Fluorescence-detected Fourier transform electronic spectroscopy by phase-tagged photon counting.

Fluorescence-detected Fourier transform (FT) spectroscopy is a technique in which the relative paths of an optical interferometer are controlled to excite a material sample, and the ensuing fluorescence is detected as a function of the interferometer path delay and relative phase. A common approach to enhance the signal-to-noise ratio in these experiments is to apply a continuous phase sweep to the relative optical path, and to detect the resulting modulated fluorescence using a phase-sensitive lock-in amplifier. In many important situations, the fluorescence signal is too weak to be measured using a lock-in amplifier, so that photon counting techniques are preferred. Here we introduce an approach to low-signal fluorescence-detected FT spectroscopy, in which individual photon counts are assigned to a modulated interferometer phase ('phase-tagged photon counting,' or PTPC), and the resulting data are processed to construct optical spectra. We studied the fluorescence signals of a molecular sample excited resonantly by a pulsed coherent laser over a range of photon flux and visibility levels. We compare the performance of PTPC to standard lock-in detection methods and establish the range of signal parameters over which meaningful measurements can be carried out. We find that PTPC generally outperforms the lock-in detection method, with the dominant source of measurement uncertainty being associated with the statistics of the finite number of samples of the photon detection rate.

Measuring local conformations and conformational disorder of (Cy3)2 dimer labeled DNA fork junctions using absorbance, circular dichroism and two-dimensional fluorescence spectroscopy.

The sugar-phosphate backbone of DNA near single-stranded (ss)-double-stranded (ds) junctions likely fluctuates within a broad distribution of conformations to permit the proper binding of genome regulatory proteins that function at these sites. In this work we use absorbance, circular dichroism (CD), and two-dimensional fluorescence spectroscopy (2DFS) to study the local conformations and conformational disorder within chromophore-labeled DNA constructs. These constructs employ dimers of the fluorescent chromophore Cy3 that are site-specifically incorporated into the sugar-phosphate backbones of DNA strands at ss-ds DNA fork junctions. We show that these data can be analyzed to determine the local conformations of the (Cy3)2 dimer, and the degree of conformational disorder. Our analysis employs an essential-state Holstein-Frenkel Hamiltonian model, which takes into account the internal electronic-vibrational motions within each Cy3 chromophore, and the resonant electronic interaction that couples the two chromophores together. Our results suggest that this approach may be applied generally to understand local backbone conformation and conformational disorder at ss-ds DNA fork junctions.

Dynamics in a Room-Temperature Ionic Liquid from the Cation Perspective: 2D IR Vibrational Echo Spectroscopy.

The dynamics of the room-temperature ionic liquid (RTIL) 1-butyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide (BmimNTf2) were investigated with two-dimensional infrared (2D IR) vibrational echo spectroscopy and polarization selective pump-probe (PSPP) experiments. The CN stretch frequency of a modified Bmim+ cation (2-SeCN-Bmim+), in which a SeCN moiety was substituted onto the C-2 position of the imidazolium ring, was used as a vibrational probe. A major result of the 2D IR experiments is the observation of a long time scale structural spectral diffusion component of 600 ps in addition to short and intermediate time scales similar to those measured for selenocyanate anion (SeCN-) dissolved in BmimNTf2. In contrast to 2-SeCN-Bmim+, SeCN- samples its inhomogeneous line width nearly an order of magnitude faster than the complete structural randomization time of neat BmimNTf2 liquid (870 ± 20 ps) measured with optical heterodyne-detected optical Kerr effect (OHD-OKE) experiments. The orientational correlation function obtained from PSPP experiments on 2-SeCN-Bmim+ exhibits two periods of restricted angular diffusion (wobbling-in-a-cone) followed by complete orientational randomization on a time scale of 900 ± 20 ps, significantly slower than observed for SeCN- but identical within experimental error to the complete structural randomization time of BmimNTf2. The experiments indicate that 2-SeCN-Bmim+ is sensitive to local motions of the ionic region that influence the spectral diffusion and reorientation of small, anionic, and neutral molecules as well as significantly slower, longer-range fluctuations that are responsible for complete randomization of the liquid structure.

Alkyl Chain Length Dependence of the Dynamics and Structure in the Ionic Regions of Room-Temperature Ionic Liquids.

The dynamics of four 1-alkyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide room-temperature ionic liquids (RTILs) with carbon chain lengths of 2, 4, 6, and 10 were studied by measuring the orientational and spectral diffusion dynamics of the vibrational probe SeCN(-). Vibrational absorption spectra, two-dimensional infrared (2D IR), and polarization-selective pump-probe (PSPP) experiments were performed on the CN stretch. In addition, optical heterodyne-detected optical Kerr effect (OHD-OKE) experiments were performed on the bulk liquids. The PSPP experiments yielded triexponential anisotropy decays, which were analyzed with the wobbling-in-a-cone model. The slowest decay, the complete orientational randomization, slows with increasing chain length in a hydrodynamic trend consistent with the increasing viscosity. The shortest time scale wobbling motions are insensitive to chain length, while the intermediate time scale wobbling slows mildly as the chain length increases. The 2D IR spectra measured in parallel (⟨XXXX⟩) and perpendicular (⟨XXYY⟩) polarization configurations gave different decays, showing that reorientation-induced spectral diffusion (RISD) contributes to the dynamics. The spectral diffusion caused by the RTIL structural fluctuations was obtained by removing the RISD contributions. The faster structural fluctuations are relatively insensitive to chain length. The slowest structural fluctuations slow substantially when going from Emim (2 carbon chain) to Bmim (4 carbon chain) and slow further, but more gradually, as the chain length is increased. It was shown previously that K(+) causes local ion clustering in the Emim RTIL. The K(+) effect increases with increasing chain length. The OHD-OKE measured complete structural randomization times slow substantially with increasing chain length and are much slower than the dynamics experienced by the SeCN(-) located in the ionic regions of the RTILs.

Structural and Rotational Dynamics of Carbon Dioxide in 1-Alkyl-3-methylimidazolium Bis(trifluoromethylsulfonyl)imide Ionic Liquids: The Effect of Chain Length.

Ionic liquids (ILs) have been proposed as possible carbon dioxide (CO2) capture media; thus, it is useful to understand the dynamics of both the dissolved gas and its IL environment as well as how altering an IL affects these dynamics. With increasing alkyl chain length, it is well-established that ILs obtain a mesoscopic structural feature assigned to polar-apolar segregation, and the change in structure with chain length affects the dynamics. Here, the dynamics of CO2 in a series of 1-alkyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide ILs, in which the alkyl group is ethyl, butyl, hexyl, or decyl, were investigated using ultrafast infrared spectroscopy by measuring the reorientation and spectral diffusion of carbon dioxide in the ILs. It was found that reorientation of the carbon dioxide occurs on three time scales, which correspond to two different time scales of restricted wobbling-in-a-cone motions and a long-time complete diffusive reorientation. Complete reorientation slows with increasing chain length but less than the increases in viscosity of the bulk liquids. Spectral diffusion, measured with two-dimensional IR spectroscopy, is caused by a combination of the liquids' structural fluctuations and reorientation of the CO2. The data were analyzed using a recent theory that takes into account both contributions to spectral diffusion and extracts the structural spectral diffusion. Different components of the structural fluctuations have distinct dependences on the alkyl chain length. All of the dynamics are fast compared to the complete orientational randomization of the bulk ILs, as measured with optical heterodyne-detected optical Kerr effect measurements. The results indicate a hierarchy of constraint releases in the liquids that give rise to increasingly slower dynamics.

Carbon dioxide in an ionic liquid: Structural and rotational dynamics.

Ionic liquids (ILs), which have widely tunable structural motifs and intermolecular interactions with solutes, have been proposed as possible carbon capture media. To inform the choice of an optimal ionic liquid system, it can be useful to understand the details of dynamics and interactions on fundamental time scales (femtoseconds to picoseconds) of dissolved gases, particularly carbon dioxide (CO2), within the complex solvation structures present in these uniquely organized materials. The rotational and local structural fluctuation dynamics of CO2 in the room temperature ionic liquid 1-ethyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide (EmimNTf2) were investigated by using ultrafast infrared spectroscopy to interrogate the CO2 asymmetric stretch. Polarization-selective pump probe measurements yielded the orientational correlation function of the CO2 vibrational transition dipole. It was found that reorientation of the carbon dioxide occurs on 3 time scales: 0.91 ± 0.03, 8.3 ± 0.1, 54 ± 1 ps. The initial two are attributed to restricted wobbling motions originating from a gating of CO2 motions by the IL cations and anions. The final (slowest) decay corresponds to complete orientational randomization. Two-dimensional infrared vibrational echo (2D IR) spectroscopy provided information on structural rearrangements, which cause spectral diffusion, through the time dependence of the 2D line shape. Analysis of the time-dependent 2D IR spectra yields the frequency-frequency correlation function (FFCF). Polarization-selective 2D IR experiments conducted on the CO2 asymmetric stretch in the parallel- and perpendicular-pumped geometries yield significantly different FFCFs due to a phenomenon known as reorientation-induced spectral diffusion (RISD), revealing strong vector interactions with the liquid structures that evolve slowly on the (independently measured) rotation time scales. To separate the RISD contribution to the FFCF from the structural spectral diffusion contribution, the previously developed first order Stark effect RISD model is reformulated to describe the second order (quadratic) Stark effect--the first order Stark effect vanishes because CO2 does not have a permanent dipole moment. Through this analysis, we characterize the structural fluctuations of CO2 in the ionic liquid solvation environment, which separate into magnitude-only and combined magnitude and directional correlations of the liquid's time dependent electric field. This new methodology will enable highly incisive comparisons between CO2 dynamics in a variety of ionic liquid systems.

Ionic Liquid Dynamics Measured with 2D IR and IR Pump-Probe Experiments on a Linear Anion and the Influence of Potassium Cations.

The room-temperature ionic liquid EmimNTf2 (1-ethyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide) was studied with two-dimensional infrared (2D IR) spectroscopy and polarization selective pump-probe (PSPP) experiments using low-concentration selenocyanate (SeCN(-)) as the vibrational probe. SeCN(-) was added as EmimSeCN, which keeps the cation the same. KSeCN was also used, so K(+) was added. Two 2D IR polarization configurations were employed: ⟨XXXX⟩ (all pulses have the same polarization) and ⟨XXYY⟩ (the first two pulse polarizations are perpendicular to that of the third pulse and the echo). The spectral diffusion differs for the two configurations, demonstrating that reorientation-induced spectral diffusion, in addition to structural spectral diffusion (SSD), plays a role in the observed dynamics. The SSD was extracted from the 2D IR time-dependent data. The samples with EmimSeCN have dynamics on several fast time scales; however, when KSeCN is used, both the PPSP anisotropy decay and the 2D IR decays have low amplitude offsets (nondecaying values at long times). The size of the offsets increased with increased K(+) concentration. These results are explained in terms of a two-ensemble model. A small fraction of the SeCN(-) is located in the regions modified by the presence of K(+), causing a substantial slowing of the SeCN(-) orientational relaxation and spectral diffusion. Having a small ensemble of SeCN(-) that undergoes very slow dynamics is sufficient to explain the offsets. For the major ensemble, the dynamics with and without K(+) are the same.

Coupling of Carbon Dioxide Stretch and Bend Vibrations Reveals Thermal Population Dynamics in an Ionic Liquid.

The population relaxation of carbon dioxide dissolved in the room temperature ionic liquid 1-ethyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide (EmimNTf2) was investigated using polarization-selective ultrafast infrared pump-probe spectroscopy and two-dimensional infrared (2D IR) spectroscopy. Due to the coupling of the bend with the asymmetric stretch, excitation of the asymmetric stretch of a molecule with a thermally populated bend leads to an additional peak, a hot band, which is red-shifted from the main asymmetric absorption band by the combination band shift. This hot band peak exchanges population with the main peak through the gain and loss of bend excitation quanta. The isotropic pump-probe signal originating from the unexcited bend state displays a fast, relatively small amplitude, initial growth followed by a longer time scale exponential decay. The signal is analyzed over its full time range using a kinetic model to determine both the vibrational lifetime (the final decay) and rate constant for the loss of the bend energy. This bend relaxation manifests as the fast initial growth of the stretch/no bend signal because the hot band (stretch with bend) is "over pumped" relative to the ground state equilibrium. The nonequilibrium pumping occurs because the hot band has a larger transition dipole moment than the stretch/no bend peak. The system is then prepared, utilizing an acousto-optic mid-infrared pulse shaper to cut a hole in the excitation pulse spectrum, such that the hot band is not pumped. The isotropic pump-probe signal from the stretch/no bend state is altered because the initial excited state population ratio has changed. Instead of a growth due to relaxation of bend quanta, a fast initial decay is observed because of thermal excitation of the bend. Fitting this curve gives the rate constant for thermal excitation of the bend and the lifetime, which agree with those determined in the pump-probe experiments without frequency-selective pumping.

Molecular Anion Hydrogen Bonding Dynamics in Aqueous Solution.

The dynamic nature of hydrogen bonding between a molecular anion, selenocyanate (SeCN(-)), and water in aqueous solution (D2O) is addressed using FT-IR spectroscopy, two-dimensional infrared (2D IR) vibrational echo spectroscopy, and polarization selective IR pump-probe (PSPP) experiments performed on the CN stretching mode. The CN absorption spectrum is asymmetric with a wing on the low frequency (red) side of the line in contrast to the spectrum in the absence of hydrogen bonding. It is shown that the red wing is the result of an increase in the CN stretch transition dipole moment due to the effect of hydrogen bonding (non-Condon effect). This non-Condon effect is similar in nature to observations on pure water and other nonionic systems where hydrogen bonding enhances the extinction coefficient. The 2D IR measurements of spectral diffusion (solvent structural evolution) yield a time constant of 1.5 ps, which is within error the same as that of the OH stretch of HOD in D2O (1.4 ps). The orientational relaxation of SeCN(-) measured by PSPP experiments is long (4.04 ps) compared to the spectral diffusion time. The population decay at or near the absorption line center is a single-exponential decay of 37.4 ± 0.3 ps, the vibrational lifetime. However, on the red side of the line the decay is biexponential with a low amplitude, fast component; on the blue side of the line there is a low amplitude, fast growth followed by the lifetime decay. Both of the fast components have 1.5 ps time constants, which is the spectral diffusion time. The fast components of the population decays are the results of the non-Condon effect that causes the red side of the line to be over pumped by the pump pulse. Spectral diffusion then produces the fast decay component on the red side of the line and the growth on the blue side of the line as the excess initial population on the red side produces a net population flow from red to blue.

Observation and theory of reorientation-induced spectral diffusion in polarization-selective 2D IR spectroscopy.

In nearly all applications of ultrafast multidimensional infrared spectroscopy, the spectral degrees of freedom (e.g., transition frequency) and the orientation of the transition dipole are assumed to be decoupled. We present experimental results which confirm that frequency fluctuations can be caused by rotational motion and observed under appropriate conditions. A theory of the frequency-frequency correlation function (FFCF) observable under various polarization conditions is introduced, and model calculations are found to reproduce the qualitative trends in FFCF rates. The FFCF determined with polarization-selective two-dimensional infrared (2D IR) spectroscopy is a direct reporter of the frequency-rotational coupling. For the solute methanol in a room temperature ionic liquid, the FFCF of the hydroxyl (O-D) stretch decays due to spectral diffusion with different rates depending on the polarization of the excitation pulses. The 2D IR vibrational echo pulse sequence consists of three excitation pulses that generate the vibrational echo, a fourth pulse. A faster FFCF decay is observed when the first two excitation pulses are polarized perpendicular to the third pulse and the echo, 〈XXY Y〉, than in the standard all parallel configuration, 〈XXXX〉, in which all four pulses have the same polarization. The 2D IR experiment with polarizations 〈XY XY〉 ("polarization grating" configuration) gives a FFCF that decays even more slowly than in the 〈XXXX〉 configuration. Polarization-selective 2D IR spectra of bulk water do not exhibit polarization-dependent FFCF decays; spectral diffusion is effectively decoupled from reorientation in the water system.

The Influence of Cholesterol on Fast Dynamics Inside of Vesicle and Planar Phospholipid Bilayers Measured with 2D IR Spectroscopy.

Phospholipid bilayers are frequently used as models for cell membranes. Here the influence of cholesterol on the structural dynamics in the interior of 1,2-dilauroyl-sn-glycero-3-phosphocholine (dilauroylphosphatidylcholine, DLPC) vesicles and DLPC planar bilayers are investigated as a function of cholesterol concentration. 2D IR vibrational echo spectroscopy was performed on the antisymmetric CO stretch of the vibrational probe molecule tungsten hexacarbonyl, which is located in the interior alkyl regions of the bilayers. The 2D IR experiments measure spectral diffusion, which is caused by the structural fluctuations of the bilayers. The 2D IR measurements show that the bilayer interior alkyl region dynamics occur on time scales ranging from a few picoseconds to many tens of picoseconds. These are the time scales of the bilayers' structural dynamics, which act as the dynamic solvent bath for chemical processes of membrane biomolecules. The results suggest that at least a significant fraction of the dynamics arise from density fluctuations. Samples are studied in which the cholesterol concentration is varied from 0% to 40% in both the vesicles (72 nm diameter) and fully hydrated planar bilayers in the form of aligned multibilayers. At all cholesterol concentrations, the structural dynamics are faster in the curved vesicle bilayers than in the planar bilayers. As the cholesterol concentration is increased, at a certain concentration there is a sudden change in the dynamics, that is, the dynamics abruptly slow down. However, this change occurs at a lower concentration in the vesicles (between 10% and 15% cholesterol) than in the planar bilayers (between 25% and 30% cholesterol). The sudden change in the dynamics, in addition to other IR observables, indicates a structural transition. However, the results show that the cholesterol concentration at which the transition occurs is influenced by the curvature of the bilayers.

Structural dynamics inside a functionalized metal-organic framework probed by ultrafast 2D IR spectroscopy.

The structural elasticity of metal-organic frameworks (MOFs) is a key property for their functionality. Here, we show that 2D IR spectroscopy with pulse-shaping techniques can probe the ultrafast structural fluctuations of MOFs. 2D IR data, obtained from a vibrational probe attached to the linkers of UiO-66 MOF in low concentration, revealed that the structural fluctuations have time constants of 7 and 670 ps with no solvent. Filling the MOF pores with dimethylformamide (DMF) slows the structural fluctuations by reducing the ability of the MOF to undergo deformations, and the dynamics of the DMF molecules are also greatly restricted. Methodology advances were required to remove the severe light scattering caused by the macroscopic-sized MOF particles, eliminate interfering oscillatory components from the 2D IR data, and address Förster vibrational excitation transfer.

Size-dependent ultrafast structural dynamics inside phospholipid vesicle bilayers measured with 2D IR vibrational echoes.

The ultrafast structural dynamics inside the bilayers of dilauroylphosphatidylcholine (DLPC) and dipalmitoylphosphatidylcholine vesicles with 70, 90, and 125 nm diameters were directly measured with 2D IR vibrational echo spectroscopy. The antisymmetric CO stretch of tungsten hexacarbonyl was used as a vibrational probe and provided information on spectral diffusion (structural dynamics) in the alkyl region of the bilayers. Although the CO stretch absorption spectra remain the same, the interior structural dynamics become faster as the size of the vesicles decrease, with the size dependence greater for dipalmitoylphosphatidylcholine than for DLPC. As DLPC vesicles become larger, the interior dynamics approach those of the planar bilayer.

Ultrafast structural dynamics inside planar phospholipid multibilayer model cell membranes measured with 2D IR spectroscopy.

The ultrafast dynamics in the interior of planar aligned multibilayers of 1,2-dilauroyl-sn-glycero-3-phosphocholine (dilauroylphosphatidylcholine, DLPC) are investigated using 2D IR vibrational echo spectroscopy. The nonpolar and water insoluble vibrational dynamics probe, tungsten hexacarbonyl (W(CO)6), is located in the alkane interior of the membranes. The 2D IR experiments conducted on the antisymmetric CO stretching mode measure spectral diffusion caused by the structural dynamics of the membrane from ~200 fs to ~200 ps as a function of the number of water molecules hydrating the head groups and as a function of cholesterol content for a fixed hydration level. FT-IR studies of the lipid bilayers and the model liquids, hexadecane and bis(2-ethylhexyl) succinate, indicate that as the number of hydrating water molecules increases from 2 to 16, there are structural changes in the membrane that partition some of the W(CO)6 into the ester region of DLPC. However, the 2D IR measurements, which are made solely on the W(CO)6 in the alkane regions, show that the level of hydration has no observable impact on the interior membrane dynamics. FT-IR spectra and 2D IR experiments on samples with cholesterol concentrations from 0 to 60% demonstrate that there is a change in the membrane structure and an abrupt change in dynamics at 35% cholesterol. The dynamics are independent of cholesterol content from 10 to 35%. At 35%, the dynamics become slower and remain unchanged from 35 to 60% cholesterol.