Molecular dynamics simulations of reversible hydrogen bond network dynamics under external force

外力作用下可逆氢键网络动力学的分子动力学模拟

• 批准号: 264597009
• 负责人: Professor Dr. Gregor Diezemann
• 金额: --
• 依托单位: Department Chemie
• 依托单位国家: 德国
• 项目类别: Research Grants
• 财政年份: 2014
• 资助国家: 德国
• 起止时间: 2013-12-31 至 2017-12-31
• 项目状态: 已结题
• 来源: https://gepris.dfg.de/gepris/projekt/264597009?language=en
• 关键词: Molecular; dynamics; simulations; reversible; hydrogen

The application of a mechanical force allows to break adhesion bonds in supramolecular assemblies or to unfold biomolecules. The force-dependence of the unbinding rate yields important information about the kinetics on a single molecule level.In the project molecular dynamics simulations under the influence of an external force will be performed on systems showing reversible unbinding and rebinding. In contrast to the much studied systems showing only irreversible unbinding, here the opportunity to observe both, unbinding and rebinding, allows for a detailed study of the kinetics. In particular, it should be possible to observe deviations from a simple two-state kinetics and to analyze the impact of intermediates. Furthermore, plotting the observerd force as a function of the molecular extension typical non-equilibrium features like hysteresis can be studied in detail. Most of the systems that appear reversible in experimental studies show irreversible behavior on the fast time scale of molecular dynamics simulations. Therefore, we will use a class of entangled molecules with a catenane structure (calixarene catenanes) as model systems because complete dissociation in these systems is prevented by the loop structure and reversible opening of the structure can be observed. The most important goal of the project is to understand the force-dependence of relevant energy landscape parameters like the kinetic rates for unbinding and rebinding. Since the application of the external force via different protocols drives the system out of thermal equilibrium in different ways, it is important to investigate whether the resulting rates can be directly compared to each other. For this purpose, so-called two-state trajectories under the influence of a constant external force will be computed and analyzed. The resulting rates will be compared to those obtained from calculations of the potential of mean force as a function of the molecular extension along the pulling direction. Changing the loop length of the calixarene dimers investigated gives rise to a change in the kinetic behavior of bond rupture and bond formation. For short loops a simple two-state kinetics is observed while for longer loops one finds not only an open and a closed state but also an intermediate. Thus, a slight modification of the model system allows to study deviations from a simple kinetics and to investigate the impact of an intermediate in the reversible dynamics. The investigations allow to validate existing theoretical models for the force-dependent properties of adhesion bonds and may help to deepen the understanding of the kinetic behavior of complex systems.

在机械力的作用下，可以打破超分子组件中的粘附键或展开生物分子。解离速率的力依赖关系提供了关于单分子水平上的动力学的重要信息。在该项目中，将对呈现可逆解结合和再结合的体系进行外力影响下的分子动力学模拟。与大量研究只显示不可逆解结合的体系不同，这里有机会同时观察解结合和重新结合，从而允许详细研究动力学。特别是，应该有可能观察到与简单的两态动力学的偏差，并分析中间体的影响。此外，绘制作为分子伸展函数的观察力可以详细地研究典型的非平衡特征，如滞后。大多数在实验研究中看似可逆的系统在分子动力学模拟的快时间尺度上显示出不可逆行为。因此，我们将使用一类具有环状结构的纠缠分子(杯芳烃环状分子)作为模型体系，因为这些体系中的环状结构阻止了完全解离，并且可以观察到结构的可逆打开。该项目最重要的目标是了解相关能量景观参数的力依赖关系，如解除结合和重新结合的动力学速率。由于通过不同的协议施加外力会以不同的方式使系统脱离热平衡，因此研究所产生的速率是否可以直接相互比较是很重要的。为此，将计算和分析恒定外力影响下的所谓两状态轨迹。所得到的速率将与通过计算作为分子沿牵引方向延伸的函数的平均力势而获得的速率进行比较。改变所研究的杯芳烃二聚体的环长会引起键断裂和键形成的动力学行为的变化。对于较短的环，观察到简单的两态动力学，而对于较长的环，人们不仅可以看到开态和闭态，而且还可以看到中间态。因此，对模型系统稍作修改，就可以研究与简单动力学的偏差，并研究中间体在可逆动力学中的影响。这些研究结果验证了现有的粘附键与力相关的理论模型，有助于加深对复杂体系动力学行为的理解。