Monitoring conical intersections in the ring opening of furan by attosecond stimulated X-ray Raman spectroscopy.

Attosecond X-ray pulses are short enough to capture snapshots of molecules undergoing nonadiabatic electron and nuclear dynamics at conical intersections (CoIns). We show that a stimulated Raman probe induced by a combination of an attosecond and a femtosecond pulse has a unique temporal and spectral resolution for probing the nonadiabatic dynamics and detecting the ultrafast (∼4.5 fs) passage through a CoIn. This is demonstrated by a multiconfigurational self-consistent-field study of the dynamics and spectroscopy of the furan ring-opening reaction. Trajectories generated by surface hopping simulations were used to predict Attosecond Stimulated X-ray Raman Spectroscopy signals at reactant and product structures as well as representative snapshots along the conical intersection seam. The signals are highly sensitive to the changes in nonadiabatically coupled electronic structure and geometry.

Characterizing the Intermediates Compound I and II in the Cytochrome P450 Catalytic Cycle with Nonlinear X-ray Spectroscopy: A Simulation Study.

Cytochrome P450 enzymes are an important family of biocatalysts that oxidize chemically inert CH bonds. There are many unresolved questions regarding the catalytic reaction intermediates, in particular P450 Compound I (Cpd-I) and II (Cpd-II). By using simple molecular models, we simulate various X-ray spectroscopy signals, including X-ray absorption near-edge structure (XANES), resonant inelastic X-ray scattering (RIXS), and stimulated X-ray Raman spectroscopy (SXRS) of the low- and high-spin states of Cpd-I and II. Characteristic peak patterns are presented and connected to the corresponding electronic structures. These X-ray spectroscopy techniques are complementary to more conventional infrared and optical spectroscopy and they help to elucidate the evolving electronic structures of transient species along the reaction path.

Monitoring Long-Range Electron Transfer Pathways in Proteins by Stimulated Attosecond Broadband X-ray Raman Spectroscopy.

Long-range electron transfer (ET) is a crucial step in many energy conversion processes and biological redox reactions in living organisms. We show that newly developed X-ray pulses can directly probe the evolving oxidation states and the electronic structure around selected atoms with detail not available through conventional time-resolved infrared or optical techniques. This is demonstrated in a simulation study of the stimulated X-ray Raman (SXRS) signals in Re-modified azurin, which serves as a benchmark system for photoinduced ET in proteins. Nonlinear SXRS signals offer a direct novel window into the long-range ET mechanism.

Three-dimensional attosecond resonant stimulated X-ray Raman spectroscopy of electronic excitations in core-ionized glycine.

We investigate computationally the valence electronic excitations of the amino acid glycine prepared by a sudden nitrogen core ionization induced by an attosecond X-ray pump pulse. The created superposition of cationic excited states is probed by two-dimensional transient X-ray absorption and by three dimensional attosecond stimulated X-ray Raman signals. The latter, generated by applying a second broadband X-ray pulse combined with a narrowband pulse tuned to the carbon K-edge, reveal the complex coupling between valence and core-excited manifolds of the cation.

Femtosecond stimulated Raman spectroscopy of the cyclobutane thymine dimer repair mechanism: a computational study.

Cyclobutane thymine dimer, one of the major lesions in DNA formed by exposure to UV sunlight, is repaired in a photoreactivation process, which is essential to maintain life. The molecular mechanism of the central step, i.e., intradimer C-C bond splitting, still remains an open question. In a simulation study, we demonstrate how the time evolution of characteristic marker bands (C═O and C═C/C-C stretch vibrations) of cyclobutane thymine dimer and thymine dinucleotide radical anion, thymidylyl(3'→5')thymidine, can be directly probed with femtosecond stimulated Raman spectroscopy (FSRS). We construct a DFT(M05-2X) potential energy surface with two minor barriers for the intradimer C5-C5' splitting and a main barrier for the C6-C6' splitting, and identify the appearance of two C5═C6 stretch vibrations due to the C6-C6' splitting as a spectroscopic signature of the underlying bond splitting mechanism. The sequential mechanism shows only absorptive features in the simulated FSRS signals, whereas the fast concerted mechanism shows characteristic dispersive line shapes.

Understanding Excitation Energy Transfer in Metalloporphyrin Heterodimers with Different Linkers, Bonding Structures and Geometries through Stimulated X-Ray Raman Spectroscopy.

We present simulations of stimulated X-ray Raman (SXRS) signals from covalent porphyrin heterodimers with different linkers, chemical bonding structures and geometries. The signals are interpreted in terms of valence electron wavepacket motion. One- and two-color SXRS signals can jointly indicate excitation energy transfer (EET) between the porphyrin monomers. It is shown that the SXRS signals provide a novel window into EET dynamics in multiporphyrin systems, and can be used as a powerful tool to monitor the subtle chemical environment which affects EET.

Time-, frequency-, and wavevector-resolved x-ray diffraction from single molecules.

Using a quantum electrodynamic framework, we calculate the off-resonant scattering of a broadband X-ray pulse from a sample initially prepared in an arbitrary superposition of electronic states. The signal consists of single-particle (incoherent) and two-particle (coherent) contributions that carry different particle form factors that involve different material transitions. Single-molecule experiments involving incoherent scattering are more influenced by inelastic processes compared to bulk measurements. The conditions under which the technique directly measures charge densities (and can be considered as diffraction) as opposed to correlation functions of the charge-density are specified. The results are illustrated with time- and wavevector-resolved signals from a single amino acid molecule (cysteine) following an impulsive excitation by a stimulated X-ray Raman process resonant with the sulfur K-edge. Our theory and simulations can guide future experimental studies on the structures of nano-particles and proteins.

Two-dimensional x-ray correlation spectroscopy of remote core states.

Nonlinear all-X-ray signals that involve large core-atom separation compared to the X-ray wavelengths may not be described by the dipole approximation since they contain additional phase factors. Expressions for the rotationally averaged 2D X-ray photon echo signals from randomly oriented systems that take this position-dependent phase into account for arbitrary ratio between the core separation and the resonant wavelength are presented. Application is made to the Se K-edge of a selenium dipeptide system.

Multiple Core and Vibronic Coupling Effects in Attosecond Stimulated X-Ray Raman Spectroscopy (SXRS).

Attosecond Stimulated X-ray Raman Spectroscopy (SXRS) is a promising technique for investigating molecular electronic structure and photochemical processes with high spatial and temporal resolution. We present a theoretical study of SXRS from multiple core excitation sites of the same element. Two issues are addressed: interference between pathways contributing the signals from different sites; and how nuclear vibrations influence the signals. Taking furan as a model system, which contains two types of carbons Cα and Cß, we performed time-dependent density functional theory calculations and computed the SXRS signals with two pulses tuned at the carbon K-edge. Our simulations demonstrate that the SXRS signal from the Cα and Cß sites are non-additive, owing to the significant mixed contributions (Cα 1s excitations by the pump pulse followed by Cß 1s excitations by the probe, or vice verse). Harmonic vibrations linearly coupled to the electronic transitions are incorporated using the cumulant expansion. The nuclei act as a bath for electronic transitions which accelerate the decay of time-domain signal. The frequency-domain spectrum is modified by a small red shift and high-resolution fine-structure features are introduced.

Simulations of Two-dimensional Infrared and Stimulated Resonance Raman Spectra of Photoactive Yellow Protein.

We present simulations of one and two-dimensional infrared (2DIR) and stimulated resonance Raman (SRR) spectra of the dark state (pG) and early red-shifted intermediate (pR) of photoactive yellow protein (PYP). Shifts in the amide I and Glu46 COOH stretching bands distinguish between pG and pR in the IR absorption and 2DIR spectra. The one-dimensional SRR spectra are similar to the spontaneous RR spectra. The two-dimensional SRR spectra show large changes in cross peaks involving the C=O stretch of the two species and are more sensitive to the chromophore structure than 2DIR spectra.

Two-dimensional stimulated resonance Raman spectroscopy study of the Trp-cage peptide folding.

We report a combined molecular dynamics (MD) and ab initio simulation study of the ultrafast broadband ultraviolet (UV) stimulated resonance Raman (SRR) spectra of the Trp-cage mini protein. Characteristic two dimensional (2D) SRR features of various folding states are identified. Structural fluctuations erode the cross peaks and the correlation between diagonal peaks is a good indicator of the α-helix formation.

Watching energy transfer in metalloporphyrin heterodimers using stimulated X-ray Raman spectroscopy.

Understanding the excitation energy transfer mechanism in multiporphyrin arrays is key for designing artificial light-harvesting devices and other molecular electronics applications. Simulations of the stimulated X-ray Raman spectroscopy signals of a Zn/Ni porphyrin heterodimer induced by attosecond X-ray pulses show that these signals can directly reveal electron-hole pair motions. These dynamics are visualized by a natural orbital decomposition of the valence electron wavepackets.

Two-Dimensional Stimulated Ultraviolet Resonance Raman Spectra of Tyrosine and Tryptophan; A Simulation Study.

We report an ab-initio simulation study of the ultrafast broad bandwidth ultraviolet (UV) stimulated resonance Raman spectra (SRRS) of L-tyrosine, L-tryptophan and trans-L-tryptophan-L-tyrosine (WY) dipeptide. Two-pulse one-dimensional (1D) SRRS and three-pulse 2D SRRS that reveal inter- and intra-residue vibrational coorelations are simulated using electronically resonant or preresonant pulse configurations that select the Raman signal and discriminate against excited state pathways. Multimode effects are incorporated via the cumulant expansion. The 2D SRRS technique is more sensitive to residue couplings than spontaneous Raman.

Double-core excitations in formamide can be probed by X-ray double-quantum-coherence spectroscopy.

The attosecond, time-resolved X-ray double-quantum-coherence four-wave mixing signals of formamide at the nitrogen and oxygen K-edges are simulated using restricted excitation window time-dependent density functional theory and the excited core hole approximation. These signals, induced by core exciton coupling, are particularly sensitive to the level of treatment of electron correlation, thus providing direct experimental signatures of electron and core-hole many-body effects and a test of electronic structure theories.

Multidimensional x-ray spectroscopy of valence and core excitations in cysteine.

Several nonlinear spectroscopy experiments which employ broadband x-ray pulses to probe the coupling between localized core and delocalized valence excitation are simulated for the amino acid cysteine at the K-edges of oxygen and nitrogen and the K- and L-edges of sulfur. We focus on two-dimensional (2D) and 3D signals generated by two- and three-pulse stimulated x-ray Raman spectroscopy (SXRS) with frequency-dispersed probe. We show how the four-pulse x-ray signals [Formula: see text] and [Formula: see text] can give new 3D insight into the SXRS signals. The coupling between valence- and core-excited states can be visualized in three-dimensional plots, revealing the origin of the polarizability that controls the simpler pump-probe SXRS signals.

Multidimensional attosecond resonant X-ray spectroscopy of molecules: lessons from the optical regime.

New free-electron laser and high-harmonic generation X-ray light sources are capable of supplying pulses short and intense enough to perform resonant nonlinear time-resolved experiments in molecules. Valence-electron motions can be triggered impulsively by core excitations and monitored with high temporal and spatial resolution. We discuss possible experiments that employ attosecond X-ray pulses to probe the quantum coherence and correlations of valence electrons and holes, rather than the charge density alone, building on the analogy with existing studies of vibrational motions using femtosecond techniques in the visible regime.

Core and valence excitations in resonant X-ray spectroscopy using restricted excitation window time-dependent density functional theory.

We report simulations of X-ray absorption near edge structure (XANES), resonant inelastic X-ray scattering (RIXS) and 1D stimulated X-ray Raman spectroscopy (SXRS) signals of cysteine at the oxygen, nitrogen, and sulfur K and L(2,3) edges. Comparison of the simulated XANES signals with experiment shows that the restricted window time-dependent density functional theory is more accurate and computationally less expensive than the static exchange method. Simulated RIXS and 1D SXRS signals give some insights into the correlation of different excitations in the molecule.

Coherent nonlinear optical studies of elementary processes in biological complexes: diagrammatic techniques based on the wave function versus the density matrix.

Two types of diagrammatic approaches for the design and simulation of nonlinear optical experiments (closed-time path loops based on the wave function and double-sided Feynman diagrams for the density matrix) are presented and compared. We give guidelines for the assignment of relevant pathways and provide rules for the interpretation of existing nonlinear experiments in carotenoids.

Two-dimensional stimulated resonance Raman spectroscopy of molecules with broadband x-ray pulses.

Expressions for the two-dimensional stimulated x-ray Raman spectroscopy (2D-SXRS) signal obtained using attosecond x-ray pulses are derived. The 1D- and 2D-SXRS signals are calculated for trans-N-methyl acetamide (NMA) with broad bandwidth (181 as, 14.2 eV FWHM) pulses tuned to the oxygen and nitrogen K-edges. Crosspeaks in 2D signals reveal electronic Franck-Condon overlaps between valence orbitals and relaxed orbitals in the presence of the core-hole.

Studies of impulsive vibrational influence on ultrafast electronic excitation transfer.

We investigated electronic energy-transfer dynamics in three model dimers within which coherent intramonomer nuclear motion had been induced by impulsive Raman excitation using an optimized, electronically preresonant control pulse. Calculations of the donor-survival probability, the ultrafast pump-probe signal, and the pump-probe difference signal are presented for dithia-anthracenophane and homodimers of 2-difluoromethylanthracene and 2-trifluoromethylanthracene. Survival probabilities and signals, along with phase-space analyses, elucidated the mechanisms, extent, and spectroscopic manifestations of external vibrational or torsional control over electronic excitation transfer.