Issue 38, 2020

Establishing the accuracy of density functional approaches for the description of noncovalent interactions in biomolecules

Abstract

Biomolecules have complex structures, and noncovalent interactions are crucial to determine their conformations and functionalities. It is therefore critical to be able to describe them in an accurate but efficient manner in these systems. In this context density functional theory (DFT) could provide a powerful tool to simulate biological matter either directly for relatively simple systems or coupled with classical simulations like the QM/MM (quantum mechanics/molecular mechanics) approach. Additionally, DFT could play a fundamental role to fit the parameters of classical force fields or to train machine learning potentials to perform large scale molecular dynamics simulations of biological systems. Yet, local or semi-local approximations used in DFT cannot describe van der Waals (vdW) interactions, one of the essential noncovalent interactions in biomolecules, since they lack a proper description of long range correlation effects. However, many efficient and reasonably accurate methods are now available for the description of van der Waals interactions within DFT. In this work, we establish the accuracy of several state-of-the-art vdW-aware functionals by considering 275 biomolecules including interacting DNA and RNA bases, peptides and biological inhibitors and compare our results for the energy with highly accurate wavefunction based calculations. Most methods considered here can achieve close to predictive accuracy. In particular, the non-local vdW-DF2 functional is revealed to be the best performer for biomolecules, while among the vdW-corrected DFT methods, uMBD is also recommended as a less accurate but faster alternative.

Graphical abstract: Establishing the accuracy of density functional approaches for the description of noncovalent interactions in biomolecules

Supplementary files

Article information

Article type
Paper
Submitted
04 авг 2020
Accepted
12 сеп 2020
First published
17 сеп 2020

Phys. Chem. Chem. Phys., 2020,22, 21685-21695

Establishing the accuracy of density functional approaches for the description of noncovalent interactions in biomolecules

M. Kim, T. Gould, D. Rocca and S. Lebègue, Phys. Chem. Chem. Phys., 2020, 22, 21685 DOI: 10.1039/D0CP04137H

To request permission to reproduce material from this article, 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 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