Femtochemistry: Recent Progress in Studies of Dynamics and Control of Reactions and Their Transition States

Generation of a vector conventional soliton via a graphene oxide saturable absorber

We have experimentally observed an ultrashort conventional vector soliton in an erbium-doped fiber laser. The few-layered graphene oxide (GO) is used as a saturable absorber (SA). It is found that the saturable absorption characteristic of GO is polarization independent. Therefore, vector solitons can be obtained without polarization control by using such SA. By using a polarization beam splitter to split the mode-locked pulse obtained in the oscillator, two orthogonal polarization vector solitons with equal intensity and consistent characteristics can be obtained. It demonstrates that the initial soliton consists of two orthogonal polarization components. It is worth noting that these two orthogonal polarization component solitons improve the signal-to-noise ratio (SNR) of 3 dB compared with the initial soliton. The improvement in SNR is very significant and cannot be neglected. This phenomenon has not been reported before, to our knowledge. In addition, the conventional soliton generated by this mode-locked laser has a central wavelength of 1559 nm with 1.1 ps pulse duration. The mode-locking state of this laser can be self-started. After mode locking, the environmental stability is excellent. The experimental results indicate that GO as a broadband SA has great potential and application prospects in the field of vector soliton generation.

A Brief Discussion of Chemical Kinetics versus Chemical Dynamics

Chemical kinetics and chemical dynamics are distinct but related topics. They arise again in contemporary physical chemistry often in terms of charge carrier processes in new materials which interconvert light and electrical energy on a distribution of time scales. With this recent rise in the application of concepts in kinetics and dynamics to new problems, there has also arisen confusion about the differences and connections between the two. Here, we briefly review the relationship between kinetics and dynamics in chemical processes, with particular emphasis on the photochemical and photophysical response of a system.

Charge transfer in sodium iodide collisions

Sodium iodide (NaI) has, over the years, served as a prototype system in studies of non-adiabatic dynamics. Here, the charge transfer collision reactions Na⁺ + I^- ⇆ Na + I (mutual neutralization and ion-pair formation) are studied using an ab initio approach and the total and differential cross sections are calculated for the reactions. This involves electronic structure calculations on NaI to obtain adiabatic potential energy curves, non-adiabatic and spin-orbit couplings, followed by nuclear dynamics, treated fully quantum mechanically in a strictly diabatic representation. A single avoided crossing at 13.22 a₀ dominates the reactions, and the total cross sections are well captured by the semi-classical Landau-Zener model. Compared to the measured ion-pair formation cross section, the calculated cross section is about a factor of two smaller, and the overall shape of the calculated differential cross section is in reasonable agreement with the measured ion-pair formation differential cross section. Treating the Landau-Zener coupling as an empirical parameter of 0.05 eV, the measured total and differential cross sections are well captured when performing fully quantum mechanical cross section calculations including rotational coupling. A semi-empirical spin-orbit coupling model is also investigated, giving satisfactory estimation of the effects of spin-orbit interactions for the reactions.

Ultrafast Excited State Dynamics of Spatially Confined Organic Molecules

This Feature Article highlights the role of spatial confinement in controlling the fundamental behavior of molecules. Select examples illustrate the value of using space as a tool to control and understand excited-state dynamics through a combination of ultrafast spectroscopy and conventional steady-state methods. Molecules of interest were confined within a closed molecular capsule, derived from a cavitand known as octa acid (OA), whose internal void space is sufficient to accommodate molecules as long as tetracene and as wide as pyrene. The free space, i.e., the space that is left following the occupation of the guest within the host, is shown to play a significant role in altering the behavior of guest molecules in the excited state. The results reported here suggest that in addition to weak interactions that are commonly emphasized in supramolecular chemistry, the extent of empty space (i.e., the remaining void space within the capsule) is important in controlling the excited-state behavior of confined molecules on ultrafast time scales. For example, the role of free space in controlling the excited-state dynamics of guest molecules is highlighted by probing the cis-trans isomerization of stilbenes and azobenzenes within the OA capsule. Isomerization of both types of molecule are slowed when they are confined within a small space, with encapsulated azobenzenes taking a different reaction pathway compared to that in solution upon excitation to S₂. In addition to steric constraints, confinement of reactive molecules in a small space helps to override the need for diffusion to bring the reactants together, thus enabling the measurement of processes that occur faster than the time scale for diffusion. The advantages of reducing free space and confining reactive molecules are illustrated by recording unprecedented excimer emission from anthracene and by measuring ultrafast electron transfer rates across the organic molecular wall. By monitoring the translational motion of anthracene pairs in a restricted space, it has been possible to document the pathway undertaken by excited anthracene from inception to the formation of the excimer on the excited-state surface. Similarly, ultrafast electron transfer experiments pursued here have established that the process is not hindered by a molecular wall. Apparently, the electron can cross the OA capsule wall provided the donor and acceptor are in close proximity. Measurements on the ultrafast time scale provide crucial insights for each of the examples presented here, emphasizing the value of both "space" and "time" in controlling and understanding the dynamics of excited molecules.

Mechanism of ultrafast energy transfer between the organic-inorganic layers in multiple-ring aromatic spacers for 2D perovskites

Lead halide based perovskite semiconductors self-assemble with distinct organic cations in natural multi-quantum-well structures. The emerging electronic properties of these two-dimensional (2D) materials can be controlled by the combination of the halide content and choice of chromophore in the organic layer. Understanding the photophysics of the perovskite semiconductor materials is critical for the optimization of stable and efficient optoelectronic devices. We use femtosecond transient absorption spectroscopy (fs-TAS) to study the mechanism of energy transfer between the organic and inorganic layers in a series of three lead-based mixed-halide perovskites such as benzylammonium (BA), 1-naphthylmethylammonium (NMA), and 1-pyrenemethylammonium (PMA) cations in 2D-lead-based perovskite thin films under similar experimental conditions. After optical excitation of the 2D-confined exciton in the lead halide layer, ultrafast energy transfer is observed to organic singlet and triplet states of the incorporated chromophores. This is explained by an effective Dexter energy transfer, which operates via a correlated electron exchange between the donating 2D-confined exciton and the accepting chromophore under spin conservation.

Ultrafast-nonlinear ultraviolet pulse modulation in an AlInGaN polariton waveguide operating up to room temperature

Ultrafast nonlinear photonics enables a host of applications in advanced on-chip spectroscopy and information processing. These rely on a strong intensity dependent (nonlinear) refractive index capable of modulating optical pulses on sub-picosecond timescales and on length scales suitable for integrated photonics. Currently there is no platform that can provide this for the UV spectral range where broadband spectra generated by nonlinear modulation can pave the way to new on-chip ultrafast (bio-) chemical spectroscopy devices. We demonstrate the giant nonlinearity of UV hybrid light-matter states (exciton-polaritons) up to room temperature in an AlInGaN waveguide. We experimentally measure ultrafast nonlinear spectral broadening of UV pulses in a compact 100 μm long device and deduce a nonlinearity 1000 times that in common UV nonlinear materials and comparable to non-UV polariton devices. Our demonstration promises to underpin a new generation of integrated UV nonlinear light sources for advanced spectroscopy and measurement.

Nonlinearity enhancement in different materials is relevant for many scientific applications. Here the authors demonstrate pulse modulation in the UV regime due to polariton-based nonlinearity in an AlInGaN waveguide structure, including at room temperature.

Photoinduced Intermolecular Electron Transfer in Gas Phase Ion Pairs of the 1-Ethyl-3-methylimidazolium Cation and the Bis(trifluoromethylsulfonyl)imide Anion

In this study, the UV photodissociation of gas phase ion pairs of the ionic liquid 1-ethyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide, [emim]⁺[tf2n]^-, is shown to proceed primarily through radical intermediates. [emim]⁺[tf2n]^- ion pairs have been shown previously to undergo two-photon-dependent dissociation, but the mechanisms of this have not been probed in detail. By employing a two-laser pump probe spectroscopy and time-dependent density functional theory (TD-DFT) calculations, we have illustrated that one of the major UV photodissociation pathways in [emim]⁺[tf2n]^- ion pairs is an intermolecular electron transfer wherein the anion transfers an electron to the cation resulting in two neutral open-shelled products. These products were observable for at least 1.6 μs post photodissociation, the experimental limit, via detection of the [emim]⁺ cation. This data demonstrates that the likely photoproducts of [emim]⁺[tf2n]^- UV photodissociation are two neutral species that separate spatially, demonstrated through lack of observed relaxation pathways such as electron recombination. TD-DFT and frontier molecular orbital analysis calculations at the MN15/6-311++G(d,p) level are employed to aid in identifying excited state characteristics and support the interpretations of the experimental data. The energetic onset of the intermolecular electron transfer is consistent with previously observed [emim]⁺[tf2n]^- absorption spectra in the bulk and gas phases. The similarities between bulk and gas phase UV spectra imply that this electron-transfer pathway may be a major photodissociation channel in both phases.

Recent advances in real-time spectrum measurement of soliton dynamics by dispersive Fourier transformation

Mode-locking lasers have not only produced huge economic benefits in industrial fields and scientific research, but also provided an excellent platform to study diverse soliton phenomena. However, the real-time characterization of the ultrafast soliton dynamics remains challenging for traditional electronic instruments due to their relatively low response bandwidth and slow scan rate. Consequently, it is urgent for researchers to directly observe these ultrafast evolution processes, rather than just indirectly understand them from numerical simulations or averaged measurement data. Fortunately, dispersive Fourier transformation (DFT) provides a powerful real-time measurement technique to overcome the speed limitations of traditional electronic measurement devices by mapping the frequency spectrum onto the temporal waveform. In this review, the operation principle of DFT is discussed and the recent progress in characterizing the ultrafast transient soliton dynamics of mode-locking lasers is summarized, including soliton explosions, soliton molecules, noise-like pulses, rogue waves, and mode-locking buildup processes.

An experimental approach for controlling confinement effects at catalyst interfaces

Catalysts are conventionally designed with a focus on enthalpic effects, manipulating the Arrhenius activation energy. This approach ignores the possibility of designing materials to control the entropic factors that determine the pre-exponential factor. Here we investigate a new method of designing supported Pt catalysts with varying degrees of molecular confinement at the active site. Combining these with fast and precise online measurements, we analyse the kinetics of a model reaction, the platinum-catalysed hydrolysis of ammonia borane. We control the environment around the Pt particles by erecting organophosphonic acid barriers of different heights and at different distances. This is done by first coating the particles with organothiols, then coating the surface with organophosphonic acids, and finally removing the thiols. The result is a set of catalysts with well-defined "empty areas" surrounding the active sites. Generating Arrhenius plots with >300 points each, we then compare the effects of each confinement scenario. We show experimentally that confining the reaction influences mainly the entropy part of the enthalpy/entropy trade-off, leaving the enthalpy unchanged. Furthermore, we find this entropy contribution is only relevant at very small distances (<3 Å for ammonia borane), where the "empty space" is of a similar size to the reactant molecule. This suggests that confinement effects observed over larger distances must be enthalpic in nature.

Approaching black-box calculations of pump-probe fragmentation dynamics of polyatomic molecules

A general framework for the simulation of ultrafast pump-probe time resolved experiments based on Born-Oppenheimer molecular dynamics (BOMD) is presented. Interaction of the molecular species with a laser is treated by a simple maximum entropy distribution of the excited state occupancies. The latter decay of the electronic excitation into the vibrations is based on an on-the-fly estimation of the rate of the internal conversion, while the energy is distributed in a thermostat-like fashion. The approach was tested by reproducing the results of previous femtosecond studies on ethylene, naphthalene and new results for phenanthrene.

Revisiting the von Neumann–Wigner noncrossing rule and validity of a dynamic correlation diagram method

The noncrossing rule for potential energy surfaces can be applied only, as originally postulated by von Neumann and Wigner, to slowly occurring changes; it has, however, over many years, been widely used to rationalize fast chemical reactions. Taking the conversion of Dewar benzene to benzene as an example, we demonstrate a reaction that has a timescale for which crossings are allowed. Since it is now established that elementary chemical reactions proceed over ca. 10–100[Formula: see text]fs, as revealed experimentally by Zewail, the noncrossing rule cannot any longer be said to be valid for most chemical reactions. We further demonstrate that the mechanism of the chemiluminescent conversion of Dewar benzene to benzene is explained by an electronic state diagram derived using a dynamic correlation diagram method which allows crossings, whereas the reaction is not explained by a conventional approach, applying the noncrossing rule using a static correlation diagram method.

Nonlinear XUV signal generation probed by transient grating spectroscopy with attosecond pulses

Nonlinear spectroscopies are utilized extensively for selective measurements of chemical dynamics in the optical, infrared, and radio-frequency regimes. The development of these techniques for extreme ultraviolet (XUV) light sources facilitates measurements of electronic dynamics on attosecond timescales. Here, we elucidate the temporal dynamics of nonlinear signal generation by utilizing a transient grating scheme with a subfemtosecond XUV pulse train and two few-cycle near-infrared pulses in atomic helium. Simultaneous detection of multiple diffraction orders reveals delays of ≥1.5 fs in higher-order XUV signal generation, which are reproduced theoretically by solving the coupled Maxwell–Schrödinger equations and with a phase grating model. The delays result in measurable order-dependent differences in the energies of transient light induced states. As nonlinear methods are extended into the attosecond regime, the observed higher-order signal generation delays will significantly impact and aid temporal and spectral measurements of dynamic processes.

Ultrafast dynamics following light-matter interaction are governed by nonlinear processes. Here the authors show that initial nonlinear signal time-evolution is a consequence of phase grating accumulation using transient grating measurements with attosecond and near-infrared pulses.

Electrons dynamics control by shaping femtosecond laser pulses in micro/nanofabrication: modeling, method, measurement and application

During femtosecond laser fabrication, photons are mainly absorbed by electrons, and the subsequent energy transfer from electrons to ions is of picosecond order. Hence, lattice motion is negligible within the femtosecond pulse duration, whereas femtosecond photon-electron interactions dominate the entire fabrication process. Therefore, femtosecond laser fabrication must be improved by controlling localized transient electron dynamics, which poses a challenge for measuring and controlling at the electron level during fabrication processes. Pump-probe spectroscopy presents a viable solution, which can be used to observe electron dynamics during a chemical reaction. In fact, femtosecond pulse durations are shorter than many physical/chemical characteristic times, which permits manipulating, adjusting, or interfering with electron dynamics. Hence, we proposed to control localized transient electron dynamics by temporally or spatially shaping femtosecond pulses, and further to modify localized transient materials properties, and then to adjust material phase change, and eventually to implement a novel fabrication method. This review covers our progresses over the past decade regarding electrons dynamics control (EDC) by shaping femtosecond laser pulses in micro/nanomanufacturing: (1) Theoretical models were developed to prove EDC feasibility and reveal its mechanisms; (2) on the basis of the theoretical predictions, many experiments are conducted to validate our EDC-based femtosecond laser fabrication method. Seven examples are reported, which proves that the proposed method can significantly improve fabrication precision, quality, throughput and repeatability and effectively control micro/nanoscale structures; (3) a multiscale measurement system was proposed and developed to study the fundamentals of EDC from the femtosecond scale to the nanosecond scale and to the millisecond scale; and (4) As an example of practical applications, our method was employed to fabricate some key structures in one of the 16 Chinese National S&T Major Projects, for which electron dynamics were measured using our multiscale measurement system.

Dynamic correlation diagrams for sigmatropic reactions based on orbital phase conservation theory

For sigmatropic reactions, such as [1,3] and [1,5] hydrogen shifts, the Cope and Claisen rearrangements, and the Berson–Nelson rearrangement, no correlation diagrams consistent with the classical electronic formulas have been reported. Here, we report dynamic correlation diagrams for these sigmatropic reactions based on orbital phase conservation theory. The diagrams are consistent with both the selection rules of sigmatropic reactions proposed by Woodward and Hoffmann and classical electronic formulas.

Dissolution-and-reduction CVD synthesis of few-layer graphene on ultra-thin nickel film lifted off for mode-locking fiber lasers

The in-situ dissolution-and-reduction CVD synthesized few-layer graphene on ultra-thin nickel catalyst film is demonstrated at temperature as low as 550 °C, which can be employed to form transmission-type or reflection-type saturable absorber (SA) for mode-locking the erbium-doped fiber lasers (EDFLs). With transmission-type graphene SA, the EDFL shortens its pulsewidth from 483 to 441 fs and broadens its spectral linewidth from 4.2 to 6.1 nm with enlarging the pumping current from 200 to 900 mA. In contrast, the reflection-type SA only compresses the pulsewidth from 875 to 796 fs with corresponding spectral linewidth broadened from 2.2 to 3.3 nm. The reflection-type graphene mode-locker increases twice of its equivalent layer number to cause more insertion loss than the transmission-type one. Nevertheless, the reflection-type based saturable absorber system can generate stabilized soliton-like pulse easier than that of transmission-type system, because the nonlinearity induced self-amplitude modulation depth is simultaneously enlarged when passing through the graphene twice under the retro-reflector design.

Excited-state wavepacket and potential reconstruction by coherent anti-Stokes Raman scattering

We propose a methodology for reconstructing polyatomic excited-state molecular wavepackets and potential energy surfaces by multiple pulse optical spectroscopy.

First-Principles Calculations on the Kinetics and Mechanism of the Retro-Ene Reaction of Diallyl Amine in the Gas Phase

A computational study has been carried out on the gas-phase retro-ene reaction of diallyl amine. The energies of the stationary points have also been evaluated with the B3LYP and MP2 methods on the optimized structure using the different basis sets. The kinetic activation parameters were calculated at 648 K to enable comparison with experimental data. Two probable mechanisms are suggested for the reaction. Since the radical mechanism produced a high activation energy conflicting with the experimental results, the concerted cyclic pathway of the retro-ene reaction was considered completely and comprehensively. Natural bond orbital analysis showed that the acidic character of the HI atom plays an important role in the reaction process. Wiberg bond indices were calculated throughout the reaction, and an asynchronousity value of 70% was obtained, confirming a distorted chair-like geometry for the transition state with the early and advanced natures of bond formation and bond cleavage. To provide a reasonable analysis of the critical points and the Laplacian of the electronic charge density in the TS, the atoms-in-molecule method was applied. Topological analysis showed the expected ring point for the best transition state corresponding to the cyclic six- membered structure. Comparison between the computational data and experiment showed a good agreement.

QUANTIZATION OF CHEMICAL REACTION: THE DYNAMIC CORRELATION DIAGRAM METHOD FREE FROM NONCROSSING RULE

Both Fukui's frontier orbital (FO) theory and Woodward–Hoffmann's orbital symmetry conservation (W–H) theory are based on the molecular orbital theory. However, there are some obvious inconsistencies between the two theories in explaining the electron movement. The process of chemical reactions has been explained by the potential surface analysis based on the time-independent Schrödinger equation. However, this approach is not always appropriate for describing unsteady states, because the variable of reaction coordinate should be time t by its very nature. When considering the time-scale of chemical reactions for molecules, there is inherent uncertainty in the energy levels for the midway state of chemical reactions owing to the Heisenberg uncertainty principle. The states which can be accurately described by quantum mechanics exist discontinuously in chemical reactions. Such quantization of chemical reactions solves all noncrossing problems. We also show that such an essential fact leads to new concepts and theories in chemical reactions such as stable molecule, elementary reaction and minimum deformation of orbital phases. Finally, taking the regularity in organic reactions as an example, we demonstrate that FO theory and W–H theory can be unified consistently by the universally applicable "dynamic correlation diagram method."

SELECTIVE EXCITATION OF HIGH VIBRATIONAL STATES OF HYDROGEN FLUORIDE IN A THERMAL ENVIRONMENT BY ULTRAFAST INFRARED LASER PULSES

The selective excitation of the high ground vibrational state of rotationless HF in an unobserved quasi-resonant thermal environment under the control of a single pulse and pulse train is studied using the reduced density matrix theory. It is shown that the pulse train can enhance the population transfer probability. The numerical results reveal that the vibrational relaxation process is affected by the distribution of the environment frequency and the molecule–environment coupling intensity. The effects of the molecule–environment coupling parameter and the overlapping pulses on the population of the target state of HF are also discussed.

THEORETICAL INVESTIGATION OF ULTRAFAST DYNAMICS OF THE RHODAMINE-700 MOLECULE IN SOLVENTS

The density matrix theory is used to calculate the fluorescence depletion spectra and the internal conversion (IC) times of rhodamine-700 (R-700) in methanol, ethanol, and DMSO solvents. The calculated IC times from Sx to S1 states of R-700 in methanol, ethanol, and DMSO solvents are about 20, 33, and 70 fs, respectively. The times of the excited solvation processes for R-700 in methanol, ethanol, and DMSO solvents are about 8.0, 7.0, and 3.0 ps, respectively.

Femtosecond interferometry of molecular dynamics – the role of relative and absolute phase of two individual laser pulses

Dynamical implications of the dissociation of a molecular ion under the influence of interferometrically generated light fields have been investigated by numerical solution of time dependent Schrödinger equations. As an example the dissociation of DCl+ ions by means of two interfering 7 fs laser pulses at 800 nm has been chosen. We demonstrate that product branching ratios D+:Cl+ can be manipulated from 10:1 to 1:10 not only by adjusting the appropriate delay time in the time-shifted two-pulse approach, but also by choosing the proper carrier envelope phase (CEP) of the two partial light fields. The effects of the phase shift related to the time shift and that of the CEP can be clearly distinguished.

Low threshold power density for the generation of frequency up-converted pulses in bismuth glass by two crossing chirped femtosecond pulses

We investigated the generation of frequency up-converted femtosecond laser pulses by nondegenerate cascaded four-wave mixing (CFWM) in a bismuth-oxide glass (BI glass). Broad-bandwidth light pulses with different propagation directions were simultaneously obtained by using two small-angle crossing femtosecond laser pulses in BI glass. Experimental results show that the threshold power density for the generation of broad-bandwidth femtosecond pulses in BI glass is one order of magnitude lower than that in fused silica.

Enhancement of vibrational coherence by femtosecond degenerate four-wave-mixing for a chromophore in 1-propanol glass

The enhancement effect of vibrational coherence by femtosecond degenerate four-wave-mixing (DFWM) technique was investigated with a dye, NK-2990, doped in low temperature 1-propanol glass. The strongest enhancement was observed with the delay between the first and the second pulses, t(13), set at about quarter of the oscillation period, which does not coincide with the theoretical prediction of half the period. One of the enhanced vibrational modes at ca. 90 cm(-1) became significantly broader below the glass transition temperature, indicating its sensitivity towards microscopic viscosity of the environment.

Electronic effects on photochemistry: the diverse reaction dynamics of highly excited stilbenes and azobenzene

Ultrafast time-resolved mass spectrometry and structural dynamics experiments on trans-stilbene, cis-stilbene, and azobenzene, with excitation to high-lying electronic states, reveal a rich diversity of photochemical reaction dynamics. All processes are found to be quite unlike the well-known photochemistry on lower electronic surfaces. While in trans-stilbene, excitation at 6 eV induces a phenyl twisting motion, in cis-stilbene it leads to an ultrafast ring-closing to form 4a,4b-dihydrophenanthrene. Azobenzene dissociates on an ultrafast time scale, rather than isomerizing as it does on a lower surface. The photochemical dynamics of the sample molecules proceed along steep potential energy surfaces and conical intersections. Because of that, the dynamics are much faster than vibrational relaxation, the randomizing effects from vibrational energy scrambling are avoided, and excitation-energy specific reaction dynamics results.

Theoretical study of the tautomerism in the one-electron oxidized guanine-cytosine base pair

Ionizing radiation on DNA mainly generates one-electron oxidized guanine-cytosine base pair (G(+·):C), and in the present paper we study all possible tautomers of G(+·):C by using ab initio approaches. Our calculations reveal that the tautomeric equilibrium follows a peculiar path, characterized by a stepwise mechanism: first the proton in the central hydrogen bond N1(G)-H1-N3(C) migrates from guanine to cytosine, and then the cytosine cation releases one proton from its amino group. During this second step, water acts as a proton acceptor, localizing the positive charge on one of the water molecules interacting with the guanine radical. In agreement with experimental findings, the computed energy barriers show that the deprotonation of the cytosine cation is the speed-limiting step in the tautomeric equilibrium. The influence of the number of water molecules incorporated in the theoretical model is analyzed in detail. The evolution of electronic properties along the reaction path is also discussed on the basis of partial atomic charges and spin density distributions. This work demonstrates that water indeed plays a crucial role in the tautomeric equilibra of base pairs.

One-electron oxidation of DNA by ionizing radiation: competition between base-to-base hole-transfer and hole-trapping

The distance of hole migration through DNA determines the degree to which radiation-induced lesions are clustered. It is the degree of clustering that confers to ionizing radiation its high toxicity. The migration distance is governed by a competition between hole transfer and irreversible trapping reactions. An important type of trapping is reactions that lead to the formation of deoxyribose radicals, which are precursors to free base release (fbr). Using HPLC, fbr was measured in X-irradiated films of d(CGCGCGCGCG)(2) and d(CGCGAATTCGCG)(2) as well as three genomic DNAs: M. luteus, calf thymus, and C. perfringens. The level of DNA hydration was varied from Gamma = 2.5 to 22 mol waters/mol nucleotide. The chemical yields of each base, G(base), were measured and used to calculate the modification factor, M(base). This factor compensates for differences in the GC/AT ratio, providing a measure of the degree to which a given base influences its own release. In the DNA oligomers, M(Gua) > M(Cyt), a result ascribed to the previously observed end effect in short oligomers. In the highly polymerized genomic DNA, we found that M(Cyt) > M(Gua) and that M(Thy) is consistently the smallest of the M factors. For these same DNA films, the yields of total DNA trapped radicals, G(tot)(fr), were measured using EPR spectroscopy. The yield of deoxyribose radicals was calculated using G(dRib)(fr) = approximately 0.11 x G(tot)(fr). Comparing G(dRib)(fr) with total fbr, we found that only about half of the fbr is accounted for by deoxyribose radical intermediates. We conclude that for a hole on cytosine, Cyt(*+), base-to-base hole transfer competes with irreversible trapping by the deoxyribose. In the case of a hole on thymine, Thy(*+), base-to-base hole transfer competes with irreversible trapping by methyl deprotonation. Close proximity of Gua protects the deoxyribose of Cyt but sensitizes the deoxyribose of Thy.

Use of ruthenium dyes for subnanosecond detector fidelity testing in real time transient absorption

Transient absorption spectroscopy is a powerful tool for the study of photoreactions on time scales from femtoseconds to seconds. Typically, reactions slower than approximately 1 ns are recorded by the "classical" technique; the reaction is triggered by an excitation flash, and absorption changes accompanying the reaction are recorded in real time using a continuous monitoring light beam and a detection system with sufficiently fast response. The pico- and femtosecond region can be accessed by the more recent "pump-probe" technique, which circumvents the difficulties of real time detection on a subnanosecond time scale. This is paid for by accumulation of an excessively large number of shots to sample the reaction kinetics. Hence, it is of interest to extend the classical real time technique as far as possible to the subnanosecond range. In order to identify and minimize detection artifacts common on a subnanosecond scale, like overshoot, ringing, and signal reflections, rigorous testing is required of how the detection system responds to fast changes of the monitoring light intensity. Here, we introduce a novel method to create standard signals for detector fidelity testing on a time scale from a few picoseconds to tens of nanoseconds. The signals result from polarized measurements of absorption changes upon excitation of ruthenium complexes {[Ru(bpy)(3)](2+) and a less symmetric derivative} by a short laser flash. Two types of signals can be created depending on the polarization of the monitoring light with respect to that of the excitation flash: a fast steplike bleaching at magic angle and a monoexponentially decaying bleaching for parallel polarizations. The lifetime of the decay can be easily varied via temperature and viscosity of the solvent. The method is applied to test the performance of a newly developed real time transient absorption setup with 300 ps time resolution and high sensitivity.