Crystal structure, vibrational frequencies and polarizability distribution in hydrogen-bonded salts of pyromellitic acid

Distributed functional-group polarizabilities in polypeptides and peptide clusters toward accurate prediction of electro-optical properties of biomacromolecules

CONTEXT

Aiming at accurately predicting electro-optical properties of biomolecules, this work presents distributed atomic and functional-group polarizability tensors for a series of polypeptides and peptide clusters constructed from glycine and its residuals. By partitioning the electron density using the quantum theory of atoms in molecules, we demonstrated a very good transferability of the group polarizabilities. We were able to identify and extract the most efficient functional groups capable of generating the largest electrical susceptibility in condensed phases. Both the isotropic polarizability and its anisotropy were used to understand the way functional groups act as sources of linear optical responses, how they interact with each other reinforcing the macroscopic optical behavior within the material, and how covalent bonds and non-covalent interactions, such as hydrogen bonds, determine refractive indices and birefringence. Particular attention is devoted to the peptide bonds as they provide links to build biomacromolecules or polymers. An adequate quantum-mechanical treatment of at least the first interaction sphere of a given functional group is required to properly describe the effects of mutual polarization, but we identified optimum cluster size and shape to better estimate polarizabilities and dipole moments of larger molecules or molecular aggregates from the knowledge of the electron density of a central molecule or amino acid residual that is representative of the bulk. The strategy outlined here is a fast yet effective tool for estimating the optical properties of proteins but could eventually find application in the rational design of optical organic materials as well.

METHODS

Electronic-structure calculations were performed on the Gaussin16 program at the DFT level using the CAMB3LYP functional and the double-ζ quality Dunning basis set aug-cc-pVDZ. Electron density partitioning followed the concepts of the Quantum Theory of Atoms and Molecules (QTAIM) and was performed using the AIMAll program. The locally developed Polaber routine was applied to calculate dipole moment vectors and polarizability tensors. It was amended to include the effects of the local field on a given central molecule by means of a modified Atom-Dipole Interaction Model (ADIM).

Accurate Atom-Dipole Interaction Model for Prediction of Electro-optical Properties: From van der Waals Aggregates to Covalently Bonded Clusters

This work aims at the accurate estimation of the electro-optical properties of atoms and functional groups in organic crystals. A better understanding of the nature of building blocks and the way they interact with each other enables more efficient prediction of self-assembly, and thus physical properties in condensed matter. We propose a modified version of an atom-dipole interaction model that is based on atomic dipole moments calculated from the quantum theory of atoms in molecules. The method is very reliable for the prediction of various optical and electric properties in diverse chemical environments, ranging from hydrocarbon molecules bonded by dispersive interactions to polar rings connected by hydrogen bonds, or even polymeric structures whose monomers are covalently linked. Distributed polarizabilities and electrostatic potentials are compared to those obtained using a complete quantum-mechanical approach on finite-size aggregates. Our electrostatic approximation recovers isotropic polarizabilities with an accuracy of ca. 5 au and electrostatic potentials of ca. 0.05 au, even in the worst-case scenario in which polarization and charge-transfer effects are large. Functional groups are highly exportable, estimating the properties of small peptides and polyaromatics with a maximum deviation as low as ca. 15%.