• 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.

• Journal of Integrative Natural Science
• /
• v.15 no.4
• /
• pp.179-186
• /
• 2022

The c-Jun N-terminal kinase (JNK3) play major role in neurodegenerative diseases like Alzheimer's disease, Parkinson's disease, cerebral ischemia and other Central Nervous System disorders. Since JNK3 is primarily stated in the brain and stimulated by stress-stimuli, this situation is conceivable that inhibiting JNK3 could be a possible treatment for the mechanisms underlying neurodegenerative diseases. In this study drugs from Zinc15 database were screened to identify the JNK3 inhibitors by Molecular docking and Density functional theory approach. Molecular docking was done by Autodock vina and the ligands were selected based on the binding affinity. Our results identified top ten novel ligands as potential inhibitors against JNK3. Molecular docking revealed that Venetoclax, Fosaprepitant and Avapritinib exhibited better binding affinity and interacting with proposed binding site residues of JNK3. Density functional theory was used to compute the values for energy gap, lowest unoccupied molecular orbital (LUMO), and highest occupied molecular orbital (HOMO). The results of Density functional theory study showed that Venetoclax, Fosaprepitant and Avapritinib serves as a lead compound for the development of JNK3 small molecule inhibitors.

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

• Textile Coloration and Finishing
• /
• v.21 no.5
• /
• pp.35-40
• /
• 2009

Computational calculations of molecular orbital and electrochemical redox/oxidation potentials are of very importance to determine the compound properties. The energy levels of molecular orbital were calculated by the density function theory (DFT) with exchange correction functional of local density approximation (LSA) based on the Perdew-Wang (PWC) setting and cyclic voltammetry.

• 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.

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

• Proceedings of the Korean Institute of Electrical and Electronic Material Engineers Conference
• /
• 2003.11a
• /
• pp.148-151
• /
• 2003

The spin density of ${\beta}-MnO_2$ structure was theoretically investigated by $DV-X_{\alpha}$ (the discrete variation $X{\alpha}$) method, which is a sort of the first principle molecular orbital method using Hatre-Fock-Slater approximation. The used cluster model was $[Mn_{14}O_{56}]^{-52}$. The ${\beta}-MnO_2$ is a paramagnetic oxide semiconductor material having the energy band gap of 0.18 eV and an 3 loan-pair electrons in the 3d orbital of an cation. This material exhibits spin-only magnetism and has the magnetic ordering temperature of 94 K. Below this temperature its magnetism appears as antiferromagnetism. The calculations of electronic state showed that if the initial spin condition of input parameters changed, the magnetic state changed from paramagnetic to antiferromagnetic. When d orbital of all Mn atoms in cluster had same initial spin state as only up spin, paramagnetic spin density distribution appeared by the calculation. On the other way, d orbital had alternately changed spin state along special direction the resulted spin distribution showed antiferromagnetism.

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

• Journal of the Korean Electrochemical Society
• /
• v.16 no.3
• /
• pp.177-183
• /
• 2013

As the development of available binder in the harsh conditions is needed, we propose the proper binder for high-voltage lithium-ion secondary batteries based on the quantum chemistry modeling. The optimized structures, HOMO (Highest Occupied Molecular Orbital) energies and ionization potentials of 4 binders, which were considered from monomer to tetramer, were investigated by the semi-empirical and DFT (Density Functional Theory) calculations. The results show that the ionization potential values by calculation tend to be close to the oxidation potentials from the measurement of linear sweep voltametry (LSV). The order of oxidative resistance from high value to low value is following: poly(hexafluropropylene), poly(vinylidene fluoride), poly(methyl acrylate) and poly(acryl amide). Also these results correspond with the experimental values. Thus, we find the reason why HOMO (Highest Occupied Molecular Orbital) energy of PHFP has the highest value than other binders by analysis of HOMO orbital structures.

• Bulletin of the Korean Chemical Society
• /
• v.25 no.7
• /
• pp.1061-1064
• /
• 2004

Molecular visualization software has the common objective of manipulation and interpretation of data from numerical simulations. They visualize many complicated molecular structures with personal computer and workstation, to help analyze a large quantity of data produced by various computational methods. However, users are often discouraged from using these tools for visualization and analysis due to the difficult and complicated user interface. In this regard, we have developed an easy-to-use three-dimensional molecular visualization and analysis program named POSMOL. This has been developed on the Microsoft Windows platform for the easy and convenient user environment, as a compact program which reads outputs from various computational chemistry software without editing or changing data. The program animates vibration modes which are needed for locating minima and transition states in computational chemistry, draws two and three dimensional (2D and 3D) views of molecular orbitals (including their atomic orbital components and these partial sums) together with molecular systems, measures various geometrical parameters, and edits molecules and molecular structures.