Molecular shape dynamics, reaction paths and conformational transitions in biomolecules. Theory and simulations.

生物分子的分子形状动力学、反应路径和构象转变。

• 批准号: 138157-2009
• 负责人: Arteca, Gustavo
• 金额: $ 3.64万
• 依托单位: Laurentian University of Sudbury
• 依托单位国家: 加拿大
• 项目类别: Discovery Grants Program - Individual
• 财政年份: 2011
• 资助国家: 加拿大
• 起止时间: 2011-01-01 至 2012-12-31
• 项目状态: 已结题
• 来源: https://www.nserc-crsng.gc.ca/ase-oro/Details-Detailles_eng.asp?id=475781
• 关键词: Molecular; shape; dynamics; reaction; paths

Our research program focuses on developing and applying the tools of theoretical & computational chemistry to study the interplay between shape and dynamics in flexible molecules. Our approach blends the notions of structure, shape, energetics, and configurational transitions in an original manner: molecules are seen as topological entities, instead of isolated conformers at optimal geometries. By studying how these properties persist under external perturbations, we establish: (i) the stability of molecular shape, (ii) the factors that control the onset of configurational transitions, (iii) the occurrence of new species along reaction paths, and (iv) a measure of dynamic shape similarity for comparing these species. Molecular shape is conveyed differently depending on scale. For macromolecules, we use chain geometry and topology to monitor configurational transitions in constrained polymers and protein ions. In smaller systems, we focus on how quantum states and electronic structure are affected by external fields or non-adiabatic changes in nuclear geometry. Our long-term goal is to integrate these areas into a single protocol to study the interplay between local electronic properties and global conformational motions in biopolymers. The work projected for the next five years will extend our methods and apply them to the analysis of selected phenomena. The following main themes will be our priorities: (a) Configurational transitions in grafted and externally-driven polymers with distinct topologies. (b) The stability and unfolding of anhydrous protein ions in conditions that simulate time-of-flight mass spectrometry. (c) Effect of external fields and nuclear geometry on the curvature for reaction paths for electronic processes. The themes (a) and (b) rely on a combination of polymer theory, computer simulations, and our techniques to study chain entanglement. Theme (c) deals with non-adiabatic effects caused by the motions and local fields associated with a protein native state. This latter analysis requires the computation of diabatic amplitudes in coherent quantum states that vary with external fields. I will continue to train HQPs in these areas, and pursue collaborative research with colleagues in Sweden during my sabbatical in 2010/2011.

我们的研究项目侧重于开发和应用理论和计算化学工具来研究柔性分子的形状和动力学之间的相互作用。我们的方法以一种原始的方式融合了结构、形状、能量学和构型转变的概念：分子被视为拓扑实体，而不是最佳几何形状的孤立构象。通过研究这些性质在外部扰动下如何持续，我们建立了：(i)分子形状的稳定性，（ii）控制构型转变开始的因素，（iii）沿着反应路径新物种的发生，以及（iv）用于比较这些物种的动态形状相似性的度量。分子形状的传递取决于尺度的不同。对于大分子，我们使用链几何和拓扑结构来监测约束聚合物和蛋白质离子的构型转变。在较小的系统中，我们关注的是量子态和电子结构如何受到外场或核几何形状的非绝热变化的影响。我们的长期目标是将这些领域整合到一个单一的协议中，以研究生物聚合物中局部电子特性和全局构象运动之间的相互作用。预计今后五年的工作将扩展我们的方法，并将它们应用于对选定现象的分析。以下主题将是我们的重点：(a)具有不同拓扑结构的接枝和外部驱动聚合物的构型转变。(b)模拟飞行时间质谱法条件下无水蛋白离子的稳定性和展开。(c)外场和核几何形状对电子过程反应路径曲率的影响。主题(a)和(b)依赖于聚合物理论、计算机模拟和我们的技术的结合来研究链缠结。主题(c)处理与蛋白质天然状态相关的运动和局部场引起的非绝热效应。后一种分析需要计算随外场变化的相干量子态的非绝热振幅。我将在2010/2011年休假期间继续在这些领域培训hqp，并与瑞典的同事进行合作研究。