Abstract
The amide I region of the infrared spectrum is related to the protein backbone conformation and can provide important structural information. However, the interpretation of the experimental results is hampered because the theoretical description of the amide I spectrum is still under development. Quantum mechanical calculations, for example, using density functional theory (DFT), can be used to study the amide I spectrum of small systems, but the high computational cost makes them inapplicable to proteins. Other approaches that solve the eigenvalues of the coupled amide I oscillator system are used instead. An important interaction to be considered is transition dipole coupling (TDC). Its calculation depends on the parameters of the transition dipole moment. This work aims to find the optimal parameters for TDC in three major secondary structures: α-helices, antiparallel β-sheets, and parallel β-sheets. The parameters were suggested through a comparison between DFT and TDC calculations. The comparison showed a good agreement for the spectral shape and for the wavenumbers of the normal modes for all secondary structures. The matching between the two methods improved when hydrogen bonding to the amide oxygen was considered. Optimal parameters for individual secondary structures were also suggested.
Highlights
The main application of infrared (IR) spectroscopy in the biological sciences is the analysis of the amide I region of the spectrum
Because of the large computational cost, density functional theory (DFT) calculations cannot be applied to entire proteins, fragmentation approaches are possible.[18−20] Even though these are successful in the hand of specialists, there is a demand in the vibrational spectroscopy community for widely applicable and rapid computational methods to model experimental spectra
Such methods are often based on the floating oscillator model,[12] where each amide group is considered as a vibrating oscillator with a specific, intrinsic frequency of vibration and a local transition dipole moment (TDM)
Summary
The main application of infrared (IR) spectroscopy in the biological sciences is the analysis of the amide I region of the spectrum. Because of the large computational cost, DFT calculations cannot be applied to entire proteins, fragmentation approaches are possible.[18−20] Even though these are successful in the hand of specialists, there is a demand in the vibrational spectroscopy community for widely applicable and rapid computational methods to model experimental spectra. Such methods are often based on the floating oscillator model,[12] where each amide group is considered as a vibrating oscillator with a specific, intrinsic frequency of vibration and a local transition dipole moment (TDM). The individual oscillators are coupled electrostatically, which is often described by the transition dipole coupling (TDC) approximation.[2,4,12,21−23] TDC is known not to reproduce nearest neighbor couplings, which are taken from quantum chemical calculations of small peptides.[13,14,24−27] Additional properties can influence the intrinsic frequency of the individual amide I oscillators, such as the local dihedral angles[13,14,26] and hydrogen bonding, which causes a downshift of the intrinsic frequencies of vibration.[28−30]
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