Theoretical Investigation of Positional Substitution and Solvent Effects on n-Cyanoindole Fluorescent Probes

Modeling the effect of substituents on the electronically excited states of indole derivatives

A proper understanding of excited state properties of indole derivatives can lead to rational design of efficient fluorescent probes. The optically activeL a andL b excited states of a series of substituted indoles, where a substituent was placed on position four, were calculated using equation of motion coupled cluster and time dependent density functional theory. The results indicate that most substituted indoles have a brighter second excited state corresponding to experimental absorption maxima, but a few with electron withdrawing substituents absorb more on the first excited state. Absorption on the first excited state may increase their fluorescence quantum yield, making them better probes. Electronic structure methods were found to predict the energies of the systems with electron withdrawing substituents more accurately than those with electron donating substituents. The excited states of both states correlated well with electrophilicity, similar to the experimental trends for the absorption maxima. Overall, these computational studies indicate that theory can be used to predict excited state properties of substituted indoles, when the substituent is an electron withdrawing group.

Blueshift or redshift? Effect of hydrogen bonding interactions on the C≡N stretching frequency of 5-cyanoindole

The nitrile (C≡N) stretching vibration is widely used as a site-specific environmental probe of proteins and, as such, many computational studies have been used to investigate the factors that affect its frequency (νCN). These studies, most of which were carried out in the ground electronic state of the molecule of interest, revealed that the formation of a normal or linear hydrogen bond (H-bond) with the nitrile group results in a blueshift in its νCN. Recently, however, several experimental studies showed that for certain aromatic nitriles, solvent relaxations in their excited electronic state(s) induce a redshift (blueshift) in νCN in protic (aprotic) solvents, suggesting that the effect of hydrogen-bonding (H-bonding) interactions on νCN may depend on the electronic state of the molecule. To test this possibility, herein we combine molecular dynamics simulations and quantum mechanical calculations to assess the effect of H-bonding interactions on the νCN of 5-cyanoindole (5-CNI) in its different electronic states. We find that its C≡N group can form either one H-bond (single-H-bond) or two H-bonds (d-H-bonds) with the solvent molecules and that in the ground electronic state, a single-H-bond can lead νCN to shift either to a higher or lower frequency, depending on its angle, which is consistent with previous studies, whereas the d-H-bonds cause νCN to redshift. However, in its lowest-lying excited electronic state (i.e., S1), which has the characteristics of a charge-transfer state, all H-bonds induce a redshift in νCN, with the d-H-bonds being most effective in this regard.

Modeling the temperature dependence of the fluorescence properties of Indole in aqueous solution

In a recent paper, we proposed a scheme to describe the relaxation mechanism of the excited Indole in aqueous solution, involving the fluctuations among the diabatic electronic states 1Lb, 1La and 1πσ∗. Such a theoretical and computational model reproduced accurately the available experimental data at room temperature. Following these results, in the present work, we model the complex temperature dependence of the fluorescence properties of Indole in aqueous solution, with results further validating the proposed relaxation scheme. This scheme is able to explain the temperature effects on the fluorescence behavior indicating the water fluctuations as the main cause of (i) the stabilization of the dark state (1πσ∗) and (ii) the increase in temperature of the kinetics of the irreversible transition towards such a state.

Excited state hydrogen or proton transfer pathways in microsolvated n-cyanoindole fluorescent probes

The sensitivity of the fluorescence properties of n-cyanoindole (n-CNI) fluorescent probes to the microenvironment makes them potential reporters of protein conformation and hydration. The fluorescence intensity of 5-CNI, 6-CNI, and 7-CNI is quenched when exposed to water solvent whereas substitution on position 4 of indoles dramatically increases it. A potential mechanism for this sensitivity to water may be similar to that found in indole. The fluorescence of indole is found to be quenched when interacting with water and ammonia solvent molecules via radiationless decay through an S1 (πσ*)/S0 conical intersection caused by excited state proton or hydrogen transfer to the solvent molecules. In this study we examine this fluorescence quenching mechanism along the N-H bond stretch of n-CNI probes using water cluster models and quantum mechanical calculations of the excited states. We find that n-CNI-(H2O)1-2 clusters form cyclic or non-cyclic structures via hydrogen bonds which lead to different photochemical reaction paths that can potentially quench the fluorescence by undergoing internal conversion from S1 to S0. However, the existence of a high energy barrier along the potential energy surface of the S1 state in most cases prevents this from occurring. We show that substitution on position 4 leads to the highest energy barrier that prevents the fluorophore from accessing these non-radiative channels, in agreement with its high intensity. We also find that the energy barrier in the S1 state of non-cyclic 5-CNI-(H2O)1-2 excited complexes decreases as the number of water molecules increases, which suggests great sensitivity of the fluorescence quenching on the aqueous environment.

Blue Fluorescence of Cyano-tryptophan Predicts Local Electrostatics and Hydrogen Bonding in Biomolecules

Cyano-tryptophan is an unnatural fluorescent amino acid that emits in the visible region. Along with the structural similarity with tryptophan, the unique photophysical properties of this fluorophore make it an ideal probe for biophysical research. Herein, combining fluorescence spectroscopy, infrared spectroscopy, and molecular dynamics simulations, we show that the cyano-tryptophan's emission energy quantifies the underlying bond-specific noncovalent interactions in terms of the electric field. We further report the use of fluorophore's emission energy to predict its hydrogen bond characteristics. We demonstrate that combining experiments with molecular dynamics simulations can provide the hydrogen bonding status of the nitrile moiety. In addition, we report a method to differentiate between aqueous and nonaqueous hydrogen-bonding partners. Using a phenomenological approach, we demonstrate that the presence of the cyano-indole moiety is responsible for the distinct correlations between the fluorophore's emission and the electrostatic forces on the nitrile bond. As indole is a privileged scaffold for both native amino acids and nucleobases, cyano-indoles will have many multifaceted applications.

The photophysics of 2-cyanoindole probed by femtosecond spectroscopy

The photophysics of 2-cyanoindole (2-CI) in solution (water, 2,2,2-trifluoroethanol, acetonitrile‚ and tetrahydrofuran) was investigated by steady-state as well as time resolved fluorescence and absorption spectroscopy. The fluorescence quantum yield of 2-cyanoindole is strongly sensitive to the solvent. In water the quantum yield is as low as 4.4 × 10–4. In tetrahydrofuran, it amounts to a yield of 0.057. For 2-CI dissolved in water, a bi-exponential fluorescence decay with time constants of ∼1 ps and ∼8 ps is observed. For short wavelength excitation (266 nm) the initial fluorescence anisotropy is close to zero. For excitation with 310 nm it amounts to 0.2. In water, femtosecond transient absorption reveals that the fluorescence decay is solely due to internal conversion to the ground state. In aprotic solvents, the fluorescence decay takes much longer (acetonitrile: ∼900 ps, tetrahydrofuran: ∼2.6 ns) and intersystem crossing contributes.

Graphical abstract

A Simplified Treatment for Efficiently Modeling the Spectral Signal of Vibronic Transitions: Application to Aqueous Indole

In this paper, we introduce specific approximations to simplify the vibronic treatment in modeling absorption and emission spectra, allowing us to include a huge number of vibronic transitions in the calculations. Implementation of such a simplified vibronic treatment within our general approach for modelling vibronic spectra, based on molecular dynamics simulations and the perturbed matrix method, provided a quantitative reproduction of the absorption and emission spectra of aqueous indole with higher accuracy than the one obtained when using the existing vibronic treatment. Such results, showing the reliability of the approximations employed, indicate that the proposed method can be a very efficient and accurate tool for computational spectroscopy.

Indole Facilitates Antimicrobial Uptake in Bacteria

Indole signaling in bacteria plays an important role in antibiotic resistance, persistence, and tolerance. Here, we used the nonlinear optical technique, second-harmonic light scattering (SHS), to examine the influence of exogenous indole on the bacterial uptake of the antimicrobial quaternary ammonium cation (qac), malachite green. The transport rates of the antimicrobial qac across the individual membranes of Escherichia coli and Pseudomonas aeruginosa, as well as liposomes composed of the polar lipid extract of E. coli, were directly measured using time-resolved SHS. Whereas exogenous indole was shown to induce a 2-fold increase in the transport rate of the qac across the cytoplasmic membranes of the wild-type bacteria, it had no influence on a knockout strain of E. coli lacking the tryptophan-specific transport protein (Δmtr). Likewise, indole did not affect the transport rate of the qac diffusing across the liposome membrane. Our findings suggest that indole increases the bacterial uptake of antimicrobials through an interaction with the Mtr permease.

Tryptophan as a Template for Development of Visible Fluorescent Amino Acids

Most biological systems, at both molecular and cellular levels, are intrinsically complex, diverse, and nonfluorescent. Therefore, studying their structures, dynamics, and interactions via fluorescence-based methods requires incorporation of one or multiple external fluorophores that would not significantly affect any native property of the system in question. This requirement necessitates the development of a diverse set of fluorescence reporters that differ in chemical, physical, and photophysical properties. Herein, we offer our perspective on the need for, recent progress in, and future directions of developing tryptophan-based fluorescent amino acids.

Excited state dipole moments and lifetimes of 2-cyanoindole from rotationally resolved electronic Stark spectroscopy

The permanent dipole moments of 2-cyanoindole (cyanoindole = CNI) in its ground and lowest excited singlet states have been determined from rotationally resolved electronic Stark spectroscopy under jet-cooled conditions. From the orientation of the transition dipole moment and the geometry changes upon electronic excitation the lowest excited singlet state could be shown to be of L_b-symmetry. The general statement, that the L_a-state has the larger permanent dipole moment of the two lowest excited singlet states, will be challenged in this contribution. On the basis of the different electronic nature of the first excited singlet state the behavior of 2-, 3-, 4- and 5-CNI is discussed. The excited state lifetime of isolated 2-CNI in the gas phase has been determined to be 9.4 ns. This value is compared to the excited state lifetime in ethyl acetate solution of 2.6 ns, which was quantified with a Strickler-Berg analysis. Using water as solvent shortens the 2-CNI lifetime to <40 ps. The reason for this drastic shortening is discussed in detail. Additionally, the rotationally resolved electronic spectrum of 2-CNI(1-d₁) has been measured and analyzed.

Tuning the electronic transition energy of indole via substitution: application to identify tryptophan-based chromophores that absorb and emit visible light

Fluorescent amino acids (FAAs) offer significant advantages over fluorescent proteins in applications where the fluorophore size needs to be limited or minimized. A long-sought goal in biological spectroscopy/microcopy is to develop visible FAAs by modifying the indole ring of tryptophan. Herein, we examine the absorption spectra of a library of 4-substituted indoles and find that the frequency of the absorption maximum correlates linearly with the global electrophilicity index of the substituent. This finding permits us to identify two promising candidates, 4-formyltryptophan (4CHO-Trp) and 4-nitrotryptophan (4NO₂-Trp), both of which can be excited by visible light. Further fluorescence measurements indicate that while 4CHO-indole (and 4CHO-Trp) emits cyan fluorescence with a reasonably large quantum yield (ca. 0.22 in ethanol), 4NO₂-indole is essentially non-fluorescent, suggesting that 4CHO-Trp (4NO₂-Trp) could be useful as a fluorescence reporter (quencher). In addition, we present a simple method for synthesizing 4CHO-Trp.

Modeling solvation effects on absorption and fluorescence spectra of indole in aqueous solution

Modeling the optical spectra of molecules in solution presents a challenge, so it is important to understand which of the solvation effects (i.e., electrostatics, mutual polarization, and hydrogen bonding interactions between solute and solvent molecules) are crucial in reproducing the various features of the absorption and fluorescence spectra and to identify a sufficient theoretical model that accurately captures these effects with minimal computational cost. In this study, we use various implicit and explicit solvation models, such as molecular dynamics coupled with non-polarizable and polarizable force fields, as well as Car-Parrinello molecular dynamics, to model the absorption and fluorescence spectra of indole in aqueous solution. The excited states are computed using the equation of motion coupled cluster with single and double excitations combined with the effective fragment potential to represent water molecules, which we found to be a computationally efficient approach for modeling large solute-solvent clusters at a high level of quantum theory. We find that modeling mutual polarization, compared to other solvation effects, is a dominating factor for accurately reproducing the position of the peaks and spectral line shape of the absorption spectrum of indole in solution. We present an in-depth analysis of the influence that different solvation models have on the electronic excited states responsible for the features of the absorption spectra. Modeling fluorescence is more challenging since it is hard to reproduce even the correct emitting state, and force field parameters need to be re-evaluated.