1. Computational Modeling of the Nitrile Stretching Vibration of 5-Cyanoindole in Water
Matthias M Waegele, Feng Gai J Phys Chem Lett. 2010 Feb 1;1(4):781-786. doi: 10.1021/jz900429z.
The bandwidth of the nitrile (C≡N) stretching vibration of 5-cyanotryptophan shows a significant broadening upon hydration. Thus, it has been proposed to be a useful infrared probe of the local hydration environment of proteins. However, the molecular mechanism underlying this hydration-induced spectral broadening is not known, making interpretation of the experimental results difficult. Herein, we investigate how interactions of water with various sites of 5-cyanoindole, the sidechain of 5-cyanotryptophan, affect its C≡N stretching vibration via a combined electronic structure/molecular dynamics approach. It is found that, besides those interactions with the nitrile group, interactions of water with the indole ring also play a significant role in mediating the C≡N stretching frequency. Thus, this study provides a molecular basis for understanding how hydration affects the C≡N stretching band of 5-cyanotryptophan. In addition, an empirical model, which includes interactions of water with both the nitrile and indole groups, is developed for predicting the C≡N stretching vibrational band via molecular dynamics simulations.
2. A vibrational probe for local nucleic acid environments: 5-cyano-2'-deoxyuridine
Matthew D Watson, Xin Sonia Gai, Anne T Gillies, Scott H Brewer, Edward E Fenlon J Phys Chem B. 2008 Oct 23;112(42):13188-92. doi: 10.1021/jp8067238. Epub 2008 Sep 25.
Nitriles have been shown to be effective vibrational probes of local environments in proteins but have yet to be fully utilized for the study of nucleic acids. The potential utility of 5-cyano-2'-deoxyuridine ( 1) as a probe of local nucleic acid environment was investigated by measuring the dependence of the IR nitrile stretching frequency (nu CN), line shape, and absorbance on solvent and temperature. The nu CN was found to be sensitive to solvent with an observed blue shift of 9.2 cm (-1) in going from THF to water. The dependence of the nitrile IR absorbance band was further investigated in water-THF mixtures. Global line shape analysis, difference FTIR spectroscopy, and singular value decomposition (SVD) were used to show the presence of three distinct local environments around the nitrile group of 1 in these mixtures. A modest blue shift in nu CN was observed upon a hydrogen-bond-mediated heterodimer formation between 2 (a silyl ether analogue of 1) and 2,6-diheptanamido-pyridine ( 3a) in chloroform. The intrinsic temperature dependence of the nu CN was found to be minimal and linear over the temperature range studied. The experimental studies were complemented by density functional theory (DFT) calculations on the dependence of the nitrile stretching frequency on solute-solvent interactions and upon heterodimer formation with model systems.
3. C≡N stretching vibration of 5-cyanotryptophan as an infrared probe of protein local environment: what determines its frequency?
Wenkai Zhang, Beatrice N Markiewicz, Rosalie S Doerksen, Amos B Smith III, Feng Gai Phys Chem Chem Phys. 2016 Mar 14;18(10):7027-34. doi: 10.1039/c5cp04413h.
Recently it has been suggested that the C≡N stretching vibration of a tryptophan analog, 5-cyanotryptophan, could be used as an infrared probe of the local environment, especially the hydration status, of tryptophan residues in proteins. However, the factors that influence the frequency of this vibrational mode are not understood. To determine these factors, herein we carried out linear and nonlinear infrared measurements on the C≡N stretching vibration of the sidechain of 5-cyanotryptophan, 3-methyl-5-cyanoindole, in a series of protic and aprotic solvents. We found that while the C≡N stretching frequencies obtained in these solvents do not correlate well with any individual Kamlet-Taft solvent parameter, i.e., π* (polarizability), β (hydrogen bond accepting ability), and α (hydrogen bond donating ability), they do however, collapse on a straight line when plotted against σ = π* + β - α. This linear relationship provides a firm indication that both specific interactions, i.e., hydrogen-bonding interactions with the C≡N (through α) and indole N-H (through β) groups, and non-specific interactions with the molecule (through π*) work together to determine the C≡N stretching frequency, thus laying a quantitative framework for applying 5-cyanotryptophan to investigate the microscopic environment of proteins in a site-specific manner. Furthermore, two-dimensional and pump-probe infrared measurements revealed that a significant portion (~31%) of the ground state bleach signal has a decay time constant of ~12.3 ps, due to an additional vibrational relaxation channel, making it possible to use 5-cyanotryptophan to probe dynamics occurring on a timescale on the order of tens of picoseconds.
