• 대한화학회지
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• 제30권2호
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• pp.166-171
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• 1986

반경험적 분자궤도함수법인 MINDO/3방법을 사용하여 수소원자 전달반응인$ RNH_2+CH_3{\to} RNH+CH_4$(여기서 R=H, $CH_3$)에 관해 연구하였다. 그결과 $CH_3$와 $NH_3$간에 안정한 착물의 존재가 예상되었다. 또한 이들 반응들에 대한 활성화엔트로피를 포함해서 활성화파라메타를 결정하였으며 그 결과 절대엔트로피와 활성화 엔트로피의 경우에 비교가 가능한 곳에는 ab initio 및 실험결과와 잘 일치하였다.

• 대한화학회지
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• 제57권4호
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• pp.461-471
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• 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.

• 한국진공학회:학술대회논문집
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• 한국진공학회 2011년도 제40회 동계학술대회 초록집
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• pp.61-61
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• 2011

Using ab initio calculations, we study the MgO(001) and Fe/MgO(001) surface phases and the effects of interface structure on the Fe/MgO magnetic anisotropy. The surface phase diagrams of MgO(001) and Fe/MgO(001) show that the most stable surface structures are either defect-free surface or the surfaces with oxygen vacancies in c($2{\times}1$) periodicity for the systems. By the formations of the oxygen vacancy rows on MgO(001) surface, the in-plane magnetic anisotropy energy of Fe overlayer is reduced while the perpendicular magnetic anisotropy energy is increased from 0.1 to 0.5 meV per Fe atom.

• 한국진공학회:학술대회논문집
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• 한국진공학회 2011년도 제40회 동계학술대회 초록집
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• pp.314-314
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• 2011

Using first principles calculations, we investigated the interface structure effects on the magnetic properties of the Fe/BaTiO3 system. On the BaO-terminated surface, a Fe monolayer is formed as two Fe atoms are adsorbed on the top sites of Ba and O in the ($1{\times}1$) surface unit and a Fe ML is formed on the TiO2-terminated surface as two Fe atoms are adsorbed on the two O top sites. The magnetic anisotropy energy of Fe was higher on the TiO2?-erminated surface (1.5 eV) than on the BaO-terminated surface (0.5 eV). The decomposed electron density of the states showed that the stronger hybridization of Fe with the TiO2 layer than with the BaO layer is the most important reason for the higher magnetic anisotropy energy.

• EDISON SW 활용 경진대회 논문집
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• 제3회(2014년)
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• pp.141-155
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• 2014

Peptide bond hydrolysis는 세포 내외의 생화학반응에 있어서 핵심이다. 하지만 amide Hydrolysis Mechanism은 아직 명확하게 규명되지 않았다. pH가 중성인 물에서의 비 촉매 가수분해가 발생하는 몇몇 실험적 증거가 있지만, 해당 반응 매커니즘은 4 가지(non-assisted concerted, non-assisted step-wise, assisted concerted, assisted step-wise)로 여전히 논란이 있다. 이번 연구에서는, Formamide의 가능한 Hydrolysis Mechanism을 자세히 연구해보고자 한다. 먼저, Ab-initio 계산을 통해 4가지 반응 메커니즘의 다시 한번 확인하고, quantum chemical calculations과 quantum mechanical molecular dynamic이 결합된 (QMMD) simulation을 통하여 water solvent에서의 반응 메커니즘의 에너지관계를 규명하였다. 결론적으로 아직 계산이 끝나지 않은 supported concerted mechanism을 제외한 모든 계산에서 non-supported, supported 두 system 모두에서 step-wise가 일어나기 쉬웠고, non-supported 보다 supported mechanism이 선호됨을 보였다. Intermediate인 amino-gem-diol의 수용액 상에서 안정화 또한 나타났다. 이는 Ab-initio 계산만 통해서는 정확하게 산출할 수 없는 엔트로피의 영향을 잘 보여준다.

• EDISON SW 활용 경진대회 논문집
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• 제4회(2015년)
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• pp.91-98
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• 2015

Formamide의 중성가수분해 mechanism은 QM/MM (quantum mecahnics/molecular mechanics) molecular dynamics simulations 및 CPMD과 같은 방법으로 연구되어왔다. 본 연구에서는. Umbrella sampling을 이용한 QM/MM-MD simulation을 사용하여 4가지 반응의 free energy surface를 도출해냈다. 전체적으로, 가장 선호되는 메커니즘은 two step으로 구성된 water assisted stepwise mechanism이었으며 모든 mechanism은 ab-initio calculation과 QM/MM-MD simulation이 수행되었다. water assisted stepwise mechanism을 살펴보면, 첫 번째 step에서 formamide의 carbonyl group이 hydrate되면서 gem-diol intermediate를 형성한다. 다음 step에서, intermediate의 hydroxyl group으로부터 amino group으로 water-assisted proton transfer이 일어난다. 두 반응 모두에서 물이 proton transfer를 직접적으로 도와주는 것을 관찰할 수 있었다. 특히, ab-initio calculation과는 다르게 QM/MM-MD에서는 gem-diol intermediate가 안정화되는 것으로 solvent effect를 잘 보여준다.

• Bulletin of the Korean Chemical Society
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• 제23권6호
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• pp.891-896
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• 2002

The structures and energies of p-tert-butylcalix[4]crown-6-ether(1) in various conformers and their alkyl ammonium complexes have been calculated by ab initio HF/6-31G quantum mechanics method. We have tried to obtain the relative affinity of partial-cone and 1,3-alternate conformers of 1 for alkyl ammonium guests by comparison with its cone-shaped analogue. We have also calculated the relative complexation efficiency of these host-guest complexes focusing on the binding sites of $crown-\sigma-enther$ moiety or benzene-rings pocket of the host molecule 1. These calculations revealed that the crown moiey has better complexation efficiency than upper rim part of calyx[4]arene that is in similar trend to the cone-shaped complexes.

• 한국결정학회지
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• 제19권1호
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• pp.1-6
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• 2008

Dilithio-o-carborane과 dipenyl disulfide를 반응(反應)하여 a phenyl thiolated o-carborane compound가 얻어 졌으며 X-ray crystallography로 밝혀진 이 compound의 구조(構造)와 ab initio 및 density functional theory로 계산(計算)한 이 compound의 구조문(構造間)에 conformational similarity가 있음을 확인(確認)하였다.

• 한국균학회소식:학술대회논문집
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• 한국균학회 2018년도 춘계학술대회 및 임시총회
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• pp.22-22
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• 2018

Fungal genome sequencing and assembly have been trivial in these days. Genome analysis relies on high quality of gene prediction and annotation. Automatic fungal genome annotation pipeline is essential for handling genomic sequence data accumulated exponentially. However, building an automatic annotation procedure for fungal genomes is not an easy task. FunGAP (Fungal Genome Annotation Pipeline) is developed for precise and accurate prediction of gene models from any fungal genome assembly. To make high-quality gene models, this pipeline employs multiple gene prediction programs encompassing ab initio, evidence-, and homology-based evaluation. FunGAP aims to evaluate all predicted genes by filtering gene models. To make a successful filtering guide for removal of false-positive genes, we used a scoring function that seeks for a consensus by estimating each gene model based on homology to the known proteins or domains. FunGAP is freely available for non-commercial users at the GitHub site (https://github.com/CompSynBioLab-KoreaUniv/FunGAP).

• Journal of Microbiology
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• 제44권2호
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• pp.137-144
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• 2006

The problems associated with gene identification and the prediction of gene structure in DNA sequences have been the focus of increased attention over the past few years with the recent acquisition by large-scale sequencing projects of an immense amount of genome data. A variety of prediction programs have been developed in order to address these problems. This paper presents a review of the computational approaches and gene-finders used commonly for gene prediction in eukaryotic genomes. Two approaches, in general, have been adopted for this purpose: similarity-based and ab initio techniques. The information gleaned from these methods is then combined via a variety of algorithms, including Dynamic Programming (DP) or the Hidden Markov Model (HMM), and then used for gene prediction from the genomic sequences.