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

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Abstract

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).

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Data availability

The datasets generated during the current study are available from the corresponding author on reasonable request.

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Funding

This work was partially supported by the Brazilian agency FAPEMIG (project APQ-01465–21) and by the Polish PLGrid Infrastructure.

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Authors and Affiliations

  1. Departamento de Química, Universidade Federal de Minas Gerais, Av. Pres. Antônio Carlos 6627, Belo Horizonte, MG, 31270-901, Brazil

    José L. Rodrigues, Renata Diniz & Leonardo H. R. Dos Santos

  2. Departamento de Química, Instituto Federal de Educação, Ciência e Tecnologia do Maranhão – Campus Grajaú, Br 226 S/N, Grajaú, MA, 65940-000, Brazil

    José L. Rodrigues

  3. Institut für Anorganische Chemie, Universität Göttingen, Tammannstrasse 4, 37077, Göttingen, Germany

    Raphael F. Ligorio & Anna Krawczuk

Authors
  1. José L. Rodrigues
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  2. Raphael F. Ligorio
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  4. Renata Diniz
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  5. Leonardo H. R. Dos Santos
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Contributions

Rodrigues J. L and Ligorio R. F. carried out theoretical calculations and data analyses. Rodrigues J. L made all pictures and tables. All authors discussed the results, commented, and wrote the manuscript.

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Correspondence to Leonardo H. R. Dos Santos.

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Rodrigues, J.L., Ligorio, R.F., Krawczuk, A. et al. Distributed functional-group polarizabilities in polypeptides and peptide clusters toward accurate prediction of electro-optical properties of biomacromolecules. J Mol Model 29, 49 (2023). https://doi.org/10.1007/s00894-023-05451-5

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