Issue 41, 2019

Electron density learning of non-covalent systems

Abstract

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 ρ(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 Schrödinger equation, but this approach becomes rapidly demanding if the electron density has to be evaluated for thousands of different molecules or 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 ρ(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.

Graphical abstract: Electron density learning of non-covalent systems

Supplementary files

Article information

Article type
Edge Article
Submitted
03 juin 2019
Accepted
08 sept. 2019
First published
09 sept. 2019
This article is Open Access

All publication charges for this article have been paid for by the Royal Society of Chemistry
Creative Commons BY-NC license

Chem. Sci., 2019,10, 9424-9432

Electron density learning of non-covalent systems

A. Fabrizio, A. Grisafi, B. Meyer, M. Ceriotti and C. Corminboeuf, Chem. Sci., 2019, 10, 9424 DOI: 10.1039/C9SC02696G

This article is licensed under a Creative Commons Attribution-NonCommercial 3.0 Unported Licence. You can use material from this article in other publications, without requesting further permission from the RSC, provided that the correct acknowledgement is given and it is not used for commercial purposes.

To request permission to reproduce material from this article in a commercial publication, please go to the Copyright Clearance Center request page.

If you are an author contributing to an RSC publication, you do not need to request permission provided correct acknowledgement is given.

If you are the author of this article, you do not need to request permission to reproduce figures and diagrams provided correct acknowledgement is given. If you want to reproduce the whole article in a third-party commercial publication (excluding your thesis/dissertation for which permission is not required) please go to the Copyright Clearance Center request page.

Read more about how to correctly acknowledge RSC content.

Social activity

Spotlight

Advertisements