机器学习热化学估算器。

IF 5.6 2区 化学 Q1 CHEMISTRY, MEDICINAL Journal of Chemical Information and Modeling Pub Date : 2024-12-16 DOI:10.1021/acs.jcim.4c00989
Tianjun Xie, Gerhard R Wittreich, Matthew T Curnan, Geun Ho Gu, Kayla N Seals, Justin S Tolbert
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引用次数: 0

摘要

为单晶金属上的吸附物建模对于合理的催化剂设计和其他需要详细热化学信息的研究至关重要。通过密度泛函理论(DFT)进行第一原理模拟是获取表面物种信息的常用工具之一。虽然密度泛函理论计算非常可靠,但通常需要密集的计算资源和运行时间。在研究重贵金属上的大量复杂分子时,这些限制因素变得尤为突出。因此,我们探索这些物种及其相应能量学的能力受到了限制。在这项工作中,我们建立了一个新颖的框架,利用分子编码、描述符合成和机器学习等技术来克服昂贵的 DFT 模拟的限制。同时,我们在 DFT 精确度水平上高效地估算了热化学信息。更具体地说,我们通过简化的分子输入行输入系统,将训练分子转化为基于文本的标识符。随后,我们用基于群方法的短程描述符集对训练矩阵进行参数化,首先应用近邻描述符来考虑线性贡献。这与第二近邻的长程描述符相结合,以考虑非线性修正。最后,我们使用线性回归和机器学习技术,如高斯过程回归,分别对线性和非线性矩阵系统进行回归。据我们所知,这是第一项在整个特征化、训练和部署阶段都包含基于群理论的第一和第二近邻的工作。我们用铂(111)、钌(0001)和铱(111)表面上的 459 个表面物种训练和验证了我们的模型。结果表明,在不同温度下,我们的模型在重现焓、熵和热容量等相关能效方面表现出色。值得注意的是,与经典分组方法相比,平均绝对误差在训练过程中可减少 48%,在预测过程中至少可减少 19%。利用新颖的框架,我们的机器学习热化学估算器极大地增强了我们研究金属催化剂上复杂物种热化学的能力。
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Machine-Learning-Enabled Thermochemistry Estimator.

Modeling adsorbates on single-crystal metals is critical in rational catalyst design and other research that requires detailed thermochemistry. First-principles simulations via density functional theory (DFT) are among the prevalent tools to acquire such information about surface species. While they are highly dependable, DFT calculations often require intensive computational resources and runtime. These limiting factors become particularly pronounced when investigating large sets of complex molecules on heavy noble metals. Consequently, our ability to explore these species and their corresponding energetics is limited. In this work, we establish a novel framework that utilizes techniques including molecular encoding, descriptor synthesis, and machine learning to overcome the limitation of costly DFT simulations. Simultaneously, we estimate thermochemical information efficiently at the DFT accuracy level. More specifically, we translated our training molecules into text-based identifiers through a simplified molecular-input line-entry system. Following that, we parametrize our training matrices with sets of short-range descriptors based on group methods, applying first the nearest neighbors to account for linear contributions. This is coupled with the long-range descriptors characterizing second nearest neighbors to account for nonlinear corrections. Finally, we use linear regression and machine learning techniques, such as Gaussian process regressions to regress over the linear and nonlinear matrix systems, respectively. This is the first work to our knowledge that encompasses both the first and second nearest neighbors based on the group theory throughout the featurization, training, and deployment stages. We trained and validated our models with 459 surface species on Pt(111), Ru(0001), and Ir(111) surfaces. Results exhibit robust performance to reproduce the energetics of interest, such as enthalpies, entropies, and heat capacities, at various temperatures. Notably, the mean absolute errors can be reduced by 48% during training and 19% during prediction at a minimum, when compared to the classical group method. Leveraging the novel framework, our machine-learning-enabled thermochemistry estimator significantly empowers us to research the thermochemistry of complex species on metal catalysts.

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来源期刊
CiteScore
9.80
自引率
10.70%
发文量
529
审稿时长
1.4 months
期刊介绍: The Journal of Chemical Information and Modeling publishes papers reporting new methodology and/or important applications in the fields of chemical informatics and molecular modeling. Specific topics include the representation and computer-based searching of chemical databases, molecular modeling, computer-aided molecular design of new materials, catalysts, or ligands, development of new computational methods or efficient algorithms for chemical software, and biopharmaceutical chemistry including analyses of biological activity and other issues related to drug discovery. Astute chemists, computer scientists, and information specialists look to this monthly’s insightful research studies, programming innovations, and software reviews to keep current with advances in this integral, multidisciplinary field. As a subscriber you’ll stay abreast of database search systems, use of graph theory in chemical problems, substructure search systems, pattern recognition and clustering, analysis of chemical and physical data, molecular modeling, graphics and natural language interfaces, bibliometric and citation analysis, and synthesis design and reactions databases.
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