Benjamin P. Fingerhut

Mechanism of UV-Induced Formation of Dewar Lesions in DNA †

The importance of a backbone: The mechanism of formation of Dewar lesions has been investigated by using femtosecond IR spectroscopy and ab initio calculations of the exited state. The 4π electrocyclization is rather slow, occurs with an unusual high quantum yield, and--surprisingly--is controlled by the phosphate backbone.

Probing the Conical Intersection Dynamics of the RNA Base Uracil by UV-Pump Stimulated-Raman-Probe Signals; Ab Initio Simulations

Nonadiabatic electron and nuclear dynamics of photoexcited molecules involving conical intersections is of fundamental importance in many reactions such as the self-protection mechanism of DNA and RNA bases against UV irradiation. Nonlinear vibrational spectroscopy can provide an ultrafast sensitive probe for these processes. We employ a simulation protocol that combines nonadiabatic on-the-fly molecular dynamics with a mode-tracking algorithm for the simulation of femtosecond stimulated Raman spectroscopy (SRS) signals of the high frequency C–H- and N–H-stretch vibrations of the photoexcited RNA base uracil. The simulations rely on a microscopically derived expression that takes into account the path integral of the excited state evolution and the pulse shapes. Analysis of the joint time/frequency resolution of the technique reveals a matter chirp contribution that limits the inherent temporal resolution. Characteristic signatures of relaxation dynamics mediated in the vicinity of conical intersection are predicted. The C–H and N–H spectator modes provide high sensitivity to their local environment and act as local probes with submolecular and high temporal resolution.

Suppression of population transport and control of exciton distributions by entangled photons.

Entangled photons provide an important tool for secure quantum communication, computing and lithography. Low intensity requirements for multi-photon processes make them idealy suited for minimizing damage in imaging applications. Here we show how their unique temporal and spectral features may be used in nonlinear spectroscopy to reveal properties of multiexcitons in chromophore aggregates. Simulations demostrate that they provide unique control tools for two-exciton states in the bacterial reaction centre of Blastochloris viridis. Population transport in the intermediate single-exciton manifold may be suppressed by the absorption of photon pairs with short entanglement time, thus allowing the manipulation of the distribution of two-exciton states. The quantum nature of the light is essential for achieving this degree of control, which cannot be reproduced by stochastic or chirped light. Classical light is fundamentally limited by the frequency-time uncertainty, whereas entangled photons have independent temporal and spectral characteristics not subjected to this uncertainty.

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.

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.

The Hydrated Excess Proton in the Zundel Cation H5O2+: 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.

ONIOM approach for non-adiabatic on-the-fly molecular dynamics demonstrated for the backbone controlled Dewar valence isomerization

Non-adiabatic on-the-fly molecular dynamics (NA-O-MD) simulations require the electronic wavefunction, energy gradients, and derivative coupling vectors in every timestep. Thus, they are commonly restricted to the excited state dynamics of molecules with up to ≈20 atoms. We discuss an approximation that combines the ONIOM(QM:QM) method with NA-O-MD simulations to allow calculations for larger molecules. As a proof of principle we present the excited state dynamics of a (6-4)-lesion containing dinucleotide (63 atoms), and especially the importance to include the confinement effects of the DNA backbone. The method is able to include electron correlation on a high level of theory and offers an attractive alternative to QM:MM approaches for moderate sized systems with unknown force fields.

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.

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.