Structure and stability of polydiacetylene membrane systems: Molecular dynamics simulation studies,Journal of Computational Chemistry

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Structure and stability of polydiacetylene membrane systems: Molecular dynamics simulation studies
Journal of Computational Chemistry ( IF 3.4 ) Pub Date : 2022-12-08 , DOI: 10.1002/jcc.27053
Youhyun Nam ₁ , Songyi Lee ₂ , Rakwoo Chang ₁

Affiliation

We have performed full atomistic molecular dynamics (MD) simulations to investigate structure and stability of bilayer membrane systems consisting of monomeric or polymeric 10,12-pentacosadiynoic acid (PCDA) units connected with lysine groups by amide bonds. The PCDA monomer molecules show a twisted three-rod-domain structure with two kinks but upon polymerization, they possess more elongated conformation. The resulting polydiacetylene (PDA) membrane systems have stable membrane structures at room temperature, which is similar to biological lipid bilayer membranes and maintain their gel-like membrane integrity even up to as high as 370 K. Structural properties such as area per monomer, membrane thickness, density profile, 2D pair distribution function, and orientational correlation function are also calculated to understand the membrane structure and check its stability upon thermal fluctuation with atomistic resolution. This study is expected to provide the understanding about PDA membrane systems in atomistic details as well as significant insights into designing new novel PDA sensors.

中文翻译：

聚丁二炔膜系统的结构和稳定性：分子动力学模拟研究

我们进行了完整的原子分子动力学 (MD) 模拟，以研究双层膜系统的结构和稳定性，该系统由通过酰胺键与赖氨酸基团连接的单体或聚合 10,12-二十五碳二炔酸 (PCDA) 单元组成。PCDA 单体分子显示出带有两个扭结的扭曲三杆域结构，但在聚合后，它们具有更细长的构象。由此产生的聚二乙炔 (PDA) 膜系统在室温下具有稳定的膜结构，类似于生物脂质双层膜，即使高达 370 K 也能保持其凝胶状膜的完整性。结构特性，例如每个单体的面积、膜厚度，密度分布，二维对分布函数，还计算了方向相关函数，以了解膜结构，并通过原子分辨率检查其在热波动时的稳定性。这项研究有望在原子细节方面提供对 PDA 膜系统的理解，以及对设计新型 PDA 传感器的重要见解。

更新日期：2022-12-08

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