Nile blue shows its true colors in gas-phase absorption and luminescence ion spectroscopy

Turning on the Fluorescence from Isolated GFP Chromophore Anions at Cryogenic Temperatures

The chromophore anion derived from the green fluorescent protein is one of the best-studied chromophores in the gas phase, but attempts to measure fluorescence have failed at room temperature. Here we unequivocally show that the chromophore exhibits fluorescence in the gas phase when cooled to low temperatures (<150  K), thereby validating previous hypotheses. The experimental confirmation is enabled by a unique mass-spectroscopy setup, allowing for fluorescence observation near or at the 0-0 transition without inducing heat in the ions upon photon absorption. The low-temperature conditions effectively simulate the restricted motion experienced within the protein, inhibiting internal conversion via a conical intersection along a twist motion coordinate. Fluorescence-excitation experiments at 100 K reveal an absorption-band maximum at 481.6±0.2  nm, while the dispersed fluorescence spectrum shows maximum emission at 483.6±0.5  nm. Remarkably, both values closely resemble those for proteins cooled to 77 K. We estimate that after excitation at the band maximum, radiation is the only pathway back to the ground state. Franck-Condon simulations at the ωB97XD/aug-cc-pVDZ level of theory nicely reproduce the experimental spectra and identify the fluorescent form to be planar, and that an in-plane scissoring mode (80  cm^{-1}) is active for both absorption and emission.

Gas-phase Förster resonance energy transfer in mass-selected and trapped ions

Förster Resonance Energy transfer (FRET) is a nonradiative process that may occur from an electronically excited donor to an acceptor when the emission spectrum of the donor overlaps with the absorption spectrum of the acceptor. FRET experiments have been done in the gas phase based on specially designed mass-spectroscopy setups with the goal to obtain structural information on biomolecular ions labeled with a FRET pair (i.e., donor and acceptor dyes) and to shed light on the energy-transfer process itself. Ions are accumulated in a radio-frequency ion trap or a Penning trap where mass selection of those of interest takes place, followed by photoexcitation. Gas-phase FRET is identified from detection of emitted light either from the donor, the acceptor, or both, or from a fragmentation channel that is specific to the acceptor when electronically excited. The challenge associated with the first approach is the collection and detection of photons emitted from a thin ion cloud that is not easily accessible while the second approach relies both on the photophysical and chemical behavior of the acceptor. In this review, we present the different instrumentation used for gas-phase FRET, including a discussion of advantages and disadvantages, and examples on how the technique has provided important structural information that is not easily obtainable otherwise. Furthermore, we describe how the spectroscopic properties of the dyes are affected by nearby electric fields, which is readily discernable from experiments on simple model systems with alkyl or π-conjugated bridges. Such spectral changes can have a significant effect on the FRET efficiency. Ideas for new directions are presented at the end with special focus on cold-ion spectroscopy.

Empirical Calibration of a Cylindrical Ion Trap for Mass-Selected Gas-Phase Fluorescence Spectroscopy

The ion motion in a quadrupole ion trap of hyperbolic geometry is well described by the Mathieu equations. A simpler cylindrical ion trap has also gained significance and has been used by us for fluorescence-spectroscopy experiments. This design allows for the easy replacement of the end-cap with a mesh, enhancing the photon collection. It is crucial to obtain a firm understanding of the ion motion in cylindrical ion traps and their capability as mass spectrometers. We present here an empirical method of calibrating a cylindrical ion trap based on fluorescence detection. This can be done nearly background-free in a pulsed experiment. The ions are located at the center of the trap, where the field is primarily quadrupolar, and here an effective Mathieu description is found through an effective geometry parameter. In spectroscopy experiments, high buffer-gas pressures are needed to efficiently cool the ions, which complicates the ions' motion and hence their stability. Still, simulations show that the stability diagram closely aligns with the Mathieu diagram, albeit shifted due to collisions. We map the stability diagram for six molecular ions by fluorescence collection from four cations and two anions spanning m/z from 212 to 647. The stability diagram is parametrized through the Mathieu functions with an m/z-dependent effective geometry parameter and a q-dependent shrinkage of the diagram. Based on the calibration, we estimate the mass resolution to be +7/-3 Da for ions with masses in the hundreds of Da.

Cryogenic fluorescence spectroscopy of oxazine ions isolated in vacuo

Recent developments in fluorescence spectroscopy have made it possible to measure both absorption and dispersed fluorescence spectra of isolated molecular ions at liquid-nitrogen temperatures. Absorption is here obtained from fluorescence-excitation experiments and does not rely on ion dissociation. One large advantage of reduced temperature compared to room-temperature spectroscopy is that spectra are narrow, and they provide information on vibronic features that can better be assigned from theoretical simulations. We report on the intrinsic spectroscopic properties of oxazine dyes cooled to about 100 K. They include six cations (crystal violet, darrow red, oxazine-1, oxazine-4, oxazine-170 and nile blue) and one anion (resorufin). Experiments were done with a home-built setup (LUNA2) where ions are stored, mass-selected, cooled, and photoexcited in a cylindrical ion trap. We find that the Stokes shifts are small (14-50 cm-1), which is ascribed to rigid geometries, that is, there are only small geometrical changes between the electronic ground and excited states. However, both the absorption and the emission spectra of darrow-red cations are broader than those of the other ionic dyes, which is likely associated with a less symmetric electronic structure and more non-zero Franck-Condon factors for the vibrational progressions. In the case of resorufin, the smallest ion under study, vibrational features are assigned based on calculated spectra.

Laser-Induced Fluorescence (LIF) Spectroscopy of Trapped Molecular Ions in the Gas Phase

This review focuses on the laser-induced fluorescence (LIF) spectroscopy of trapped gas-phase molecular ions, a developing field of research. Following a brief description of the theory and experimental approaches employed in general for fluorescence spectroscopy, the review summarizes the current state-of-the-art intrinsic fluorescence measurement techniques employed for gas-phase ions. Whereas the LIF spectroscopy of condensed matter systems is a well-developed area of research, the instrumentation used for such studies is not directly applicable to gas-phase ions. However, some measurement schemes employed in condensed-phase experiments could be highly beneficial for gas-phase investigations. We have included a brief discussion on some of these techniques as well. Quadrupole ion traps are commonly used for spatial confinement of ions in the ion-trap-based LIF. One of the main challenges involved in such experiments is the poor signal-to-noise ratio (SNR) arising due to weak gas-phase fluorescence emission, high background noise, and small solid angle for the fluorescence collection optics. The experimental approaches based on the integrated high-finesse optical cavities employed for the condensed-phase measurements provide a better (typically an order of magnitude more) SNR in the detected fluorescence than the single-pass detection schemes. Another key to improving the SNR is to exploit the maximum solid angle of light collection by choosing high numerical aperture (NA) collection optics. A combination of these two approaches integrated with ion traps could transmogrify this field, allowing one to study even weak fluorescence emission from gas-phase molecular ions. The review concludes by discussing the scope of the advances in the LIF instrumentation for detailed spectral characterization of fluorophores of weak gas-phase fluorescence emission, considering fluorescein as one example.

Effect of Freezing out Vibrational Modes on Gas-Phase Fluorescence Spectra of Small Ionic Dyes

While action spectroscopy of cold molecular ions is a well-established technique to provide vibrationally resolved absorption features, fluorescence experiments are still challenging. Here we report the fluorescence spectra of pyronin-Y and resorufin ions at 100 K using a newly constructed setup. Spectra narrow upon cooling, and the emission maxima blueshift. Temperature effects are attributed to the population of vibrational excited levels in S₁, and that frequencies are lower in S₁ than in S₀. This picture is supported by calculated spectra based on a Franck-Condon model that not only predicts the observed change in maximum, but also assigns Franck-Condon active vibrations. In-plane vibrational modes that preserve the mirror plane present in both S₀ and S₁ of resorufin and pyronin Y account for most of the observed vibrational bands. Finally, at low temperatures, it is important to pick an excitation wavelength as far to the red as possible to not reheat the ions.

Broadband visible two-dimensional spectroscopy of molecular dyes

Two-dimensional Fourier transform spectroscopy is a promising technique to study ultrafast molecular dynamics. Similar to transient absorption spectroscopy, a more complete picture of the dynamics requires broadband laser pulses to observe transient changes over a large enough bandwidth, exceeding the inhomogeneous width of electronic transitions, as well as the separation between the electronic or vibronic transitions of interest. Here, we present visible broadband 2D spectra of a series of dye molecules and report vibrational coherences with frequencies up to ∼1400 cm^-1 that were obtained after improvements to our existing two-dimensional Fourier transform setup [Al Haddad et al., Opt. Lett. 40, 312-315 (2015)]. The experiment uses white light from a hollow core fiber, allowing us to acquire 2D spectra with a bandwidth of 200 nm, in a range between 500 and 800 nm, and with a temporal resolution of 10-15 fs. 2D spectra of nile blue, rhodamine 800, terylene diimide, and pinacyanol iodide show vibronic spectral features with at least one vibrational mode and reveal information about structural motion via coherent oscillations of the 2D signals during the population time. For the case of pinacyanol iodide, these observations are complemented by its Raman spectrum, as well as the calculated Raman activity at the ground- and excited-state geometry.

Triangular Rhodamine Triads and Their Intrinsic Photophysics Revealed from Gas-Phase Ion Fluorescence Experiments

When ionic dyes are close together, the internal Coulomb interaction may affect their photophysics and the energy-transfer efficiency. To explore this, we have prepared triangular architectures of three rhodamines connected to a central triethynylbenzene unit (1,3,5-tris(buta-1,3-diyn-1-yl)benzene) based on acetylenic coupling reactions and measured fluorescence spectra of the isolated, triply charged ions in vacuo. We find from comparisons with previously reported monomer and dimer spectra that while polarization of the π-system causes redshifted emission, the separation between the rhodamines is too large for a Stark shift. This picture is supported by electrostatic calculations on model systems composed of three linear and polarizable ionic dyes in D_3h configuration: The electric field that each dye experiences from the other two is too small to induce a dipole moment, both in the ground and the excited state. In the case of heterotrimers that contain either two rhodamine 575 (R575) and one R640 or one R575 and two R640, emission is almost purely from R640 although the polarization of the π-system expectedly diminishes the dipole-dipole interaction.

A new setup for low-temperature gas-phase ion fluorescence spectroscopy

Here, we present a new instrument named LUNA2 (LUminescence iNstrument in Aarhus 2), which is purpose-built to measure dispersed fluorescence spectra of gaseous ions produced by electrospray ionization and cooled to low temperatures (<100 K). LUNA2 is, as an earlier room-temperature setup (LUNA), optimized for a high collection efficiency of photons and includes improvements based on our operational experience with LUNA. The fluorescence cell is a cylindrical Paul trap made of copper with a hole in the ring electrode to permit laser light to interact with the trapped ions, and one end-cap electrode is a mesh grid combined with an aspheric condenser lens. The entrance and exit electrodes are both in physical contact with the liquid-nitrogen cooling unit to reduce cooling times. Mass selection is done in a two-step scheme where, first, high-mass ions are ejected followed by low-mass ions according to the Mathieu stability region. This scheme may provide a higher mass resolution than when only one DC voltage is used. Ions are irradiated by visible light delivered from a nanosecond 20-Hz pulsed laser, and dispersed fluorescence is measured with a spectrometer combined with an iCCD camera that allows intensification of the signal for a short time interval. LUNA2 contains an additional Paul trap that can be used for mass selection before ions enter the fluorescence cell, which potentially is relevant to diminishing RF heating in the cold trap. Successful operation of the setup is demonstrated from experiments with rhodamine dyes and oxazine-4, and spectral changes with temperature are identified.

Breaking the Brightness Barrier: Design and Characterization of a Selected-Ion Fluorescence Measurement Setup with High Optical Detection Efficiency

A quadrupole ion trap (QIT) mass spectrometer has been modified and coupled with tunable laser excitation and highly sensitive fluorescence detection systems to perform fluorescence studies on mass-selected ions. Gaseous ions, generated using nanoelectrospray ionization (nano-ESI), are trapped in the QIT that allows optical access for laser irradiation. The emitted fluorescence is collected from a 5.0 mm diameter hole drilled into the ring electrode of the QIT and is directed toward the detection setup. Due to the small inner diameter (7.07 mm) of the ring electrode and a relatively large opening for fluorescence collection, a fluorescence collection efficiency of 2.3% is achieved. After some losses in transmission, around 1.8% of the emitted fluorescence reaches the detectors, more than any other similar instrument reported in the literature. This improved fluorescence collection translates to a much shorter measurement time for a fluorescence signal. Another key feature of this setup is the ability to perform a variety of fluorescence experiments on trapped ions including excitation and emission spectroscopy, lifetime measurement, and ion imaging. The capabilities of the instrument are demonstrated by measuring fluorescence spectra of dyes and biomolecules labeled with dyes in a range of different excitation and emission wavelengths, quantum yields, m/z, and different polarities. A fluorescence lifetime measurement and ion image of trapped rhodamine 6G cations are also shown. With a wide array of functionality and high fluorescence detection performance, this setup provides an opportunity to study biomolecular structures and photophysics of fluorophores in well-controlled environments.

Photophysics of Isolated Rose Bengal Anions

Dye molecules based on the xanthene moiety are widely used as fluorescent probes in bioimaging and technological applications due to their large absorption cross-section for visible light and high fluorescence quantum yield. These applications require a clear understanding of the dye's inherent photophysics and the effect of a condensed-phase environment. Here, the gas-phase photophysics of the rose bengal doubly deprotonated dianion [RB - 2H]^2-, deprotonated monoanion [RB - H]^-, and doubly deprotonated radical anion [RB - 2H]^•- is investigated using photodetachment, photoelectron, and dispersed fluorescence action spectroscopies, and tandem ion mobility spectrometry (IMS) coupled with laser excitation. For [RB - 2H]^2-, photodetachment action spectroscopy reveals a clear band in the visible (450-580 nm) with vibronic structure. Electron affinity and repulsive Coulomb barrier (RCB) properties of the dianion are characterized using frequency-resolved photoelectron spectroscopy, revealing a decreased RCB compared with that of fluorescein dianions due to electron delocalization over halogen atoms. Monoanions [RB - H]^- and [RB - 2H]^•- differ in nominal mass by 1 Da but are difficult to study individually using action spectroscopies that isolate target ions using low-resolution mass spectrometry. This work shows that the two monoanions are readily distinguished and probed using the IMS-photo-IMS and photo-IMS-photo-IMS strategies, providing distinct but overlapping photodissociation action spectra in the visible spectral range. Gas-phase fluorescence was not detected from photoexcited [RB - 2H]^2- due to rapid electron ejection. However, both [RB - H]^- and [RB - 2H]^•- show a weak fluorescence signal. The [RB - H]^- action spectra show a large Stokes shift of ∼1700 cm^-1, while the [RB - 2H]^•- action spectra show no appreciable Stokes shift. This difference is explained by considering geometries of the ground and fluorescing states.

Gas-phase action and fluorescence spectroscopy of mass-selected fluorescein monoanions and two derivatives

Gaseous fluorescein monoanions are weakly fluorescent; they display a broad fluorescence spectrum and a large Stokes shift. This contrasts with the situation in aqueous solution. One explanation of the intriguing behavior in vacuo is based on internal proton transfer from the pendant carboxyphenyl group to one of the xanthene oxygens in the excited state; another that rotation of the carboxyphenyl group relative to the xanthene leads to a partial charge transfer from one chromophore (xanthene) to the other (carboxyphenyl) when the π orbitals start to overlap. To shed light on the mechanism at play, we synthesized two fluorescein derivatives where the carboxylic acid group is replaced with either an ester or a tertiary amide functionality and explored their gas-phase ion fluorescence using the home-built LUminescence iNstrument in Aarhus (LUNA) setup. Results on the fluorescein methyl ester that has no acidic proton clearly disprove the former explanation: The spectrum remains broad, and the band center (at 605 nm) is shifted even more to the red than that of fluorescein (590 nm). Experiments on the other variant that contains a piperidino amide are also in favor of the second explanation as here the piperidino already causes the dihedral angle between the planes defining the xanthene and the benzene ring to be less than 90° in the ground state (i.e., 63°), according to density functional theory calculations. As a result of the closer similarity between the ground-state and excited-state structures, the fluorescence spectrum is narrower than those of the other two ions, and the band maximum is further to the blue (575 nm). In accordance with a more delocalized ground state of the amide derivative, action spectra associated with photoinduced dissociation recorded at another setup show that the absorption-band maximum for the amide derivative is redshifted compared to that of fluorescein (538 nm vs. 525 nm).

Gas-phase Förster resonance energy transfer in mass-selected ions with methylene or peptide linkers between two dyes: a concerted dance of charges

Emission from gaseous rhodamine 640 is redshifted when the dye is tethered to rhodamine 575 due to internal Coulomb interaction.

Luminescence spectroscopy of oxazine dye cations isolated in vacuo

Gas-phase luminescence spectroscopy reveals transition energies of oxazine dye cations with no disturbance from counter ions or solvent molecules.

Storage time dependent photodissociation action spectroscopy of polycyclic aromatic hydrocarbon cations in the cryogenic electrostatic storage ring DESIREE

The intrinsic absorption profile and radiative cooling rate of coronene cations are reported.

Ion mobility action spectroscopy of flavin dianions reveals deprotomer-dependent photochemistry

Photo-induced proton transfer, deprotomer-dependent photochemistry, and intramolecular charge transfer in flavin anions are investigated using action spectroscopy.

The intrinsic optical properties and photochemistry of flavin adenine dinucleotide (FAD) dianions are investigated using a combination of tandem ion mobility spectrometry and action spectroscopy. Two principal isomers are observed, the more stable form being deprotonated on the isoalloxazine group and a phosphate (N-3,PO₄ deprotomer), and the other on the two phosphates (PO₄,PO₄ deprotomer). Ion mobility data and electronic action spectra suggest that photo-induced proton transfer occurs from the isoalloxazine group to a phosphate group, converting the PO₄,PO₄ deprotomer to the N-3,PO₄ deprotomer. Comparisons of the isomer selective action spectra of FAD dianions and flavin monoanions with solution spectra and gas-phase photodissociation action spectra suggests that solvation shifts the electronic absorption of the deprotonated isoalloxazine group to higher energy. This is interpreted as evidence for significant charge transfer in the lowest optical transition of deprotonated isoalloxazine. Overall, this work demonstrates that the site of deprotonation of flavin anions strongly affects their electronic absorptions and photochemistry.

Absorption and luminescence spectroscopy of mass-selected flavin adenine dinucleotide mono-anions

We report the absorption profile of isolated Flavin Adenine Dinucleotide (FAD) mono-anions recorded using photo-induced dissociation action spectroscopy. In this charge state, one of the phosphoric acid groups is deprotonated and the chromophore itself is in its neutral oxidized state. These measurements cover the first four optical transitions of FAD with excitation energies from 2.3 to 6.0 eV (210-550 nm). The S₀ → S₂ transition is strongly blue shifted relative to aqueous solution, supporting the view that this transition has a significant charge-transfer character. The remaining bands are close to their solution-phase positions. This confirms that the large discrepancy between quantum chemical calculations of vertical transition energies and solution-phase band maxima cannot be explained by solvent effects. We also report the luminescence spectrum of FAD mono-anions in vacuo. The gas-phase Stokes shift for S₁ is 3000 cm^-1, which is considerably larger than any previously reported for other molecular ions and consistent with a significant displacement of the ground and excited state potential energy surfaces. Consideration of the vibronic structure is thus essential for simulating the absorption and luminescence spectra of flavins.

Laser-induced- and dispersed-fluorescence studies of rhodamine 590 and 640 ions formed by electrospray ionization: observation of fluorescence from highly-excited vibrational levels of S1 states

Fluorescence spectra of vibrationally very “hot” S₁ states were observed for the first time under gas phase conditions.

Luminescence spectroscopy of chalcogen substituted rhodamine cations in vacuo

A library of fluorescent rhodamine cations has been characterized with view to their potential use in gas-phase structural biology experiments.

Sibling rivalry: intrinsic luminescence from two xanthene dye monoanions, resorufin and fluorescein, provides evidence for excited-state proton transfer in the latter

Excited-state proton transfer in gas-phase fluorescein monoanions results in a broad, featureless emission band and a large Stokes shift compared to resorufin, which shares the same xanthene core structure.