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 materials behavior, including biomaterials. For this reason, computational approaches based on partitioning schemes have been developed aiming...

Unveiling GruPol: Predicting Electric and Electrostatic Properties of Macromolecules via the Building Block Approach

“…Since the introduction of the techniques used in GruPol, − a number of significant improvements were developed to better describe the electric and electrostatic properties of macromolecules. In particular, a hydrogen bond scan is implemented, which significantly improves the prediction of the magnitude and orientation of dipole moments as well as the anisotropy of polarizability tensors.…”

“…Although our first attempts 10,11 to reproduce ESP of polypeptide chains, employing group dipole moments, gave very promising results, a closer look at some functional groups, e.g., carboxylic groups or peptide bonds, indicated an incorrect distribution of the electrostatic potential. In particular, one could expect that the most electronegative ESP shall be located on the oxygen atoms in the region of lone pairs.…”

“…Polarization effects experienced by highly polarizable atoms are too sensitive to subtle changes of the chemical environment; thus, the transferability concept may not be effective, leading to inaccurate property prediction. Instead, bigger building blocks such as functional groups have demonstrated efficacy in resolving this matter, and numerous advances on expanding that idea, particularly for biological systems, have been published. − …”

Current developments and trends in quantum crystallography

“…Such a simplified approach, which makes use of functionalgroup electrostatic potentials (GEP) and distributed polarizabilities (GDP), enables an in-depth analysis of the correlation between structural features and a build-up of molecular properties. The efficiency and accuracy of the database for biomolecules, including macromolecules, were benchmarked against quantum chemical calculations (Ligorio et al, 2022;Rodrigues et al, 2022). Aiming at the simulation of condensed phase properties, the dipole interaction model (DIM) was additionally implemented into the polarizability database (Ligorio et al, 2020(Ligorio et al, , 2021.…”

“…However, very soon after, it became apparent that the stored dipole moments and polarizabilities of common functional groups could also be used for larger systems (e.g. macromolecules) to predict optoelectronic and electric-response properties, including electrostatic potential (Ligorio et al, 2022(Ligorio et al, , 2023; see Fig. 11).…”