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Insights into Non-Covalent Interactions with a Machine-Learned Electron Density

preprint
submitted on 03.06.2019 and posted on 04.06.2019 by Alberto Fabrizio, Andrea Grisafi, Benjamin Meyer, Michele Ceriotti, Clemence Corminboeuf
Chemists continuously harvest the power of non-covalent interactions to control phenomena in both the micro- and macroscopic worlds. From the quantum chemical perspective, the strategies essentially rely upon an in-depth understanding of the physical origin of these interactions, the quantification of their magnitude and their visualization in real-space.
The total electron density rho(r) represents the simplest yet most comprehensive piece of information available for fully characterizing bonding patterns and non-covalent interactions. The charge density of a molecule can be computed by solving the Schrodinger equation, but this approach becomes rapidly demanding if the electron density has to be evaluated for thousands of different molecules or for very large chemical systems, such as peptides and proteins.
Here we present a transferable and scalable machine-learning model capable of predicting the total electron density directly from the atomic coordinates. The regression model is used to access qualitative and quantitative insights beyond the underlying rho(r) in a diverse ensemble of sidechain-sidechain dimers extracted from the BioFragment database (BFDb). The transferability of the model to more complex chemical systems is demonstrated by predicting and analyzing the electron density of a collection of 8 polypeptides.

Funding

The National Centre of Competence in Research (NCCR) Materials' Revolution: Computational Design and Discovery of Novel Materials (MARVEL) of the Swiss National Science Foundation (SNSF) and the EPFL are acknowledged for financial support. AG acknowledges funding from the Max Planck-EPFL center.

History

Email Address of Submitting Author

clemence.corminboeuf@epfl.ch

Institution

EPFL

Country

Switzerland

ORCID For Submitting Author

0000-0001-7993-2879

Declaration of Conflict of Interest

no conflict of interest

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