Issue 48, 2022

Benchmark of a functional-group database for distributed polarizability and dipole moment in biomolecules

Abstract

The extraction of functional-group properties in condensed phases is very useful for predicting material behaviors, including those of biomaterials. For this reason, computational approaches based on partitioning schemes have been developed aiming at rapidly and accurately estimating properties from chemically meaningful building blocks. A comprehensive database of group polarizabilities and dipole moments is useful not only to predict the optical properties of biomacromolecules but also to improve molecular force fields focused on simulating biochemical processes. In this work we benchmark a database of distributed polarizabilities and dipole moments for functional groups extracted from a series of polypeptides. This allows reconstruction of a variety of relevant chemical environments. The accuracy of our database was tested to predict the electro-optical properties of larger peptides and also simpler amino acids for which density functional theory calculations at the M06-HF/aug-cc-pVDZ level of theory was chosen as the reference. This approach is reasonably accurate for the diagonal components of the polarizability tensor, with errors not larger than 15–20%. The anisotropy of the polarizability is predicted with smaller efficacy though. Solvent effects were included explicitly by surrounding the database entries by a box of water molecules whose distribution was optimized using the CHARMM force field.

Graphical abstract: Benchmark of a functional-group database for distributed polarizability and dipole moment in biomolecules

Supplementary files

Article information

Article type
Paper
Submitted
31 8 2022
Accepted
21 11 2022
First published
22 11 2022
This article is Open Access
Creative Commons BY-NC license

Phys. Chem. Chem. Phys., 2022,24, 29495-29504

Benchmark of a functional-group database for distributed polarizability and dipole moment in biomolecules

R. F. Ligorio, J. L. Rodrigues, A. Zuev, L. H. R. Dos Santos and A. Krawczuk, Phys. Chem. Chem. Phys., 2022, 24, 29495 DOI: 10.1039/D2CP04052B

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