Abstract
The isonitrile (NC) group has been shown to be a promising infrared probe for studying the structure and dynamics of biomolecules. However, there have been no systematic studies performed on the NC group as an infrared probe, when it is bonded to an indole ring. Here, we systematically study the NC stretching mode of two model compounds, 5-isocyano-1H-indole (5ICI) and 5-isocyano-1-methyl-1H-indole (NM5ICI), using Fourier transform infrared (FTIR) spectroscopy. The NC stretching frequency is shown to be strongly dependent on the polarizability of protic solvents and the density of hydrogen-bond donor groups in the solvent when NC is bonded to an indole ring. Infrared pump–probe studies of 5ICI in DMSO and in EtOH further support that the NC stretching mode could be used as a site-specific infrared probe for local environments when NC is bonded to an indole ring.
Highlights
Infrared (IR) probes have been widely employed as vibrational reporters to investigate site-specific information for protein conformations, local environments, and dynamics in various biomolecular systems using linear and non-linear spectroscopy [1,2,3,4,5,6,7,8]
All the results indicate that the NC group could be used as a sensitive site-specific IR probe of the local environments
We found that the NC stretching frequency was not dependent on the polarizability of aprotic solvents but showed a strong linear correlation with the polarizability of protic solvents
Summary
Infrared (IR) probes have been widely employed as vibrational reporters to investigate site-specific information for protein conformations, local environments, and dynamics in various biomolecular systems using linear and non-linear spectroscopy [1,2,3,4,5,6,7,8]. Many probes have been used to provide useful information about proteins or polypeptides, their application in time-resolved non-linear IR spectroscopy has been limited. The azido group has become a desirable IR probe in biological environments at very low concentration owing to its larger transition dipole strength [12,13,14]. The cyanamide group has been reported as an optimized version of the nitrile group, owing to its larger transition dipole strength and longer vibrational lifetime [16]. Site-specific IR probes have been widely used in protein structure studies, researchers are still actively working on the development of new IR probes
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