Molecular applications of attosecond laser pulses

Demir G, Demir D. Quantum tunneling time delay investigation of [Formula: see text] ion in human telomeric G-quadruplex systems

Guanine-rich quadruplex DNA (G-quadruplex) is of interest both in cell biology and nanotechnology. Its biological functions necessitate a G-quadruplex to be stabilized against escape of the monovalent metal cations. The potassium ion ([Formula: see text]) is particularly important as it experiences a potential energy barrier while it enters and exits the G-quadruplex systems which are normally found in human telomere. In the present work, we analyzed the time it takes for the [Formula: see text] cations to get in and out of the G-quadruplex. Our time estimate is based on entropic tunneling time-a time formula which gave biologically relevant results for DNA point mutation by proton tunneling. The potential energy barrier experienced by [Formula: see text] ions is determined from a quantum mechanical simulation study, Schrodinger equation is solved using MATLAB, and the computed eigenfunctions and eigenenergies are used in the entropic tunneling time formula to compute the time delay and charge accumulation rate during the tunneling of [Formula: see text] in G-quadruplex. The computations have shown that ion tunneling takes picosecond times. In addition, average [Formula: see text] accumulation rate is found to be in the picoampere range. Our results show that time delay during the [Formula: see text] ion tunneling is in the ballpark of the conformational transition times in biological systems, and it could be an important parameter for understanding its biological role in human DNA as well as for the possible applications in biotechnology. To our knowledge, for the first time in the literature, time delay during the ion tunneling from and into G-quadruplexes is computed.

Time delay during intra-base proton tunneling in the guanine base of the single stranded DNA

Spontaneous point mutations are one of the main actors in evolution, and the tautomerization of organic bases in the DNA is hypothesized to be the underlying mechanism of this crucial process. Tautomerization can be induced by proton tunneling, and if it occurs in single-stranded DNA (ssDNA) during the replication process, tautomerized bases might give rise to a mismatch, which will eventually defect the genetic code. In the present work, we report on the tautomerization time in the guanine base of the ssDNA. The model we use includes an intra-base tunneling mechanism such that time tunneling (delay time) is estimated to be around a few pico-seconds. The time delay is found to be biologically relevant which indicates that it is long enough to induce point mutations. Our results close a gap in the literature and sheds light on the importance of point mutations originating from quantum effects in the ssDNA.

Time delay during the proton tunneling in the base pairs of the DNA double helix

DNA undergoes spontaneous point mutations, which are believed to be central to the evolution of the organisms and which are thought to occur by tautomerization of the canonical Guanine-Cytosine (G-C) base pair into non-canonical G∗-C∗ base pair via the double proton tunneling. In the present work, we close a gap in the literature by computing the time delay during the proton tunneling. Our results, based on the well-known dwell time and our model of the entropic time, range from femtoseconds to picoseconds, and completely agree with the time scales of the structural changes in molecules (mutation processes not the complete replication processes). The tunneling delay times are thus nonnegligible and imply that the DNA mutations can be resolved using the attosecond laser technology, if not the femtosecond technology. Our results can be relevant also for other tunneling-enabled biological processes.

Time-Resolved Photoelectron Spectroscopy of Conical Intersections with Attosecond Pulse Trains

Conical Intersections (CIs), which are believed to be ubiquitous in molecular and biological systems, open up ultrafast nonradiative decay channels. A superposition of electronic states is created when a molecule passes through a CI and the nuclear wave packet branches. The resulting electronic coherence can be considered a unique signature of the CI. The involved electronic states can be resolved in the energy domain with photoelectron spectroscopy using a femtosecond pulse as a probe. However, the observation of the created electronic coherence in the time domain requires probe pulses with several electron volts of bandwidth. Attosecond pulses can probe the electronic coherence but are unable to resolve the involved electronic states. In this Letter, we propose to address this restriction by using time-resolved photoelectron spectroscopy with an attosecond pulse train as a probe. We theoretically demonstrate that the resulting photoelectron spectrum may yield energy resolution as well as the information on the created coherences in the time domain.

Onset of ionic coherence and ultrafast charge dynamics in attosecond molecular ionisation

Here is presented a fully ab initio theoretical framework for simulating the correlated many-electron dynamics occurring during and emerging from molecular ionisation by attosecond laser pulses. This is based on the time-dependent (TD) version of the B-spline restricted correlation space (RCS)-algebraic diagrammatic construction (ADC) method, with the full description of the photoelectron and inclusion of electron correlation effects, such as shakeup processes and inter-channel couplings. The nature of the ultrafast charge dynamics in the molecular ion is elucidated by quantitatively predicting the degree of electronic coherence and eigenstate content of the prepared molecular cationic state, beyond the commonly used sudden approximation. The results presented here for the acetylene and ethylene molecules show that even in the high photon energy regime the simulated hole dynamics is quantitatively different from the prediction of the sudden approximation. Moreover, for high-bandwidth ionising pulse, the residual interaction between the cation, in highly-excited shake-up states, and the emitted slow photoelectron gives rise to a loss of coherence in the ionic system which can persist for the first few femtoseconds after ionisation.

Attosecond single-cycle undulator light: a review

Research at modern light sources continues to improve our knowledge of the natural world, from the subtle workings of life to matter under extreme conditions. Free-electron lasers, for instance, have enabled the characterization of biomolecular structures with sub-ångström spatial resolution, and paved the way to controlling the molecular functions. On the other hand, attosecond temporal resolution is necessary to broaden our scope of the ultrafast world. Here we discuss attosecond pulse generation beyond present capabilities. Furthermore, we review three recently proposed methods of generating attosecond x-ray pulses. These novel methods exploit the coherent radiation of microbunched electrons in undulators and the tailoring of the emitted wavefronts. The computed pulse energy outperforms pre-existing technologies by three orders of magnitude. Specifically, our simulations of the proposed Soft X-ray Laser at MAX IV (Lund, Sweden) show that a pulse duration of 50-100 as and a pulse energy up to 5 [Formula: see text]J is feasible with the novel methods. In addition, the methods feature pulse shape control, enable the incorporation of orbital angular momentum, and can be used in combination with modern compact free-electron laser setups.

Photoinduced Ultrafast Charge Transfer and Charge Migration in Small Gold Clusters Passivated by a Chromophoric Ligand

Because the development of attopulses, charge migration induced by short optical pulses has been extensively investigated. We report a computational purely electronic dynamical study of ultrafast few femtoseconds (fs) charge transfer and charge migration in realistic passivated stoichiometric Au₁₁ and Au₂₀ gold nanoclusters functionalized by a bipyridine ligand. We show that a net significant amount of electronic charge (0.1 to 0.4 |e| where |e| is the electron charge) is permanently transferred from the bipyridine chromophore to the gold cluster during the short 5-6 fs UV-vis strong pulse. This electron transfer to the metallic core is induced by the optical excitation of electronic states with a partial charge transfer character involving the chromophore before the onset of nuclei motion. In addition, the photoexcitation by the strong fs pulse builds a nonequilibrium electronic density that beats between the chromophore and the metallic core around the average of the transferred value. Modular systems made of a donor chromophore that can be photoexcited in the UV-vis range coupled to an efficient acceptor that could trap the charge are of interest for applications to nanodevices. Our study provides understanding on the very early, purely electronic dynamics built by the fs optical excitation and the initial charge separation step.

A simple technique to overcome self-focusing, filamentation, supercontinuum generation, aberrations, depth dependence and waveguide interface roughness using fs laser processing

Several detrimental effects limit the use of ultrafast lasers in multi-photon processing and the direct manufacture of integrated photonics devices, not least, dispersion, aberrations, depth dependence, undesirable ablation at a surface, limited depth of writing, nonlinear optical effects such as supercontinuum generation and filamentation due to Kerr self-focusing. We show that all these effects can be significantly reduced if not eliminated using two coherent, ultrafast laser-beams through a single lens - which we call the Dual-Beam technique. Simulations and experimental measurements at the focus are used to understand how the Dual-Beam technique can mitigate these problems. The high peak laser intensity is only formed at the aberration-free tightly localised focal spot, simultaneously, suppressing unwanted nonlinear side effects for any intensity or processing depth. Therefore, we believe this simple and innovative technique makes the fs laser capable of much more at even higher intensities than previously possible, allowing applications in multi-photon processing, bio-medical imaging, laser surgery of cells, tissue and in ophthalmology, along with laser writing of waveguides.

Communication: XFAIMS-eXternal Field Ab Initio Multiple Spawning for electron-nuclear dynamics triggered by short laser pulses

Attoscience is an emerging field where attosecond pulses or few cycle IR pulses are used to pump and probe the correlated electron-nuclear motion of molecules. We present the trajectory-guided eXternal Field Ab Initio Multiple Spawning (XFAIMS) method that models such experiments "on-the-fly," from laser pulse excitation to fragmentation or nonadiabatic relaxation to the ground electronic state. For the photoexcitation of the LiH molecule, we show that XFAIMS gives results in close agreement with numerically exact quantum dynamics simulations, both for atto- and femtosecond laser pulses. We then show the ability of XFAIMS to model the dynamics in polyatomic molecules by studying the effect of nuclear motion on the photoexcitation of a sulfine (H₂CSO).

Ultrafast Spin-State Dynamics in Transition-Metal Complexes Triggered by Soft-X-Ray Light

Recent advances in attosecond physics provide access to the correlated motion of valence and core electrons on their intrinsic timescales. For valence excitations, processes related to the electron spin are usually driven by nuclear motion. For core-excited states, where the core hole has a nonzero angular momentum, spin-orbit coupling is strong enough to drive spin flips on a much shorter time scale. Here, unprecedented short spin crossover is demonstrated for L-edge (2p→3d) excited states of a prototypical Fe(II) complex. It occurs on a time scale, which is faster than the core-hole lifetime of about 4 fs and can be manipulated by the excitation conditions. A detailed analysis of such phenomena will help to gain a fundamental understanding of spin-crossover processes and establish the basis for their control by light.

Towards the analysis of attosecond dynamics in complex systems

We study from a theoretical perspective the ionization of molecules and clusters induced by irradiation of a combined two-color laser field consisting of a train of attosecond XUV pulses in the presence of an IR field.

Quantum Nuclear Dynamics Pumped and Probed by Ultrafast Polarization Controlled Steering of a Coherent Electronic State in LiH

The quantum wave packet dynamics following a coherent electronic excitation of LiH by an ultrashort, polarized, strong one-cycle infrared optical pulse is computed on several electronic states using a grid method. The coupling to the strong field of the pump and the probe pulses is included in the Hamiltonian used to solve the time-dependent Schrodinger equation. The polarization of the pump pulse allows us to control the localization in time and in space of the nonequilibrium coherent electronic motion and the subsequent nuclear dynamics. We show that transient absorption, resulting from the interaction of the total molecular dipole with the electric fields of the pump and the probe, is a very versatile probe of the different time scales of the vibronic dynamics. It allows probing both the ultrashort, femtosecond time scale of the electronic coherences as well as the longer dozens of femtoseconds time scales of the nuclear motion on the excited electronic states. The ultrafast beatings of the electronic coherences in space and in time are shown to be modulated by the different periods of the nuclear motion.

Using high harmonic radiation to reveal the ultrafast dynamics of radiosensitiser molecules

5-Fluorouracil (5FU) is a radiosensitiser molecule routinely used in combined chemo- and radio-therapies to enhance and localize cancer treatments. We have employed ultra-short XUV pulses produced by high harmonic generation (HHG) as a pump pulse to study the dynamics underlying the photo-stability and the radiation damage of this molecule. This work shows that it is possible to resolve individual dynamics even when using unselected HH. By comparing the results with those obtained in the multiphoton absorption at 400 nm, we were able to identify the frequencies of the HH comb relevant to the recorded dynamics: HH5 and HH3. The latter excites a high-lying Rydberg state interacting with a valence state and its dynamics is revealed by a 30 fs decay signal in the parent ion transient. Our results suggest that the same photoprotection mechanisms as those conferring photostability to the neutral nucleobases and to the DNA appear to be activated: HH5 excites the molecule to a state around 10.5 eV that undergoes an ultrafast relaxation on a timescale of 30 fs due to nonadiabatic interactions. This is followed sequentially by a 2.3 ps internal conversion as revealed by the dynamics observed for another fragment ion. These dynamics are extracted from the fragment ion signals. Proton or hydrogen transfer processes are required for the formation of three fragments and we speculate that the time scale of one of the processes is revealed by a H⁺ transient signal.

Bright attosecond soft X-ray pulse trains by transient phase-matching in two-color high-order harmonic generation

We study two-color high-order harmonic generation in Neon with 790 nm and 1300 nm driving laser fields and observe an extreme-ultraviolet continuum that extends to photon energies of 160 eV. Using a 6-mm-long, high pressure gas cell, we optimize the HHG yield at high photon energies and investigate the effect of ionization and propagation under phase-matching conditions that allow us to control the temporal structure of the XUV emission. Numerical simulations that include the 3D propagation of the two-color laser pulse show that a bright isolated attosecond pulse with exceptionally high photon energies can be generated in our experimental conditions due to an efficient hybrid optical and phase-matching gating mechanism.

Generating Isolated Elliptically Polarized Attosecond Pulses Using Bichromatic Counterrotating Circularly Polarized Laser Fields

We theoretically demonstrate the possibility to generate both trains and isolated attosecond pulses with high ellipticity in a practical experimental setup. The scheme uses circularly polarized, counterrotating two-color driving pulses carried at the fundamental and its second harmonic. Using a model Ne atom, we numerically show that highly elliptic attosecond pulses are generated already at the single-atom level. Isolated pulses are produced by using few-cycle drivers with controlled time delay between them.

Coherent electronic wave packet motion in C(60) controlled by the waveform and polarization of few-cycle laser fields

Strong laser fields can be used to trigger an ultrafast molecular response that involves electronic excitation and ionization dynamics. Here, we report on the experimental control of the spatial localization of the electronic excitation in the C_{60} fullerene exerted by an intense few-cycle (4 fs) pulse at 720 nm. The control is achieved by tailoring the carrier-envelope phase and the polarization of the laser pulse. We find that the maxima and minima of the photoemission-asymmetry parameter along the laser-polarization axis are synchronized with the localization of the coherent electronic wave packet at around the time of ionization.

Analysis of a measurement scheme for ultrafast hole dynamics by few femtosecond resolution X-ray pump–probe Auger spectroscopy

Ultrafast hole dynamics created in molecular systems as a result of sudden ionisation is the focus of much attention in the field of attosecond science. Using the molecule glycine we show through ab initio simulations that the dynamics of a hole, arising from ionisation in the inner valence region, evolves with a timescale appropriate to be measured using X-ray pulses from the current generation of SASE free electron lasers. The examined pump–probe scheme uses X-rays with photon energy below the K edge of carbon (275–280 eV) that will ionise from the inner valence region. A second probe X-ray at the same energy can excite an electron from the core to fill the vacancy in the inner-valence region. The dynamics of the inner valence hole can be tracked by measuring the Auger electrons produced by the subsequent refilling of the core hole as a function of pump–probe delay. We consider the feasibility of the experiment and include numerical simulation to support this analysis. We discuss the potential for all X-ray pump-X-ray probe Auger spectroscopy measurements for tracking hole migration.