Modified Ehrenfest Formalism for Efficient Large-Scale ab initio Molecular Dynamics

Optical force and torque in near-field excitation of C3H6: A first-principles study using RT-TDDFT

Optical trapping is an effective tool for manipulating micrometer-sized particles, although its application to nanometer-sized particles remains difficult. The field of optical trapping has advanced significantly, incorporating more advanced techniques such as plasmonic structures. However, single-molecule trapping remains a challenge. To achieve a deeper understanding of optical forces acting on molecular systems, a first-principles approach to analyze the optical force on molecules interacting with a plasmonic field is crucial. In our study, the optical force and torque induced by the near-field excitation of C3H6 were investigated using real-time time-dependent density functional theory calculations on real-space grids. The near field from the scanning tunneling probe was adopted as the excitation source for the molecule. The optical force was calculated using the polarization charges induced in the molecule based on Lorentz force. While the optical force and torque calculated as functions of the light energy were in moderate agreement with the oscillator strengths obtained from the far-field excitation of C3H6, a closer correspondence was achieved with the power spectrum of the induced dipole moment using near-field excitation. Time-domain analysis of the optical force suggests that the simultaneous excitation of multiple excited states generally weakens the force because of mismatches between the directions of the induced polarization and the electric field. This study revealed a subtle damping mechanism for the optical force arising from intrinsic electronic states and the influence of beating.

Asynchronous propagation of atomic force and excited electronic charge in GaAs under proton irradiation

The studies for the interaction of energetic particles with matter have greatly contributed to the exploration of material properties under irradiation conditions, such as nuclear safety, medical physics and aerospace applications. In this work, we theoretically simulate the non-adiabatic process for GaAs upon proton irradiation using time-dependent density functional theory, and find that the radial propagation of force on atoms and the excitation of electron in GaAs are non-synchronous process. We calculated the electronic stopping power on proton with the velocity of 0.1-0.6 a.u., agreement with the previous empirical results. After further analyzing the force on atoms and the population of excited electrons, we find that under proton irradiation, the electrons around the host atoms at different distances from the proton trajectories are excited almost simultaneously, especially those regions with relatively high charge density. However, the distant atoms have a significant hysteresis in force, which occurs after the surrounding electrons are excited. In addition, hysteresis in force and electron excitation behavior at different positions are closely related to the velocity of proton. This non-synchronous propagation reveals the microscopic dynamic mechanism of energy deposition into the target material under ion irradiation.

Applications and Advances in Machine Learning Force Fields

Force fields (FFs) form the basis of molecular simulations and have significant implications in diverse fields such as materials science, chemistry, physics, and biology. A suitable FF is required to accurately describe system properties. However, an off-the-shelf FF may not be suitable for certain specialized systems, and researchers often need to tailor the FF that fits specific requirements. Before applying machine learning (ML) techniques to construct FFs, the mainstream FFs were primarily based on first-principles force fields (FPFF) and empirical FFs. However, the drawbacks of FPFF and empirical FFs are high cost and low accuracy, respectively, so there is a growing interest in using ML as an effective and precise tool for reconciling this trade-off in developing FFs. In this review, we introduce the fundamental principles of ML and FFs in the context of machine learning force fields (MLFF). We also discuss the advantages and applications of MLFF compared to traditional FFs, as well as the MLFF toolkits widely employed in numerous applications.

Short-Range Charge Transfer in DNA Base Triplets: Real-Time Tracking of Coherent Fluctuation Electron Transfer

The short-range charge transfer of DNA base triplets has wide application prospects in bioelectronic devices for identifying DNA bases and clinical diagnostics, and the key to its development is to understand the mechanisms of short-range electron dynamics. However, tracing how electrons are transferred during the short-range charge transfer of DNA base triplets remains a great challenge. Here, by means of ab initio molecular dynamics and Ehrenfest dynamics, the nuclear-electron interaction in the thymine-adenine-thymine (TAT) charge transfer process is successfully simulated. The results show that the electron transfer of TAT has an oscillating phenomenon with a period of 10 fs. The charge density difference proves that the charge transfer proportion is as high as 59.817% at 50 fs. The peak position of the hydrogen bond fluctuates regularly between -0.040 and -0.056. The time-dependent Marcus-Levich-Jortner theory proves that the vibrational coupling between nucleus and electron induces coherent electron transfer in TAT. This work provides a real-time demonstration of the short-range coherent electron transfer of DNA base triplets and establishes a theoretical basis for the design and development of novel biological probe molecules.

The contribution of inner electron excitation to the electronic stopping power of palladium for protons

The electronic stopping power of palladium (Pd) for protons is investigated based on time-dependent density functional theory combined with Ehrenfest molecular dynamics simulations. The electronic stopping power of Pd with explicitly considering inner electrons for protons is calculated and the excitation mechanism for the inner electrons of Pd is revealed. The velocity proportionality of the low-energy stopping power of Pd is reproduced. Our study verified that the inner electron excitation contributes significantly to the electronic stopping power of Pd in the high energy range, which is strongly dependent on the impact parameter. The electronic stopping power obtained from the off-channeling geometry is in quantitative agreement with the experimental data in a wide velocity range, and the discrepancy around the stopping maximum is further reduced by considering the relativistic correction on the binding energy of inner electrons. The velocity dependence of the mean steady-state charge of protons is quantified, and the results showed that the participation of 4p-electrons reduces the mean steady-state charge of protons, and consequently decreases the electronic stopping power of Pd in the low energy range.

Shining light on the microscopic resonant mechanism responsible for cavity-mediated chemical reactivity

Strong light-matter interaction in cavity environments is emerging as a promising approach to control chemical reactions in a non-intrusive and efficient manner. The underlying mechanism that distinguishes between steering, accelerating, or decelerating a chemical reaction has, however, remained unclear, hampering progress in this frontier area of research. We leverage quantum-electrodynamical density-functional theory to unveil the microscopic mechanism behind the experimentally observed reduced reaction rate under cavity induced resonant vibrational strong light-matter coupling. We observe multiple resonances and obtain the thus far theoretically elusive but experimentally critical resonant feature for a single strongly coupled molecule undergoing the reaction. While we describe only a single mode and do not explicitly account for collective coupling or intermolecular interactions, the qualitative agreement with experimental measurements suggests that our conclusions can be largely abstracted towards the experimental realization. Specifically, we find that the cavity mode acts as mediator between different vibrational modes. In effect, vibrational energy localized in single bonds that are critical for the reaction is redistributed differently which ultimately inhibits the reaction.

Hybrid Carbon Nanotubes-Graphene Nanostructures: Modeling, Formation, Characterization

A technology for the formation and bonding with a substrate of hybrid carbon nanostructures from single-walled carbon nanotubes (SWCNT) and reduced graphene oxide (rGO) by laser radiation is proposed. Molecular dynamics modeling by the real-time time-dependent density functional tight-binding (TD-DFTB) method made it possible to reveal the mechanism of field emission centers formation in carbon nanostructures layers. Laser radiation stimulates the formation of graphene-nanotube covalent contacts and also induces a dipole moment of hybrid nanostructures, which ensures their orientation along the force lines of the radiation field. The main mechanical and emission characteristics of the formed hybrid nanostructures were determined. By Raman spectroscopy, the effect of laser radiation energy on the defectiveness of all types of layers formed from nanostructures was determined. Laser exposure increased the hardness of all samples more than twice. Maximum hardness was obtained for hybrid nanostructure with a buffer layer (bl) of rGO and the main layer of SWCNT-rGO(bl)-SWCNT and was 54.4 GPa. In addition, the adhesion of rGO to the substrate and electron transport between the substrate and rGO(bl)-SWCNT increased. The rGO(bl)-SWCNT cathode with an area of ~1 mm2 showed a field emission current density of 562 mA/cm2 and stability for 9 h at a current of 1 mA. The developed technology for the formation of hybrid nanostructures can be used both to create high-performance and stable field emission cathodes and in other applications where nanomaterials coating with good adhesion, strength, and electrical conductivity is required.

Nonadiabatic Molecular Dynamics Simulations Based on Time-Dependent Density Functional Tight-Binding Method

Nonadiabatic excited-state molecular dynamics underpin many photophysical and photochemical phenomena, such as exciton dynamics, charge separation and transport. In this work, we present an efficient nonadiabatic molecular dynamic (NAMD) simulation method based on time-dependent density functional tight-binding (TDDFTB) theory. Specifically, the adiabatic electronic structure, an essential NAMD input, is described at the TDDFTB level. The nonadiabatic effects originating from the coupled motions of electrons and nuclei are treated by the trajectory surface hopping algorithm. To improve the computational efficiency, nonadiabatic couplings between excited states within the TDDFTB method are derived and implemented using an analytical approach. Further, the time-dependent nonadiabatic coupling scalars are calculated based on the overlap between molecular orbitals rather than the Slater determinants to speed up the simulations. In addition, the electronic decoherence scheme and a state reassigned unavoided crossings algorithm, which has been implemented in the NEXMD software, are used to improve the accuracy of the simulated dynamics and handle trivial unavoided crossings. Finally, the photoinduced nonadiabatic dynamics of a benzene molecule are simulated to demonstrate our implementation. The results for excited state NAMD simulations of benzene molecule based on TDDFTB method compare well that obtained with numerically expensive time-dependent density functional theory. The proposed methodology provides an attractive theoretical simulation tool for predicting the photophysical and photochemical properties of complex materials.

Probing phonon dynamics with multidimensional high harmonic carrier-envelope-phase spectroscopy

We explore pump-probe high harmonic generation (HHG) from monolayer hexagonal-boron-nitride, where a terahertz pump excites coherent optical phonons that are subsequently probed by an intense infrared pulse that drives HHG. We find, through state-of-the-art ab initio calculations, that the structure of the emission spectrum is attenuated by the presence of coherent phonons and no longer comprises discrete harmonic orders, but rather a continuous emission in the plateau region. The HHG yield strongly oscillates as a function of the pump-probe delay, corresponding to ultrafast changes in the lattice such as specific bond compression or stretching dynamics. We further show that in the regime where the excited phonon period and the pulse duration are of the same order of magnitude, the HHG process becomes sensitive to the carrier-envelope phase (CEP) of the driving field, even though the pulse duration is so long that no such sensitivity is observed in the absence of coherent phonons. The degree of CEP sensitivity versus pump-probe delay is shown to be a highly selective measure for instantaneous structural changes in the lattice, providing an approach for ultrafast multidimensional HHG spectroscopy. Remarkably, the obtained temporal resolution for phonon dynamics is ∼1 femtosecond, which is much shorter than the probe pulse duration because of the inherent subcycle contrast mechanism. Our work paves the way toward routes of probing phonons and ultrafast material structural changes with subcycle temporal resolution and provides a mechanism for controlling the HHG spectrum.

Cavity-Modified Unimolecular Dissociation Reactions via Intramolecular Vibrational Energy Redistribution

While the emerging field of vibrational polariton chemistry has the potential to overcome traditional limitations of synthetic chemistry, the underlying mechanism is not yet well understood. Here, we explore how the dynamics of unimolecular dissociation reactions that are rate-limited by intramolecular vibrational energy redistribution (IVR) can be modified inside an infrared optical cavity. We study a classical model of a bent triatomic molecule, where the two outer atoms are bound by anharmonic Morse potentials to the center atom coupled to a harmonic bending mode. We show that an optical cavity resonantly coupled to particular anharmonic vibrational modes can interfere with IVR and alter unimolecular dissociation reaction rates when the cavity mode acts as a reservoir for vibrational energy. These results lay the foundation for further theoretical work toward understanding the intriguing experimental results of vibrational polaritonic chemistry within the context of IVR.

Analytical Nonadiabatic Couplings and Gradients within the State-Averaged Orbital-Optimized Variational Quantum Eigensolver

We introduce several technical and analytical extensions to our recent state-averaged orbital-optimized variational quantum eigensolver (SA-OO-VQE) algorithm (see Yalouz et al. Quantum Sci. Technol. 2021, 6, 024004). Motivated by the limitations of current quantum computers, the first extension consists of an efficient state-resolution procedure to find the SA-OO-VQE eigenstates, and not just the subspace spanned by them, while remaining in the equi-ensemble framework. This approach avoids expensive intermediate resolutions of the eigenstates by postponing this problem to the very end of the full algorithm. The second extension allows for the estimation of analytical gradients and nonadiabatic couplings, which are crucial in many practical situations ranging from the search of conical intersections to the simulation of quantum dynamics, in, for example, photoisomerization reactions. The accuracy of our new implementations is demonstrated on the formaldimine molecule CH₂NH (a minimal Schiff base model relevant for the study of photoisomerization in larger biomolecules), for which we also perform a geometry optimization to locate a conical intersection between the ground and first-excited electronic states of the molecule.

Inq, a Modern GPU-Accelerated Computational Framework for (Time-Dependent) Density Functional Theory

We present inq, a new implementation of density functional theory (DFT) and time-dependent DFT (TDDFT) written from scratch to work on graphic processing units (GPUs). Besides GPU support, inq makes use of modern code design features and takes advantage of newly available hardware. By designing the code around algorithms, rather than against specific implementations and numerical libraries, we aim to provide a concise and modular code. The result is a fairly complete DFT/TDDFT implementation in roughly 12 000 lines of open-source C++ code representing a modular platform for community-driven application development on emerging high-performance computing architectures.

Laser-Induced Electronic and Vibronic Dynamics in the Pyrene Molecule and Its Cation

Among polycyclic aromatic hydrocarbons, pyrene is widely used as an optical probe thanks to its peculiar ultraviolet absorption and infrared emission features. Interestingly, this molecule is also an abundant component of the interstellar medium, where it is detected via its unique spectral fingerprints. In this work, we present a comprehensive first-principles study on the electronic and vibrational response of pyrene and its cation to ultrafast, coherent pulses in resonance with their optically active excitations in the ultraviolet region. The analysis of molecular symmetries, electronic structure, and linear optical spectra is used to interpret transient absorption spectra and kinetic energy spectral densities computed for the systems excited by ultrashort laser fields. By disentangling the effects of the electronic and vibrational dynamics via ad hoc simulations with stationary and moving ions, and, in specific cases, with the aid of auxiliary model systems, we rationalize that the nuclear motion is mainly harmonic in the neutral species, while strong anharmonic oscillations emerge in the cation, driven by electronic coherence. Our results provide additional insights into the ultrafast vibronic dynamics of pyrene and related compounds and set the stage for future investigations on more complex carbon-conjugated molecules.

High-order geometric integrators for representation-free Ehrenfest dynamics

Ehrenfest dynamics is a useful approximation for ab initio mixed quantum-classical molecular dynamics that can treat electronically nonadiabatic effects. Although a severe approximation to the exact solution of the molecular time-dependent Schrödinger equation, Ehrenfest dynamics is symplectic, is time-reversible, and conserves exactly the total molecular energy as well as the norm of the electronic wavefunction. Here, we surpass apparent complications due to the coupling of classical nuclear and quantum electronic motions and present efficient geometric integrators for "representation-free" Ehrenfest dynamics, which do not rely on a diabatic or adiabatic representation of electronic states and are of arbitrary even orders of accuracy in the time step. These numerical integrators, obtained by symmetrically composing the second-order splitting method and exactly solving the kinetic and potential propagation steps, are norm-conserving, symplectic, and time-reversible regardless of the time step used. Using a nonadiabatic simulation in the region of a conical intersection as an example, we demonstrate that these integrators preserve the geometric properties exactly and, if highly accurate solutions are desired, can be even more efficient than the most popular non-geometric integrators.

Simulating electronic excitation and dynamics with real-time propagation approach to TDDFT within plane-wave pseudopotential formulation

We give a perspective on simulating electronic excitation and dynamics using the real-time propagation approach to time-dependent density functional theory (RT-TDDFT) in the plane-wave pseudopotential formulation. RT-TDDFT is implemented in various numerical formalisms in recent years, and its practical application often dictates the most appropriate implementation of the theory. We discuss recent developments and challenges, emphasizing numerical aspects of studying real systems. Several applications of RT-TDDFT simulation are discussed to highlight how the approach is used to study interesting electronic excitation and dynamics phenomena in recent years.

Three-state harmonic models for photoinduced charge transfer

A widely used strategy for simulating the charge transfer between donor and acceptor electronic states in an all-atom anharmonic condensed-phase system is based on invoking linear response theory to describe the system in terms of an effective spin-boson model Hamiltonian. Extending this strategy to photoinduced charge transfer processes requires also taking into consideration the ground electronic state in addition to the excited donor and acceptor electronic states. In this paper, we revisit the problem of describing such nonequilibrium processes in terms of an effective three-state harmonic model. We do so within the framework of nonequilibrium Fermi's golden rule (NE-FGR) in the context of photoinduced charge transfer in the carotenoid-porphyrin-C₆₀ (CPC₆₀) molecular triad dissolved in explicit tetrahydrofuran (THF). To this end, we consider different ways for obtaining a three-state harmonic model from the equilibrium autocorrelation functions of the donor-acceptor, donor-ground, and acceptor-ground energy gaps, as obtained from all-atom molecular dynamics simulations of the CPC₆₀/THF system. The quantum-mechanically exact time-dependent NE-FGR rate coefficients for two different charge transfer processes in two different triad conformations are then calculated using the effective three-state model Hamiltonians as well as a hierarchy of more approximate expressions that lead to the instantaneous Marcus theory limit. Our results show that the photoinduced charge transfer in CPC₆₀/THF can be described accurately by the effective harmonic three-state models and that nuclear quantum effects are small in this system.

Direct Measurement of Electron-Phonon Coupling with Time-Resolved ARPES

Time- and angular- resolved photoelectron spectroscopy is a powerful technique to measure electron dynamics in solids. Recent advances in this technique have facilitated band and energy resolved observations of the effect that excited phonons, have on the electronic structure. Here, we show with the help of ab initio simulations that the Fourier analysis of the time-resolved measurements of solids with excited phonon modes enables the determination of the band- and mode-resolved electron-phonon coupling directly from the experimental data without any additional input from theory. Such an observation is not restricted to regions of strong electron-phonon coupling and does not require strongly excited or hot phonons, but can be employed to monitor the dynamical renormalization of phonons in driven phases of matter.

Understanding real-time time-dependent density-functional theory simulations of ultrafast laser-induced dynamics in organic molecules

Real-time time-dependent density functional theory, in conjunction with the Ehrenfest molecular dynamics scheme, is becoming a popular methodology to investigate ultrafast phenomena on the nanoscale. Thanks to recent developments, it is also possible to explicitly include in the simulations a time-dependent laser pulse, thereby accessing the transient excitation regime. However, the complexity entailed in these calculations calls for in-depth analysis of the accessible and yet approximate (either "dressed" or "bare") quantities in order to evaluate their ability to provide us with a realistic picture of the simulated processes. In this work, we analyze the ultrafast dynamics of three small molecules (ethylene, benzene, and thiophene) excited by a resonant laser pulse in the framework of the adiabatic local-density approximation. The electronic response to the laser perturbation in terms of induced dipole moment and excited-state population is compared to the results given by an exactly solvable two-level model. In this way, we can interpret the charge-carrier dynamics in terms of simple estimators, such as the number of excited electrons. From the computed transient absorption spectra, we unravel the appearance of nonlinear effects such as excited-state absorption and vibronic coupling. In this way, we observe that the laser excitation affects the vibrational spectrum by enhancing the anharmonicities therein, while the coherent vibrational motion contributes to stabilizing the electronic excitation already within a few tens of femtoseconds.

Real-Time Time-Dependent Nuclear-Electronic Orbital Approach: Dynamics beyond the Born-Oppenheimer Approximation

The quantum mechanical treatment of both electrons and nuclei is crucial in nonadiabatic dynamical processes such as proton-coupled electron transfer. The nuclear-electronic orbital (NEO) method provides an elegant framework for including nuclear quantum effects beyond the Born-Oppenheimer approximation. To enable the study of nonequilibrium properties, we derive and implement a real-time NEO (RT-NEO) approach based on time-dependent Hatree-Fock or density functional theory, in which the electronic and nuclear degrees of freedom are propagated in a time-dependent variational framework. Nuclear and electronic spectral features can be resolved from the time-dependent dipole moment computed using the RT-NEO method. The test cases show the dynamical interplay between the quantum nuclei and the electrons through vibronic coupling. Moreover, vibrational excitation in the RT-NEO approach is demonstrated by applying a resonant driving field, and electronic excitation is demonstrated by simulating excited state intramolecular proton transfer. This work shows that the RT-NEO approach is a promising tool to study nonadiabatic quantum dynamical processes within a time-dependent variational description for the coupled electronic and nuclear degrees of freedom.

Octopus, a computational framework for exploring light-driven phenomena and quantum dynamics in extended and finite systems

Over the last few years, extraordinary advances in experimental and theoretical tools have allowed us to monitor and control matter at short time and atomic scales with a high degree of precision. An appealing and challenging route toward engineering materials with tailored properties is to find ways to design or selectively manipulate materials, especially at the quantum level. To this end, having a state-of-the-art ab initio computer simulation tool that enables a reliable and accurate simulation of light-induced changes in the physical and chemical properties of complex systems is of utmost importance. The first principles real-space-based Octopus project was born with that idea in mind, i.e., to provide a unique framework that allows us to describe non-equilibrium phenomena in molecular complexes, low dimensional materials, and extended systems by accounting for electronic, ionic, and photon quantum mechanical effects within a generalized time-dependent density functional theory. This article aims to present the new features that have been implemented over the last few years, including technical developments related to performance and massive parallelism. We also describe the major theoretical developments to address ultrafast light-driven processes, such as the new theoretical framework of quantum electrodynamics density-functional formalism for the description of novel light-matter hybrid states. Those advances, and others being released soon as part of the Octopus package, will allow the scientific community to simulate and characterize spatial and time-resolved spectroscopies, ultrafast phenomena in molecules and materials, and new emergent states of matter (quantum electrodynamical-materials).

Electronic stopping power for slow ions in the low-hardness semimetal HgTe using first-principles calculations

The electronic stopping power for low-velocity ions (including protons, [Formula: see text]-particles, and [Formula: see text]) is investigated in a novel semimetal HgTe system, where the data are obtained with the aid of Ehrenfest dynamics combined with time-dependent density functional theory. For the light projectile ions (protons and [Formula: see text]-particles), the linear and nonlinear behaviors of electronic stopping power in three different channel directions are analyzed in detail. In the case where the projectile ion is a proton, the linear results for the threshold velocity are correlated with an indirect band gap; the direction of the electronic stopping power depends on the radial drag force, the channeling electronic density and the trapped charge. More notably, we report an interesting channel-geometry fact, i.e. that the electronic stopping power of HgTe is powerfully modulated by the impact parameters. The parallel off-center tracks increase the electronic stopping power, making it more consistent with the SRIM data. In the case of an [Formula: see text]-particle as the projectile ion, nonlinear behavior that varies with velocity can be ascribed to the charge transfer, which is another mode of energy dissipation. In addition, when the slightly heavier projectile [Formula: see text] travels through the medium HgTe, the projectile [Formula: see text] can capture more free charges than the protons and [Formula: see text]-particles under the same circumstances. Especially, for the projectile in the off-channel, the electronic stopping power is close to the SRIM data with the decrease of the impact parameter. These results extend the study of radiation damage to a new field of materials.

Cavity-Correlated Electron-Nuclear Dynamics from First Principles

The rapidly developing and converging fields of polaritonic chemistry and quantum optics necessitate a unified approach to predict strongly correlated light-matter interactions with atomic-scale resolution. Toward this overarching goal, we introduce a general time-dependent density-functional theory to study correlated electron, nuclear, and photon interactions on the same quantized footing. We complement our theoretical formulation with the first ab initio calculation of a correlated electron-nuclear-photon system. For a CO_{2} molecule in an optical cavity, we construct the infrared spectra exhibiting Rabi splitting between the upper and lower polaritonic branches, time-dependent quantum-electrodynamical observables such as the electric displacement field, and observe cavity-modulated molecular motion. Our work opens an important new avenue in introducing ab initio methods to the nascent field of collective strong vibrational light-matter interactions.

Propagators for the Time-Dependent Kohn-Sham Equations: Multistep, Runge-Kutta, Exponential Runge-Kutta, and Commutator Free Magnus Methods

We examine various integration schemes for the time-dependent Kohn-Sham equations. Contrary to the time-dependent Schrödinger's equation, this set of equations is nonlinear, due to the dependence of the Hamiltonian on the electronic density. We discuss some of their exact properties, and in particular their symplectic structure. Four different families of propagators are considered, specifically the linear multistep, Runge-Kutta, exponential Runge-Kutta, and the commutator-free Magnus schemes. These have been chosen because they have been largely ignored in the past for time-dependent electronic structure calculations. The performance is analyzed in terms of cost-versus-accuracy. The clear winner, in terms of robustness, simplicity, and efficiency is a simplified version of a fourth-order commutator-free Magnus integrator. However, in some specific cases, other propagators, such as some implicit versions of the multistep methods, may be useful.

Computational Methods for Ab Initio Molecular Dynamics

Ab initio molecular dynamics is an irreplaceable technique for the realistic simulation of complex molecular systems and processes from first principles. This paper proposes a comprehensive and self-contained review of ab initio molecular dynamics from a computational perspective and from first principles. Quantum mechanics is presented from a molecular dynamics perspective. Various approximations and formulations are proposed, including the Ehrenfest, Born–Oppenheimer, and Hartree–Fock molecular dynamics. Subsequently, the Kohn–Sham formulation of molecular dynamics is introduced as well as the afferent concept of density functional. As a result, Car–Parrinello molecular dynamics is discussed, together with its extension to isothermal and isobaric processes. Car–Parrinello molecular dynamics is then reformulated in terms of path integrals. Finally, some implementation issues are analysed, namely, the pseudopotential, the orbital functional basis, and hybrid molecular dynamics.

Assessment of Real-Time Time-Dependent Density Functional Theory (RT-TDDFT) in Radiation Chemistry: Ionized Water Dimer

Ionization in the condensed phase and molecular clusters leads to a complicated chain of processes with coupled electron-nuclear dynamics. It is difficult to describe such dynamics with conventional nonadiabatic molecular dynamics schemes since the number of states swiftly increases as the molecular system grows. It is therefore attractive to use a direct electron and nuclear propagation such as the real-time time-dependent density functional theory (RT-TDDFT). Here we report a RT-TDDFT benchmark study on simulations of singly and doubly ionized states of a water monomer and dimer as a prototype for more complex processes in a condensed phase. We employed the RT-TDDFT based Ehrenfest molecular dynamics with a generalized gradient approximate (GGA) functional and compared it with wave-function-based surface hopping (SH) simulations. We found that the initial dynamics of a singly HOMO ionized water dimer is similar for both the RT-TDDFT/GGA and the SH simulations but leads to completely different reaction channels on a longer time scale. This failure is attributed to the self-interaction error in the GGA functionals and it can be avoided by using hybrid functionals with large fraction of exact exchange (represented here by the BHandHLYP functional). The simulations of doubly ionized states are reasonably described already at the GGA level. This suggests that the RT-TDDFT/GGA method could describe processes following the autoionization processes such as Auger emission, while its applicability to more complex processes such as intermolecular Coulombic decay remains limited.

Quantum modeling of ultrafast photoinduced charge separation

Phenomena involving electron transfer are ubiquitous in nature, photosynthesis and enzymes or protein activity being prominent examples. Their deep understanding thus represents a mandatory scientific goal. Moreover, controlling the separation of photogenerated charges is a crucial prerequisite in many applicative contexts, including quantum electronics, photo-electrochemical water splitting, photocatalytic dye degradation, and energy conversion. In particular, photoinduced charge separation is the pivotal step driving the storage of sun light into electrical or chemical energy. If properly mastered, these processes may also allow us to achieve a better command of information storage at the nanoscale, as required for the development of molecular electronics, optical switching, or quantum technologies, amongst others. In this Topical Review we survey recent progress in the understanding of ultrafast charge separation from photoexcited states. We report the state-of-the-art of the observation and theoretical description of charge separation phenomena in the ultrafast regime mainly focusing on molecular- and nano-sized solar energy conversion systems. In particular, we examine different proposed mechanisms driving ultrafast charge dynamics, with particular regard to the role of quantum coherence and electron-nuclear coupling, and link experimental observations to theoretical approaches based either on model Hamiltonians or on first principles simulations.

Real-space grids and the Octopus code as tools for the development of new simulation approaches for electronic systems

Real-space grids are a powerful alternative for the simulation of electronic systems. One of the main advantages of the approach is the flexibility and simplicity of working directly in real space where the different fields are discretized on a grid, combined with competitive numerical performance and great potential for parallelization. These properties constitute a great advantage at the time of implementing and testing new physical models. Based on our experience with the Octopus code, in this article we discuss how the real-space approach has allowed for the recent development of new ideas for the simulation of electronic systems. Among these applications are approaches to calculate response properties, modeling of photoemission, optimal control of quantum systems, simulation of plasmonic systems, and the exact solution of the Schrödinger equation for low-dimensionality systems.

Optical field terahertz amplitude modulation by graphene nanoribbons

In this study, first-principles time-dependent density functional theory calculations were used to demonstrate the possibility to modulate the amplitude of the optical electric field (E-field) near a semiconducting graphene nanoribbon. A significant enhancement of the optical E-field was observed 3.34 Å above the graphene nanoribbon sheet, with an amplitude modulation of approximately 100 fs, which corresponds to a frequency of 10 THz. In general, a six-fold E-field enhancement could be obtained, which means that the power of the obtained THz is about 36 times that of incident UV light. We suggest the use of semiconducting graphene nanoribbons for converting visible and UV light into a THz signal.

Modifying the interlayer interaction in layered materials with an intense IR laser

We propose a transient interlayer compression in two-dimensional compound materials by using an intense IR laser resonant with the out-of-plane optical phonon mode (A(2u) mode). As a test case, we studied bilayer hexagonal boron nitride (h-BN), which is one of the compound layered materials. Excited state molecular dynamics calculations using time-dependent density functional theory show an 11.3% transient interlayer contraction of h-BN due to an interlayer dipole-dipole attraction of the laser-pumped A(2u) mode. These results are applicable to other layered compound materials. Such layered materials are a good material for nanospace chemistry, e.g., intercalating molecules and acting with them, and IR irradiation to contract the interlayer distance could provide a new route for chemical reactions under pressure. The duration of the contraction is at least 1 ps in the current simulation, which is observable by high-speed electron-beam diffraction measurements.

The effects of electron transfer on the energy loss of slow He²⁺, C²⁺, and C⁴⁺ ions penetrating a graphene fragment

Electronic energy loss in the collision processes of slow ions with a graphene fragment is investigated by combining ab initio time-dependent density functional theory calculations for electrons with molecular dynamics simulations for ions in real time and real space. We study the electronic energy loss of slow He²⁺, C²⁺, and C⁴⁺ ions penetrating the graphene fragment as a function of the ion velocity, and establish the velocity-proportional energy loss for low-charged ions down to 0.1 a.u. One mechanism clarified in the simulations for electron transfer is polarization capture, which is effective for bare ions at low velocities. The other one is resonance capture, by which the incident ion can capture electrons from the graphene fragment to its electron affinity levels, which have the same, or nearly the same, energy as those of the electron donor levels. The results demonstrate that the nonlinear behavior of energy loss of C⁴⁺ is attributed to the large number of electrons captured by this multi-charged ion during the collision.

Quantum coherence controls the charge separation in a prototypical artificial light-harvesting system

The efficient conversion of light into electricity or chemical fuels is a fundamental challenge. In artificial photosynthetic and photovoltaic devices, this conversion is generally thought to happen on ultrafast, femto-to-picosecond timescales and to involve an incoherent electron transfer process. In some biological systems, however, there is growing evidence that the coherent motion of electronic wavepackets is an essential primary step, raising questions about the role of quantum coherence in artificial devices. Here we investigate the primary charge-transfer process in a supramolecular triad, a prototypical artificial reaction centre. Combining high time-resolution femtosecond spectroscopy and time-dependent density functional theory, we provide compelling evidence that the driving mechanism of the photoinduced current generation cycle is a correlated wavelike motion of electrons and nuclei on a timescale of few tens of femtoseconds. We highlight the fundamental role of the interface between chromophore and charge acceptor in triggering the coherent wavelike electron-hole splitting.

In artificial photosynthetic devices, conversion of light into electricity is thought to involve an incoherent electron transfer process. Rozzi et al. provide evidence for quantum-correlated wavelike motion inducing the ultrafast photoinduced electronic charge transfer in a light-harvesting supramolecular triad.

Ab initio molecular dynamics

In this chapter, an introduction to ab initio molecular dynamics (AIMD) has been given. Many of the basic concepts, like the Hellman-Feynman forces, the difference between the Car-Parrinello molecular dynamics and AIMD, have been explained. Also a very versatile AIMD code, the CP2K, has been introduced. On the application, the emphasis was on the aqueous systems and chemical reactions. The biochemical applications have not been discussed in depth.