• Bulletin of the Korean Chemical Society
• /
• v.19 no.5
• /
• pp.527-530
• /
• 1998

This paper presents the electrochemistry and molecular orbital (MO) picture of a series of conformationally-restricted thioxantone derivatives. A series of $C_2-substituted$ thioxanthones were examined to probe the electronic influence of the substituent on the electrooxidation and electroreduction sites (i.e., on the electron densities at the 10-and 9-positions), respectively. In the presence of "electrophoric" groups such as C=O and S, characteristic electrochemical reduction and oxidation responses are observed. The electrochemical reaction was diffusion-controlled, because the $I_p/{\upsilon}^{1/2}$ ratio was constant for the anodic and cathodic wave of thioxantone derivatives. These substituent effects are presented in terms of correlations of oxidation (or reduction) potentials with the highest occupied molecular orbital (HOMO), or lowest unoccupied molecular orbital (LUMO) energies, respectively. There is good correlation between energies of the HOMO vs. $E_{pa}^{(+)}$ and energies of the LUMO vs. $E_{pc}^{(-)}$. Frontier Molecular Orbital (FMO) is changed by the functional group of thioxanthones. FMO energy level was offered us the information about the electron transfer direction, and the coefficient of FMO was offered the information about the electron transfer position. Sulfur atom has an important effect on oxidation potential, $E_{pa}^{(+)}$ and the carbonyl carbon has an important effect on reduction potential, $E_{pc}^{(-)}$. Therefore we were appreciated that the contribution of sulfur atom for the $E_{pa}^{(+)}$ and HOMO energies is larger than the contribution of carbonyl group for the $E_{pc}^{(-)}$ and LUMO energies.

• Interdisciplinary Bio Central
• /
• v.2 no.2
• /
• pp.6.1-6.5
• /
• 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.

• Journal of the Korean Chemical Society
• /
• v.34 no.2
• /
• pp.136-142
• /
• 1990

PMO (Pertubation Molecular Orbital) energies, ${\delta}E$, have been calculated from NBMO (Nonbonding Molecular Orbital) coefficient for some hydrocarbons by PMO method. It was found that the stabilization energies are correlated with activation energies, bond dissociation energies, and G-values observed from vapor phase radiolysis in the free radical reactions.

• Journal of the Korean Ceramic Society
• /
• v.42 no.5 s.276
• /
• pp.304-307
• /
• 2005

The possible configurations of hydroxyl group in hexagonal hydroxyapatite were identified through molecular orbital calculation. The molecular orbital interaction between O and H in hydroxyl column was analyzed using charge variation and Bond Overlap Population (BOP). We supposed 5 kinds of O-H bond configurations as cluster types of I, II, III, IV, and V. Mulliken's population analysis was applied to evaluate ionic charges of O, H, P, and Ca ions, and BOPs (Bond Overlap Populations) in order to discuss the bond strength change by the atomic arrangement. The stability of each O-H bond configuration was analyzed using bond overlap and ionic charge.

• Journal of Microbiology and Biotechnology
• /
• v.17 no.11
• /
• pp.1789-1796
• /
• 2007

A ${\beta}$-glucosidase with the molecular mass of 160,000 Da was purified to homogeneity from cell extract of a cellulolytic bacterium, Cellulomonas uda CS1-1. The kinetic parameters ($K_m$ and $V_{max}$) of the enzyme were determined with pNP-cellooligosccharides (DP 1-5) and cellobiose. The molecular orbital theoretical studies on the cellulolytic reactivity between the pNP-cellooligosaccharides as substrate (S) molecules and the purified ${\beta}$-glucosidase (E) were conducted by applying the frontier molecular orbital (FMO) interaction theory. The results of the FMO interaction between E and S molecules verified that the first stage of the reaction was induced by exocyclic cleavage, which occurred in an electrophilic reaction based on a strong charge-controlled reaction between the highest occupied molecular orbital (HOMO) energy of the S molecule and the lowest occupied molecular orbital (LUMO) energy of the hydronium ion ($H_3O^+$), more than endocyclic cleavage, whereas a nucleophilic substitution reaction was induced by an orbital-controlled reaction between the LUMO energy of the oxonium ion ($SH^+$) protonated to the S molecule and the HOMO energy of the $H_2O_2$ molecule. A hypothetic reaction route was proposed with the experimental results in which the enzymatic acid-catalyst hydrolysis reaction of E and S molecules would be progressed via $SN_1$ and $SN_2$ reactions. In addition, the quantitative structure-activity relationships (QSARs) between these kinetic parameters showed that $K_m$ has a significant correlation with hydrophobicity (logP), and specific activity has with dipole moment, respectively.

• Journal of Integrative Natural Science
• /
• v.3 no.4
• /
• pp.231-236
• /
• 2010

Partial charge is an important and fundamental concept which can explain many aspects of chemistry. Since a molecule can be regarded as neclei surrounded by electron cloud, there is no way to define a partial charge accurately. Nevertheless, there have been many attempts to define these seemingly impossible parameters, since they would facilitate the understanding of molecular properties such as molecular dipole moment, solvation, hydrogen bonding, molecular spectroscopy, chemical reaction, etc. Common methods are based on the charge equalization, orbital occupancy, charge density, and electric multipole moments, and electrostatic potential fitting. Methods based on the charge equalization using electronegativity are very fast, and therefore they have been used to study many compounds. Methods to subdivide orbital occupancy using basis set conversion, relies on the notion that molecular orbitals are composed of atomic orbitals. The main idea is to reduce overlap integral between two nuclei using converted orthogonal basis sets. Using some quantum mechanical observables like electrostatic potential or charge multipole moments. Using potential grids obtained from wavefunction, partial charges can be fitted. these charges are most useful to describe intermolecular electrostatic interactions. Methods to using dipole moment and its derivatives, seems to be sensitive the level of theory, Dividing electron density using density gradient being the most rigorous theoretically among various schemes, bears best potential to describe the charge the most adequately in the future.

• Bulletin of the Korean Chemical Society
• /
• v.31 no.3
• /
• pp.595-598
• /
• 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.

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

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

• Textile Coloration and Finishing
• /
• v.6 no.1
• /
• pp.28-32
• /
• 1994

The synthesis and absorption spectra of squarvlium(SQ) dyes and croconium(CR) dyes were .studied. Absorption spectra of SQ dye in various solvents exhibited a negative solvatochrornism. Thus, it was suggested that the structure of SQ dye may be a highly polar structure. The λ$_{max}$ of CR dyes undergoes a bathochromic shift of about 100nm compared with the corresponding SQ dyes. This shift can be calculated by the Pariser-Parr-Pople molecular orbital method. From the PPP MO calculation results, we found that SQ dye and CR dye have a almost same Highest Occupied Molecular Orbital(HOMO) level(SQ : -8.0eV, CR : -8.09eV). On the other hand, energy levels of Lowest Unoccupied Molecular Orbital(LUMO) of SQ and CR dyes are -4.09eV and -4.13eV respectively. Thus, replacement of five membered ring by four membered ring in SQ dye causes a large bathochromic shift.t.