Raman Spectra of Amino Acids and Peptides from Machine Learning Polarizabilities
Berger, Ethan; Niemelä, Juha; Lampela, Outi; Juffer, André H; Komsa, Hannu-Pekka (2024-06-03)
American chemical society
03.06.2024
Berger, E., Niemelä, J., Lampela, O., Juffer, A. H., & Komsa, H.-P. (2024). Raman spectra of amino acids and peptides from machine learning polarizabilities. Journal of Chemical Information and Modeling, 64(12), 4601–4612. https://doi.org/10.1021/acs.jcim.4c00077
https://rightsstatements.org/vocab/InC/1.0/
This document is the Accepted Manuscript version of a Published Work that appeared in final form in Journal of chemical information and modeling, copyright © 2024 American Chemical Society after peer review and technical editing by the publisher. To access the final edited and published work see https://doi.org/10.1021/acs.jcim.4c00077.
https://rightsstatements.org/vocab/InC/1.0/
This document is the Accepted Manuscript version of a Published Work that appeared in final form in Journal of chemical information and modeling, copyright © 2024 American Chemical Society after peer review and technical editing by the publisher. To access the final edited and published work see https://doi.org/10.1021/acs.jcim.4c00077.
https://rightsstatements.org/vocab/InC/1.0/
Julkaisun pysyvä osoite on
https://urn.fi/URN:NBN:fi:oulu-202406174607
https://urn.fi/URN:NBN:fi:oulu-202406174607
Tiivistelmä
Abstract
Raman spectroscopy is an important tool in the study of vibrational properties and composition of molecules, peptides, and even proteins. Raman spectra can be simulated based on the change of the electronic polarizability with vibrations, which can nowadays be efficiently obtained via machine learning models trained on first-principles data. However, the transferability of the models trained on small molecules to larger structures is unclear, and direct training on large structures is prohibitively expensive. In this work, we first train two machine learning models to predict the polarizabilities of all 20 amino acids. Both models are carefully benchmarked and compared to density functional theory (DFT) calculations, with the neural network method being found to offer better transferability. By combination of machine learning models with classical force field molecular dynamics, Raman spectra of all amino acids are also obtained and investigated, showing good agreement with experiments. The models are further extended to small peptides. We find that adding structures containing peptide bonds to the training set greatly improves predictions, even for peptides not included in training sets.
Raman spectroscopy is an important tool in the study of vibrational properties and composition of molecules, peptides, and even proteins. Raman spectra can be simulated based on the change of the electronic polarizability with vibrations, which can nowadays be efficiently obtained via machine learning models trained on first-principles data. However, the transferability of the models trained on small molecules to larger structures is unclear, and direct training on large structures is prohibitively expensive. In this work, we first train two machine learning models to predict the polarizabilities of all 20 amino acids. Both models are carefully benchmarked and compared to density functional theory (DFT) calculations, with the neural network method being found to offer better transferability. By combination of machine learning models with classical force field molecular dynamics, Raman spectra of all amino acids are also obtained and investigated, showing good agreement with experiments. The models are further extended to small peptides. We find that adding structures containing peptide bonds to the training set greatly improves predictions, even for peptides not included in training sets.
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