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Abstract
Single-molecule measurements represent a remarkable frontier in spectroscopy, offering unparalleled insights into the heterogeneity and dynamics of individual molecules that are often obscured in ensemble measurements. Techniques like vibrational spectroscopy, which detect structural changes at the scale of a chemical bond, are challenging to perform with single-molecule sensitivity. However, near-field strategies enable single-molecule vibrational measurements, though their application in solution remains a challenge.
Fluorescence-Encoded Infrared Spectroscopy (FEIR) uses sequential absorption of IR and visible photons, creating a double resonance condition that excites molecular vibrations in its electronic ground state, followed by selective up-conversion to a higher-lying fluorescent electronic state. The resulting fluorescence is encoded with vibrational information of the molecular ground state. FEIR combines the single-molecule sensitivity of fluorescence with the structural specificity of vibrational spectroscopy, enabling solution-phase vibrational measurements in the optical far field with single-molecule sensitivity.
This thesis describes the factors that collectively contribute to achieving single-molecule sensitivity with FEIR. Instrumental factors play a vital role in determining the signal-to-noise ratio at the single-molecule level, resulting from a combination of FEIR brightness and contrast. An FEIR spectrometer employing high-energy sub-picosecond ultrafast infrared and visible pulses at a 1 MHz repetition rate, generated from home-built optical parametric amplifiers pumped with a Yb-fiber laser source, and a microscope for high-sensitivity fluorescence detection are described. Proof-of-principle experiments using Coumarin 6 as the model system are discussed, along with the impact of FEIR resonance condition on molecular brightness, through a comparative study across a series of coumarin chromophores. The effect of tuning the visible encoding frequency on the FEIR brightness and contrast is explored using Rhodamine 6G as the model system, demonstrating the need for precise tuning of the resonance condition when setting up an FEIR experiment.
The thesis further presents a discussion on the collective role played by various factors intrinsic to the electronic structure of the chromophore, in shaping the FEIR selection rules. These molecular factors include the magnitudes and relative orientation of vibrational and electronic transition dipoles, vibronic coupling, and fluorescence quantum yield. A computational model based on electronic structure calculations is described, which predicts the FEIR activity of a normal mode within a chromophore. The impact of these molecular factors on the mode-specific FEIR activities is demonstrated through correlations with measured FEIR cross-sections. The discussion includes an illustration of the effect of vibrational dynamics and interaction with finite light pulses on these correlations, and a description of FEIR selection rules from the perspective of normal mode symmetry, supported by an illustrative example of a comparative study of FEIR cross-sections of a symmetric and an asymmetric molecule with similar FEIR resonance condition.
The work concludes by defining a "good FEIR probe" and provides computational tools to guide the choice of a chromophore with an FEIR-active vibrational reporter for single-molecule applications to study the dynamics of chemical interactions in solution by probing structural changes down at the length-scale of a chemical bond.