Structures, dipole moments and excited state lifetime of isolated 4-cyanoindole in its ground and lowest electronically excited singlet states

Transient spectroscopic insights into nitroindole's T1 state: Elucidating its intermediates and unique photochemical properties

Indoles are notable for their distinct photophysical and photochemical properties, making them useful indicators in biological systems and promising candidates for a variety of pharmaceutical applications. While some indoles exhibit room temperature phosphorescence, such a phenomenon has not been observed in nitroindoles. Typically, adding of a nitro group into aromatic compounds promotes ultrafast intersystem crossing and increases the formation quantum yield of the lowest excited triplet (T1). Therefore, understanding the reactivity of nitroindoles' T1 states is imperative. This study investigated the physical properties and chemical reactivities of the T1 state of 6-nitroindole (3HN-6NO2) in both polar aprotic and protic solvents, using transient absorption spectroscopy. Our results demonstrate the basicity and acidity of 3HN-6NO2, emphasizing its potential for protonation and dissociation in mildly acidic and basic conditions, respectively. Furthermore, 3HN-6NO2 has a high oxidizing capacity, participating in electron transfer reactions and proton-coupled electron transfer to produce radicals. Interestingly, in protic solvents like alcohols, 3HN-6NO2 dissociates at the -NH group and forms N-H…O hydrogen-bonded complexes with the nitro group. By identifying transient absorption spectra of intermediates and quantifying kinetic reaction rate constants, we illuminate the unique properties of the T1 state nitroindoles, enriching our understanding of their photophysical and photochemical behaviors. The results of this study have significant implications for their potential application in both biological systems and materials science.

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.

Conformational preferences of modified nucleobases in RNA aptamers and their effect on Förster resonant energy transfer

Förster resonant energy transfer (FRET) can be utilized in the study of tertiary structures of RNA aptamers, which bind specific fluorophoric ligands to form a fluorogenic aptamer complex. By introducing the emissive nucleobase analog 4-cyanoindole into the fluorogenic Chili RNA aptamer a FRET pair was established. The interpretation of studies aiming to investigate those tertiary structures using FRET, however, relies on prior knowledge about conformational properties of the nucleobase, which govern exciton transfer capabilities. Herein we employed classical molecular dynamics combined with Förster exciton theory to elucidate the preferred orientation relative to proximate bases and the influence on exciton transfer efficiency in multiple substitution sites. We did this by comparing the chromophoric distances emergent from MD simulations with experimental FRET data based on structural data of the native aptamer. We present the outlined methodology as a means to reliably evaluate future nucleobase analogue candidates in terms of their structural behavior and emergent exciton transfer properties as exemplified in the study of the preferred orientation of 4-cyanoindole in the Chili RNA aptamer.

Charge Transfer and Level Lifetime in Molecular Photon-Absorption upon the Quantum Impedance Lorentz Oscillator

On the strength of the new quantum impedance Lorentz oscillator (QILO) model, a charge-transfer method in molecular photon-absorption is proposed and imaged via the numerical simulations of 1- and 2-photon-absorption (1PA and 2PA) behaviors of the organic compounds LB3 and M4 in this paper. According to the frequencies at the peaks and the full width at half-maximums (FWHMs) of the linear absorptive spectra of the two compounds, we first calculate the effective quantum numbers before and after the electronic transitions. Thus, we obtain the molecular average dipole moments, i.e., 1.8728 × 10^-29 C·m (5.6145 D) for LB3 and 1.9626 × 10^-29 C·m (5.8838 D) for M4 in the ground state in the tetrahydrofuran (THF) solvent. Then, the molecular 2PA cross sections corresponding to wavelength are theoretically inferred and figured out by QILO. As a result, the theoretical cross sections turn out to be in good agreement with the experimental ones. Our results reveal such a charge-transfer image in 1PA near wavelength 425 nm, where an atomic electron of LB3 jumps from the ground-state ellipse orbit with the semimajor axis a_i = 1.2492 × 10^-10m = 1.2492 Å and semiminor axis b_i = 0.4363 Å to the excited-state circle (a_j = b_j = 2.5399 Å). In addition, during its 2PA process, the same transitional electron in the ground state is excited to the elliptic orbit with a_j = 2.5399 Å and b_j =1.3808 Å, in which the molecular dipole moment reaches as high as 3.4109 × 10^-29 C·m (10.2256 D). In addition, we obtain a level-lifetime formula with the microparticle collision idea of thermal motion, which indicates that the level lifetime is proportional (not inverse) to the damping coefficient or FWHM of an absorptive spectrum. The lifetimes of the two compounds at some excited states are calculated and presented. This formula may be used as an experimental method to verify 1PA and 2PA transition selection rules. The QILO model exhibits the advantage of simplifying the calculation complexity and reducing the high cost associated with the first principle in dealing with quantum properties of optoelectronic materials.

Photophysics of Two Indole-Based Cyan Fluorophores

For the purpose of searching for new biological fluorophore, we assess the photophysical properties of two indole derivatives, 4-cyano-7-azaindole (4CN7AI) and 1-methyl-4-cyano-7-azaindole (1M4CN7AI), in a series of solvents. We find that (1) the absorption spectra of both derivatives are insensitive to solvents and are red-shifted from that of indole, having a maximum absorption wavelength of ca. 318 nm and a broad profile that extends beyond 370 nm; (2) both derivatives emit in the blue to green spectral range with a large Stokes shift, for example, in H₂O, the maximum emission wavelength of 4CN7AI (1M4CN7AI) is at ca. 455 nm (470 nm); (3) 4CN7AI has a higher fluorescence quantum yield (QY) and a longer fluorescence lifetime (τ_F) in aprotic solvents than in protic solvents, for example, QY (τ_F) = 0.72 ± 0.04 (7.6 ± 0.8 ns) in tetrahydrofuran and QY (τ_F) = 0.29 ± 0.03 (6.2 ± 0.6 ns) in H₂O; (4) in all of the solvents used except H₂O, the fluorescence QY (τ_F) of 1M4CN7AI is equal to or higher (longer) than 0.69 ± 0.03 (11.2 ± 0.7 ns). Taken together, these results suggest that the corresponding non-natural amino acids, 4-cyano-7-azatryptophan and 1-methyl-4-cyano-7-azatryptophan, could be useful as biological fluorophores.

Dipole Moments and Transition Dipole Moments Calculated by Pair-Density Functional Theory with State Interaction

We develop response-function algorithms for dipole moments and transition dipole moments for compressed multistate pair-density functional theory (CMS-PDFT). We use the method of undetermined Lagrange multipliers to derive analytical expressions and validate them using numerical differentiation. We test the accuracy of the magnitudes of predicted ground-state and excited-state dipole moments, the orientations of these dipole moments, and the orientation of transition dipole moments by comparison to experimental data. We show that CMS-PDFT has good accuracy for these quantities, and we also show that, unlike methods that neglect state interaction, CMS-PDFT yields correct behavior for the dipole moment curves in the vicinity of conical intersections. This work, therefore, opens the door to molecular dynamic simulations in strong electric fields, and we envision that CMS-PDFT can now be used to discover chemical reactions that can be controlled by an oriented external electric field upon photoexcitation of the reactants.

4-Cyanotryptophan as a Sensitive Fluorescence Probe of Local Electric Field of Proteins

Electrostatic interactions are key determinants of protein structure, dynamics, and function. Since protein electrostatics are nonuniform, assessment of the internal electric fields (EFs) of proteins requires spatial resolution at the amino acid residue level. In this regard, vibrational Stark spectroscopy, in conjunction with various unnatural amino acid-based vibrational probes, has become a common method for site-specific interrogation of protein EFs. However, application of this method is often limited to proteins with relatively high solubility, due to the intrinsically low oscillator strength of vibrational transitions. Therefore, it would be useful to develop an alternative method that can overcome this limitation. To this end, we show that, using solvatochromic study and molecular dynamics simulations, the frequency of maximum emission intensity of the fluorophore of 4-cyanotryptophan (4CN-Trp), 3-methyl-1H-indole-4-carbonitrile, exhibits a linear dependence on the local EF. Since the absorption and emission spectra of 4CN-Trp are easily distinguishable from those of naturally occurring aromatic amino acids, we believe that this linear relationship provides an easier and more sensitive means to determine the local EF of proteins.

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

Explicit Projection of Stokes Shifts onto Solvent Motion in an Aqueous Liquid and Linear Response Theory

We investigate the molecular origin of the fluorescence Stokes shift in an aqueous liquid. By examining the speed of energy change, the solvation response function is explicitly projected onto the translational and rotational motions of water molecules for both nonequilibrium relaxation and equilibrium fluctuations. Molecular dynamics simulations of a tryptophan solution show that these two processes have highly consistent dynamics, not only for the total response function but also for the decomposed components in terms of specific molecular movements. We found that the rotational mode governs the relaxation of the Stokes shift, whereas the translational mode contributes non-negligibly with slower dynamics. This consistency implies the similarity of the underlying translational and rotational movements of water molecules as the system is far away from and at equilibrium, supporting the validity of the linear response theory at the molecular level. The decomposition methodology is also applicable to a rigid solvent.

Photoenhancement of the C≡N Stretching Vibration Intensity of Aromatic Nitriles

The C≡N stretching vibration is a versatile infrared (IR) reporter that is useful for a wide range of applications. Aiming to further expand its spectroscopic utility, herein, we show that, using 4-cyanoindole and 4-cyano-7-azaindole as examples, photoexcitation can significantly shift the frequency (ν_CN) and enhance the molar extinction coefficient (ε_CN) of this vibrational mode of aromatic nitriles and that, for these indole derivatives, the enhancement factor can reach 13. Moreover, we find that while solvent relaxation at the excited electronic state(s) always leads to an increase in ε_CN, its effect on ν_CN depends on the solute and the solvent. Taken together, these results demonstrate that solvent relaxation can differently affect the local environment of the nitrile group and its conjugation with the indole ring and, more importantly, that the C≡N stretching vibration can serve as a sensitive IR probe of charge and electron transfer processes in which an aromatic nitrile is involved.

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.

Unitary coupled cluster ground- and excited-state molecular properties

A scheme for the calculation of molecular properties within the framework of unitary coupled-cluster (UCC) theory in both the electronic ground and excited states is presented. The scheme is based on an expectation-value ansatz, similar to the equation-of-motion coupled-cluster method or the intermediate state representation (ISR) approach of the algebraic-diagrammatic construction (ADC) scheme. Due to the UCC ansatz, the resulting equations cannot be given by closed-form expressions but need to be approximated. Explicit expressions for the expectation value of a general one-particle operator correct through second order in perturbation theory have been derived and coded for the electronic ground state as well as for excited states of predominant single-excitation character. The resulting equations are shown to be equivalent to those of the second-order ADC/ISR procedure. As first computational tests, the second-order UCC method (UCC2) and the one employing third-order amplitudes (also eigenvectors) together with the second-order density matrix, denoted as UCC3(2), are applied to the calculation of dipole moments for a series of small closed- and open-shell systems as well as 4-cyanoindole and 2,3-benzofuran and compared to full configuration interaction or experimental results. For the aromatic organic molecules, the UCC2 method is shown to be sufficient for the ground-state dipole moment, whereas the UCC3(2) scheme is superior for excited-state dipole moments.

Rotationally resolved UV spectroscopy of the rotamers of indole-4-carboxylic acid: Evidence for charge transfer quenching

Rotationally resolved electronic spectra of two conformational isomers of jet-cooled indole-4-carboxylic acid (I4CA) and the deuterated forms of the acid (-COOD) and amide (-ND) groups have been obtained using a UV laser/molecular beam spectrometer. The in-plane orientation of the acid group defines the two lowest energy rotamers of I4CA. The S1 ← S0 origin bands of the two rotamers and four isotopologues have been fit to asymmetric rotor Hamiltonians in both electronic states. From the best-fit parameters, the positions of the H-atoms in the principal axis frames of each conformer have been determined and serve to unambiguously identify the syn forms (i.e., COH⋯O) of the cis and trans rotamers. The experimental S0 and S1 inertial parameters, hydrogen atom positions, and transition dipole moment (TDM) orientations are compared with the results of theoretical calculations. The TDM orientation indicates that the S1 state is the 1La state in contrast to most substituted indoles. The molecular orbital properties and natural charges are investigated to better understand the 1La/1Lb state reversal and the extent of photoinduced intramolecular charge transfer that impacts the rotamer-dependent fluorescence lifetimes.