Vibrational Exciton Models for Biomolecules from Quantum Chemistry
Biophysics
Final Report Abstract
Vibrational spectroscopy can provide insights into fast processes occurring during protein folding and in disordered or unfolded proteins. In this project, we have developed efficient computational methods for reliably predicting vibrational spectra of biomolecular systems, in particular for two-dimensional infrared (2D-IR) and vibrational Raman optical activity (ROA) spectroscopy of conformationally flexible polypeptides and proteins. The key idea of all these developments is the use of localized vibrational modes as starting point. In this project, we have (a) further developed efficient L-VSCF/L-VCI methods for the calculation of anharmonic vibrational spectra, (b) explored the use of localized modes for constructing efficient vibrational exciton models from quantum-chemical calculations, and (c) pursued the calculation of ROA and 2D-IR spectra based on these novel methods. Specifically, we have (a) performed the first L-VSCF/L-VCI calculation of the anharmonic ROA spectrum of a system as large as (Ala)20 , which revealed that anharmonicities do not alter ROA band shapes significantly, (b) performed the first quantum-chemical calculations of 2D-IR spectra of polypeptides, and made the first predictions for 2D-IR spectra in the extended amide III region. The developments made in this project open the door to large-scale computational studies of advanced vibrational spectroscopy for realistic models of biomolecular systems.
Link to the final report
https://doi.org/10.24355/dbbs.084-202501161006-0
Publications
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Anharmonic Theoretical Vibrational Spectroscopy of Polypeptides. The Journal of Physical Chemistry Letters, 7(16), 3084-3090.
Panek, Paweł T. & Jacob, Christoph R.
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On the benefits of localized modes in anharmonic vibrational calculations for small molecules. The Journal of Chemical Physics, 144(16).
Panek, Paweł T. & Jacob, Christoph R.
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On the choice of coordinates in anharmonic theoretical vibrational spectroscopy: Harmonic vs. anharmonic coupling in vibrational configuration interaction. The Journal of Chemical Physics, 150(5).
Panek, Paweł T.; Hoeske, Adrian A. & Jacob, Christoph R.
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Data Set: Quantum-chemical calculation of two-dimensional infrared spectra using localized-mode VSCF/VCI
J. Brüggemann; M. Wolter; Ch. R. Jacob
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Quantum-chemical calculation of two-dimensional infrared spectra using localized-mode VSCF/VCI. The Journal of Chemical Physics, 157(24).
Brüggemann, Julia; Wolter, Mario & Jacob, Christoph R.
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Data Set: Structural Dependence of Extended Amide III Vibrations in Two-Dimensional Infrared Spectra
J. Brüggemann; M. Chekmeneva; M. Wolter; Ch. R. Jacob
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Python tools for localizing normal modes, Version 1.3
Ch. R. Jacob; P. T. Panek; T. Bergmann; J. Brüggemann; M. O. Welzel; M. Wolter
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Structural Dependence of Extended Amide III Vibrations in Two-Dimensional Infrared Spectra. The Journal of Physical Chemistry Letters, 14(41), 9257-9264.
Brüggemann, Julia; Chekmeneva, Maria; Wolter, Mario & Jacob, Christoph R.
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VIBRATIONS — a Python Code for Anharmonic Theoretical Vibrational Spectroscopy, Version 0.96
P. T. Panek; A. A. Hoeske; J. Brüggemann; M. O. Welzel; Ch. J. Jacob
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Benchmarking of Vibrational Exciton Models Against Quantum-Chemical Localized-Mode Calculations. (2024, 11, 21). American Geophysical Union (AGU).
van Bodegraven, Anna M.; Focke, Kevin; Wolter, Mario & Jacob, Christoph
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Data Set: Benchmarking of Vibrational Exciton Models Against Quantum-Chemical Localized-Mode Calculations
A. M. van Bodegraven; K. Focke; M. Wolter; Ch. R. Jacob
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PYADF Version 1.5
Ch. R. Jacob; T. Bergmann; S. M. B Eyhan; J. Brüggemann; R. E. Bulo, Rosa; M. Chekmeneva; T. Dresselhaus; K. Focke; A. S. P. Gomes; A. W. Goetz; M. Handzlik; K. K Iewisch; M. Klammler; L. Ridder; J. Sikkema; L. Visscher; J. Vornweg; M. O. Welzel; M. Wolter
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VIBRATIONS 2D, Version 0.9
J. Brüggemann; M. O. W Elzel; K. Focke; Ch. R. Jacob
