Step-by-step state-selective tracking of fragmentation dynamics of water dications by momentum imaging.

The double photoionization of a molecule by one photon ejects two electrons and typically creates an unstable dication. Observing the subsequent fragmentation products in coincidence can reveal a surprisingly detailed picture of the dynamics. Determining the time evolution and quantum mechanical states involved leads to deeper understanding of molecular dynamics. Here in a combined experimental and theoretical study, we unambiguously separate the sequential breakup via D+ + OD+ intermediates, from other processes leading to the same D+ + D+ + O final products of double ionization of water by a single photon. Moreover, we experimentally identify, separate, and follow step by step, two pathways involving the b 1Σ+ and a 1Δ electronic states of the intermediate OD+ ion. Our classical trajectory calculations on the relevant potential energy surfaces reproduce well the measured data and, combined with the experiment, enable the determination of the internal energy and angular momentum distribution of the OD+ intermediate.

The kinetic landscape of an RNA-binding protein in cells.

Gene expression in higher eukaryotic cells orchestrates interactions between thousands of RNA-binding proteins (RBPs) and tens of thousands of RNAs1. The kinetics by which RBPs bind to and dissociate from their RNA sites are critical for the coordination of cellular RNA-protein interactions2. However, these kinetic parameters have not been experimentally measured in cells. Here we show that time-resolved RNA-protein cross-linking with a pulsed femtosecond ultraviolet laser, followed by immunoprecipitation and high-throughput sequencing, allows the determination of binding and dissociation kinetics of the RBP DAZL for thousands of individual RNA-binding sites in cells. This kinetic cross-linking and immunoprecipitation (KIN-CLIP) approach reveals that DAZL resides at individual binding sites for time periods of only seconds or shorter, whereas the binding sites remain DAZL-free for markedly longer. The data also indicate that DAZL binds to many RNAs in clusters of multiple proximal sites. The effect of DAZL on mRNA levels and ribosome association correlates with the cumulative probability of DAZL binding in these clusters. Integrating kinetic data with mRNA features quantitatively connects DAZL-RNA binding to DAZL function. Our results show how kinetic parameters for RNA-protein interactions can be measured in cells, and how these data link RBP-RNA binding to the cellular function of RBPs.

Time-resolved ultrafast transient polarization spectroscopy to investigate nonlinear processes and dynamics in electronically excited molecules on the femtosecond time scale.

We report a novel experimental technique to investigate ultrafast dynamics in photoexcited molecules by probing the 3rd-order nonlinear optical susceptibility. A non-collinear 3-pulse scheme is developed to probe the ultrafast dynamics of excited electronic states using the optical Kerr effect. Optical homodyne and optical heterodyne detections are demonstrated to measure the 3rd-order nonlinear optical response for the S1 excited state of liquid nitrobenzene, which is populated by 2-photon absorption of a 780 nm 40 fs excitation pulse.

On the Origin of the Photostability of DNA and RNA Monomers: Excited State Relaxation Mechanism of the Pyrimidine Chromophore.

Today's genetic composition is the result of continual refinement processes on primordial heterocycles present in prebiotic Earth and at least partially regulated by ultraviolet radiation. Femtosecond transient absorption spectroscopy and state-of-the-art ab initio calculations are combined to unravel the electronic relaxation mechanism of pyrimidine, the common chromophore of the nucleobases. The excitation of pyrimidine at 268 nm populates the S1(nπ*) state directly. A fraction of the population intersystem crosses to the triplet manifold within 7.8 ps, partially decaying within 1.5 ns, while another fraction recovers the ground state in >3 ns. The pyrimidine chromophore is not responsible for the photostability of the nucleobases. Instead, C2 and C4 amino and/or carbonyl functionalization is essential for shaping the topography of pyrimidine's potential energy surfaces and results in accessible conical intersections between the initially populated electronic excited state and the ground state.

Ultrafast Dynamics of Excited Electronic States in Nitrobenzene Measured by Ultrafast Transient Polarization Spectroscopy.

We investigate ultrafast dynamics of the lowest singlet excited electronic state in liquid nitrobenzene using ultrafast transient polarization spectroscopy, extending the well-known technique of optical Kerr effect spectroscopy to excited electronic states. The third-order nonlinear response of the excited molecular ensemble is measured using a pair of femtosecond pulses following a third femtosecond pulse that populates the S1 excited state. By measuring this response, which is highly sensitive to details of the excited state character and structure, as a function of time delays between the three pulses involved, we extract the dephasing time of the wave packet on the excited state. The dephasing time, measured as a function of time delay after pump excitation, shows oscillations indicating oscillatory wave packet dynamics on the excited state. From the experimental measurements and supporting theoretical calculations, we deduce that the wave packet completely leaves the S1 state potential energy surface after three traversals of the intersystem crossing between the singlet S1 and triplet T2 states.

Excited State Lifetimes of Sulfur-Substituted DNA and RNA Monomers Probed Using the Femtosecond Fluorescence Up-Conversion Technique.

Sulfur-substituted DNA and RNA nucleobase derivatives (a.k.a., thiobases) are an important family of biomolecules. They are used as prodrugs and as chemotherapeutic agents in medical settings, and as photocrosslinker molecules in structural-biology applications. Remarkably, excitation of thiobases with ultraviolet to near-visible light results in the population of long-lived and reactive triplet states on a time scale of hundreds of femtoseconds and with near-unity yields. This efficient nonradiative decay pathway explains the vanishingly small fluorescence yields reported for the thiobases and the scarcity of fluorescence lifetimes in the literature. In this study, we report fluorescence lifetimes for twelve thiobase derivatives, both in aqueous solution at physiological pH and in acetonitrile. Excitation is performed at 267 and 362 nm, while fluorescence emission is detected at 380, 425, 450, 525, or 532 nm. All the investigated thiobases reveal fluorescence lifetimes that decay in a few hundreds of femtoseconds and with magnitudes that depend and are sensitive to the position and degree of sulfur-atom substitution and on the solvent environment. Interestingly, however, three thiopyrimidine derivatives (i.e., 2-thiocytidine, 2-thiouridine, and 4-thiothymidine) also exhibit a small amplitude fluorescence component of a few picoseconds in aqueous solution. Furthermore, the N-glycosylation of thiobases to form DNA or RNA nucleoside analogues is demonstrated as affecting their fluorescence lifetimes. In aqueous solution, the fluorescence decay signals exciting at 267 nm are equal or slower than those collected exciting at 362 nm. In acetonitrile, however, the fluorescence decay signals recorded upon 267 nm excitation are, in all cases, faster than those measured exciting at 362 nm. A comparison to the literature values show that, while both the DNA and RNA nucleobase and thiobase derivatives exhibit sub-picosecond fluorescence lifetimes, the 1ππ* excited-state population in the nucleobase monomers primarily decay back to the ground state, whereas it predominantly populates long-lived and reactive triplet states in thiobase monomers.

Excited-State Dynamics in the RNA Nucleotide Uridine 5'-Monophosphate Investigated Using Femtosecond Broadband Transient Absorption Spectroscopy.

Damage to RNA from ultraviolet radiation induces chemical modifications to the nucleobases. Unraveling the excited states involved in these reactions is essential; however, investigations aimed at understanding the electronic-energy relaxation pathways of the RNA nucleotide uridine 5'-monophosphate (UMP) have not received enough attention. In this Letter, the excited-state dynamics of UMP is investigated in aqueous solution. Excitation at 267 nm results in a trifurcation event that leads to the simultaneous population of the vibrationally excited ground state, a long-lived 1nπ* state, and a receiver triplet state within 200 fs. The receiver state internally converts to the long-lived 3ππ* state in an ultrafast time scale. The results elucidate the electronic relaxation pathways and clarify earlier transient absorption experiments performed for uracil derivatives in solution. This mechanistic information is important because long-lived nπ* and ππ* excited states of both singlet and triplet multiplicities are thought to lead to the formation of harmful photoproducts.

Heavy-Atom-Substituted Nucleobases in Photodynamic Applications: Substitution of Sulfur with Selenium in 6-Thioguanine Induces a Remarkable Increase in the Rate of Triplet Decay in 6-Selenoguanine.

Sulfur substitution of carbonyl oxygen atoms of DNA/RNA nucleobases promotes ultrafast intersystem crossing and near-unity triplet yields that are being used for photodynamic therapy and structural-biology applications. Replacement of sulfur with selenium or tellurium should significantly red-shift the absorption spectra of the nucleobases without sacrificing the high triplet yields. Consequently, selenium/tellurium-substituted nucleobases are thought to facilitate treatment of deeper tissue carcinomas relative to the sulfur-substituted analogues, but their photodynamics are yet unexplored. In this contribution, the photochemical relaxation mechanism of 6-selenoguanine is elucidated and compared to that of the 6-thioguanine prodrug. Selenium substitution leads to a remarkable enhancement of the intersystem crossing lifetime both to and from the triplet manifold, resulting in an efficiently populated, yet short-lived triplet state. Surprisingly, the rate of triplet decay in 6-selenoguanine increases by 835-fold compared to that in 6-thioguanine. This appears to be an extreme manifestation of the classical heavy-atom effect in organic photochemistry, which challenges conventional wisdom.

Photochemical Relaxation Pathways in Dinitropyrene Isomer Pollutants.

Dinitropyrenes are polycyclic aromatic pollutants prevalent in the environment. While their transformations by sunlight in the environment have been documented, the effect that the nitro-group substitution pattern has on the relaxation pathways has not been extensively studied. In this contribution, the steady-state and femtosecond-to-microsecond excited-state dynamics of 1,3-dinitropyrene and 1,8-dinitropyrene isomers are investigated upon visible light excitation at 425 nm and compared with those recently reported for the 1,6-dinitropyrene isomer. The experimental results are complemented with ground- and excited-state density functional calculations. It is shown that excitation at 425 nm results in the ultrafast branching of the excited-state population in the S1 state to populate the triplet state in ca. 90% yield and to form a nitropyrenoxy radical in less than 10% yield. In addition, the position of the NO2 group does not affect significantly the excited-state relaxation mechanism, while it does influence the absorption and fluorescence spectra, the fluorescence, triplet, singlet oxygen, and photodegradation yields, as well as the relative yield of radical formation. Radical formation is implicated in the photodegradation of these pollutants, while in the presence of hydrogen donors, direct reactions from the triplet state are also observed.

The Photochemical Branching Ratio in 1,6-Dinitropyrene Depends on the Excitation Energy.

Nitropolycyclic aromatic hydrocarbons constitute one of the most disconcerting classes of pollutants. Photochemical degradation is thought to be a primary mode of their natural removal from the environment, but the microscopic mechanism leading to product formation as a function of excitation wavelength is poorly understood. In this Letter, it is revealed that excitation of 1,6-dinitropyrene with 425, 415, or 340 nm radiation leads to an increasing amount of radical production through photodissociation at the expense of triplet-state population-the two primary reaction pathways in this class of pollutants. Radical formation requires overcoming an energy barrier in the excited singlet manifold. This activation energy explains the large fraction of the initial singlet-state population that intersystem crosses to a doorway triplet state, instead of leading overwhelmingly to photodissociation. The unforeseen excitation wavelength dependence of this branching process is expected to regulate the photochemistry of 1,6-dinitropyrene and possibly of other nitroaromatic pollutants in the environment.

Direct Observation of Triplet-State Population Dynamics in the RNA Uracil Derivative 1-Cyclohexyluracil.

Investigation of the excited-state dynamics in nucleic acid monomers is an area of active research due to the crucial role these early events play in DNA and RNA photodamage. The dynamics and rate at which the triplet state is populated are key mechanistic pathways yet to be fully elucidated. Direct spectroscopic evidence is presented in this contribution for intersystem crossing dynamics in a uracil derivative, 1-cyclohexyluracil. It is shown that intersystem crossing to the triplet manifold occurs in one picosecond or less in acetonitrile solution-at least an order of magnitude faster than previously estimated experimentally. Broadband transient absorption measurements also reveal the primary electronic relaxation pathways of the uracil chromophore, including the absorption spectra of the (1)ππ*, (1)nπ*, and (3)ππ* states and the rates of vibrational cooling in the ground and (3)ππ* states. The experimental results are supported by density functional calculations.