Institute of Nanotechnology (INT), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz Platz 1, Eggenstein-Leopoldshafen 76344, Germany.
Institute of Theoretical Informatics (ITI), Karlsruhe Institute of Technology (KIT), Am Fasanengarten 5, Karlsruhe 76131, Germany.
J Chem Theory Comput. 2021 Nov 9;17(11):7195-7202. doi: 10.1021/acs.jctc.1c00506. Epub 2021 Oct 8.
Adsorption and desorption of molecules are key processes in extraction and purification of biomolecules, engineering of drug carriers, and designing of surface-specific coatings. To understand the adsorption process on the atomic scale, state-of-the-art quantum mechanical and classical simulation methodologies are widely used. However, studying adsorption using a full quantum mechanical treatment is limited to picoseconds simulation timescales, while classical molecular dynamics simulations are limited by the accuracy of the existing force fields. To overcome these challenges, we propose a systematic way to generate flexible, application-specific highly accurate force fields by training artificial neural networks. As a proof of concept, we study the adsorption of the amino acid alanine on graphene and gold (111) surfaces and demonstrate the force field generation methodology in detail. We find that a molecule-specific force field with Lennard-Jones type two-body terms incorporating the 3rd and 7th power of the inverse distances between the atoms of the adsorbent and the surfaces yields optimal results, which is surprisingly different from typical Lennard-Jones potentials used in traditional force fields. Furthermore, we present an efficient and easy-to-train machine learning model that incorporates system-specific three-body (or higher order) interactions that are required, for example, for gold surfaces. Our final machine learning-based force field yields a mean absolute error of less than 4.2 kJ/mol at a speed-up of ∼10 times compared to quantum mechanical calculation, which will have a significant impact on the study of adsorption in different research areas.
分子的吸附和解吸是生物分子提取和纯化、药物载体工程以及表面特异性涂层设计中的关键过程。为了在原子尺度上理解吸附过程,广泛使用了最先进的量子力学和经典模拟方法。然而,使用全量子力学处理研究吸附受到模拟时间尺度限于皮秒的限制,而经典分子动力学模拟则受到现有力场准确性的限制。为了克服这些挑战,我们提出了一种通过训练人工神经网络生成灵活、特定于应用的高精度力场的系统方法。作为概念验证,我们研究了氨基酸丙氨酸在石墨烯和金(111)表面上的吸附,并详细展示了力场生成方法。我们发现,带有 Lennard-Jones 型两体项的分子特异性力场,其中包含吸附剂和表面之间原子的倒数的第 3 次和第 7 次幂,可产生最佳结果,这与传统力场中使用的典型 Lennard-Jones 势能惊人地不同。此外,我们提出了一种高效且易于训练的机器学习模型,该模型包含特定于系统的三体(或更高阶)相互作用,例如对于金表面。我们最终的基于机器学习的力场在与量子力学计算相比加速约 10 倍的情况下,产生的平均绝对误差小于 4.2 kJ/mol,这将对不同研究领域的吸附研究产生重大影响。