The secondary structure of diatom silaffin peptide R5 determined by two-dimensional infrared spectroscopy

Thomassen, Asger Berg; Jansen, Thomas L. C.; Weidner, Tobias

doi:10.1039/d4cp00970c

Phys. Chem. Chem. Phys.

2024

DOI: 10.1039/d4cp00970c

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The secondary structure of diatom silaffin peptide R5 determined by two-dimensional infrared spectroscopy

Asger Berg Thomassen,

Thomas L. C. Jansen,

Tobias Weidner

Abstract: Diatoms, unicellular marine organisms, harness short peptide repeats of the protein silaffin to transform silicic acid into biosilica nanoparticles. This process have been a white wale for material scientists for...

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Modeling Infrared Spectroscopy of Nucleic Acids: Integrating Vibrational Non-Condon Effects with Machine Learning Schemes

Qian,

Liu,

Meng

et al. 2024

J. Chem. Theory Comput.

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Vibrational non-Condon effects, which describe how molecular vibrational transitions are influenced by a system's rotational and translational degrees of freedom, are often overlooked in spectroscopy studies of biological macromolecules. In this work, we explore these effects in the modeling of infrared (IR) spectra for nucleic acids in the 1600−1800 cm −1 region. Through electronic structure calculations, we reveal that the transition dipole moments of the C�O and C�C stretching modes in nucleobases are highly sensitive to solvation, hydrogen bonding, and base stacking conditions. To incorporate vibrational non-Condon effects into spectroscopy modeling, we use local electric fields on chromophore atoms as collective coordinates and leverage experimental IR spectra of oligonucleotides to develop deep neural network-based transition dipole strength (TDS) maps for the C�O and C�C chromophores. By integrating molecular dynamics simulations with a mixed quantum/classical treatment of the line shape theory, we apply the TDS maps to calculate the IR spectra of nucleoside 5′-monophosphates, DNA double helices and yeast phenylalanine tRNA. The resulting theoretical spectra show quantitative agreement with experimental measurements. While the predictions for nucleoside 5′-monophosphates are comparable to baseline performance, the TDS maps yield significantly improved IR peak intensities across all oligonucleotides. This theoretical framework effectively bridges atomistic simulations and IR spectroscopy experiments, offering molecular insights into how vibrational non-Condon effects impact the observed spectral features.

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Modeling Infrared Spectroscopy of Nucleic Acids: Integrating Vibrational Non-Condon Effects with Machine Learning Schemes

Qian,

Liu,

Meng

et al. 2024

J. Chem. Theory Comput.

View full text Add to dashboard Cite

show abstract

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The secondary structure of diatom silaffin peptide R5 determined by two-dimensional infrared spectroscopy

Abstract: Diatoms, unicellular marine organisms, harness short peptide repeats of the protein silaffin to transform silicic acid into biosilica nanoparticles. This process have been a white wale for material scientists for...

Cited by 1 publication

References 83 publications

Modeling Infrared Spectroscopy of Nucleic Acids: Integrating Vibrational Non-Condon Effects with Machine Learning Schemes

Modeling Infrared Spectroscopy of Nucleic Acids: Integrating Vibrational Non-Condon Effects with Machine Learning Schemes

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