CNRS, Université de Paris, UPR 9080, Laboratoire de Biochimie Théorique, 13 rue Pierre et Marie Curie, 75005 Paris, France.
Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, Prague 6 166 10, Czech Republic.
J Chem Phys. 2020 Aug 7;153(5):050901. doi: 10.1063/5.0017775.
Molecular simulations can elucidate atomistic-level mechanisms of key biological processes, which are often hardly accessible to experiment. However, the results of the simulations can only be as trustworthy as the underlying simulation model. In many of these processes, interactions between charged moieties play a critical role. Current empirical force fields tend to overestimate such interactions, often in a dramatic way, when polyvalent ions are involved. The source of this shortcoming is the missing electronic polarization in these models. Given the importance of such biomolecular systems, there is great interest in fixing this deficiency in a computationally inexpensive way without employing explicitly polarizable force fields. Here, we review the electronic continuum correction approach, which accounts for electronic polarization in a mean-field way, focusing on its charge scaling variant. We show that by pragmatically scaling only the charged molecular groups, we qualitatively improve the charge-charge interactions without extra computational costs and benefit from decades of force field development on biomolecular force fields.
分子模拟可以阐明关键生物过程的原子级机制，而这些机制通常很难通过实验来研究。然而，模拟的结果只能与基础的模拟模型一样可靠。在许多这样的过程中，带电荷部分之间的相互作用起着至关重要的作用。当涉及多价离子时，当前的经验力场往往会以戏剧性的方式高估这种相互作用。这种缺陷的根源在于这些模型中缺少电子极化。鉴于此类生物分子系统的重要性，人们非常希望以不使用可极化力场的计算成本低廉的方式来纠正这种缺陷。在这里，我们回顾了电子连续体修正方法，该方法以平均场的方式考虑了电子极化，重点介绍了其电荷标度变体。我们表明，通过实际仅对带电分子基团进行标度，我们可以在不增加额外计算成本的情况下定性地改善电荷-电荷相互作用，并受益于数十年来在生物分子力场方面的力场发展。
