• Title/Summary/Keyword: Molecular Modeling

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Molecular Modeling and its Experimental Verification for the Catalytic Mechanism of Candida antarctica Lipase B

  • Kwon, Cheong-Hoon;Shin, Dae-Young;Lee, Jong-Ho;Kim, Seung-Wook;Kang, Jeong-Won
    • Journal of Microbiology and Biotechnology
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    • 제17권7호
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    • pp.1098-1105
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    • 2007

  • Quantum mechanical and molecular dynamics simulation analysis has been performed on the model system for CALB (Candida antarctica lipase B) with esters to study the reaction mechanism and conformational preference of catalytic hydrolysis and the esterification reaction. Using quantum mechanical analysis, the ping-pong bi-bi mechanism was applied and energies and 3-dimensional binding configurations of the whole reaction pathways were calculated. Further molecular dynamics simulation analysis was performed on the basis of the transition state obtained from quantum mechanical study to observe the effect of structures of the substrates. Calculation results using substrates of different chain length and chiral configurations were compared for conformational preference. The calculated results showed very small influence on chain length, whereas chiral conformation showed big differences. Calculated results from molecular modeling studies have been compared qualitatively with the experimental data using racemic mixtures of (${\pm}$)-cis-4-acetamido-cyclopent-2-ene-1-ethyl acetate as substrates.

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Molecular Modeling of Enantio-discrimination of α-Methoxy-α-trifluoromethylphenylacetic Acid (MTPA) by Cyclomaltoheptaose (β-Cyclodextrin) and 6-Amino-6-deoxy-cyclomaltoheptaose

  • Jung, Eun-Kyoung;Jeong, Karp-Joo;Lee, Sang-San;Kim, Jee-In;Jung, Seun-Ho
    • Bulletin of the Korean Chemical Society
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    • 제24권11호
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    • pp.1627-1631
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    • 2003

  • Molecular modeling was performed to comprehend the chiral recognition of ${\alpha}$-methoxy-${\alpha}$-trifluoromethylphenylacetic acid (MTPA) enantiomers by cyclomaltoheptaose (${\beta}$-cyclodextrin,${\beta}$-CD) and 6-amino-6-deoxy-cyclomaltoheptaose (am-${\beta}$-CD). Monte Carlo (MC) docking coupled to constant temperature molecular dynamics (MD) simulations was applied to the investigation for the ${\alpha}$-methoxy-${\alpha}$-trifluoromethylphenylacetic acid complexation with two different CDs in terms of the relative distribution of the interaction energies. The calculated results are finely correlated with the experimental observations in chiral recognition thermodynamics. Am-${\beta}$-CD as a host showed the superior enantio-discrimination ability to the native ${\beta}$-CD where the amino group of am-${\beta}$-CD was critically involved in enhancing the ability of chiral discrimination via the Coulombic interaction with MTPA.

  • https://doi.org/10.5012/bkcs.2003.24.11.1627 인용 PDF KSCI

Molecular Connectivity法을 이용한 有機化合物과 二成分 混合物에 對한 物理化學的 性質에 關한 硏究 (Ⅱ) (The Study of Physical Properties for the Organic Compounds and their Binary Mixture according to Molecular Connectivity Method)

  • 김의락;민경섭;이명재;김상해;정봉진
    • 대한화학회지
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    • 제36권4호
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    • pp.485-495
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    • 1992

  • 기체 및 액체 상태의 여러가지 유기화합물(alcohol, acetate, alkane, acid 및 substituted NH$_2$)과 이성분계 혼합용액(n-alkane/1-chloroalkane)에 대한 점성도를 계산하기 위하여, 분자의 크기, 가지의 형태, 환상구조, 불포화의 정도, 분극성 등이 분자의 성질에 미치는 영향을 잘 설명하여 주는 molecular connectivity index, Wiener index 및 ad hoc descriptor 방법을 이용하였다. 그 결과 기체 상태에 대해서는 Wiener index 방법이, 액체 상태에 대해서는 ad hoc descriptor 방법이 그리고 이성분계에 대해서는 molecular connectivity index 방법이 우수한 방법임을 알 수 있었으며, 각각의 방법으로 구한 최적 상관관계식을 이용하여 점성도를 계산하였고, 이와 같이 구한 이론치와 점성도의 실측치를 비교할 때, 매우 잘 일치하는 결과를 얻을 수 있었다.

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