Charge migration in photo-ionized aromatic amino acids

Simulating Real-Time Molecular Electron Dynamics Efficiently Using the Time-Dependent Density Matrix Renormalization Group

Compared to ground-state electronic structure optimizations, accurate simulations of molecular real-time electron dynamics are usually much more difficult to perform. To simulate electron dynamics, the time-dependent density matrix renormalization group (TDDMRG) has been shown to offer an attractive compromise between accuracy and cost. However, many simulation parameters significantly affect the quality and efficiency of a TDDMRG simulation. So far, it is unclear whether common wisdom from ground-state DMRG carries over to the TDDMRG, and a guideline on how to choose these parameters is missing. Here, in order to establish such a guideline, we investigate the convergence behavior of the main TDDMRG simulation parameters, such as time integrator, the choice of orbitals, and the choice of matrix-product-state representation for complex-valued nonsinglet states. In addition, we propose a method to select orbitals that are tailored to optimize the dynamics. Lastly, we showcase the TDDMRG by applying it to charge migration ionization dynamics in furfural, where we reveal a rapid conversion from an ionized state with a σ character to one with a π character within less than a femtosecond.

Simulating Attochemistry: Which Dynamics Method to Use?

Attochemistry aims to exploit the properties of coherent electronic wavepackets excited via attosecond pulses to control the formation of photoproducts. Such molecular processes can, in principle, be simulated with various nonadiabatic dynamics methods, yet the impact of the approximations underlying the methods is rarely assessed. The performances of widely used mixed quantum-classical approaches, Tully surface hopping, and classical Ehrenfest methods are evaluated against the high-accuracy DD-vMCG quantum dynamics. This comparison is conducted for the valence ionization of fluorobenzene. Analyzing the nuclear motion induced in the branching space of the nearby conical intersection, the results show that the mixed quantum-classical methods reproduce quantitatively the average motion of a quantum wavepacket when initiated on a single electronic state. However, they fail to properly capture the nuclear motion induced by an electronic wavepacket along the derivative coupling, the latter originating from the quantum electronic coherence property, key to attochemistry.

Time-resolved photoelectron spectroscopy: the continuing evolution of a mature technique

Time-resolved photoelectron spectroscopy (TRPES) has become one of the most widespread techniques for probing nonadiabatic dynamics in the excited electronic states of molecules. Furthermore, the complementary development of ab initio approaches for the simulation of TRPES signals has enabled the interpretation of these transient spectra in terms of underlying coupled electronic-nuclear dynamics. In this perspective, we discuss the current state-of-the-art approaches, including efforts to push femtosecond pulses into vacuum ultraviolet and soft X-ray regimes as well as the utilization of novel polarizations to use time-resolved optical activity as a probe of nonadiabatic dynamics. We close this perspective with a forward-looking prospectus on the new areas of application for this technique.

Attosecond charge migration following oxygen K-shell ionization in DNA bases and base pairs

Core ionization of DNA begins a cascade of events which could lead to cellular inactivation or death. The created core-hole following an impulse inner-shell ionization of molecules naturally decays in the auger timescale. We simulated charge migration (CM) phenomena following an impulsive core ionization of individual DNA bases at the oxygen K-edge which occurs before Auger decay of the oxygen. Our approach is based on real-time time dependent density functional theory (RT-TDDFT). It is shown that the pronounced hole fluctuation observed around bonds of the initial core-hole results in various valence orbital migrations. Also, the same photo-core-ionized dynamics is studied for the related base pairs. We investigate the role of base pairing and H-bonding interactions in the attosecond CM dynamics. In particular, the creation of a core-hole in the oxygen involved in H-bonding leads to an enhancement of charge migration relative to the respective single bases. Importantly, the hole oscillation of the adenine-thymine base pair upon creation of a core-hole at the oxygen, which does not contribute to the donor-acceptor interactions (not H-bonded), decreases compared to the single thymine base. Understanding the detailed dynamics of the localized core-hole initiating CM process would open the way for chemically controlling DNA damage/repair in the future.

Observation of intra- and intermolecular vibrational coherences of the aqueous tryptophan radical induced by photodetachment

The study of the photodetachment of amino acids in aqueous solution is pertinent to the understanding of elementary processes that follow the interaction of ionizing radiation with biological matter. In the case of tryptophan, the tryptophan radical that is produced by electron ejection also plays an important role in numerous redox reactions in biology, although studies of its ultrafast molecular dynamics are limited. Here, we employ femtosecond optical pump-probe spectroscopy to elucidate the ultrafast structural rearrangement dynamics that accompany the photodetachment of the aqueous tryptophan anion by intense, ∼5-fs laser pulses. The observed vibrational wave packet dynamics, in conjunction with density functional theory calculations, identify the vibrational modes of the tryptophan radical, which participate in structural rearrangement upon photodetachment. Aside from intramolecular vibrational modes, our results also point to the involvement of intermolecular modes that drive solvent reorganization about the N-H moiety of the indole sidechain. Our study offers new insight into the ultrafast molecular dynamics of ionized biomolecules and suggests that the present experimental approach can be extended to investigate the photoionization- or photodetachment-induced structural dynamics of larger biomolecules.

The mystery of sub-picosecond charge transfer following irradiation of hydrated uridine monophosphate

The early mechanisms by which ionizing rays damage biological structures by so-called direct effects are largely elusive. In a recent picosecond pulse radiolysis study of concentrated uridine monophosphate solutions [J. Ma, S. A. Denisov, J.-L. Marignier, P. Pernot, A. Adhikary, S. Seki and M. Mostafavi, J. Phys. Chem. Lett., 2018, 9, 5105], unexpected results were found regarding the oxidation of the nucleobase. The signature of the oxidized nucleobase could not be detected 5 ps after the electron pulse, but only the oxidized phosphate, raising intriguing questions about the identity of charge-transfer mechanisms that could explain the absence of U⁺. We address here this question by means of advanced first-principles atomistic simulations of solvated uridine monophosphate, combining Density Functional Theory (DFT) with polarizable embedding schemes. We contrast three very distinct mechanisms of charge transfer covering the atto-, femto- and pico-second timescales. We first investigate the ionization mechanism and subsequent hole/charge migrations on a timescale of attoseconds to a few femtoseconds under the frozen nuclei approximation. We then consider a nuclear-driven phosphate-to-oxidized-nucleobase electron transfer, showing that it is an uncompetitive reaction channel on the sub-picosecond timescale, despite its high exothermicity and significant electronic coupling. Finally, we show that non-adiabatic charge transfer is enabled by femtosecond nuclear relaxation after ionization. We show that electronic decoherence and the electronic coupling strength are the key parameters that determine the hopping probabilities. Our results provide important insight into the interplay between electronics and nuclear motions in the early stages of the multiscale responses of biological matter subjected to ionizing radiation.

First-Principles Simulations of Biological Molecules Subjected to Ionizing Radiation

Ionizing rays cause damage to genomes, proteins, and signaling pathways that normally regulate cell activity, with harmful consequences such as accelerated aging, tumors, and cancers but also with beneficial effects in the context of radiotherapies. While the great pace of research in the twentieth century led to the identification of the molecular mechanisms for chemical lesions on the building blocks of biomacromolecules, the last two decades have brought renewed questions, for example, regarding the formation of clustered damage or the rich chemistry involving the secondary electrons produced by radiolysis. Radiation chemistry is now meeting attosecond science, providing extraordinary opportunities to unravel the very first stages of biological matter radiolysis. This review provides an overview of the recent progress made in this direction, focusing mainly on the atto- to femto- to picosecond timescales. We review promising applications of time-dependent density functional theory in this context.

Ultrafast Quantum Interference in the Charge Migration of Tryptophan

Extreme-ultraviolet-induced charge migration in biorelevant molecules is a fundamental step in the complex path leading to photodamage. In this work we propose a simple interpretation of the charge migration recently observed in an attosecond pump-probe experiment on the amino acid tryptophan. We find that the decay of the prominent low-frequency spectral structure with increasing pump-probe delay is due to a quantum beating between two geometrically distinct, almost degenerate charge oscillations. Quantum beating is ubiquitous in these systems, and at least on the few-to-tens of femtosecond time scales, it may dominate over decoherence the line intensities of time-resolved spectra. We also address the experimentally observed phase shift in the charge oscillations of two different amino acids, tryptophan and phenylalanine. Our results indicate that a beyond mean-field treatment of the electron dynamics is necessary to reproduce the correct behavior.

The physical stage of radiolysis of solvated DNA by high-energy-transfer particles: insights from new first principles simulations

Electron dynamics simulations based on density functional theory are carried out on nanometric molecular systems to decipher the primary processes following irradiation of bio-macromolecules by high energy transfer charged particles.

Competition between charge migration and charge transfer induced by nuclear motion following core ionization: Model systems and application to Li2. J Chem Phys 2019;151:124108. [PMID: 31575213 DOI: 10.1063/1.5117246]

Attosecond and femtosecond spectroscopies present opportunities for the control of chemical reaction dynamics and products, as well as for quantum information processing; we address the somewhat unique situation of core-ionization spectroscopy which, for dimeric chromophores, leads to strong valence charge localization and hence tightly paired potential-energy surfaces of very similar shape. Application is made to the quantum dynamics of core-ionized Li₂ ⁺. This system is chosen as Li₂ is the simplest stable molecule facilitating both core ionization and valence ionization. First, the quantum dynamics of some model surfaces are considered, with the surprising result that subtle differences in shape between core-ionization paired surfaces can lead to dramatic differences in the interplay between electronic charge migration and charge transfer induced by nuclear motion. Then, equation-of-motion coupled-cluster calculations are applied to determine potential-energy surfaces for 8 core-excited state pairs, calculations believed to be the first of their type for other than the lowest-energy core-ionized molecular pair. While known results for the lowest-energy pair suggest that Li₂ ⁺ is unsuitable for studying charge migration, higher-energy pairs are predicted to yield results showing competition between charge migration and charge transfer. Central is a focus on the application of Hush's 1975 theory for core-ionized X-ray photoelectron spectroscopy to understand the shapes of the potential-energy surfaces and hence predict key features of charge migration.

The measurement of ultrafast electronic and structural dynamics with X-rays

In this theme issue, leading researchers discuss recent work on the measurement of ultrafast electronic and structural dynamics in matter using a new generation of short duration X-ray photon sources. These photon sources, based upon high harmonic generation from lasers and X-ray free-electron lasers, look set to have a high impact on ultrafast science. This article is part of the theme issue 'Measurement of ultrafast electronic and structural dynamics with X-rays'.