A building‐block database of distributed polarizabilities and dipole moments to estimate optical properties of biomacromolecules in isolation or in an explicitly solvated medium

Abstract

Since atomic or functional-group properties in the bulk are generally not available from experimental methods, computational approaches based on partitioning schemes have emerged as a rapid yet accurate pathway to estimate the materials behavior from chemically meaningful building blocks. Among several applications, a comprehensive and systematically built database of atomic or group polarizabilities and related opto-electronic quantities would be very useful not only to envisage linear or non-linear optical properties of biomacromolecules but also to improve the accuracy of classical force fields devoted to simulate biochemical processes. In this work, we propose the first entries of such database that contains distributed polarizabilities and dipole moments extracted from fragments of peptides. Twenty three prototypical conformers of the dipeptides alanine-alanine and glycine-glycine were used to extract functional groups such as CH 2 , CHCH 3 , NH 2 , COOH, CONH , thus allowing construction of a diversity of chemically relevant environments. To evaluate the accuracy of our database, reconstructed properties of larger peptides containing up to six residues of alanine and glycine were tested against density functional theory calculations at the M06-HF/aug-cc-pVDZ level of theory. The procedure is particularly accurate for the diagonal components of the polarizability tensor with errors up to 15%. In order to include solvent effects explicitly, the peptides were also surrounded by a box of water molecules whose distribution was optimized using the CHARMM force field. Solvent effects introduced by a classical dipole-dipole interaction model were compared to those obtained from polarizablecontinuum model calculations.

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

“…Although our first attempts , 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.…”

“…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.…”

“…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. − …”