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J Chem Phys. 2013 Sep 14;139(10):104311. doi: 10.1063/1.4820532.

Observation of exclusively π-stacked heterodimer of indole and hexafluorobenzene in the gas phase.

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  • 1Department of Chemistry, Indian Institute of Science Education and Research (IISER), 900 NCL Innovation Park, Dr. Homi Bhabha Road, Pune 411008, Maharashtra, India.


In this study, the structure of the indole···hexafluorobenzene dimer has been investigated in the gas phase by using resonant two photon ionzation (R2PI) and IR-UV double resonance spectroscopy combined with quantum chemistry calculations. We have confirmed the presence of exclusively π-stacked structure of the dimer from both experimental and theoretical IR spectra in the N-H stretching region. Observation of a single stable structure of the dimer has also been verified through 3D potential energy surface scan of the π-stacked dimer by varying the parallel displacement of the hexafluorobenzene unit simultaneously along the major and minor axes of the indole moiety. π-stacking interaction is present very often between the tryptophan and phenylalanine residues in proteins. But this interaction has not been observed earlier in the gas phase experiment by studying indole···benzene dimer because the N-H group of indole predominately directs towards the N-H···π hydrogen bonded T-shaped structure. The chosen molecular systems in this study not only rule out the possibility of the formation of the N-H···π bound T-shaped dimer but also enable the determination of the structure by probing the N-H group. The π-stacked indole···hexafluorobenzene dimer has a unique structure where the center of the hexafluorobenznene ring is aligned with the center of the shared bond of the indole ring. Our work provides useful insight in designing unnatural proteins having strong π-stacking interaction between the tryptophan and phenylalanine residues.

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