Nitrile Infrared Intensities Characterize Electric Fields and Hydrogen Bonding in Protic, Aprotic, and Protein Environments

Abstract

Nitriles are widely used vibrational probes; however, the interpretation of their IR frequencies is complicated by hydrogen bonding (H-bonding) in protic environments. We report a new vibrational Stark effect (VSE) that correlates the electric field projected on the −CN bond to the transition dipole moment and, by extension, the nitrile peak area or integrated intensity. This linear VSE applies to both H-bonding and non-H-bonding interactions. It can therefore be generally applied to determine electric fields in all environments. Additionally, it allows for semiempirical extraction of the H-bonding contribution to the blueshift of the nitrile frequency. Nitriles were incorporated at H-bonding and non-H-bonding protein sites using amber suppression, and each nitrile variant was structurally characterized at high resolution. We exploited the combined information available from variations in frequency and integrated intensity and demonstrate that nitriles are a generally useful probe for electric fields.

Genetically encoded non-canonical amino acids reveal asynchronous dark reversion of chromophore, backbone and side-chains in EL222

“…Introducing CNF groups at many different positions in EL222 provided us with information about site-specific light-induced changes on the local electric field from variations in the nitrile band area. We also resolved changes in the nitrile frequency, whose interpretation is more challenging by its dual dependence on local electric fields and H-bonding ( 45 ). In H-bonding environments, e.g.…”

“…We also looked at the band areas, proportional to the integrated extinction coefficient: larger areas indicate a larger transition dipole moment for the C≡N bond. Recently, it has been proposed that this dipole senses the local electric field by a Stark effect and, thus, the average local electric field projected on the C≡N direction can be derived from the peak area of the C≡N stretch ( 45 ). Hence, we finally extracted two parameters from the C≡N band of 39 single-CNF mutants: ν max and ( Note S1 and Table S4 ).…”

“…DMSO, the nitrile stretching frequency red-shifts as the electric field increases ( 47 ). A combined analysis of peak frequency and band area of nitrile probes has been recently proposed to characterize their H-bonding ( Note S1 ) ( 45 ). We applied this analysis to our data, and the estimated frequency shifts ascribable to H-bonding (Δν HB ) are listed in Table S4 for each CNF group.…”

Potential Distribution across Model Membranes

“…The constant D is analogous to the Stark tuning rate and proportional but not identical with the quantity determined in solution. 26 Using the value for E pzc,eff obtained from the analysis of the SEIRA frequencies (method I) and the calculated electric field for E pzc , we determined I SEIRA 0 and subsequently D from eqs 3 and 5 (vide supra). Because we were using the normalized intensities, D was identical for all three systems.…”

“…For all three MBN systems, i.e., pure MBN SAM, mixed SAM, and bilayer, we noted an increase of the intensities and a red shift of the nitrile stretching frequencies upon varying the electrode potential from +0.4 to −0.4 V, reflecting the variation of the transition dipole moment (proportional to the square root of the intensity, I SEIRA , abbreviated as SRI herein) and the frequency (ν SEIRA ) with the electric field acting on the nitrile bond (Figure 4). 26 To compare the data for MBN in all three systems, we must consider that, first, the SEIRA intensities depend on the electric field and the number of light-absorbing MBN molecules which is smaller in the mixed SAM and the bilayer as compared to the pure SAM. Second, the nitrile stretching frequencies do not only shift with the electric field but also vary with hydrogen-bonding interactions.…”