Fluorescence-Encoded Infrared Spectroscopy: Ultrafast Vibrational Spectroscopy on Small Ensembles of Molecules in Solution

Vibrational-Mode-Selective Modulation of Electronic Excitation

Vibrational-mode-selective modulation of electronic excitation is conducted with a synchronized femtosecond (fs) visible (vis) pulse and a picosecond (ps) infrared (IR) pulse. The mechanism of modulation of vibrational and vibronic relaxation behavior of excited state is investigated with ultrafast vis/IR, IR/IR, and vis-IR/IR transient spectroscopy, optical gating experiments and theoretical calculations. An organic molecule, 4'-(N,N-dimethylamino)-3-methoxyflavone (DMA3MHF) is chosen as the model system. Upon 1608 cm-1 excitation, the skeleton stretching vibration of DMA3MHF is energized, which can significantly change the shape of the absorption, facilitate the radiative decay and promote emission from vibrational excited states. As results, a remarkable enhancement and a slight blueshift in fluorescence are observed. The mode-selective modulation of electronic excitation is not limited in luminescence or photophysics. It is expected to be widely applicable in tuning many photochemical processes.

Molecular factors determining brightness in fluorescence-encoded infrared vibrational spectroscopy

Fluorescence-encoded infrared (FEIR) spectroscopy is a recently developed technique for solution-phase vibrational spectroscopy with detection sensitivity at the single-molecule level. While its spectroscopic information content and important criteria for its practical experimental optimization have been identified, a general understanding of the electronic and nuclear properties required for highly sensitive detection, i.e., what makes a molecule a "good FEIR chromophore," is lacking. This work explores the molecular factors that determine FEIR vibrational activity and assesses computational approaches for its prediction. We employ density functional theory (DFT) and its time-dependent version (TD-DFT) to compute vibrational and electronic transition dipole moments, their relative orientation, and the Franck-Condon factors involved in FEIR activity. We apply these methods to compute the FEIR activities of normal modes of chromophores from the coumarin family and compare these predictions with experimental FEIR cross sections. We discuss the extent to which we can use computational models to predict the FEIR activity of individual vibrations in a candidate molecule. The results discussed in this work provide the groundwork for computational strategies for choosing FEIR vibrational probes or informing the structure of designer chromophores for single-molecule spectroscopic applications.

Transient stimulated Raman scattering spectroscopy and imaging

Stimulated Raman scattering (SRS) has been developed as an essential quantitative contrast for chemical imaging in recent years. However, while spectral lines near the natural linewidth limit can be routinely achieved by state-of-the-art spontaneous Raman microscopes, spectral broadening is inevitable for current mainstream SRS imaging methods. This is because those SRS signals are all measured in the frequency domain. There is a compromise between sensitivity and spectral resolution: as the nonlinear process benefits from pulsed excitations, the fundamental time-energy uncertainty limits the spectral resolution. Besides, the spectral range and acquisition speed are mutually restricted. Here we report transient stimulated Raman scattering (T-SRS), an alternative time-domain strategy that bypasses all these fundamental conjugations. T-SRS is achieved by quantum coherence manipulation: we encode the vibrational oscillations in the stimulated Raman loss (SRL) signal by femtosecond pulse-pair sequence excited vibrational wave packet interference. The Raman spectrum was then achieved by Fourier transform of the time-domain SRL signal. Since all Raman modes are impulsively and simultaneously excited, T-SRS features the natural-linewidth-limit spectral line shapes, laser-bandwidth-determined spectral range, and improved sensitivity. With ~150-fs laser pulses, we boost the sensitivity of typical Raman modes to the sub-mM level. With all-plane-mirror high-speed time-delay scanning, we further demonstrated hyperspectral SRS imaging of live-cell metabolism and high-density multiplexed imaging with the natural-linewidth-limit spectral resolution. T-SRS shall find valuable applications for advanced Raman imaging.

Multidimensional Widefield Infrared-Encoded Spontaneous Emission Microscopy: Distinguishing Chromophores by Ultrashort Infrared Pulses

Photoluminescence (PL) imaging has broad applications in visualizing biological activities, detecting chemical species, and characterizing materials. However, the chemical information encoded in the PL images is often limited by the overlapping emission spectra of chromophores. Here, we report a PL microscopy based on the nonlinear interactions between mid-infrared and visible excitations on matters, which we termed MultiDimensional Widefield Infrared-encoded Spontaneous Emission (MD-WISE) microscopy. MD-WISE microscopy can distinguish chromophores that possess nearly identical emission spectra via conditions in a multidimensional space formed by three independent variables: the temporal delay between the infrared and the visible pulses (t), the wavelength of visible pulses (λvis), and the frequencies of the infrared pulses (ωIR). This method is enabled by two mechanisms: (1) modulating the optical absorption cross sections of molecular dyes by exciting specific vibrational functional groups and (2) reducing the PL quantum yield of semiconductor nanocrystals, which was achieved through strong field ionization of excitons. Importantly, MD-WISE microscopy operates under widefield imaging conditions with a field of view of tens of microns, other than the confocal configuration adopted by most nonlinear optical microscopies, which require focusing the optical beams tightly. By demonstrating the capacity of registering multidimensional information into PL images, MD-WISE microscopy has the potential of expanding the number of species and processes that can be simultaneously tracked in high-speed widefield imaging applications.

Multimode vibrational dynamics and orientational effects in fluorescence-encoded infrared spectroscopy. II. Analysis of early-time signals

Developing fluorescence-encoded infrared (FEIR) vibrational spectroscopy for single-molecule applications requires a detailed understanding of how the molecular response and external experimental parameters manifest in the detected signals. In Paper I [L. Whaley-Mayda, A. Guha, and A. Tokmakoff, J. Chem. Phys. 159, 194201 (2023)] we introduced a nonlinear response function theory to describe vibrational dynamics, vibronic coupling, and transition dipole orientation in FEIR experiments with ultrashort pulses. In this second paper, we apply the theory to investigate the role of intermode vibrational coherence, the orientation of vibrational and electronic transition dipoles, and the effects of finite pulse durations in experimental measurements. We focus on measurements at early encoding delays-where signal sizes are largest and therefore of most value for single-molecule experiments, but where many of these phenomena are most pronounced and can complicate the appearance of data. We compare experiments on coumarin dyes with finite-pulse response function simulations to explain the time-dependent behavior of FEIR spectra. The role of the orientational response is explored by analyzing polarization-dependent experiments and their ability to resolve relative dipole angles in the molecular frame. This work serves to demonstrate the molecular information content of FEIR experiments, and develop insight and guidelines for their interpretation.

Multimode vibrational dynamics and orientational effects in fluorescence-encoded infrared spectroscopy. I. Response function theory

Fluorescence-encoded infrared (FEIR) spectroscopy is an emerging technique for performing vibrational spectroscopy in solution with detection sensitivity down to single molecules. FEIR experiments use ultrashort pulses to excite a fluorescent molecule's vibrational and electronic transitions in a sequential, time-resolved manner, and are therefore sensitive to intervening vibrational dynamics on the ground state, vibronic coupling, and the relative orientation of vibrational and electronic transition dipole moments. This series of papers presents a theoretical treatment of FEIR spectroscopy that describes these phenomena and examines their manifestation in experimental data. This first paper develops a nonlinear response function description of Fourier-transform FEIR experiments for a two-level electronic system coupled to multiple vibrations, which is then applied to interpret experimental measurements in the second paper [L. Whaley-Mayda et al., J. Chem. Phys. 159, 194202 (2023)]. Vibrational coherence between pairs of modes produce oscillatory features that interfere with the vibrations' population response in a manner dependent on the relative signs of their respective Franck-Condon wavefunction overlaps, leading to time-dependent distortions in FEIR spectra. The orientational response of population and coherence contributions are analyzed and the ability of polarization-dependent experiments to extract relative transition dipole angles is discussed. Overall, this work presents a framework for understanding the full spectroscopic information content of FEIR measurements to aid data interpretation and inform optimal experimental design.

Increasing Pump-Probe Signal toward Asymptotic Limits

Optimization of pump-probe signal requires a complete understanding of how signal scales with experimental factors. In simple systems, signal scales quadratically with molar absorptivity, and linearly with fluence, concentration, and path length. In practice, scaling factors weaken beyond certain thresholds (e.g., OD > 0.1) due to asymptotic limits related to optical density, fluence and path length. While computational models can accurately account for subdued scaling, quantitative explanations often appear quite technical in the literature. This Perspective aims to present a simpler understanding of the subject with concise formulas for estimating absolute magnitudes of signal under both ordinary and asymptotic scaling conditions. This formulation may be more appealing for spectroscopists seeking rough estimates of signal or relative comparisons. We identify scaling dependencies of signal with respect to experimental parameters and discuss applications for improving signal under broad conditions. We also review other signal enhancement methods, such as local-oscillator attenuation and plasmonic enhancement, and discuss respective benefits and challenges regarding asymptotic limits that signal cannot exceed.

Simulation of two-dimensional infrared Raman spectroscopy with application to proteins

Two-dimensional infrared Raman spectroscopy is a powerful technique for studying the structure and interaction in molecular and biological systems. Here, we present a new implementation of the simulation of the two-dimensional infrared Raman signals. The implementation builds on the numerical integration of the Schrödinger equation approach. It combines the prediction of dynamics from molecular dynamics with a map-based approach for obtaining Hamiltonian trajectories and response function calculations. The new implementation is tested on the amide-I region for two proteins, where one is dominated by α-helices and the other by β-sheets. We find that the predicted spectra agree well with experimental observations. We further find that the two-dimensional infrared Raman spectra at least of the studied proteins are much less sensitive to the laser polarization used compared to conventional two-dimensional infrared experiments. The present implementation and findings pave the way for future applications for the interpretation of two-dimensional infrared Raman spectra.

Resonance conditions, detection quality, and single-molecule sensitivity in fluorescence-encoded infrared vibrational spectroscopy

Fluorescence-encoded Infrared (FEIR) spectroscopy is a vibrational spectroscopy technique that has recently demonstrated the capability of single-molecule sensitivity in solution without near-field enhancement. This work explores the practical experimental factors that are required for successful FEIR measurements in both the single-molecule and bulk regimes. We investigate the role of resonance conditions by performing measurements on a series of coumarin fluorophores of varying electronic transition frequencies. To analyze variations in signal strength and signal to background between molecules, we introduce an FEIR brightness metric that normalizes out measurement-specific parameters. We find that the effect of the resonance condition on FEIR brightness can be reasonably well described by the electronic absorption spectrum. We discuss strategies for optimizing detection quality and sensitivity in bulk and single-molecule experiments.

Highly Sensitive Low-Frequency Time-Domain Raman Spectroscopy via Fluorescence Encoding

Fluorescence-encoded vibrational spectroscopy has become increasingly more popular by virtue of its high chemical specificity and sensitivity. However, current fluorescence-encoded vibrational spectroscopy methods lack sensitivity in the low-frequency region, which if addressed could further enhance their capabilities. Here, we present a method for highly sensitive low-frequency fluorescence-encoded vibrational spectroscopy, termed fluorescence-encoded time-domain coherent Raman spectroscopy (FLETCHERS). By first exciting molecules into vibrationally excited states and then promoting the vibrating molecules to electronic states at varying times, the molecular vibrations can be encoded onto the emitted time-domain fluorescence intensity. We demonstrate the sensitive low-frequency detection capability of FLETCHERS by measuring vibrational spectra in the lower fingerprint region of rhodamine 800 solutions as dilute as 250 nM, which is ∼1000 times more sensitive than conventional vibrational spectroscopy. These results, along with further improvement of the method, open up the prospect of performing single-molecule vibrational spectroscopy in the low-frequency region.

Fluorescence-Detected Mid-Infrared Photothermal Microscopy

Mid-infrared photothermal microscopy is a new chemical imaging technology in which a visible beam senses the photothermal effect induced by a pulsed infrared laser. This technology provides infrared spectroscopic information at submicrometer spatial resolution and enables infrared spectroscopy and imaging of living cells and organisms. Yet, current mid-infrared photothermal imaging sensitivity suffers from a weak dependence of scattering on the temperature, and the image quality is vulnerable to the speckles caused by scattering. Here, we present a novel version of mid-infrared photothermal microscopy in which thermosensitive fluorescent probes are harnessed to sense the mid-infrared photothermal effect. The fluorescence intensity can be modulated at the level of 1% per Kelvin, which is 100 times larger than the modulation of scattering intensity. In addition, fluorescence emission is free of interference, thus much improving the image quality. Moreover, fluorophores can target specific organelles or biomolecules, thus augmenting the specificity of photothermal imaging. Spectral fidelity is confirmed through fingerprinting a single bacterium. Finally, the photobleaching issue is successfully addressed through the development of a wide-field fluorescence-detected mid-infrared photothermal microscope which allows video rate bond-selective imaging of biological specimens.

Elucidation of Quantum-Well-Specific Carrier Mobilities in Layered Perovskites

Layered organohalide perovskite films consist of quantum wells with concentration distributions tailored to enhance long-range charge transport. Whereas cascaded energy and charge funneling behaviors have been detected with conventional optical spectroscopies, it is not clear that such dynamics contribute to the efficiencies of photovoltaic cells. In this Letter, we use nonlinear photocurrent spectroscopy to selectively target charge transport processes within devices based on layered perovskite quantum wells. The photocurrent induced by a pair of laser pulses is directly measured in this "action" spectroscopy to remove ambiguities in signal interpretation. By varying the external bias, we determine carrier mobilities for quantum-well-specific trajectories taken through the active layers of the devices. The results suggest that the largest quantum wells are primarily responsible for photocurrent production, whereas the smallest quantum wells trap charge carriers and are a major source of energy loss in photovoltaic cells.

Combining the best of two worlds: Stimulated Raman excited fluorescence

The pursuit of a hybrid spectroscopy that combines the superb sensitivity of fluorescence and the high chemical specificity of Raman scattering has lasted for 40 years, with multiple experimental and theoretical attempts in the literature. It was only recently that the stimulated Raman excited fluorescence (SREF) process was successfully observed in a broad range of fluorophores. SREF allows single-molecule vibrational spectroscopy and imaging in the optical far field without relying on plasmonic enhancement. In this perspective, we will first review the historical efforts that lead to the successful excitation and detection of SREF, followed by the underlying physical principles, then the remaining technical challenges will be discussed, and, at last, the future opportunities in this old but yet newly emerged spectroscopy are outlined.

Infrared Difference Spectroscopy of Proteins: From Bands to Bonds

Infrared difference spectroscopy probes vibrational changes of proteins upon their perturbation. Compared with other spectroscopic methods, it stands out by its sensitivity to the protonation state, H-bonding, and the conformation of different groups in proteins, including the peptide backbone, amino acid side chains, internal water molecules, or cofactors. In particular, the detection of protonation and H-bonding changes in a time-resolved manner, not easily obtained by other techniques, is one of the most successful applications of IR difference spectroscopy. The present review deals with the use of perturbations designed to specifically change the protein between two (or more) functionally relevant states, a strategy often referred to as reaction-induced IR difference spectroscopy. In the first half of this contribution, I review the technique of reaction-induced IR difference spectroscopy of proteins, with special emphasis given to the preparation of suitable samples and their characterization, strategies for the perturbation of proteins, and methodologies for time-resolved measurements (from nanoseconds to minutes). The second half of this contribution focuses on the spectral interpretation. It starts by reviewing how changes in H-bonding, medium polarity, and vibrational coupling affect vibrational frequencies, intensities, and bandwidths. It is followed by band assignments, a crucial aspect mostly performed with the help of isotopic labeling and site-directed mutagenesis, and complemented by integration and interpretation of the results in the context of the studied protein, an aspect increasingly supported by spectral calculations. Selected examples from the literature, predominately but not exclusively from retinal proteins, are used to illustrate the topics covered in this review.

Stimulated Raman Excited Fluorescence Spectroscopy of Visible Dyes

Fluorescence spectroscopy and Raman spectroscopy are two major classes of spectroscopy methods in physical chemistry. Very recently, stimulated Raman excited fluorescence (SREF) has been demonstrated ( Xiong, H.; et al. Nature Photonics , 2019 , 13 , 412 - 417 ) as a new hybrid spectroscopy that combines the vibrational specificity of Raman spectroscopy with the superb sensitivity of fluorescence spectroscopy (down to the single-molecule level). However, this proof-of-concept study was limited by both the tunability of the commercial laser source and the availability of the excitable molecules in the near-infrared. As a result, the generality of SREF spectroscopy remains unaddressed, and the understanding of the critical electronic preresonance condition is lacking. In this work, we built a modified excitation source to explore SREF spectroscopy in the visible region. Harnessing a large palette of red dyes, we have systematically studied SREF spectroscopy on a dozen different cases with a fine spectral interval of several nanometers. The results not only establish the generality of SREF spectroscopy for a wide range of molecules but also reveal a tight window of proper electronic preresonance for the stimulated Raman pumping process. Our theoretical modeling and further experiments on newly synthesized dyes also support the obtained insights, which would be valuable in designing and optimizing future SREF experiments for single-molecule vibrational spectroscopy and supermultiplex vibrational imaging.