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%.

Crystal Field Effects on Atomic and Functional-Group Distributed Polarizabilities of Molecular Materials.

To rationally design new molecular materials with desirable linear optical properties, such as refractive index or birefringence, we investigated how atomic and functional-group polarizability tensors of prototypical molecules respond to crystal field effects. By building finite aggregates of urea, succinic acid, p-nitroaniline, 4-mercaptopyridine, or methylbenzoate, and by partitioning the cluster electronic density using quantum theory of atoms in molecules, we could extract atoms and functional groups from the aggregates and estimate their polarizability enhancements with respect to values calculated for molecules in isolation. The isotropic polarizability and its anisotropy for the molecular building blocks are used to understand the functional-group sources of optical properties in these model systems, which could help the synthetic chemist to fabricate efficient materials. This analysis is complemented by benchmarking density functionals for atomic distributed polarizabilities in gas phase, by comparing the results with refractive-index calculations under periodic boundary conditions, and by estimating functional-group optical properties from a classical electrostatic atom-dipole interaction model.

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

Structural features of moderate-to-strong O-H...O hydrogen bonds are related to the frequencies of O-H stretching vibrations and to the electric polarizability distribution in the donor and acceptor functional groups for crystals synthesized from the 1,2,4,5-benzenetetracarboxylic (pyromellitic) acid, namely: bis(3-aminopyridinium) dihydrogen pyromellitate tetrahydrate, (1); bis(3-carboxypyridinium) dihydrogen pyromellitate, (2); bis(3-carboxyphenylammonium) dihydrogen pyromellitate dihydrate, (3); and bis(4-carboxyphenylammonium) dihydrogen pyromellitate, (4). A combination of single-crystal X-ray diffraction, powder Raman spectroscopy and first-principle calculations in both crystalline and gaseous phases has shown that changes in the O-H...O hydrogen-bond geometry can be followed by changes in the corresponding spectral modes. Vibrational properties of moderate hydrogen bonds can be estimated from correlations based on statistical analysis of several compounds [Novak (1974). Struct. Bond. 18, 177-216]. However, frequencies related to very short O-H...O bonds can only be predicted by relationships built from a subset of structurally similar systems. Moreover, the way in which hydrogen bonds affect the polarizability of donor and acceptor groups depends on their strength. Moderate interactions enhance the polarizability and make it more anisotropic. Shorter hydrogen bonds may decrease the polarizability of a group as a consequence of the volume restraint implied by the neighbour molecule within a hydrogen-bonded aggregate. This is significant for evaluation of the electric susceptibility in crystals and, therefore, for estimation of refractive indices and birefringence.