Fast and Accurate Ring Strain Energy Predictions with Machine Learning and Application in Strain-Promoted Reactions

AbstractThe potential energy of molecular species and their conformers can be computed with a wide range of computational chemistry methods, from molecular mechanics to ab initio quantum chemistry. However, the proper choice of the computational approach based on computational cost and reliability of calculated energies is a dilemma, especially for large molecules. This dilemma is proved to be even more problematic for studies that require hundreds and thousands of calculations, such as drug discovery. On the other hand, driven by their pattern recognition capabilities, neural networks started to gain popularity in the computational chemistry community. During the last decade, many neural network potentials have been developed to predict a variety of chemical information of different systems. Neural network potentials are proved to predict chemical properties with accuracy comparable to quantum mechanical approaches but with the cost approaching molecular mechanics calculations. As a result, the development of more reliable, transferable, and extensible neural network potentials became an attractive field of study for researchers. In this review, we outlined an overview of the status of current neural network potentials and strategies to improve their accuracy. We provide recent examples of studies that prove the applicability of these potentials. We also discuss the capabilities and shortcomings of the current models and the challenges and future aspects of their development and applications. It is expected that this review would provide guidance for the development of neural network potentials and the exploitation of their applicability.This article is categorized under:Data Science > Artificial Intelligence/Machine LearningMolecular and Statistical Mechanics > Molecular InteractionsSoftware > Molecular Modeling

Deep learning models have demonstrated outstanding results in many data-rich areas of research, such as computer vision and natural language processing. Currently, there is a rise of deep learning in computational chemistry and materials informatics, where deep learning could be effectively applied in modeling the relationship between chemical structures and their properties. With the immense growth of chemical and materials data, deep learning models can begin to outperform conventional machine learning techniques such as random forest, support vector machines, and nearest neighbor. Herein, we introduce OpenChem, a PyTorch-based deep learning toolkit for computational chemistry and drug design. OpenChem offers easy and fast model development, modular software design, and several data preprocessing modules. It is freely available via the GitHub repository.

Machine learning (ML) methods have become powerful, predictive tools in a wide range of applications, such as facial recognition and autonomous vehicles. In the sciences, computational chemists and physicists have been using ML for the prediction of physical phenomena, such as atomistic potential energy surfaces and reaction pathways. Transferable ML potentials, such as ANI-1x, have been developed with the goal of accurately simulating organic molecules containing the chemical elements H, C, N, and O. Here, we provide an extension of the ANI-1x model. The new model, dubbed ANI-2x, is trained to three additional chemical elements: S, F, and Cl. Additionally, ANI-2x underwent torsional refinement training to better predict molecular torsion profiles. These new features open a wide range of new applications within organic chemistry and drug development. These seven elements (H, C, N, O, F, Cl, and S) make up ∼90% of drug-like molecules. To show that these additions do not sacrifice accuracy, we have tested this model across a range of organic molecules and applications, including the COMP6 benchmark, dihedral rotations, conformer scoring, and nonbonded interactions. ANI-2x is shown to accurately predict molecular energies compared to density functional theory with a ∼10⁶ factor speedup and a negligible slowdown compared to ANI-1x and shows subchemical accuracy across most of the COMP6 benchmark. The resulting model is a valuable tool for drug development which can potentially replace both quantum calculations and classical force fields for a myriad of applications.

Reactive potentials serve as essential tools for investigating chemical reactions with moderate computational costs. However, traditional reactive potentials often depend on fixed, semiempirical parameters, which limits their accuracy and transferability. Overcoming these limitations can significantly expand the applicability of reactive potentials, enabling the simulation of a broader range of reactions under diverse conditions and the prediction of reaction properties, such as barrier heights. This work introduces ANI-1xBB, a novel ANI-based reactive ML potential trained on off-equilibrium molecular conformers generated through an automated bond-breaking workflow. ANI-1xBB significantly enhances the prediction of reaction energetics, barrier heights, and bond dissociation energies, surpassing those of conventional ANI models. Our results show that ANI-1xBB improves transition state modeling and reaction pathway prediction while generalizing effectively to pericyclic reactions and radical-driven processes. Furthermore, the automated data generation strategy supports the efficient construction of large-scale, high-quality reactive data sets, reducing reliance on expensive QM calculations. This work highlights ANI-1xBB as a practical model for accelerating the development of reactive machine learning potentials, offering new opportunities for modeling reaction phenomena.