Ultrafast terahertz Stark spectroscopy reveals the excited-state dipole moments of retinal in bacteriorhodopsin.

The photoinduced all-trans to 13-cis isomerization of the retinal Schiff base represents the ultrafast first step in the reaction cycle of bacteriorhodopsin (BR). Extensive experimental and theoretical work has addressed excited-state dynamics and isomerization via a conical intersection with the ground state. In conflicting molecular pictures, the excited state potential energy surface has been modeled as a pure S[Formula: see text] state that intersects with the ground state, or in a 3-state picture involving the S[Formula: see text] and S[Formula: see text] states. Here, the photoexcited system passes two crossing regions to return to the ground state. The electric dipole moment of the Schiff base in the S[Formula: see text] and S[Formula: see text] state differs strongly and, thus, its measurement allows for assessing the character of the excited-state potential. We apply the method of ultrafast terahertz (THz) Stark spectroscopy to measure electric dipole changes of wild-type BR and a BR D85T mutant upon electronic excitation. A fully reversible transient broadening and spectral shift of electronic absorption is induced by a picosecond THz field of several megavolts/cm and mapped by a 120-fs optical probe pulse. For both BR variants, we derive a moderate electric dipole change of 5 [Formula: see text] 1 Debye, which is markedly smaller than predicted for a neat S[Formula: see text]-character of the excited state. In contrast, S[Formula: see text]-admixture and temporal averaging of excited-state dynamics over the probe pulse duration gives a dipole change in line with experiment. Our results support a picture of electronic and nuclear dynamics governed by the interaction of S[Formula: see text] and S[Formula: see text] states in a 3-state model.

Terahertz Polaron Oscillations of Electrons Solvated in Liquid Water.

The terahertz (THz) response of solvated electrons in liquid water is studied in nonlinear ultrafast pump-probe experiments. Free electrons with concentrations from c_{e}=4 to 140×10^{-6} moles/liter are generated by high-field THz or near-infrared multiphoton excitation. The time-resolved change of the dielectric function as mapped by broadband THz pulses exhibits pronounced oscillations persisting up to 30 ps. Their frequency increases with electron concentration from 0.2 to 1.5 THz. The oscillatory response is assigned to impulsively excited coherent polarons involving coupled electron and water shell motions with a frequency set by the local electric field.

Infrared and NMR Spectroscopic Fingerprints of the Asymmetric H7+ O3 Complex in Solution.

Infrared (IR) absorption in the 1000-3700 cm-1 range and 1 H NMR spectroscopy reveal the existence of an asymmetric protonated water trimer, H7+ O3, in acetonitrile. The core H7+ O3 motif persists in larger protonated water clusters in acetonitrile up to at least 8 water molecules. Quantum mechanics/molecular mechanics (QM/MM) molecular dynamics (MD) simulations reveal irreversible proton transport promoted by propagating the asymmetric H7+ O3 structure in solution. The QM/MM calculations allow for the successful simulation of the measured IR absorption spectra of H7+ O3 in the OH stretch region, which reaffirms the assignment of the H7+ O3 spectra to a hybrid-complex structure: a protonated water dimer strongly hydrogen-bonded to a third water molecule with the proton exchanging between the two possible shared-proton Zundel-like centers. The H7+ O3 structure lends itself to promoting irreversible proton transport in presence of even one additional water molecule. We demonstrate how continuously evolving H7+ O3 structures may support proton transport within larger water solvates.

Infrared and NMR Spectroscopic Fingerprints of the Asymmetric H7 + O3 Complex in Solution.

The front cover artwork is provided by the groups of Prof. Ehud Pines (BGU, Israel) and Dr. Benjamin Fingerhut (MBI, Berlin). The image shows a scientist integrating experiments with theory for resolving the structural diffusion of the aqueous proton in acetonitrile providing a novel view on the Grotthuss mechanism. Read the full text of the Article at 10.1002/cphc.202001046.

On the role of non-diagonal system-environment interactions in bridge-mediated electron transfer.

Bridge-mediated electron transfer (ET) between a donor and an acceptor is prototypical for the description of numerous most important ET scenarios. While multi-step ET and the interplay of sequential and direct superexchange transfer pathways in the donor-bridge-acceptor (D-B-A) model are increasingly understood, the influence of off-diagonal system-bath interactions on the transfer dynamics is less explored. Off-diagonal interactions account for the dependence of the ET coupling elements on nuclear coordinates (non-Condon effects) and are typically neglected. Here, we numerically investigate with quasi-adiabatic propagator path integral simulations the impact of off-diagonal system-environment interactions on the transfer dynamics for a wide range of scenarios in the D-B-A model. We demonstrate that off-diagonal system-environment interactions can have profound impact on the bridge-mediated ET dynamics. In the considered scenarios, the dynamics itself does not allow for a rigorous assignment of the underlying transfer mechanism. Furthermore, we demonstrate how off-diagonal system-environment interaction mediates anomalous localization by preventing long-time depopulation of the bridge B and how coherent transfer dynamics between donor D and acceptor A can be facilitated. The arising non-exponential short-time dynamics and coherent oscillations are interpreted within an equivalent Hamiltonian representation of a primary reaction coordinate model that reveals how the complex vibronic interplay of vibrational and electronic degrees of freedom underlying the non-Condon effects can impose donor-to-acceptor coherence transfer on short timescales.

Regulatory Impact of the C-Terminal Tail on Charge Transfer Pathways in Drosophila Cryptochrome.

Interconnected transcriptional and translational feedback loops are at the core of the molecular mechanism of the circadian clock. Such feedback loops are synchronized to external light entrainment by the blue light photoreceptor cryptochrome (CRY) that undergoes conformational changes upon light absorption by an unknown photoexcitation mechanism. Light-induced charge transfer (CT) reactions in Drosophila CRY (dCRY) are investigated by state-of-the-art simulations that reveal a complex, multi-redox site nature of CT dynamics on the microscopic level. The simulations consider redox-active chromophores of the tryptophan triad (Trp triad) and further account for pathways mediated by W314 and W422 residues proximate to the C-terminal tail (CTT), thus avoiding a pre-bias to specific W-mediated CT pathways. The conducted dissipative quantum dynamics simulations employ microscopically derived model Hamiltonians and display complex and ultrafast CT dynamics on the picosecond timescale, subtly balanced by the electrostatic environment of dCRY. In silicio point mutations provide a microscopic basis for rationalizing particular CT directionality and demonstrate the degree of electrostatic control realized by a discrete set of charged amino acid residues. The predicted participation of CT states in proximity to the CTT relates the directionality of CT reactions to the spatial vicinity of a linear interaction motif. The results stress the importance of CTT directional charge transfer in addition to charge transfer via the Trp triad and call for the use of full-length CRY models including the interactions of photolyase homology region (PHR) and CTT domains.

Coupled excitation energy and charge transfer dynamics in reaction centre inspired model systems.

Functional operation conditions of reaction centre core complexes require the tight coupling of exciton states to concomitant charge separation. Rigorous theoretical treatment of such integrated excitation energy transfer (EET) and charge transfer (CT) dynamics is particularly challenging due to (i) appreciable system sizes, (ii) inter-site and system-bath couplings of similar magnitude that render the Born-Markov approximation invalid, (iii) substantial reorganization energies of CT states, and (iv) the presence of complex structured spectral densities due to vibrational modes of the surroundings. We present numerical simulations on bacterial reaction centre (bRC) inspired model systems that utilize the recently developed MACGIC-iQUAPI method [Richter et al., J. Chem. Phys., 2017, 146, 214101]. The simulations demonstrate that the method provides a rigorous framework for the investigation of such integrated EET-CT dynamics. First, the applicability of the MACGIC-iQUAPI method is explored for a transition from monotonically decaying to oscillatory system-bath influence coefficients, a behavior inherently imposed by structured bath spectral densities. Tightly coupled EET and CT dynamics is further addressed for an excitonic subsystem that resembles strong coupling of special pair states and serves as donor towards a generic bridge-acceptor system. By solving the dissipative quantum dynamics of such bRC inspired model systems, the quenching of excitonic coherence on the hundreds of femtoseconds timescale is explored via a variation of the bridge state energetics, resembling a continuous transition from sequential to superexchange mediated CT regimes. Further, the simulations explore the influence of resonant vibrational modes on the quenching of excitonic coherence via CT. The results reveal a moderate influence of vibrational mode on charge separation dynamics in regimes of biologically relevant EET and CT dynamics.

Simulating Coherent Multidimensional Spectroscopy of Nonadiabatic Molecular Processes: From the Infrared to the X-ray Regime.

Crossings of electronic potential energy surfaces in nuclear configuration space, known as conical intersections, determine the rates and outcomes of a large class of photochemical molecular processes. Much theoretical progress has been made in computing strongly coupled electronic and nuclear motions at different levels, but how to incorporate them in different spectroscopic signals and the approximations involved are less established. This will be the focus of the present review. We survey a wide range of time-resolved spectroscopic techniques which span from the infrared to the X-ray regimes and can be used for probing the nonadiabatic dynamics in the vicinity of conical intersections. Transient electronic and vibrational probes and their theoretical signal calculations are classified by their information content. This includes transient vibrational spectroscopic methods (transient infrared and femtosecond off-resonant stimulated Raman), resonant electronic probes (transient absorption and photoelectron spectroscopy), and novel stimulated X-ray Raman techniques. Along with the precise definition of what to calculate for predicting the various signals, we outline a toolbox of protocols for their simulation.

Decay Pathways of Thymine Revisited.

The decay of electronically excited states of thymine (Thy) and thymidine 5'-monophosphate (TMP) was studied by time-resolved UV/vis and IR spectroscopy. In addition to the well-established ultrafast internal conversion to the ground state, a so far unidentified UV-induced species is observed. In D2O, this species decays with a time constant of 300 ps for thymine and of 1 ns for TMP. The species coexists with the lowest triplet state and is formed with a comparably high quantum yield of about 10% independent of the solvent. The experimentally determined spectral signatures are discussed in the light of quantum chemical calculations of the singlet and triplet excited states of thymine.

Coarse-grained representation of the quasi adiabatic propagator path integral for the treatment of non-Markovian long-time bath memory.

The description of non-Markovian effects imposed by low frequency bath modes poses a persistent challenge for path integral based approaches like the iterative quasi-adiabatic propagator path integral (iQUAPI) method. We present a novel approximate method, termed mask assisted coarse graining of influence coefficients (MACGIC)-iQUAPI, that offers appealing computational savings due to substantial reduction of considered path segments for propagation. The method relies on an efficient path segment merging procedure via an intermediate coarse grained representation of Feynman-Vernon influence coefficients that exploits physical properties of system decoherence. The MACGIC-iQUAPI method allows us to access the regime of biological significant long-time bath memory on the order of hundred propagation time steps while retaining convergence to iQUAPI results. Numerical performance is demonstrated for a set of benchmark problems that cover bath assisted long range electron transfer, the transition from coherent to incoherent dynamics in a prototypical molecular dimer and excitation energy transfer in a 24-state model of the Fenna-Matthews-Olson trimer complex where in all cases excellent agreement with numerically exact reference data is obtained.

The Hydrated Excess Proton in the Zundel Cation H5 O2 (+) : The Role of Ultrafast Solvent Fluctuations.

The nature of the excess proton in liquid water has remained elusive after decades of extensive research. In view of ultrafast structural fluctuations of bulk water scrambling the structural motifs of excess protons in water, we selectively probe prototypical protonated water solvates in acetonitrile on the femtosecond time scale. Focusing on the Zundel cation H5 O2 (+) prepared in room-temperature acetonitrile, we unravel the distinct character of its vibrational absorption continuum and separate it from OH stretching and bending excitations in transient pump-probe spectra. The infrared absorption continuum originates from a strong ultrafast frequency modulation of the H(+) transfer vibration and its combination and overtones. Vibrational lifetimes of H5 O2 (+) are found to be in the sub-100 fs range, much shorter than those of unprotonated water. Theoretical results support a picture of proton hydration where fluctuating electrical interactions with the solvent and stochastic thermal excitations of low-frequency modes continuously modify the proton binding site while affecting its motions.

Anharmonicities and coherent vibrational dynamics of phosphate ions in bulk H2O.

Phosphates feature prominently in the energetics of metabolism and are important solvation sites of DNA and phospholipids. Here we investigate the ion H2PO4(-) in aqueous solution combining 2D IR spectroscopy of phosphate stretching vibrations in the range from 900-1300 cm(-1) with ab initio calculations and hybrid quantum-classical molecular dynamics based simulations of the non-linear signal. While the line shapes of diagonal peaks reveal ultrafast frequency fluctuations on a sub-100 fs timescale caused by the fluctuating hydration shell, an analysis of the diagonal and cross-peak frequency positions allows for extracting inter-mode couplings and anharmonicities of 5-10 cm(-1). The excitation with spectrally broad pulses generates a coherent superposition of symmetric and asymmetric PO2(-) stretching modes resulting in the observation of a quantum beat in aqueous solution. We follow its time evolution through the time-dependent amplitude and the shape of the cross peaks. The results provide a complete characterization of the H2PO4(-) vibrational Hamiltonian including fluctuations induced by the native water environment.

Spectral lineshapes in nonlinear electronic spectroscopy.

We outline a computational approach for nonlinear electronic spectra, which accounts for the electronic energy fluctuations due to nuclear degrees of freedom and explicitly incorporates the fluctuations of higher excited states, induced by the dynamics in the photoactive state(s). This approach is based on mixed quantum-classical dynamics simulations. Tedious averaging over multiple trajectories is avoided by employing the linearly displaced Brownian harmonic oscillator to model the correlation functions. The present strategy couples accurate computations of the high-lying excited state manifold with dynamics simulations. The application is made to the two-dimensional electronic spectra of pyrene, a polycyclic aromatic hydrocarbon characterized by an ultrafast (few tens of femtoseconds) decay from the bright S2 state to the dark S1 state. The spectra for waiting times t2 = 0 and t2 = 1 ps demonstrate the ability of this approach to model electronic state fluctuations and realistic lineshapes. Comparison with experimental spectra [Krebs et al., New Journal of Physics, 2013, 15, 085016] shows excellent agreement and allows us to unambiguously assign the excited state absorption features.

Ultrafast phosphate hydration dynamics in bulk H2O.

Phosphate vibrations serve as local probes of hydrogen bonding and structural fluctuations of hydration shells around ions. Interactions of H2PO4(-) ions and their aqueous environment are studied combining femtosecond 2D infrared spectroscopy, ab-initio calculations, and hybrid quantum-classical molecular dynamics (MD) simulations. Two-dimensional infrared spectra of the symmetric (νS(PO2(-))) and asymmetric (νAS(PO2(-))) PO2(-) stretching vibrations display nearly homogeneous lineshapes and pronounced anharmonic couplings between the two modes and with the δ(P-(OH)2) bending modes. The frequency-time correlation function derived from the 2D spectra consists of a predominant 50 fs decay and a weak constant component accounting for a residual inhomogeneous broadening. MD simulations show that the fluctuating electric field of the aqueous environment induces strong fluctuations of the νS(PO2(-)) and νAS(PO2(-)) transition frequencies with larger frequency excursions for νAS(PO2(-)). The calculated frequency-time correlation function is in good agreement with the experiment. The ν(PO2(-)) frequencies are mainly determined by polarization contributions induced by electrostatic phosphate-water interactions. H2PO4(-)/H2O cluster calculations reveal substantial frequency shifts and mode mixing with increasing hydration. Predicted phosphate-water hydrogen bond (HB) lifetimes have values on the order of 10 ps, substantially longer than water-water HB lifetimes. The ultrafast phosphate-water interactions observed here are in marked contrast to hydration dynamics of phospholipids where a quasi-static inhomogeneous broadening of phosphate vibrations suggests minor structural fluctuations of interfacial water.

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.

A comprehensive microscopic picture of the benzhydryl radical and cation photogeneration and interconversion through electron transfer.

Bond cleavage and bond formation are central to organic chemistry. Carbocations play a key role in our understanding of nucleophilic substitution reactions that involve both processes. The precise understanding of the mechanism and dynamics of the photogeneration of carbocations and carbon radicals is therefore an important quest. In particular, the role of electron transfer for the generation of carbocations from the radical pair is still unclear. A quantitative femtosecond absorption study is presented, with ultrabroad probing on selected donor and acceptor substituted benzhydryl chlorides irradiated with 270 nm (35 fs) pulses. The ultrafast bond cleavage within 300 fs is almost exclusively homolytic, thus leading to a radical pair. The carbocations observable in the nanosecond regime are generated from these radicals by electron transfer from the benzhydryl to the chlorine radical within the first tens of picoseconds. Their concentration is reduced by geminate recombination within hundreds of picoseconds. In moderately polar solvents this depletion almost extinguishes the cation population; in highly polar solvents free ions are still observable on the nanosecond timescale. The explanation of the experimental findings requires the microscopic realm of the intermediates to be accounted for, including their spatial and environmental distributions. The distance dependent electron transfer described by Marcus theory is combined with Smoluchowski diffusion. The depletion of the radical pair distribution at small distances causes a temporal increase of the mean distance and the observed stretched exponential electron transfer. A close accord with experiment can only be reached for a broad distribution of the nascent radical pairs. The increase in the inter-radical and inter-ion pair distance is measured directly as a shift of the UV/Vis absorption of the products. The results demonstrate that, at least for aprotic solvents, traditional descriptions of reaction mechanisms based on the concept of contact and solvent-separated pairs have to be reassessed.

Broadband infrared and Raman probes of excited-state vibrational molecular dynamics: simulation protocols based on loop diagrams.

Vibrational motions in electronically excited states can be observed either by time and frequency resolved infrared absorption or by off resonant stimulated Raman techniques. Multipoint correlation function expressions are derived for both signals. Three representations which suggest different simulation protocols for the signals are developed. These are based on the forward and the backward propagation of the wavefunction, sum over state expansion using an effective vibrational Hamiltonian or a semiclassical treatment of a bath. We show that the effective temporal (Δt) and spectral (Δω) resolution of the techniques is not controlled solely by experimental knobs but also depends on the system dynamics being probed. The Fourier uncertainty ΔωΔt > 1 is never violated.

Time resolved photoelectron spectroscopy of thioflavin T photoisomerization: a simulation study.

The excited state isomerization of thioflavin T (ThT) is responsible for the quenching of its fluorescence in a nonrestricted environment. The fluorescence quantum yield increases substantially upon binding to amyloid fibers. Simulations reveal that the variation of the twisting angle between benzothiazole and benzene groups (φ1) is responsible for the subpicosecond fluorescence quenching. The evolution of the twisting process can be directly probed by photoelectron emission with energies ε ≥ 1.0 eV before the molecule reaches the φ1-twisted configuration (~300 fs).

Ground and excited state surfaces for the photochemical bond cleavage in phenylmethylphenylphosphonium ions.

Photolytic bond cleavage is a well-established method to generate carbocations for organic synthesis. Changes in the leaving group have a large influence on the chemical yield. The underlying potential energy surfaces governing the initial process are mostly unknown. We provide potential energy surfaces of ground and excited states on the CASSCF/CASPT2 level of theory for the charged precursor phenylmethylphenylphosphonium ion. We present the electronic and structural changes accompanying the excitation process and the subsequent bond cleavage. Inter-ring charge-transfer processes play a crucial role in the Franck-Condon region. Beyond the Franck-Condon region, competing reaction pathways emerge connected through conical intersections. The phenylmethylphenylphosphonium ion is used as a model system for the commonly used diphenylmethyltriphenylphosphonium ion. The appropriateness of the model is tested by CC2 calculations of the excitation spectrum.

Time-resolved broadband Raman spectroscopies: a unified six-wave-mixing representation.

Excited-state vibrational dynamics in molecules can be studied by an electronically off-resonant Raman process induced by a probe pulse with variable delay with respect to an actinic pulse. We establish the connection between several variants of the technique that involve either spontaneous or stimulated Raman detection and different pulse configurations. By using loop diagrams in the frequency domain, we show that all signals can be described as six wave mixing which depend on the same four point molecular correlation functions involving two transition dipoles and two polarizabilities and accompanied by a different gating. Simulations for the stochastic two-state-jump model illustrate the origin of the absorptive and dispersive features observed experimentally.