Quantum Chemical Topology of the Electron Localization Function in the Field of Attosecond Electron Dynamics

Visualizing and characterizing excited states from time-dependent density functional theory

Time-dependent density functional theory (TD-DFT) is the most widely-used electronic structure method for excited states, due to a favorable combination of low cost and semi-quantitative accuracy in many contexts, even if there are well recognized limitations. This Perspective describes various ways in which excited states from TD-DFT calculations can be visualized and analyzed, both qualitatively and quantitatively. This includes not just orbitals and densities but also well-defined statistical measures of electron-hole separation and of Frenkel-type exciton delocalization. Emphasis is placed on mathematical connections between methods that have often been discussed separately. Particular attention is paid to charge-transfer diagnostics, which provide indicators of when TD-DFT may not be trustworthy due to its categorical failure to describe long-range electron transfer. Measures of exciton size and charge separation that are directly connected to the underlying transition density are recommended over more ad hoc metrics for quantifying charge-transfer character.

Irradiation of Plutonium Tributyl Phosphate Complexes by Ionizing Alpha Particles: A Computational Study

The PUREX solvent extraction process, widely used for recovering uranium and plutonium from spent nuclear fuel, utilizes an organic solvent composed of tributyl phosphate (TBP). The emission of ionizing particles such as alpha particles, resulting from the decay of plutonium, makes the organic solvent vulnerable to degradation. Here, we study the ultrashort time alpha irradiation of tributylphosphate (TBP) and Pu(NO3)4(TBP)2 complex formed in the PUREX process. Electron dynamics is propagated by Real-Time-Dependent Auxiliary Density Functional Theory (RT-TD-ADFT). We investigate the use of previously proposed absorption boundary conditions (ABC) in the molecular orbital space to treat secondary electron emission. Basis set and exchange correlation functional effects with ABC are reported as well as a detailed analysis of the ABC parametrization. Preliminary results on the water molecule and then on TBP show that the phenomenological nature of the ABC parameters necessitates selecting appropriate values for each system under study. Irradiation of free and complexed TBP shows an influence of the ligands on the variation of atomic charges on the femtosecond time scale. An accumulation of atomic charges in the alkyl chains of TBP is observed in the case where the nitrate groups are predominantly irradiated. In addition, we find that the Pu atom regains its electric charge very rapidly after being hit by the projectile, with the coordination sphere serving as an electron reservoir to preserve its formal redox state. This study paves the road toward a full understanding of the degradation of organic extracants employed in the nuclear industry.

Modulating the Electronic Coordination Configuration and d-Band Center in Homo-Diatomic Fe2N6 Catalysts for Enhanced Peroxymonosulfate Activation

The electronic coordination configuration of metal active sites and the reaction mechanism were investigated by constructing homo-diatomic Fe sites for visible-light-assisted heterogeneous peroxymonosulfate (PMS) activation. A novel Fe₂N₆ catalyst was synthesized by selecting uniform pyridinic-N of graphitic carbon nitride (g-C₃N₄) as anchoring sites. The results demonstrated that homo-diatomic Fe sites modulated the d-band center and electron delocalization and thus enhanced the PMS activation kinetics (3.58 times vs single-atom Fe catalyst) with k_obs of 0.111 min^-1 owing to the synergistic effect between adjacent Fe atoms. New Fe-Fe coordination significantly decreased the contribution of the antibonding state in the Fe-O bond due to the coupling of the Fe-3d orbitals, which facilitated the O-O bond cleavage of the Fe₂-HOO-SO₃ complex with a reduced thermodynamic energy barrier of only -0.29 eV. This work provided comprehensive mechanistic insights into developing homo-diatomic catalysts governed by the coordination configuration and radical pathway for efficient heterogeneous PMS catalysis.

Effects of electronic correlation on the high harmonic generation in helium: a time-dependent configuration interaction singles vs time-dependent full configuration interaction study

In this paper, we investigate the effects of full electronic correlation on the high harmonic generation in the helium atom subjected to laser pulses of extremely high intensity. To do this, we perform real-time propagations of the helium atom wavefunction using quantum chemistry methods coupled to Gaussian basis sets. The calculations are done within the real-time time-dependent configuration interaction framework, at two levels of theory: time-dependent configuration interation with single excitations (TD-CIS, uncorrelated method) and time-dependent full configuration interaction (TD-FCI, fully correlated method). The electronic wavefunction is expanded in Dunning basis sets supplemented with functions adapted to describing highly excited and continuum states. We also compare the TD-CI results with grid-based propagations of the helium atom within the single-active-electron approximation. Our results show that when including the dynamical electron correlation, a noticeable improvement to the description of HHG can be achieved, in terms of e.g. a more constant intensity in the lower energy part of the harmonic plateau. However, such effects can be captured only if the basis set used suffices to reproduce the most basic features, such as the HHG cutoff position, at the uncorrelated level of theory.

Environment Effects on X-Ray Absorption Spectra With Quantum Embedded Real-Time Time-Dependent Density Functional Theory Approaches

In this work we implement the real-time time-dependent block-orthogonalized Manby-Miller embedding (rt-BOMME) approach alongside our previously developed real-time frozen density embedding time-dependent density functional theory (rt-TDDFT-in-DFT FDE) code, and investigate these methods’ performance in reproducing X-ray absorption spectra (XAS) obtained with standard rt-TDDFT simulations, for model systems comprised of solvated fluoride and chloride ions ([X@(H2O)8−, X = F, Cl). We observe that for ground-state quantities such as core orbital energies, the BOMME approach shows significantly better agreement with supermolecular results than FDE for the strongly interacting fluoride system, while for chloride the two embedding approaches show more similar results. For the excited states, we see that while FDE (constrained not to have the environment densities relaxed in the ground state) is in good agreement with the reference calculations for the region around the K and L1 edges, and is capable of reproducing the splitting of the 1s1 (n + 1)p1 final states (n + 1 being the lowest virtual p orbital of the halides), it by and large fails to properly reproduce the 1s1 (n + 2)p1 states and misses the electronic states arising from excitation to orbitals with important contributions from the solvent. The BOMME results, on the other hand, provide a faithful qualitative representation of the spectra in all energy regions considered, though its intrinsic approximation of employing a lower-accuracy exchange-correlation functional for the environment induces non-negligible shifts in peak positions for the excitations from the halide to the environment. Our results thus confirm that QM/QM embedding approaches are viable alternatives to standard real-time simulations of X-ray absorption spectra of species in complex or confined environments.

Time-dependentab initioapproaches for high-harmonic generation spectroscopy

High-harmonic generation (HHG) is a nonlinear physical process used for the production of ultrashort pulses in XUV region, which are then used for investigating ultrafast phenomena in time-resolved spectroscopies. Moreover, HHG signal itself encodes information on electronic structure and dynamics of the target, possibly coupled to the nuclear degrees of freedom. Investigating HHG signal leads to HHG spectroscopy, which is applied to atoms, molecules, solids and recently also to liquids. Analysing the number of generated harmonics, their intensity and shape gives a detailed insight of, e.g., ionisation and recombination channels occurring in the strong-field dynamics. A number of valuable theoretical models has been developed over the years to explain and interpret HHG features, with the three-step model being the most known one. Originally, these models neglect the complexity of the propagating electronic wavefunction, by only using an approximated formulation of ground and continuum states. Many effects unravelled by HHG spectroscopy are instead due to electron correlation effects, quantum interference, and Rydberg-state contributions, which are all properly captured by anab initioelectronic-structure approach. In this review we have collected recent advances in modelling HHG by means ofab initiotime-dependent approaches relying on the propagation of the time-dependent Schrödinger equation (or derived equations) in presence of a very intense electromagnetic field. We limit ourselves to gas-phase atomic and molecular targets, and to solids. We focus on the various levels of theory employed for describing the electronic structure of the target, coupled with strong-field dynamics and ionisation approaches, and on the basis used to represent electronic states. Selected applications and perspectives for future developments are also given.

Nucleic Acids under Stress: Understanding and Simulating Nucleobase Fragmentation Pathways

The effects of radiations on nucleic acids and their constituents is widely studied across several research fields using different experimental and theoretical protocols. While a large number of studies were performed in this context, many fundamental physical and chemical effects are still being investigated, particularly involving the effect of the biological environment. As an example, the interpretation of experimental nucleic acid bases mass spectra, and hence inferring their reactivity in complex environment still poses great challenge. This Minireview summarizes recent theoretical advancements aiming to predict and interpret the reactivity of nucleic acid bases. We focus not only on the understanding of the inherent fragmentation pathways of isolated nucleobases but also on the modeling of a realistic nano-environments highlighting the importance of molecular dynamics simulations and the non-innocent role of the environment and also the possibility to open novel fragmentation pathways.

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.

Role of exchange and correlation in high-harmonic generation spectra of H2, N2, and CO2: Real-time time-dependent electronic-structure approaches

This study arises from the attempt to answer the following question: how different descriptions of electronic exchange and correlation affect the high-harmonic generation (HHG) spectroscopy of H₂, N₂, and CO₂ molecules? We compare HHG spectra for H₂, N₂, and CO₂ with different ab initio electronic structure methods: real-time time-dependent configuration interaction and real-time time-dependent density functional theory (RT-TDDFT) using truncated basis sets composed of correlated wave functions expanded on Gaussian basis sets. In the framework of RT-TDDFT, we employ Perdew-Burke-Ernzerhof (PBE) and long-range corrected Perdew-Burke-Ernzerhof (LC-ωPBE) functionals. We study HHG spectroscopy by disentangling the effect of electronic exchange and correlation. We first analyze the electronic exchange alone, and in the case of RT-TDDFT with LC-ωPBE, we use ω = 0.3 and ω = 0.4 to tune the percentage of long-range Hartree-Fock exchange and short-range exchange PBE. Then, we added the correlation as described by the PBE functional. All the methods give very similar HHG spectra, and they seem not to be particularly sensitive to the different description of exchange and correlation or to the correct asymptotic behavior of the Coulomb potential. Despite this general trend, some differences are found in the region connecting the cutoff and the background. Here, the harmonics can be resolved with different accuracy depending on the theoretical schemes used. We believe that the investigation of the molecular continuum and its coupling with strong fields merits further theoretical investigations in the near future.

Analysis and visualization of energy densities. I. Insights from real-time time-dependent density functional theory simulations

In this article, we report a scheme to analyze and visualize the energy density fluctuations during the real-time time-dependent density functional theory (RT-TDDFT) simulations. Using Ag4-N2 complexes as examples, it is shown that the grid-based Kohn-Sham energy density can be computed at each time step using a procedure from Nakai and coworkers. Then the instantaneous energy of each molecular fragment (such as Ag4 and N2) can be obtained by partitioning the Kohn-Sham energy densities using Becke or fragment-based Hirshfeld (FBH) scheme. A strong orientation-dependence is observed for the energy flow between the Ag4 cluster and a nearby N2 molecule in the RT-TDDFT simulations. Future applications of such an energy density analysis in electron dynamics simulations are discussed.

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.

Molecular Simulations with in-deMon2k QM/MM, a Tutorial-Review

deMon2k is a readily available program specialized in Density Functional Theory (DFT) simulations within the framework of Auxiliary DFT. This article is intended as a tutorial-review of the capabilities of the program for molecular simulations involving ground and excited electronic states. The program implements an additive QM/MM (quantum mechanics/molecular mechanics) module relying either on non-polarizable or polarizable force fields. QM/MM methodologies available in deMon2k include ground-state geometry optimizations, ground-state Born-Oppenheimer molecular dynamics simulations, Ehrenfest non-adiabatic molecular dynamics simulations, and attosecond electron dynamics. In addition several electric and magnetic properties can be computed with QM/MM. We review the framework implemented in the program, including the most recently implemented options (link atoms, implicit continuum for remote environments, metadynamics, etc.), together with six applicative examples. The applications involve (i) a reactivity study of a cyclic organic molecule in water; (ii) the establishment of free-energy profiles for nucleophilic-substitution reactions by the umbrella sampling method; (iii) the construction of two-dimensional free energy maps by metadynamics simulations; (iv) the simulation of UV-visible absorption spectra of a solvated chromophore molecule; (v) the simulation of a free energy profile for an electron transfer reaction within Marcus theory; and (vi) the simulation of fragmentation of a peptide after collision with a high-energy proton.