Tunable Conformational Properties of POSS-Peptide Conjugate Molecule in Selective Solvents: An Atomistic Molecular Dynamics Simulation Study.

IF 2.9 2区 化学 Q3 CHEMISTRY, PHYSICAL
Junhao Dai, Wen Tang, Xianbo Huang, Rui Zhang
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引用次数: 0

Abstract

Giant molecules with precisely defined modular architectures hold promise to generate distinct structure-dynamics-property relationships in solution-phase materials. Recently, a novel class of hybrid macromolecules that combine structural rigidity of polyhedral oligomeric silsesquioxanes (POSS) with flexibility of peptide sequences (POSS-peptide conjugate molecules) have been established experimentally. To elucidate their detailed microscopic structural and dynamic features, high-precision atomistic modeling and simulation are in demand. In this study, we develop a standardized and extensible all-atom force field parametrization workflow for POSS-peptide molecules, integrating quantum chemical calculations to derive accurate force field parameters for the rigid POSS units, including bond, angle, and dihedral terms, as well as atomic charges for the whole molecule. Upon applying the parametrization framework to five representative POSS-peptide molecules with varied POSS functionality and peptide composition in water or DMF solvent, all-atom molecular dynamics simulations are performed for the ten systems to investigate the highly tunable conformational properties of POSS-peptides. We construct detailed conformational free energy landscapes that provide insight into the role of different factors in shaping the molecule's solution-phase behavior. Our analysis reveals that molecular structure and solvent polarity co-regulate the conformational preferences of POSS-peptide molecules. Of particular interest is the finding of some unusual structure-dynamics correlation behaviors driven by close-distance interactions between the POSS and peptide unit. This work expands our understanding of the conformational richness of POSS-peptides in solution and provides a methodology foundation for exploring larger-scale supramolecular structures achievable by this emergent family of giant molecules in future research.

poss -肽共轭分子在选择性溶剂中的可调构象性质:原子分子动力学模拟研究。
具有精确定义的模块化结构的大分子有望在溶液相材料中产生独特的结构-动力学-性质关系。近年来,一种结合多面体低聚硅氧烷(POSS)结构刚性和肽序列柔性的新型杂化大分子(POSS-肽共轭分子)被实验建立。为了阐明其详细的微观结构和动力学特征,需要高精度的原子建模和仿真。在这项研究中,我们为POSS-肽分子开发了一个标准化和可扩展的全原子力场参数化工作流程,整合量子化学计算来获得刚性POSS单元的准确力场参数,包括键、角和二面体项,以及整个分子的原子电荷。将参数化框架应用于5个具有代表性的POSS肽分子,这些分子在水或DMF溶剂中具有不同的POSS功能和肽组成,对这10个体系进行了全原子分子动力学模拟,以研究POSS肽的高度可调构象性质。我们构建了详细的构象自由能景观,以深入了解不同因素在塑造分子溶液相行为中的作用。我们的分析表明,分子结构和溶剂极性共同调节poss肽分子的构象偏好。特别有趣的是,POSS和肽单元之间的近距离相互作用驱动了一些不寻常的结构动力学相关行为的发现。这项工作扩大了我们对溶液中poss肽构象丰富性的理解,并为在未来的研究中探索这一新兴大分子家族可实现的更大规模超分子结构提供了方法论基础。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
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来源期刊
CiteScore
5.80
自引率
9.10%
发文量
965
审稿时长
1.6 months
期刊介绍: An essential criterion for acceptance of research articles in the journal is that they provide new physical insight. Please refer to the New Physical Insights virtual issue on what constitutes new physical insight. Manuscripts that are essentially reporting data or applications of data are, in general, not suitable for publication in JPC B.
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