Multi-scale modeling of electronic spectra of three aromatic amino acids: importance of conformational averaging and explicit solute-solvent interactions

Electronic transitions in the ultraviolet and visible spectral range can reveal a wealth of information about biomolecular geometry and interactions, such as those involved in protein folding. However, the modeling that provides the necessary link between spectral shapes and the structure is often d...

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Bibliographic Details
Published in:Physical chemistry chemical physics : PCCP 2014-09, Vol.16 (38), p.2639-2649
Main Authors: Št pánek, Petr, Bou, Petr
Format: Article
Language:English
Subjects:
Amino acids
Amino Acids, Aromatic - chemistry
Clusters
Computer Simulation
Continuums
Data Interpretation, Statistical
Dichroism
Electronics
Models, Chemical
Molecular Conformation
Molecular Dynamics Simulation
Solvents
Solvents - chemistry
Spectra
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Summary:Electronic transitions in the ultraviolet and visible spectral range can reveal a wealth of information about biomolecular geometry and interactions, such as those involved in protein folding. However, the modeling that provides the necessary link between spectral shapes and the structure is often difficult even for seemingly simple systems. To understand as to how conformational equilibria and solute-solvent interaction influence spectral intensities, we collected absorption (UV-vis), electronic circular dichroism (ECD), and magnetic circular dichroism (MCD) spectra of phenylalanine (Phe), tyrosine (Tyr) and tryptophan (Trp) zwitterions in aqueous solutions, and compared them with quantum-chemical simulations. These aromatic amino acids provide a relatively strong signal in the accessible wavelength range. At the same time, they allow for a relatively accurate modeling. Energies and intensities of spectral bands were reproduced by the time-dependent density functional theory (TD DFT). The solvent was approximated by a continuum as well as clusters containing solvent molecules from the first hydration sphere. The ECD signal was found to be strongly dependent on molecular conformation, and the dependence was much weaker in UV-vis and MCD spectra. All spectral intensities, however, were significantly affected by the solvent approximation; especially for ECD and MCD the usual polarizable continuum solvent model did not yield satisfactory spectral shapes. On the other hand, averaging of the clusters obtained from molecular dynamics simulations provided an unprecedented agreement with the experiment. Proper modeling of the interactions with the environment thus makes the information about the molecular structure, as obtained from the electronic spectra, more accurate and reliable. Electronic spectra provide a wealth of information on molecular structures. We demonstrate a very satisfactory agreement between experimental and modeled spectra, as obtained by combined molecular mechanics/quantum mechanics computations for three aromatic amino acids.
ISSN:1463-9076
1463-9084
DOI:10.1039/c4cp02668c