论文标题
通用QM/mm通用纳米级应用的方法
Universal QM/MM Approaches for General Nanoscale Applications
论文作者
论文摘要
量子力学/分子力学(QM/mm)混合模型允许在复杂的分子环境中解决化学现象。尽管这种建模方法可以以适度的计算成本来应对较大的系统大小,但这些模型通常很乏味,并且需要手动预处理和专业知识。结果,向新的应用领域的传递性可能受到限制,许多参数不容易调整到通常稀缺的参考参数。因此,希望设计具有可控精度的自动化过程,该过程可以以标准化和黑色盒子的方式进行这种建模。尽管已经为构建QM/mm型号的单个组件(例如,MM电位,嵌入类型,QM区域的选择)设置了各种最佳实践方案,但自动化程序可以调和QM/MM模型构建的所有步骤的自动化程序。在这里,我们回顾了QM/MM建模的艺术状态,重点是自动化。我们详细介绍了MM模型参数化,原子经济物理动机区域的选择以及将相互极化作为QM/MM模型的关键组件的嵌入方案。鉴于该领域的广泛范围,我们主要将讨论限制为基于第一原理数据,不确定性量化以及缓解错误的方法,这些方法具有较高的自动化潜力。最终,希望能够以快速有效的自动化方式设置可靠的QM/MM模型,而不会受到特定的化学或技术限制的约束。
Quantum mechanics/molecular mechanics (QM/MM) hybrid models allow one to address chemical phenomena in complex molecular environments. Whereas this modeling approach can cope with a large system size at moderate computational costs, the models are often tedious to construct and require manual preprocessing and expertise. As a result, transferability to new application areas can be limited and the many parameters are not easy to adjust to reference data that are typically scarce. Therefore, it is desirable to devise automated procedures of controllable accuracy, which enables such modeling in a standardized and black-box-type manner. Although diverse best-practice protocols have been set up for the construction of individual components of a QM/MM model (e.g., the MM potential, the type of embedding, the choice of the QM region), automated procedures that reconcile all steps of the QM/MM model construction are still rare. Here, we review the state of the art of QM/MM modeling with a focus on automation. We elaborate on MM model parametrization, on atom-economical physically-motivated QM region selection, and on embedding schemes that incorporate mutual polarization as critical components of the QM/MM model. In view of the broad scope of the field, we mostly restrict the discussion to methodologies that build \textit{de novo} models based on first-principles data, on uncertainty quantification, and on error mitigation with a high potential for automation. Ultimately, it is desirable to be able to set up reliable QM/MM models in a fast and efficient automated way without being constrained by specific chemical or technical limitations.