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.

Sub-100-fs energy transfer in coenzyme NADH is a coherent process assisted by a charge-transfer state.

Excitation energy transfer (EET) is a key photoinduced process in biological chromophoric assemblies. Here we investigate the factors which can drive EET into efficient ultrafast sub-ps regimes. We demonstrate how a coherent transport of electronic population could facilitate this in water solvated NADH coenzyme and uncover the role of an intermediate dark charge-transfer state. High temporal resolution ultrafast optical spectroscopy gives a 54±11 fs time constant for the EET process. Nonadiabatic quantum dynamical simulations computed through the time-evolution of multidimensional wavepackets suggest that the population transfer is mediated by photoexcited molecular vibrations due to strong coupling between the electronic states. The polar aqueous solvent environment leads to the active participation of a dark charge transfer state, accelerating the vibronically coherent EET process in favorably stacked conformers and solvent cavities. Our work demonstrates how the interplay of structural and environmental factors leads to diverse pathways for the EET process in flexible heterodimers and provides general insights relevant for coherent EET processes in stacked multichromophoric aggregates like DNA strands.

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.

WFOT: A Wave Function Overlap Tool between Single- and Multi-Reference Electronic Structure Methods for Spectroscopy Simulation.

We report the development of a novel diagnostic tool, named wave function overlap tool (WFOT), designed to evaluate the overlap between wave functions computed at single-reference [i.e., time-dependent density functional theory or configuration interaction singles (CIS)] and multireference (i.e., CASSCF/CASPT2) electronic structure levels of theory. It relies on truncating the single- and multireference WFs to CIS-like expansions spanning the same configurational space and maximizing the molecular orbital overlap by means of a unitary transformation. To demonstrate the functionality of the tool, we calculate the transient spectrum of acetylacetone by evaluating excited state absorption signals with multireference quality on top of single-reference on-the-fly dynamics simulations. Semiautomatic spectra generation is facilitated by interfacing the tool with the COBRAMM package, which also allows one to use WFOT with several quantum chemistry codes such as Gaussian, NWChem, and OpenMolcas. Other exciting possibilities for the utilization of the code beyond the simulation of transient absorption spectroscopy are eventually discussed.

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.

Water Solvent Reorganization upon Ultrafast Resonant Stimulated X-ray Raman Excitation of a Metalloporphyrin Dimer.

We propose an X-ray Raman pump-X-ray diffraction probe scheme to follow solvation dynamics upon charge migration in a solute molecule. The X-ray Raman pump selectively prepares a valence electronic wavepacket in the solute, while the probe provides information about the entire molecular ensemble. A combination of molecular dynamics and ab initio quantum chemistry simulations is applied to a Zn-Ni porphyrin dimer in water. Using time-resolved X-ray diffraction and pair distribution functions, we extracted solvation shell dynamics.

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.

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.

Ionization Pathway Interference in Photoionization Time Delays in Molecules.

The photoionization time-delay in linear conjugated molecules is computed using the Wigner scattering approach. We find that, in general, there are two additive contributions to the ionization time-delays. One originates from interferences between various ionization pathways that belong to different cationic eigenstates, while the other is due to time delays associated with each pathway and originates due to electron-electron correlations in the molecule. The former contribution scales up rapidly with the conjugation length, leading to larger time delays, as observed in recent experiments, while the latter is much less sensitive to the molecular conjugation.

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.

Time-Resolved X-ray Absorption Spectroscopy: An MCTDH Quantum Dynamics Protocol.

Expressions for linear and nonlinear spectroscopy simulation in the X-ray window in which the time evolution of a photoexcited molecular system is treated via quantum dynamics are derived. By leveraging on the peculiar properties of core-excited/ionized states, first- and third-order response functions are recast in the limit of time-scale separation between the extremely short core-state lifetime and the (comparably longer) electronic-state transfer and nuclear vibrational motion. This work is a natural extension of Segatta et al. (J. Chem. Theory Comput. 2023, 19, 2075-2091), in which some of the present authors coupled MCTDH quantum dynamics to spectroscopy simulation at different levels of sophistication. Full quantum dynamics and approximate expressions are compared by simulating X-ray transient absorption spectroscopy at the carbon K-edge in the pyrene molecule.

Intraband Exciton Transitions in Photosynthetic Complexes Revealed by Novel Five-Wave-Mixing Spectroscopy.

We calculate the χ(4) optical response of an oriented photosystem II reaction center of purple bacteria described by the Frenkel exciton model using nonlinear exciton equations (NEE). This approach treats each chromophore as an anharmonic oscillator and provides an intuitive quasiparticle picture of nonlinear spectroscopic signals of interacting excitons. It provides a computationally powerful description of nonlinear spectroscopic signals that avoids complete diagonalization of the total Hamiltonian. Expressions for the second- and the fourth-order nonlinear signals are derived. The NEE have been successfully employed in the past to describe even-order-wave-mixing. Here, we extend them to aggregates with broken inversion symmetries. Even-order susceptibilities require the introduction of permanent dipoles, which allow to directly probe low-frequency intraband transitions of excitons.

Quantum Interferometric Pathway Selectivity in Difference-Frequency-Generation Spectroscopy.

Even-order spectroscopies such as sum-frequency generation (SFG) and difference-frequency generation (DFG) can serve as direct probes of molecular chirality. Such signals are usually given by the sum of several interaction pathways that carry different information about matter. Here we focus on DFG, involving impulsive optical-optical-IR interactions, where the last IR pulse probes vibrational transitions in the ground or excited electronic state manifolds, depending on the interaction pathway. Spectroscopy with classical light can use phase matching to select the two pathways. In this theoretical study, we propose a novel quantum interferometric protocol that uses entangled photons to isolate individual pathways. This additional selectivity originates from engineering the state of light using a Zou-Wang-Mandel interferometer combined with coincidence detection.

Time-resolved enantiomer-exchange probed by using the orbital angular momentum of X-ray light.

Molecular chirality, a geometric property of utmost importance in biochemistry, is now being investigated in the time-domain. Ultrafast chiral techniques can probe the formation or disappearance of stereogenic centers in molecules. The element-sensitivity of X-rays adds the capability to probe chiral nuclear dynamics locally within the molecular system. However, the implementation of ultrafast techniques for measuring transient chirality remains a challenge because of the intrinsic weakness of chiral-sensitive signals based on circularly polarized light. We propose a novel approach for probing the enantiomeric dynamics by using the orbital angular momentum (OAM) of X-ray light, which can directly monitor the real-time chirality of molecules. Our simulations probe the oscillations in excited chiral formamide on different potential energy surfaces and demonstrate that using the X-ray OAM can increase the measured asymmetry ratio. Moreover, combining the OAM and SAM (spin angular momentum) provides stronger dichroic signals than linearly polarized light, and offers a powerful scheme for chiral discrimination.

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.

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.

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.

NEXMD v2.0 Software Package for Nonadiabatic Excited State Molecular Dynamics Simulations.

We present NEXMD version 2.0, the second release of the NEXMD (Nonadiabatic EXcited-state Molecular Dynamics) software package. Across a variety of new features, NEXMD v2.0 incorporates new implementations of two hybrid quantum-classical dynamics methods, namely, Ehrenfest dynamics (EHR) and the Ab-Initio Multiple Cloning sampling technique for Multiconfigurational Ehrenfest quantum dynamics (MCE-AIMC or simply AIMC), which are alternative options to the previously implemented trajectory surface hopping (TSH) method. To illustrate these methodologies, we outline a direct comparison of these three hybrid quantum-classical dynamics methods as implemented in the same NEXMD framework, discussing their weaknesses and strengths, using the modeled photodynamics of a polyphenylene ethylene dendrimer building block as a representative example. We also describe the expanded normal-mode analysis and constraints for both the ground and excited states, newly implemented in the NEXMD v2.0 framework, which allow for a deeper analysis of the main vibrational motions involved in vibronic dynamics. Overall, NEXMD v2.0 expands the range of applications of NEXMD to a larger variety of multichromophore organic molecules and photophysical processes involving quantum coherences and persistent couplings between electronic excited states and nuclear velocity.