• Bulletin of the Korean Chemical Society
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• v.34 no.1
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• pp.299-302
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• 2013

• Journal of the Korean Chemical Society
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• v.56 no.2
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• pp.195-200
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• 2012

In this study we present a new approach for computing the partial atomic charge derived from the wavefunctions of molecules. This charge, which we call the "y_charge", was calculated by taking into account the energy level and orbital populations in each molecular orbital (MO). The charge calculations were performed in the software, which was developed by us, developed using the C# programming language. Partial atomic charges cannot be calculated directly from quantum mechanics. According to a partitioning function, the electron density of constituent molecular atoms depends on the electrostatic attraction field of the nucleus. Taking into account the Boltzmann population of each MO as a function of its energy and temperature we obtain a formula of partial charges.

• Journal of Integrative Natural Science
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• v.3 no.4
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• pp.226-230
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• 2010

Calculation of partial charge is important in chemistry. However, because there are many methods developed, it is of considerable interest to know how to calculate and apply properly to address various chemical problems. For basis set, usually double zeta quality is acceptable, and double zeta polarization function would be enough for most cases. To describe electronic state more accurately, Many electron configurations would be necessary to describe highly strained or anionic species. The NPA population introduced new concept about amide bonds, i.e., the planar geometry of nitrogen atom may not come from resonance, but from the lowering of p-orbital energy by electronegative carbonyl carbon atom. The issues for hypervalent atomic charges was also addressed by various charge derivation scheme. When the charge schemes were applied to organolithium compounds, the ionic nature of boding was revealed. This comes from the fact that previous Mulliken partial atomic charges overemphasized the covalent character, wihout much justification. The other partial charge derivation schemes such as NPA(natural population analysis), IPP (Integrated Projected Population) showed that much more ionic picture. ESP potential derived charges are generally believed to be suitable to describe intermolecular interactions, therefore they are used for molecular dynamics simulations and CoMFA (comparative molecular field analysis). The charge derivation schemes using multipole polarization was mainly applied to reproduce experimental infrared spectroscopy. In some reports these schemes are also suitable for intermecular electrostatic interactions. Charges derived from electron density gradient have shown the some bonds are not straight, but actually bent. The proper choice of charge-calculation method along with suitable level of theory and basis set are briefly discussed.

• Journal of Integrative Natural Science
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• v.3 no.4
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• pp.231-236
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• 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
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• v.16 no.10
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• pp.915-923
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• 1995

The parameters for an empirical net atomic charge calculation method, Modified Partial Equalization of Orbital Electronegativity (MPEOE), were determined for the atoms in organosilicon compounds and zeolites. For the organosilicon family, the empirical parameters were determined by introducing both experimental and ab initio observables as constraints, these are the experimental and ab initio dipole moments, and the ab initio electrostatic potential of the organosilicon molecules. The Mulliken population was also introduced though it is not a quantum mechanical observable. For the parameter optimization of the atoms in the aluminosilicates, the dipole moments and the electrostatic potentials which calculated from the 6-31G** ab initio wave function were used as constraints. The empirically calculated atomic charges of the organosilicons could reproduce both the experimental and the ab inito dipole moments well. The empirical atomic charges of the aluminosilicates could reproduce the ab initio electrostatic potentials well also.

• Bulletin of the Korean Chemical Society
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• v.32 no.5
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• pp.1604-1612
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• 2011

We developed three-dimensional quantitative structure activity relationship (3D-QASR) models for 17 adamantyl derivatives as P-glycoprotein (P-gp) inhibitors. Eighteen different partial charge calculation methods were tested to check the feasibility of the 3D-QSAR models. Best predictive comparative molecular field analysis (CoMFA) model was obtained with the Austin Model 1-Bond Charge Correction (AM1-BCC) atomic charge. The 3D-QSAR models were derived with CoMFA and comparative molecular similarity indices analysis (CoMSIA). The final CoMFA model ($q^2$ = 0.764, $r^2$ = 0.988) was calculated with an AM1-BCC charge and electrostatic parameter, whereas the CoMSIA model ($q^2$ = 0.655, $r^2$ = 0.964) was derived with an AM1-BCC charge and combined steric, electrostatic, hydrophobic and HB-acceptor parameters. Leave-five-out (LFO) cross-validation was also performed, which yielded good correlation coefficient for both CoMFA (0.801) and CoMSIA (0.656) models. Robustness of the developed models was checked further with 1000 run bootstrapping analyses, which gave an acceptable correlation coefficient for CoMFA (BS-$r^2$ = 0.997, BS-SD = 0.003) and CoMSIA (BS-$r^2$ = 0.996, BS-SD = 0.018).

• Journal of Integrative Natural Science
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• v.7 no.1
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• pp.45-49
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• 2014

The (c-Jun N-terminal kinase 3) JNK3 is a potential therapeutic target for various neurological disorders. Here, a three dimensional quantitative structure-activity relationship (3D-QSAR) study on phenoxypyridine as JNK3 inhibitors was performed to rationalize the structural requirements responsible for the inhibitory activity of these compounds. The comparative molecular field analysis (CoMFA) using different partial atomic charges, was employed to understand the structural factors affecting JNK3 inhibitory potency. The Gasteiger-Marsili yielded a CoMFA model with cross-validated correlation coefficient ($q^2$) of 0.54 and non-cross-validated correlation coefficient ($r^2$) of 0.93 with five components. Furthermore, contour maps suggested that bulky substitution with oxygen atom in $R^3$ position could enhance the activity considerably. The work suggests that further chemical modifications of the compounds could lead to enhanced activity and could assist in the design of novel JNK3 inhibitors.

• Journal of the Korean Vacuum Society
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• v.6 no.S1
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• pp.127-132
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• 1997

Microstructure of the Fe-Ti system by ion beam mixing of multilayers at 300 K and 77 K has been studied in a wide composition range. The ion bombardment was carried out using $Ar^+$ ions at 80 keV. Using grazing angle x-ray diffraction we find that the lattice parameters of these bcc solid solutions are very close to that of $\alpha$-Fe. Extended x-ray absorption fine-structure spectroscopy have been performed to investgate the short-range order in the ion-beam-mixed state. The structure parameters, such as the interatomic distance and the coordination number are estmated from the Fe K-edge Fourier filtered EXAFS spectra. The interatomic distance is independent of the alloy concentration and it is almost constant. The study of x-ray absorption near-edge structure gives information on the individual $\rho$components of the partial densityof states of the conduction band of the Fe and Ti We also find that a charge transfer from Ti to Fe atoms takes place.

• Applied Chemistry for Engineering
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• v.31 no.1
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• pp.97-102
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• 2020

Recently, various degradation mechanisms of lithium secondary battery cathode materials have been revealed. As a result, many studies on overcoming the limitation of cathode materials and realizing new electrochemical properties by controlling the degradation mechanism have been reported. Li-rich layered oxide is one of the most promising cathode materials due to its high reversible capacity. However, the utilization of Li-rich layered oxide has been restricted, because it undergoes a unique atomic structure change during the cycle, in turn resulting in unwanted electrochemical degradations. To understand an atomic structure deterioration mechanism and suggest a research direction of Li-rich layered oxide, we deeply evaluated the atomic structure of 0.4Li₂MnO₃_0.6LiNi_1/3Co_1/3Mn_1/3O₂ Li-rich layered oxide during electrochemical cycles, by using an atomic-resolution analysis tool. During a charge process, Li-rich materials undergo a cation migration of transition metal ions from transition metal slab to lithium slab due to the structural instability from lithium vacancies. As a result, the partial structural degradation leads to discharge voltage drop, which is the biggest drawback of Li-rich materials.