Element- and enantiomer-selective visualization of molecular motion in real-time

Monitoring nuclear motion in molecules in real time became possible with ultrafast spectroscopy but optical methods lack element specificity. Time-resolved X-ray and electron diffraction and X-ray spectroscopies provide element-specific insights but were initially limited to heavy atoms; extending to the soft X-ray regime opens access to light elements (C, N, O, S, F) crucial for organic and biochemical systems. Circularly polarized soft X-ray pulses enable X-ray circular dichroism (XCD), which can probe enantiomer-specific responses at core edges with atom selectivity. Simulations show that XCD at the C K-edge depends strongly on the local chemical environment, allowing differentiation of chemically identical atoms in distinct environments. While tabletop HHG sources are emerging, reliable polarization control is established at the FERMI FEL. The goal of this study is to combine impulsive stimulated Raman scattering (ISRS) in the ground state with ultrafast circularly polarized soft X-ray absorption at the carbon K-edge, to visualize low-frequency coherent vibrations in racemic ibuprofen (RS dimer) with both element and enantiomer selectivity, revealing how specific carbon atoms within distinct enantiomers respond to coherent deformations.

Prior work established ultrafast optical spectroscopy for nuclear dynamics but without element specificity. Time-resolved X-ray and electron-based methods and X-ray absorption/emission spectroscopies map element-specific dynamics in complexes, biomolecules, and solids, historically favoring heavy atoms; recent advances extend to soft X-rays for light elements using HHG and FEL sources. Time-resolved circular dichroism (CD) has been implemented from sub-ps to ns in UV/visible/IR to study chiral dynamics in peptides, metalloproteins, and metal complexes. Theoretical studies predict that XCD signals at core edges are sensitive to local geometry, substitution, and distance to the chiral center, so chemically equivalent elements (e.g., carbons) exhibit distinct dichroic responses depending on environment. For organic molecules, combining chemical shifts with dichroic contrast can disentangle congested edges. For ibuprofen specifically, Raman studies reported low-frequency features (~20–80 cm−1) attributed to intermolecular/phonon modes in the racemate, while simulations for the S-monomer show a single low-frequency mode (~20–30 cm−1). These findings suggest that low-frequency ground-state modes (both intra- and inter-molecular) can be driven via ISRS near the first electronic absorption band and probed with core-level selectivity.

Experimental approach: An ISRS pump and soft X-ray absorption probe scheme was implemented at the EIS-TIMEX end-station of the FERMI FEL (Trieste, Italy). A 4.7 eV (∼265 nm), ∼80 fs pump pulse (≤1 µJ per pulse) resonant with the first absorption band of ibuprofen (IBP) impulsively excites coherent ground-state vibrations, including low-frequency modes (20–30 cm−1). The pump impinged at 10° relative to the surface normal onto a ∼90 × 90 µm2 FWHM spot. The probe was a circularly polarized soft X-ray pulse (∼30 fs), tuned across the carbon K-edge (∼279–294 eV) with energies selected based on ab initio predictions of atom-specific transitions. Polarization (left/right circular) was controlled via the apple II undulators. Sample: A racemic mixture of IBP was prepared by dissolving 3 mg in 1 mL ethanol; 1 µL was deposited on a 100 nm-thick silicon nitride membrane that was hydrophilized via oxygen plasma RIE (20 W, O2 30 sccm, 5 min), reducing the water contact angle from 85.1° to 28.5°. After solvent evaporation, IBP recrystallized to its native form, yielding an estimated ∼100 nm-thick layer (density ∼1.1 g/cm3). The phenyl rings are expected to lie nearly parallel to the surface. To mitigate radiation damage, the FEL spot size was ∼80 µm FWHM with ∼160 nJ energy/pulse; the sample was translated to pristine regions between scans; a tele-microscope enabled visual monitoring. Detection and acquisition: The transmitted soft X-ray intensity was measured by a multi-channel plate (MCP) on-axis. The MCP response was calibrated against a hydrophilized silicon nitride membrane: MCP signal (I1) vs FEL intensity (I0) was fit with a second-order polynomial to derive transmission shot-by-shot as measured I1 divided by the polynomial-predicted I1 for each I0. Time-resolved traces were acquired by continuously scanning the pump-probe delay at 0.5 ps/s, repeated three times per configuration, then merged and binned to 50 fs; data points represent bin means with error bars as standard deviations. Pump-off scans over 3500 shots verified stability and absence of features. Steady-state spectra: Carbon K-edge absorption spectra were recorded point-by-point by averaging 3500 shots per energy and polarization. FEL photon energies 293.5–285 eV were generated by HGHG of the 60th harmonic of a 4.9–4.7 eV seed; 283.7–279.2 eV used the 55th harmonic of a 5.16–5.1 eV seed, both tuned in ∼0.02 eV steps. XCD spectra were computed as (L−R)/(L+R). Theory: Core-excited state energies and oscillator strengths at the C K-edge were calculated using RASSCF/CASSCF with cc-pVDZ basis. Multiple active spaces (AS) were tested; AS3 provided convergence and physical plausibility. A rigid shift of 6.4 eV aligned computed energies with experiment. Specific atom transitions near 285.0 eV and 285.7 eV with appreciable oscillator strength were identified. XCD spectra were simulated at RASSCF(9/8)/cc-pVDZ, following established procedures. Data analysis: Time traces were fit to damped sinusoids y(t)=y0+θ(t)A exp(−t/τ) sin(2πt/T+mt). Fit confidence bands were obtained by uncertainty propagation; parameters are reported for each probe energy/polarization.

• Steady-state C K-edge absorption shows clear dichroism: LC yields enhanced absorption at the edge (285–286 eV), while RC is stronger above 287 eV. The XCD spectrum (difference normalized by sum) exhibits the expected energy-dependent dichroic response.
• Ab initio calculations (RASSCF/CASSCF) identify inequivalent carbon atoms contributing near the edge; among these, atoms labeled (28,12) near ∼285.7 eV and (17,3) near ∼285.0 eV possess appreciable oscillator strengths. A 6.4 eV rigid shift aligns theory with experiment; simulated XCD agrees well with measurements, confirming element- and environment-specific dichroic signatures.
• Time-resolved transmission reveals coherent oscillations with 5–10% amplitude around the mean transmission, consistent with ISRS-driven ground-state vibrations. Fitted parameters (Table 1): • 285 eV, circular left (CL): frequency 25 ± 1 cm−1, damping time 2.5 ± 1.3 ps (calc. 21.5 cm−1) • 285 eV, circular right (CR): frequency 30 ± 3 cm−1, damping time 1.5 ± 0.6 ps (calc. 28.8 cm−1) • 285.7 eV, circular right (CR): frequency 24.2 ± 0.9 cm−1, damping time 3.8 ± 3 ps (calc. 22.6 cm−1) Corresponding oscillation periods are ∼1.1–1.4 ps; damping times imply spectral widths of ∼8–25 cm−1, explaining why these modes are not resolved in steady-state Raman.
• Enantiomeric selectivity: The disparity between CL and CR signals at 285 eV indicates preferential sensitivity to vibrations of specific enantiomers via circular polarization. Element/energy selectivity: Shifting probe energy by 0.7 eV (285.0→285.7 eV) significantly alters the time-domain response, showing sensitivity to specific carbon sites and their distinct vibrational couplings.

By combining ISRS excitation with circularly polarized soft X-ray probing at the carbon K-edge, the study achieves simultaneous element and enantiomer selectivity in monitoring low-frequency ground-state vibrations. Differences between CL and CR at 285 eV directly evidence enantioselective probing, while tuning the probe to 285.7 eV shifts sensitivity to a different subset of carbon atoms, highlighting chemical-environment selectivity. Compared with vibrational optical activity (VOA) techniques, which suffer from weak chiral signals and strong achiral backgrounds and have not accessed low-frequency intermolecular modes, the present XCD-enabled approach provides robust chiroptical contrast with atom specificity in the low-frequency regime. These capabilities suggest a general strategy to identify which atoms in a given enantiomer are most affected by deformations following a perturbation, enabling targeted insights into stereospecific reactivity and intermolecular interactions in the ground state.

This work demonstrates an ultrafast, element- and enantiomer-selective method to visualize ground-state molecular motion by coupling ISRS excitation with circularly polarized soft X-ray absorption at the carbon K-edge. In racemic ibuprofen dimers, coherent low-frequency modes (∼24–30 cm−1) are observed with site and enantiomer sensitivity, corroborated by ab initio XCD simulations that resolve inequivalent carbon contributions near the edge. The approach enables differentiation of identical elements in distinct chemical environments and reveals how specific atoms within a chosen enantiomer respond to coherent deformations. Future directions include systematic studies to map atom-specific vibrational responses across enantiomers, investigation of ground-state molecular reactions via intermolecular dynamics, probing host–guest interactions (e.g., S-IBP binding to cyclodextrins), isotopic substitution strategies to engineer vibrational properties without altering electronic structure, and application to photoactive processes where the actinic ISRS pulse initiates reactivity while core-level probing tracks atom-specific dynamics.

Time-domain XCD difference traces were not plotted due to low signal-to-noise and identical phase of modes, which would wash out modulations. The measurement window did not extend to full decay, leading to significant uncertainties in damping constants. The low-frequency modes are broadened (∼8–25 cm−1), preventing resolution in steady-state Raman. Potential radiation damage required careful dose management and sample translation, and data volume considerations limit immediate open data access.