Extending the Applicability of the ANI Deep Learning Molecular Potential to Sulfur and Halogens

Author(s):  
Christian Devereux ◽  
Justin Smith ◽  
Kate Davis ◽  
Kipton Barros ◽  
Roman Zubatyuk ◽  
...  

<p>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, 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 non-bonded interactions. ANI-2x is shown to accurately predict molecular energies compared to DFT with a ~10<sup>6</sup> factor speedup and a negligible slowdown compared to ANI-1x. The resulting model is a valuable tool for drug development that can potentially replace both quantum calculations and classical force fields for myriad applications.</p>

2020 ◽  
Author(s):  
Christian Devereux ◽  
Justin Smith ◽  
Kate Davis ◽  
Kipton Barros ◽  
Roman Zubatyuk ◽  
...  

<p>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, 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 non-bonded interactions. ANI-2x is shown to accurately predict molecular energies compared to DFT with a ~10<sup>6</sup> factor speedup and a negligible slowdown compared to ANI-1x. The resulting model is a valuable tool for drug development that can potentially replace both quantum calculations and classical force fields for myriad applications.</p>


2019 ◽  
Vol 15 (S350) ◽  
pp. 148-151
Author(s):  
Malek Ben Khalifa ◽  
Emna Sahnoun ◽  
Silvia Spezzano ◽  
Laurent Wiesenfeld ◽  
Kamel Hammami ◽  
...  

AbstractCyclopropenylidene,, is a simple hydrocarbon, ubiquitous in astrophysical gases, and possessing a permanent electric dipole moment. Its readily observed multifrequency rotational transitions make it an excellent probe for the physics and history of interstellar matter. The collisional properties of with He are presented here. We computed the full Potential Energy Surfaces, and we perform quantum scattering in order to provide rates of quenching and excitation for low to medium temperature regimes. We discuss issues with the validity of the usual Local Thermodynamical Equilibrium assumption, and also the intricacies of the spectroscopy of an asymmetric top. We present the wide range of actual critical densities, as recently observed.


2019 ◽  
Vol 21 (36) ◽  
pp. 19921-19934 ◽  
Author(s):  
Balasubramanian Chandramouli ◽  
Sara Del Galdo ◽  
Marco Fusè ◽  
Vincenzo Barone ◽  
Giordano Mancini

The search for stationary points in the molecular potential energy surfaces (PES) is a problem of increasing relevance in molecular sciences especially for large, flexible systems featuring several large-amplitude internal motions.


2019 ◽  
Vol 5 (1) ◽  
Author(s):  
Noam Bernstein ◽  
Gábor Csányi ◽  
Volker L. Deringer

Abstract Interatomic potential models based on machine learning (ML) are rapidly developing as tools for material simulations. However, because of their flexibility, they require large fitting databases that are normally created with substantial manual selection and tuning of reference configurations. Here, we show that ML potentials can be built in a largely automated fashion, exploring and fitting potential-energy surfaces from the beginning (de novo) within one and the same protocol. The key enabling step is the use of a configuration-averaged kernel metric that allows one to select the few most relevant and diverse structures at each step. The resulting potentials are accurate and robust for the wide range of configurations that occur during structure searching, despite only requiring a relatively small number of single-point DFT calculations on small unit cells. We apply the method to materials with diverse chemical nature and coordination environments, marking an important step toward the more routine application of ML potentials in physics, chemistry, and materials science.


2011 ◽  
Vol 268 (1-2) ◽  
pp. 123-129 ◽  
Author(s):  
Sergei N. Yurchenko ◽  
Robert J. Barber ◽  
Jonathan Tennyson ◽  
Walter Thiel ◽  
Per Jensen

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