Quantification of transition dipole strengths using 1D and 2D spectroscopy for the identification of molecular structures via exciton delocalization: Application to α-helices

Abstract

Vibrational and electronic transition dipole strengths are often good probes of molecular structures, especially in excitonically coupled systems of chromophores. One cannot determine transition dipole strengths using linear spectroscopy unless the concentration is known, which in many cases it is not. In this paper, we report a simple method for measuring transition dipole moments from linear absorption and 2D IR spectra that does not require knowledge of concentrations. Our method is tested on several model compounds and applied to the amide I band of a polypeptide in its random coil and α-helical conformation as modulated by the solution temperature. It is often difficult to confidently assign polypeptide and protein secondary structures to random coil or α-helix by linear spectroscopy alone, because they absorb in the same frequency range. We find that the transition dipole strength of the random coil state is 0.12 ± 0.013 D 2 , which is similar to a single peptide unit, indicating that the vibrational mode of random coil is localized on a single peptide unit. In an α-helix, the lower bound of transition dipole strength is 0.26 ± 0.03 D 2 . When taking into account the angle of the amide I transition dipole vector with respect to the helix axis, our measurements indicate that the amide I vibrational mode is delocalized across a minimum of 3.5 residues in an α-helix. Thus, one can confidently assign secondary structure based on exciton delocalization through its effect on the transition dipole strength. Our method will be especially useful for kinetically evolving systems, systems with overlapping molecular conformations, and other situations in which concentrations are difficult to determine.

Communication: Nanosecond folding dynamics of an alpha helix: Time-dependent 2D-IR cross peaks observed using polarization-sensitive dispersed pump-probe spectroscopy

“…Since these responses are each sensitive in a different manner to the length of an α-helix, 4 the observation of identical time constants for each suggests that the helix behaves effectively as a two-state folder, in agreement with previous studies on α-helical folding. Combining the observed relaxation constant with the known folded unfolded equilibrium constant, we obtain folding and unfolding time constants of 260 ± 30 and 580 ± 70 ns at 298 K, in good agreement with our previous 1D-IR T-jump study on this peptide.…”

“…In particular, the amide I' chromophores in an ideal α-helix have A and E modes that are separated by a few cm −1 , 25 and the A mode has a much larger intensity than the E mode, since the local amide I' transitiondipole moments are nearly parallel to the helical axis. In our 17-residue, solvated helix, A and E modes are not exactly defined, 26 but previous work has shown that in short helices, amide I' modes are still delocalized over at least 3.5 amide units, 4 and that the dominant normal modes in finite helices still have A-like and E-like characters, with a frequency splitting on the order of 10 cm −1 . 27 Because of the small E-A frequency difference and the low intensity of the E mode, an α-helix in solution effectively has a single amide I' band.…”

“…However, the most prominent change upon unfolding is a decrease in intensity of the amide I' signal, which is caused by a loss of excitonic delocalization as a result of α-helix unfolding. 4 The coupling between the A and E amide I' modes and between the two Arg + CN-stretch modes gives rise to crosspeaks in the 2D-IR spectrum, but in the raw 2D-IR spectra, these are difficult to distinguish from the much more intense signals on the diagonal. This diagonal contribution to the 2D-IR spectrum can be eliminated efficiently by constructing the difference…”

Fully absorptive 3D IR spectroscopy using a dual mid-infrared pulse shaper

“…13. Feynman diagrams for peak G due to population or coherence transfer (dashed line) in T 4 . spectroscopy in condensed phases and in elucidating chemical reaction mechanisms.…”

“…Transition dipole moments in excitonic structures depend on the extent of delocalization of vibrational excitations and can be used to identify molecular structures. 4 With 2D IR spectroscopy now well developed, attention is turning to 3D and higher correlations. [5][6][7][8][9] Analogous to how peaks are spread into a plane in 2D IR spectroscopy; the planes will be spread over a cube in 3D IR spectra.…”