• 통합자연과학논문집
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• 제15권4호
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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.

• 대한화학회지
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• 제67권1호
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• pp.13-18
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• 2023

응축상에 존재하는 물 분자들의 OH 국소 수축 진동에 관한 0-1과 1-2 전이 에너지 계산을 위한 전자 밀도 범함수들을 평가하였다. 열세 개의 범함수와 아홉 개의 기저 함수 집합을 조사하여, 순이론적 coupled cluster 이론 CCSD(T)가 예측하는 진동수와 상관성이 매우 높게 예측되는 밀도 범함수와 활용된 기저 함수 집합은 Head-Gordon 연구진의 혼성 범함수인 ωB97X(D)/6-31+G^* 계산법임을 확인하였다.

• Bulletin of the Korean Chemical Society
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• 제34권5호
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• pp.1551-1554
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• 2013

• Bulletin of the Korean Chemical Society
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• 제19권5호
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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.

• EDISON SW 활용 경진대회 논문집
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• 제3회(2014년)
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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.

• 대한화학회지
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• 제63권2호
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• pp.73-77
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• 2019

${\pi}$-공액계 분자에 대해, density functional theory (DFT) 방법에 기반한 일반적인 삼중항 구조 최적화 방법들, 즉, 시간 의존적 DFT (TD-DFT), Tamm-Dancoff 근사법에 기반한 TD-DFT (TDA-DFT), 그리고 스핀-비제한 DFT (UDFT)에 대한 점검을 수행하였다. 모델 분자로서 1,2,3,4,5-pentacyano-6-phenyl-benzene가 이용되었고, 6-31G(d) 기저 함수와 더불어 여기 상태 계산에 최근 자주 사용되는 에너지 차 조정 영역 분리 functional인 ${\omega}B97X$ functional이 사용되었다. 계산 결과 평형 구조 근처에서, UDFT 최적화된 구조는 TD-DFT 및 TDA-DFT 계산 구조와는 다른 차이점을 보인다. 즉, 보다 안정한 바닥 상태 에너지와 보다 높은 삼중항 여기 에너지가 UDFT 최적화 구조에서 보인다. 본 논문에서는 이러한 차이에 대해 보다 자세히 토의된다.

• 한국세라믹학회지
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• 제53권3호
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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.

• 한국세라믹학회지
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• 제53권3호
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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.

• 대한화학회지
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• 제60권6호
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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.

• 대한화학회지
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• 제64권2호
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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.