The dynamics of conformational isomerization in flexible biomolecules. I. Hole-filling spectroscopy of N-acetyl tryptophan methyl amide and N-acetyl tryptophan amide

Abstract

The conformational isomerization dynamics of N-acetyl tryptophan methyl amide (NATMA) and N-acetyl tryptophan amide (NATA) have been studied using the methods of IR-UV hole-filling spectroscopy (HFS) and IR-induced population transfer spectroscopy (IR-PTS), which were developed for this purpose. Single conformations of these molecules were selectively excited in well-defined NH stretch fundamentals. This excess energy was used to drive conformational isomerization. By carrying out the infrared excitation early in a supersonic expansion, the excited molecules were recooled into their zero-point levels, partially refilling the hole created in the ground state population of one of the conformers, and creating gains in population in other conformers. These changes in population were detected using laser-induced fluorescence downstream in the expansion. In HFS, the IR wavelength is fixed and the UV laser tuned in order to determine where the population went following selective infrared excitation. In IR-PTS, the UV is fixed to monitor the population of a given conformation, and the IR is tuned to record the IR-induced changes in the population of the monitored conformer. Besides demonstrating the capability of the experiment to change the downstream conformational population distribution, the IR-PTS scans were used to extract two quantitative results: (i) The fractional populations of the conformers in the absence of the infrared, and (ii) the isomerization quantum yields for each of the six unique amide NH stretch fundamentals (three conformers each with two amide groups). The method for obtaining quantum yields is described in detail. In both NATMA and NATA, the quantum yields show modest conformational specificity, but only a hint of vibrational mode specificity. The prospects for the hole-filling technique for providing insight into energy flow in large molecules are discussed, leaving a more detailed theoretical modeling to the adjoining paper [Evans et al. J. Chem. Phys. 120, 148 (2004)].

Isolated Neutral Peptides

“…Yet, experimental techniques exist to measure conformational distribution [47], and even conformational energetics [149]. Even though conformational distributions have indeed been measured for a few peptides [47,71,72,125,126], conformational energetics have been measured only for slightly simpler systems [149,180,181]. Conclusions about conformational energetics from the majority of experiments have thus been limited so far to identifying major and minor conformations of the distribution.…”

Intramolecular Amide Stacking and Its Competition with Hydrogen Bonding in a Small Foldamer

“…These weighting factors are the relative fractional abundances of the conformers. 23 The fractional abundances derived from MRIRPT give F C ) 0.21 ( 0.01, within a factor of 2 of either of the amide-amide hydrogen bonded conformers (F A ) 0.38 ( 0.01 and F B ) 0.41 ( 0.02). This method avoids the use of S 0 -S 1 origin intensities to infer relative fractional abundances (Figure 1, top), which assume identical Franck-Condon factors, excited state lifetimes, and R2PI cross sections for each conformer.…”

“…23 MRIRPT spectra were obtained by counterpropagating the infrared laser along the molecular beam, creating a column of IR-excited molecules for interrogation. By adjusting the timing of the IR excitation relative to the UV probe laser (∆t ) 44 µs), molecules initially excited within a few millimeters of the pulsed valve orifice can isomerize and be recooled during travel to the ion source region before interrogation with the UV probe via R2PI.…”

Conformational changes in matrix-isolated 6-methoxyindole: Effects of the thermal and infrared light excitations

“…Such remote infraredinduced isomerizations were observed previously by ultrafast spectroscopy in the gas phase. [16][17][18][19][20] In matrices, however, a) Author to whom correspondence should be addressed. Electronic mail:…”