2D IR photon echo spectroscopy reveals hydrogen bond dynamics of aromatic nitriles

Abstract

The CN vibrations of two aromatic nitriles, cinnamonitrile, PhCHCH–CN and benzonitrile, PhCN, representative of components of common enzyme inhibitors, are examined by two-dimensional infrared spectroscopy. In methanol, these spectra display cross peaks between the two CN components whose evolution exposes the few picosecond (4.5 ps for CIN and 5.3 ps for BN) equilibrium dynamics of hydrogen bond making and breaking. The main features of the 2D IR spectra are reproduced by simulations only when exchange is incorporated. The lowest free energy state is the non-hydrogen bonded form. Both alkyl and aryl nitriles have now shown this picosecond exchange process.

Introduction

The vibrational spectra of nitriles have been useful as probes of the local structures [1], [2], [3], [4], [5], electric fields [6], [7], [8], [9], and solvent dynamics [10], [11], [12]. These localized –CN transitions are sharp enough that small changes in frequency can be readily quantified. Furthermore, nitriles are readily introduced into proteins [7], [8], [13] and peptides [3], [4], [14] where they have transitions that are considerably removed from the peptide backbone infrared absorption. The physical origins of the nitrile peak shifts and line shapes have been examined theoretically [15], [16], [17], [18]. For protein studies, the ability to connect the spectral shapes and frequencies of vibrational probes to specific structural and dynamical features remains an important challenge. The 2D IR experiments can help to clarify these processes and advance the applicability of nitriles as probes.

Nitrile groups are also integral components of numerous non-nucleoside anti-AIDS drugs which bind to reverse transcriptase (RT) inhibitors that have been discovered and structurally characterized by Arnold and coworkers [19], [20]. Two-dimensional infrared (2D IR) spectroscopy has been used to track frequency fluctuations and polarity differences of the drug binding sites [12]. One of the enzyme inhibitors has two aromatic arms, one consisting of a benzonitrile and the other a cinnamonitrile. The inhibitors of HIV-1 RT bind in a hydrophobic pocket between two β-sheets [21] and the motions of the drug and the nearby residues in the pocket have significant biological interest. The FTIR and 2D IR of the CN vibrations exhibit spectral diffusion in response to these polarity fluctuations in the pockets. In the present work the 2D IR of models representing the two arms of these drugs is reported along with the kinetics of their hydrogen bond making and breaking from 2D IR exchange studies.

The two-dimensional infrared spectroscopy (2D IR) is ideally suited to investigate the frequency fluctuations, dynamic exchange processes and vibrational frequency autocorrelation functions. The influence of water hydrogen bond dynamics on solute vibrational modes and structure have been examined previously by nonlinear IR spectroscopy and correlated to the frequency fluctuations of solute vibrational modes for many systems [10], [11], [22], [23], [24], [25], [26], [27]. 2D IR echo spectroscopy has been employed to measure the hydrogen bond making and breaking for the system acetonitrile in methanol [10], [11] by monitoring the exchange kinetics of such echo signals. Hamm and coworkers [23] have used 2D IR pump/probe methods [28] to follow the delay time dependence of the H-bond kinetics of an amide mode in methanol which has also been examined by molecular dynamics simulations [23], [29]. Other types of systems undergoing exchange have been reported using 2D IR echo spectroscopy involving molecules undergoing various reversible chemical processes [30], [31], [32], and there have been considerable advances in the theory of spectral diffusion of molecules and chemical exchange [29], [33], [34]. Another advantage of 2D IR is that it can identify the origins of features in linear IR spectra. Many reports can be found regarding the asymmetry or shoulders of unknown origin in the vibrational lineshapes of nitriles. Such spectral features have sometimes been attributed to anharmonic coupling [35] but linear IR spectra of molecules in condensed phases are unable to provide definitive proof of this conclusion. The distinction between exchange and anharmonic coupling is clear in 2D IR spectra because the latter introduces cross peaks that are present independently of the exchange kinetics.

Vibrational chemical exchange becomes observable in 2D IR when the vibrational frequencies of two or more chemical species at equilibrium have spectrally distinct transitions. The nonlinear and linear spectra depend critically on the relative values of the exchange rate constant, and the difference in frequency between the two exchanging states. In slow exchange two transitions appear at different frequencies, while very fast exchange results in a single time-averaged peak at the weighted average of the frequencies. 2D IR techniques have been shown to be successful in establishing exchange processes on the picosecond timescale that have not been accessible by other methods [10], [11], [30], [31], [32].

In the present work, the H-bond exchange dynamics of the CN stretching mode is reported for two aromatic nitriles in methanol where two vibrational transitions are observed when only one nitrile vibration, the CN stretch, is predicted from computations and simple force fields of the isolated molecule. Eaton and coworkers [1] had suggested that the lower frequency component corresponds to a nitrile environment of self-associated methanol. The higher frequency band coincides with the peak of nitrile in water and has been attributed to a hydrogen bonded form in methanol. Some of the inferences from FTIR experiments can be directly verified by means of nonlinear 2D IR experiments and the equilibrium kinetics can be accessed as has been shown previously for acetonitrile [10]. An important question is how the equilibrium dynamics depends on the molecular structure of the nitrile, and how general is this display of H-bond dynamics in the vibrational spectrum.