The relation between the inhibition efficiency and quantum chemical parameters have been discussed in order to elucidate the inhibition mechanism of the title compound.