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

• Journal of the Korean Chemical Society
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• v.67 no.1
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• pp.13-18
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• 2023

We evaluate electron density functional theories for the computation of 0-1 and 1-2 transition energies of local OH stretching motion of water molecules in condensed phases. By examining thirteen density functionals and nine sets of basis functions, it was found that the optimal combination that predicts the transition energies highly correlated with those calculated by the coupled cluster theory, CCSD(T), is the hybrid density functional theory developed by Head-Gordon group, ωB97X(D)/6-31+G^*.

• Bulletin of the Korean Chemical Society
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• v.34 no.5
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• pp.1551-1554
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• 2013

• Bulletin of the Korean Chemical Society
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• v.19 no.5
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• pp.553-557
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• 1998

Density functional theory calculations are reported for the carbon clusters bonded with two oxygen atoms $OC_No$ (n=2-6). The structures, vibrational frequencies and dipole moments are computed by BLYP theory with the 6-311G* basis set. Good agreement is obtained between the computed and experimentally observed properties. The ground states of these molecules are shown to be linear. Cyclic structures with higher energy are also predicted.

• Proceeding of EDISON Challenge
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• 2014.03a
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• pp.475-477
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• 2014

Self-assembly of the molecular system of perylene-3,4,9,10-tetracarboxylic-3,4,9,10-dianhydride (PTCDA) is of such potential importance for organic semiconductor devices that PTCDA molecule on a variety of substrates has been extensively studied. Therefore we studied the density of states (DOS), the charge densities, and intermolacular bond lengths for PTCDA, and investigated PTCDA absorptioni sites on Si(111)In-$8{\times}8$ at room temperature using the density functional theory calculations.

• Journal of the Korean Chemical Society
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• v.63 no.2
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• pp.73-77
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• 2019

We compared methodologies based on the density functional theory (DFT), e.g., time-dependent DFT (TD-DFT), TD-DFT within Tamm-Dancoff approximation (TDA-DFT), and spin-unrestricted DFT (UDFT), that are usually employed to optimize the geometries of ${\pi}$-conjugated molecules in their lowest lying triplet excited ($T_1$) state. As a model system for ${\pi}$-conjugated molecules, we employed 1,2,3,4,5-pentacyano-6-phenyl-benzene. In conjunction with 6-31G(d) basis sets, we made use of gap-tuned range-separated ${\omega}B97X$ functional which is often employed recently in the calculations of molecular excited states. Near the equilibrium geometries, we found that the important difference between the geometries derived at UDFT level and those at TD-DFT or TDA-DFT methods: more stable ground-state energies but higher triplet excitation energies for UDFT derived geometries. In the studies, we discuss such differences in more detail.

• Journal of the Korean Ceramic Society
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• v.53 no.3
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• pp.312-316
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• 2016

The energetics of defects in the presence of domain walls in $LiNbO_3$ are characterized using density-functional theory calculations. Domain walls show stronger interactions with antisite defects than with interstitial defects or vacancies. As a result, antisite defects act as a strong pinning center for the domain wall in $LiNbO_3$. Analysis of migration behavior of the antisite defects across the domain wall shows that the migration barrier of the antisite defects is significantly high, such that the migration of antisite defects across the domain wall is energetically not preferable. However, further study on excess electrons shows that the migration barrier of antisite defects can be lowered by changing the charge states of the antisite defects. So, excess electrons can enhance the migration of antisite defects and thus facilitate domain wall movement by weakening the pinning effect.

• Journal of the Korean Ceramic Society
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• v.53 no.3
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• pp.301-305
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• 2016

We investigate proton conduction in a nonstoichiometric ${\Sigma}3$ $BaZrO_3$ (210)[001] tilt grain boundary using density functional theory (DFT). We employ the space charge layer (SCL) and structural disorder (SD) models with the introduction of protons and oxygen vacancies into the system. The segregation energies of proton and oxygen vacancy are determined as -0.70 and -0.54 eV, respectively. Based on this data, we obtain a Schottky barrier height of 0.52 V and defect concentrations at 600K, in agreement with the reported experimental values. We calculate the energy barrier for proton migration across the grain boundary core as 0.61 eV, from which we derive proton mobility. We also obtain the proton conductivity from the knowledge of proton concentration and mobility. We find that the calculated conductivity of the nonstoichiometric grain boundary is similar to those of the stoichiometric ones in the literature.

• Journal of the Korean Chemical Society
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• v.60 no.6
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• pp.410-414
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• 2016

The anharmonic frequency of a local OH stretching mode of a water monomer and dimer was calculated using various levels of density functional theory. The quantum chemical potential energy curves as a function of the OH bond distance were calculated, and they were fitted with the Morse potential function to analytically obtain the fundamental transition frequency. By comparing those values with the frequencies similarly calculated using an ab initio quantum chemical method, the coupled cluster theory including both single and double excitations with the perturbative inclusion of triple excitation in the complete basis limit, the accuracy of various density functional methods in the calculation of anharmonic vibration frequency of water molecules was assessed. For a water monomer, X3LYP and B3LYP methods give the best accuracy, whereas for a water dimer, B972, LCBLYP, ${\omega}B97X$, ${\omega}B97$ methods show the best performance.

• Journal of the Korean Chemical Society
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• v.64 no.2
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• pp.61-66
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• 2020

In this study, we investigate the structural and electronic properties of copper oxide clusters, Cu_nO_n (n = 9 - 15). To find the lowest energy structures of copper oxide clusters, we use ReaxFF and density functional theory calculations. We calculate many initial copper oxide clusters using ReaxFF quickly. Then we calculate the lowest energy structures of copper oxide clusters using B3LYP/LANL2DZ model chemistry. We examine the atomization energies per atom, average bond angles, Bader charges, ionization potentials, and electronic affinities of copper oxide clusters. In addition, the second difference in energies is investigated for relative energies of copper oxide clusters.