Chemical bond reorganization in intramolecular proton transfer revealed by ultrafast X-ray photoelectron spectroscopy.

Time-resolved X-ray photoelectron spectroscopy (TR-XPS) is used in a simulation study to monitor the excited state intramolecular proton transfer between oxygen and nitrogen atoms in 2-(iminomethyl)phenol. Real-time monitoring of the chemical bond breaking and forming processes is obtained through the time evolution of excited-state chemical shifts. By employing individual atomic probes of the proton donor and acceptor atoms, we predict distinct signals with opposite chemical shifts of the donor and acceptor groups during proton transfer. Details of the ultrafast bond breaking and forming dynamics are revealed by extending the classical electron spectroscopy chemical analysis to real time. Through a comparison with simulated time-resolved photoelectron spectroscopy at the valence level, the distinct advantage of TR-XPS is demonstrated thanks to its atom specificity.

Manipulating ultrafast even-order nonlinear chiral responses of L-tryptophan by polarization pulse shaping.

Molecular chirality has long been monitored in the frequency domain in the ultraviolet, visible, and infrared regimes. Recently developed time-domain approaches can detect time-dependent chiral dynamics by enhancing intrinsically weak chiral signals. Even-order nonlinear signals in chiral molecules have gained attention thanks to their existence in the electric dipole approximation, without relying on the weaker higher-order multipole interactions. We illustrate the optimization of temporal polarization pulse-shaping in various frequency ranges (infrared/optical and optical/X ray) to enhance chiral nonlinear signals. These signals can be recast as an overlap integral of matter and field pseudoscalars which contain the relevant chiral information. Simulations are carried out for second- and fourth-order nonlinear spectroscopies in L-tryptophan.

Unraveling dynamic protein structures by two-dimensional infrared spectra with a pretrained machine learning model.

Dynamic protein structures are crucial for deciphering their diverse biological functions. Two-dimensional infrared (2DIR) spectroscopy stands as an ideal tool for tracing rapid conformational evolutions in proteins. However, linking spectral characteristics to dynamic structures poses a formidable challenge. Here, we present a pretrained machine learning model based on 2DIR spectra analysis. This model has learned signal features from approximately 204,300 spectra to establish a "spectrum-structure" correlation, thereby tracing the dynamic conformations of proteins. It excels in accurately predicting the dynamic content changes of various secondary structures and demonstrates universal transferability on real folding trajectories spanning timescales from microseconds to milliseconds. Beyond exceptional predictive performance, the model offers attention-based spectral explanations of dynamic conformational changes. Our 2DIR-based pretrained model is anticipated to provide unique insights into the dynamic structural information of proteins in their native environments.

Photoelectron spectroscopy with entangled photons; enhanced spectrotemporal resolution.

In this theoretical study, we show how photoelectron signals generated by time-energy entangled photon pairs can monitor ultrafast excited state dynamics of molecules with high joint spectral and temporal resolutions, not limited by the Fourier uncertainty of classical light. This technique scales linearly, rather than quadratically, with the pump intensity, allowing the study of fragile biological samples with low photon fluxes. Since the spectral resolution is achieved by electron detection and the temporal resolution by a variable phase delay, this technique does not require scanning the pump frequency and the entanglement times, which significantly simplifies the experimental setup, making it feasible with current instrumentation. Application is made to the photodissociation dynamics of pyrrole calculated by exact nonadiabatic wave packet simulations in a reduced two nuclear coordinate space. This study demonstrates the unique advantages of ultrafast quantum light spectroscopy.

Quantum interferometry and pathway selectivity in the nonlinear response of photosynthetic excitons.

We propose a time-frequency resolved spectroscopic technique which employs nonlinear interferometers to study exciton-exciton scattering in molecular aggregates. A higher degree of control over the contributing Liouville pathways is obtained as compared to classical light. We show how the nonlinear response can be isolated from the orders-of-magnitude stronger linear background by either phase matching or polarization filtering. Both arise due to averaging the signal over a large number of noninteracting, randomly oriented molecules. We apply our technique to the Frenkel exciton model which excludes charge separation for the photosystem II reaction center. We show how the sum of the entangled photon frequencies can be used to select two-exciton resonances, while their delay times reveal the single-exciton levels involved in the optical process.

Sensing ultrashort electronic coherent beating at conical intersections by single-electron pulses.

SignificanceIn a theoretical study, we present an ultrafast technique for probing time-dependent molecular charge densities. An ultrafast optical pump first brings the molecule into an electronic nonstationary state. This is followed by coherent inelastic scattering of a broadband single-electron probe pulse with a variable delay T, which is detected spectrally. The technique is applied to reveal phase-sensitive background-free coherent electron beating in the conical intersection passage in uracil and reveals the otherwise elusive coherent beating of strongly coupled electrons and nuclei.

Electronic coherences in nonadiabatic molecular photophysics revealed by time-resolved photoelectron spectroscopy.

Time-resolved photoelectron spectroscopy (TRPES) signals that monitor the relaxation of the RNA base uracil upon optical excitation are simulated. Distinguishable signatures of coherence dynamics at conical intersections are identified, with temporal and spectral resolutions determined by the duration of the ionizing probe pulse. The frequency resolution of the technique, either directly provided by the signal or retrieved at the data-processing stage, can magnify the contribution from molecular coherences, enabling the extraction of most valuable information about the nonadiabatic molecular dynamics. The predicted coherence signatures in TRPES could be experimentally observed with existing ultrashort pulses from high-order harmonic generation or free-electron lasers.

Machine learning recognition of protein secondary structures based on two-dimensional spectroscopic descriptors.

Protein secondary structure discrimination is crucial for understanding their biological function. It is not generally possible to invert spectroscopic data to yield the structure. We present a machine learning protocol which uses two-dimensional UV (2DUV) spectra as pattern recognition descriptors, aiming at automated protein secondary structure determination from spectroscopic features. Accurate secondary structure recognition is obtained for homologous (97%) and nonhomologous (91%) protein segments, randomly selected from simulated model datasets. The advantage of 2DUV descriptors over one-dimensional linear absorption and circular dichroism spectra lies in the cross-peak information that reflects interactions between local regions of the protein. Thanks to their ultrafast (∼200 fs) nature, 2DUV measurements can be used in the future to probe conformational variations in the course of protein dynamics.

Direct Probe of Conical Intersection Photochemistry by Time-Resolved X-ray Magnetic Circular Dichroism.

The direct probing of photochemical dynamics by detecting the electronic coherence generated during passage through conical intersections is an intriguing challenge. The weak coherence signal and the difficulty in preparing purely excited wave packets that exclude coherence from other sources make it experimentally challenging. We propose to use time-resolved X-ray magnetic circular dichroism to probe the wave packet dynamics around the conical intersection. The magnetic field amplifies the relative strength of the electronic coherence signal compared to populations through the magnetic field response anisotropy. More importantly, since the excited state relaxation through conical intersections involves a change of parity, the magnetic coupling matches the symmetry of the response function with the electronic coherence, making the coherence signal only sensitive to the conical intersection induced coherence and excludes the pump pulse induced coherence between the ground state and excited state. In this theoretical study, we apply this technique to the photodissociation dynamics of a pyrrole molecule and demonstrate its capability of probing electronic coherence at a conical intersection as well as population transfer. We demonstrate that a magnetic field can be effectively used to extract novel information about electron and nuclear molecular dynamics.

Cavity Control of Molecular Spectroscopy and Photophysics.

ConspectusOptical cavities have been established as a powerful platform for manipulating the spectroscopy and photophysics of molecules. Molecules placed inside an optical cavity will interact with the cavity field, even if the cavity is in the vacuum state with no photons. When the coupling strength between matter excitations, either electronic or vibrational, and a cavity photon mode surpasses all decay rates in the system, hybrid light-matter excitations known as cavity polaritons emerge. Originally studied in atomic systems, there has been growing interest in studying polaritons in molecules. Numerous studies, both experimental and theoretical, have demonstrated that the formation of molecular polaritons can significantly alter the optical, electronic, and chemical properties of molecules in a noninvasive manner.This Account focuses on novel studies that reveal how optical cavities can be employed to control electronic excitations, both valence and core, in molecules and the spectroscopic signatures of molecular polaritons. We first discuss the capacity of optical cavities to manipulate and control the intrinsic conical intersection dynamics in polyatomic molecules. Since conical intersections are responsible for a wide range of photochemical and photophysical processes such as internal conversion, photoisomerization, and singlet fission, this provides a practical strategy to control molecular photodynamics. Two examples are given for the internal conversion in pyrazine and singlet fission in a pentacene dimer. We further show how X-ray cavities can be exploited to control the core-level excitations of molecules. Core polaritons can be created from inequivalent core orbitals by exchanging X-ray cavity photons. The core polaritons can also alter the selection rules in nonlinear spectroscopy.Polaritonic states and dynamics can be monitored by nonlinear spectroscopy. Quantum light spectroscopy is a frontier in nonlinear spectroscopy that exploits the quantum-mechanical properties of light, such as entanglement and squeezing, to extract matter information inaccessible by classical light. We discuss how quantum spectroscopic techniques can be employed for probing polaritonic systems. In multimolecule polaritonic systems, there exist two-polariton states that are dark in the two-photon absorption spectrum due to destructive interference between transition pathways. We show that a time-frequency entangled photon pair can manipulate the interference between transition pathways in the two-photon absorption signal and thus capture classically dark two-polariton states. Finally, we discuss cooperative effects among molecules in spectroscopy and possibly in chemistry. When many molecules are involved in forming the polaritons, while the cooperative effects clearly manifest in the dependence of the Rabi splitting on the number of molecules, whether they can show up in chemical reactivity, which is intrinsically local, is an open question. We explore the cooperative nature of the charge migration process in a cavity and show that, unlike spectroscopy, polaritonic charge dynamics is intrinsically local and does not show collective many-molecule effects.

Ultrafast X-Ray Probes of Elementary Molecular Events.

Elementary events that determine photochemical outcomes and molecular functionalities happen on the femtosecond and subfemtosecond timescales. Among the most ubiquitous events are the nonadiabatic dynamics taking place at conical intersections. These facilitate ultrafast, nonradiative transitions between electronic states in molecules that can outcompete slower relaxation mechanisms such as fluorescence. The rise of ultrafast X-ray sources, which provide intense light pulses with ever-shorter durations and larger observation bandwidths, has fundamentally revolutionized our spectroscopic capabilities to detect conical intersections. Recent theoretical studies have demonstrated an entirely new signature emerging once a molecule traverses a conical intersection, giving detailed insights into the coupled nuclear and electronic motions that underlie, facilitate, and ultimately determine the ultrafast molecular dynamics. Following a summary of current sources and experiments, we survey these techniques and provide a unified overview of their capabilities. We discuss their potential to dramatically increase our understanding of ultrafast photochemistry.

Molecular Chirality and Its Monitoring by Ultrafast X-ray Pulses.

Major advances in X-ray sources including the development of circularly polarized and orbital angular momentum pulses make it possible to probe matter chirality at unprecedented energy regimes and with Ångström and femtosecond spatiotemporal resolutions. We survey the theory of stationary and time-resolved nonlinear chiral measurements that can be carried out in the X-ray regime using tabletop X-ray sources or large scale (XFEL, synchrotron) facilities. A variety of possible signals and their information content are discussed.

Theoretical insight into the doubly antiaromatic carbon allotrope cyclo[16]carbon.

A new carbon allotrope, cyclo[16]carbon (C16), has recently been successfully synthesized. It is hypothesized to exhibit double antiaromatic properties owing to the 4n π electrons. Theoretical calculations are a feasible method for systematically studying the structures and properties of unstable antiaromatic molecules. The results show that C16 has a planar structure characterized by alternating long and short bonds with D8h, and a strong antiaromatic characteristic originates from the two perpendicular π systems. We performed an extensive comparative analysis of C16 and the aromatic cyclo[18]carbon, C18. This study offers valuable insight into the structural and electronic characteristics of C16 and could inspire innovative applications and avenues for its utilization in various fields.

Ultrafast photochemistry and electron-diffraction spectra in n → (3s) Rydberg excited cyclobutanone resolved at the multireference perturbative level.

We study the ultrafast time evolution of cyclobutanone excited to the singlet n → Rydberg state through non-adiabatic surface-hopping simulationsperformed at extended multi-state complete active space second-order perturbation (XMS-CASPT2) level of theory. These dynamics predict relaxation to the ground-state with a timescale of 822 ± 45 fs with minimal involvement of the triplets. The major relaxation path to the ground-state involves a three-state degeneracy region and leads to a variety of fragmented photoproducts. We simulate the resulting time-resolved electron-diffraction spectra, which track the relaxation of the excited state and the formation of various photoproducts in the ground state.

Multidimensional four-wave mixing signals detected by quantum squeezed light.

Four-wave mixing (FWM) of optical fields has been extensively used in quantum information processing, sensing, and memories. It also forms a basis for nonlinear spectroscopies such as transient grating, stimulated Raman, and photon echo where phase matching is used to select desired components of the third-order response of matter. Here we report an experimental study of the two-dimensional quantum noise intensity difference spectra of a pair of squeezed beams generated by FWM in hot Rb vapor. The measurement reveals details of the [Formula: see text] susceptibility dressed by the strong pump field which induces an AC Stark shift, with higher spectral resolution compared to classical measurements of probe and conjugate beam intensities. We demonstrate how quantum correlations of squeezed light can be utilized as a spectroscopic tool which unlike their classical counterparts are robust to external noise.

Photoisomerization transition state manipulation by entangled two-photon absorption.

We demonstrate how two-photon excitation with quantum light can influence elementary photochemical events. The azobenzene trans → cis isomerization following entangled two-photon excitation is simulated using quantum nuclear wave packet dynamics. Photon entanglement modulates the nuclear wave packets by coherently controlling the transition pathways. The photochemical transition state during passage of the reactive conical intersection in azobenzene photoisomerization is strongly affected with a noticeable alteration of the product yield. Quantum entanglement thus provides a novel control knob for photochemical reactions. The distribution of the vibronic coherences during the conical intersection passage strongly depends on the shape of the initial wave packet created upon quantum light excitation. X-ray signals that can experimentally monitor this coherence are simulated.

Imaging conical intersection dynamics during azobenzene photoisomerization by ultrafast X-ray diffraction.

X-ray diffraction is routinely used for structure determination of stationary molecular samples. Modern X-ray photon sources, e.g., from free-electron lasers, enable us to add temporal resolution to these scattering events, thereby providing a movie of atomic motions. We simulate and decipher the various contributions to the X-ray diffraction pattern for the femtosecond isomerization of azobenzene, a textbook photochemical process. A wealth of information is encoded besides real-time monitoring of the molecular charge density for the cis to trans isomerization. In particular, vibronic coherences emerge at the conical intersection, contributing to the total diffraction signal by mixed elastic and inelastic photon scattering. They cause distinct phase modulations in momentum space, which directly reflect the real-space phase modulation of the electronic transition density during the nonadiabatic passage. To overcome the masking by the intense elastic scattering contributions from the electronic populations in the total diffraction signal, we discuss how this information can be retrieved, e.g., by employing very hard X-rays to record large scattering momentum transfers.

Unveiling the spatial distribution of molecular coherences at conical intersections by covariance X-ray diffraction signals.

The outcomes and timescales of molecular nonadiabatic dynamics are decisively impacted by the quantum coherences generated at localized molecular regions. In time-resolved X-ray diffraction imaging, these coherences create distinct signatures via inelastic photon scattering, but they are buried under much stronger background elastic features. Here, we exploit the rich dynamical information encoded in the inelastic patterns, which we reveal by frequency-dispersed covariance ultrafast powder X-ray diffraction of stochastic X-ray free-electron laser pulses. This is demonstrated for the photoisomerization of azobenzene involving the passage through a conical intersection, where the nuclear wave packet branches and explores different quantum pathways. Snapshots of the coherence dynamics are obtained at high frequency shifts, not accessible with conventional diffraction measurements. These provide access to the timing and to the confined spatial distribution of the valence electrons directly involved in the conical intersection passage. This study can be extended to full three-dimensional imaging of conical intersections with ultrafast X-ray and electron diffraction.

Manipulating Attosecond Charge Migration in Molecules by Optical Cavities.

The ultrafast electronic charge dynamics in molecules upon photoionization while the nuclear motions are frozen is known as charge migration. In a theoretical study of the quantum dynamics of photoionized 5-bromo-1-pentene, we show that the charge migration process can be induced and enhanced by placing the molecule in an optical cavity, and can be monitored by time-resolved photoelectron spectroscopy. The collective nature of the polaritonic charge migration process is investigated. We find that, unlike spectroscopy, molecular charge dynamics in a cavity is local and does not show many-molecule collective effects. The same conclusion applies to cavity polaritonic chemistry.

X-ray and Optical Circular Dichroism as Local and Global Ultrafast Chiral Probes of [12]Helicene Racemization.

Chirality is a fundamental molecular property that plays a crucial role in biophysics and drug design. Optical circular dichroism (OCD) is a well-established chiral spectroscopic probe in the UV-visible regime. Chirality is most commonly associated with a localized chiral center. However, some compounds such as helicenes (Figure 1) are chiral due to their screwlike global structure. In these highly conjugated systems, some electric and magnetic allowed transitions are distributed across the entire molecule, and OCD thus probes the global molecular chirality. Recent advances in X-ray sources, in particular the control of their polarization and spatial profiles, have enabled X-ray circular dichroism (XCD), which, in contrast to OCD, can exploit the localized and element-specific nature of X-ray electronic transitions. XCD therefore is more sensitive to local structures, and the chirality probed with it can be referred to as local. During the racemization of helicene, between opposite helical structures, the screw handedness can flip locally, making the molecule globally achiral while retaining a local handedness. Here, we use the racemization mechanism of [12]helicene as a model to demonstrate the capabilities of OCD and XCD as time-dependent probes for global and local chiralities, respectively. Our simulations demonstrate that XCD provides an excellent spectroscopic probe for the time-dependent local chirality of molecules.