Real-Time TD-DFT with Classical Ion Dynamics: Methodology and Applications

Total absorption spectrum of benzene aggregates obtained from two different approaches

CONTEXT

The study of molecular aggregation effects on the electronic spectrum is essential for the development of optoelectronic devices. However, investigating the entire valence absorption spectrum of aggregates using quantum mechanical methods is a challenging task. In this work, we perform systematic simulations of the absorption spectrum of benzene molecular clusters up to 35 eV applying two approaches based on time-dependent density functional theory. The results show that depending on the dimer packing, different energy shifts occur for the symmetry allowed [Formula: see text] transition, in comparison to the monomer. The transition intensity increases for the band around 6 eV for larger aggregates from the monomer to dimers and tetramer, indicating the occurrence of the symmetry forbidden (in [Formula: see text] point group) [Formula: see text] [Formula: see text] transition. The benzene crystal exhibits a large redshift following the experimental spectrum. Also, the continuum regions of all spectra show a good agreement with the experiments both in gas and solid phases.

METHODS

Geometry optimization of the monomer was carried out with Gaussian 09 software using the PBE0/def2-TZVP level of theory. We used dimers and tetramer molecular geometries extracted from the experimental crystal structure. The absorption spectra were directly obtained by the Liouville-Lanczos TDDFT approach with plane waves basis set or indirectly by TDDFT pseudo-spectra calculated in a [Formula: see text] basis followed by analytic continuation procedure to obtain complex polarizability. The former is available at Quantum ESPRESSO, and the latter was calculated using Gaussian 09 with the post-processing performed with a code previously developed in our group.

Exploration of the origin of the excellent charge-carrier dynamics in Ruddlesden-Popper oxysulfide perovskite Y2Ti2O5S2

Although the efficient separation of electron-hole (e-h) pairs is one of the most sought-after electronic characteristics of materials, due to thermally induced atomic motion and other factors, they do not remain separated during the carrier transport process, potentially leading to rapid carrier recombination. Here, we utilized real-time time-dependent density functional theory in combination with nonadiabatic molecular dynamics (NAMD) to explore the separated dynamic transport path within Ruddlesden-Popper oxysulfide perovskite Y2Ti2O5S2 caused by the dielectric layer and phonon frequency difference. The underlying origin of the efficient overall water splitting in Y2Ti2O5S2 is systematically explored. We report the existence of the bi-directional e-h separate-path transport, in which, the electrons transport in the Ti2O5 layer and the holes diffuse in the rock-salt layer. This is in contrast to the conventional e-h separated distribution with a crowded transport channel, as observed in SrTiO3 and hybrid perovskites. Such a unique feature finally results in a long carrier lifetime of 321 ns, larger than that in the SrTiO3 perovskite (160 ns) with only one carrier transport channel. This work provides insights into the carrier transport in lead-free perovskites and yields a novel design strategy for next-generation functionalized optoelectronic devices.

Optically Induced Multistage Phase Transition in Coherent Phonon-Dominated a-GeTe

Ultrafast photoexcitation can decouple the multilevel nonequilibrium dynamics of electron-lattice interactions, providing an ideal probe for dissecting photoinduced phase transition in solids. Here, real-time time-dependent density functional theory simulations combined with occupation-constrained DFT methods are employed to explore the nonadiabatic paths of optically excited a-GeTe. Results show that the short-wavelength ultrafast laser is capable of generating full-domain carrier excitation and repopulation, whereas the long-wavelength ultrafast laser favors the excitation of lone pair electrons in the antibonded state. Photodoping makes the double-valley potential energy surface shallower and allows the insertion of A_1g coherent forces in the atomic pairs, by which the phase reversal of Ge and Te atoms in the ⟨001⟩ direction is activated with ultrafast suppression of the Peierls distortion. These findings have far-reaching implications regarding nonequilibrium phase engineering strategies based on phase-change materials.

Ab initio real-time quantum dynamics of charge carriers in momentum space

Application of the non-adiabatic molecular dynamics (NAMD) approach is limited to studying carrier dynamics in the momentum space, as a supercell is required to sample the phonon excitation and electron-phonon (e-ph) interaction at different momenta in a molecular dynamics simulation. Here we develop an ab initio approach for the real-time charge carrier quantum dynamics in the momentum space (NAMD_k) by directly introducing e-ph coupling into the Hamiltonian based on the harmonic approximation. The NAMD_k approach maintains the zero-point energy and includes memory effects of carrier dynamics. The application of NAMD_k to the hot carrier dynamics in graphene reveals the phonon-specific relaxation mechanism. An energy threshold of 0.2 eV-defined by two optical phonon modes-separates the hot electron relaxation into fast and slow regions with lifetimes of pico- and nanoseconds, respectively. The NAMD_k approach provides an effective tool to understand real-time carrier dynamics in the momentum space for different materials.

Accelerating Real-Time Coupled Cluster Methods with Single-Precision Arithmetic and Adaptive Numerical Integration

We explore the framework of a real-time coupled cluster method with a focus on improving its computational efficiency. Propagation of the wave function via the time-dependent Schrödinger equation places high demands on computing resources, particularly for high level theories such as coupled cluster with polynomial scaling. Similar to earlier investigations of coupled cluster properties, we demonstrate that the use of single-precision arithmetic reduces both the storage and multiplicative costs of the real-time simulation by approximately a factor of 2 with no significant impact on the resulting UV/vis absorption spectrum computed via the Fourier transform of the time-dependent dipole moment. Additional speedups─of up to a factor of 14 in test simulations of water clusters─are obtained via a straightforward GPU-based implementation as compared to conventional CPU calculations. We also find that further performance optimization is accessible through sagacious selection of numerical integration algorithms, and the adaptive methods, such as the Cash-Karp integrator, provide an effective balance between computing costs and numerical stability. Finally, we demonstrate that a simple mixed-step integrator based on the conventional fourth-order Runge-Kutta approach is capable of stable propagations even for strong external fields, provided the time step is appropriately adapted to the duration of the laser pulse with only minimal computational overhead.

Nonadiabatic Molecular Dynamics by Multiconfiguration Pair-Density Functional Theory

We present the first implementation of multiconfiguration pair-density functional theory (MC-PDFT) ab initio molecular dynamics. MC-PDFT is a multireference electronic structure method that in many cases has a similar accuracy (or even better accuracy) the complete active space second-order perturbation theory (CASPT2) at a significantly lower computational cost. In this study, we introduced MC-PDFT analytical gradients into the SHARC molecular dynamics program for ab initio, nonadiabatic molecular dynamics simulations. We verify our implementation by examining the intersystem crossing dynamics of thioformaldehyde, and we observe excellent agreement with recent CASPT2 and experimental findings. Moreover, with MC-PDFT, we could perform dynamics simulations with the 12 electron in 10 orbitals active space that was computationally too expensive for direct dynamics with CASPT2.

Imaging of femtosecond bond breaking and charge dynamics in ultracharged peptides

X-ray free-electrons lasers have revolutionized the method of imaging biological macromolecules such as proteins, viruses and cells by opening the door to structural determination of both single particles and crystals at room temperature. By utilizing high intensity X-ray pulses on femtosecond timescales, the effects of radiation damage can be reduced. Achieving high resolution structures will likely require knowledge of how radiation damage affects the structure on an atomic scale, since the experimentally obtained electron densities will be reconstructed in the presence of radiation damage. Detailed understanding of the expected damage scenarios provides further information, in addition to guiding possible corrections that may need to be made to obtain a damage free reconstruction. In this work, we have quantified the effects of ionizing photon-matter interactions using first principles molecular dynamics. We utilize density functional theory to calculate bond breaking and charge dynamics in three ultracharged molecules and two different structural conformations that are important to the structural integrity of biological macromolecules, comparing to our previous studies on amino acids. The effects of the ultracharged states and subsequent bond breaking in real space are studied in reciprocal space using coherent diffractive imaging of an ensemble of aligned biomolecules in the gas phase.

Manipulation of Stacking Order in Td-WTe2 by Ultrafast Optical Excitation

Subtle changes in stacking order of layered transition metal dichalcogenides may have profound influence on the electronic and optical properties. The intriguing electronic properties of Td-WTe2 can be traced to the break of inversion symmetry resulting from the ground-state stacking sequence. Strategies for perturbation of the stacking order are actively pursued for intentional tuning of material properties, where optical excitation is of specific interest since it holds the potential for integration of ultrafast switches in future device designs. Here we investigate the structural response in Td-WTe2 following ultrafast photoexcitation by time-resolved electron diffraction. A 0.23 THz shear phonon, involving layer displacement along the b axis, was excited by a 515 nm laser pulse. Pump fluences in excess of a threshold of ∼1 mJ/cm2 result in formation, with an ∼5 ps time constant, of a new stacking order by layer displacement along the b axis in the direction toward the centrosymmetric 1T* phase. The shear displacement of the layers increases with pump fluence until saturation at ∼8 pm. We demonstrate that the excitation of the shear phonon and the stabilization of the metastable phase are decoupled when using an optical pump as evidenced by observation of a transition also in samples with a pinned shear phonon. The results are compared to dynamic first-principles simulations and the transition is interpreted in terms of a mechanism where transient local disorder is prominent before settling at the atomic positions of the metastable phase. This interpretation is corroborated by results from diffuse scattering. The correlation between excitation of intralayer vibrations and interlayer interaction demonstrates the importance of including both short- and long-range interactions in an accurate description of how optical fields can be employed to manipulate the stacking order in 2-dimensional transition metal dichalcogenides.

First-Principles Study on Electron-Induced Excitations of Atomic Layer Deposition Precursors: Inelastic Electron Wave Packet Scattering with Cobalt Tricarbonyl Nitrosyl Co(CO)3NO Using Time-Dependent Density Functional Theory

A quantitative study on inelastic electron scattering with a molecule is of significant importance for understanding the essential mechanisms of electron-induced gas-phase and surface chemical reactions in their excited electronic states. A key issue to be addressed is the quantitatively detailed inelastic electron collision processes with a realistic molecular target, associated with electron excitation that leads to potential ionization and dissociation reactions of the molecule. Using the real-time time-dependent density functional theory (TDDFT) modeling, we present quantitative findings on the energy transfers and internal excitations for the low energy (up to 270 eV) electron wave packet impact with the molecular target cobalt tricarbonyl nitrosyl (CTN, Co(CO)₃NO) that is used as a precursor in electron-enhanced atomic layer deposition (EE-ALD) growth of Co films. Our modeling shows the quantitative dependence of the wave packet sizes, target molecule orientations, and impact parameters on the energy transfer in this inelastic electron scattering process. It is found that the wave packet sizes have little effect on the overall profile of the internal multiple excited states, whereas different target orientations can cause significantly different internal excited states. To evaluate the quantitative prediction capability, the inelastic scattering cross-section of a hydrogen atom is calculated and compared with the experimental data, leading to a constant scaling factor over the whole energy range. The present study demonstrates the remarkable potential of TDDFT for simulating the inelastic electron scattering process, which provides critical information for future exploration of electronic excitations in a wide range of electron-induced chemical reactions in current technological applications.

Nonadiabatic dynamics of cobalt tricarbonyl nitrosyl for ligand dissociation induced by electronic excitation

We utilize real-time time-dependent density functional theory and Ehrenfest dynamics scheme to investigate excited-state nonadiabatic dynamics of ligand dissociation of cobalt tricarbonyl nitrosyl, Co(CO)3NO, which is a precursor used for cobalt growth in advanced technologies, where the precursor's reaction is enhanced by electronic excitation. Based on the first-principles calculations, we demonstrate two dissociation pathways of the NO ligand on the precursor. Detailed electronic structures are further analyzed to provide an insight into dynamics following the electronic excitations. This study sheds light on computational demonstration and underlying mechanism of the electronic-excitation-induced dissociation, especially in molecules with complex chemical bonds such as the Co(CO)3NO.

Concentric Approximation for Fast and Accurate Numerical Evaluation of Nonadiabatic Coupling with Projector Augmented-Wave Pseudopotentials

We develop an efficient and accurate method for numerical evaluation of nonadiabatic (NA) coupling in the Kohn-Sham representation with projector augmented-wave (PAW) pseudopotentials that are commonly used in electronic structure calculations on nanoscale, condensed matter, and molecular systems. Without additional cost, the method provides an order of magnitude improvement in accuracy compared to the current technique, while it is 3-4 orders of magnitude faster than the exact evaluation. Atomic displacements over typical time steps in molecular dynamics (MD) simulations are much smaller than the size of the PAW core region, and therefore, evaluation of the NA in the core is simplified. The accuracy is demonstrated with three condensed matter systems. The method is robust to variation in the MD time step. The accurate NA coupling evaluation also helps in maintaining phase-consistency of the NA coupling and identifying trivial crossings of adiabatic states. The approach stimulates NAMD applications to modeling of modern materials and processes.

Environmental Effects with Frozen-Density Embedding in Real-Time Time-Dependent Density Functional Theory Using Localized Basis Functions

Frozen-density embedding (FDE) represents a versatile embedding scheme to describe the environmental effect on electron dynamics in molecular systems. The extension of the general theory of FDE to the real-time time-dependent Kohn-Sham method has previously been presented and implemented in plane waves and periodic boundary conditions [Pavanello, M.; J. Chem. Phys. 2015, 142, 154116]. In the current paper, we extend our recent formulation of the real-time time-dependent Kohn-Sham method based on localized basis set functions and developed within the Psi4NumPy framework to the FDE scheme. The latter has been implemented in its "uncoupled" flavor (in which the time evolution is only carried out for the active subsystem, while the environment subsystems remain at their ground state), using and adapting the FDE implementation already available in the PyEmbed module of the scripting framework PyADF. The implementation was facilitated by the fact that both Psi4NumPy and PyADF, being native Python API, provided an ideal framework of development using the Python advantages in terms of code readability and reusability. We employed this new implementation to investigate the stability of the time-propagation procedure, which is based on an efficient predictor/corrector second-order midpoint Magnus propagator employing an exact diagonalization, in combination with the FDE scheme. We demonstrate that the inclusion of the FDE potential does not introduce any numerical instability in time propagation of the density matrix of the active subsystem, and in the limit of the weak external field, the numerical results for low-lying transition energies are consistent with those obtained using the reference FDE calculations based on the linear-response TDDFT. The method is found to give stable numerical results also in the presence of a strong external field inducing nonlinear effects. Preliminary results are reported for high harmonic generation (HHG) of a water molecule embedded in a small water cluster. The effect of the embedding potential is evident in the HHG spectrum reducing the number of the well-resolved high harmonics at high energy with respect to the free water. This is consistent with a shift toward lower ionization energy passing from an isolated water molecule to a small water cluster. The computational burden for the propagation step increases approximately linearly with the size of the surrounding frozen environment. Furthermore, we have also shown that the updating frequency of the embedding potential may be significantly reduced, much less than one per time step, without jeopardizing the accuracy of the transition energies.

A Perspective on Molecular Structure and Bond-Breaking in Radiation Damage in Serial Femtosecond Crystallography

X-ray free-electron lasers (XFELs) have a unique capability for time-resolved studies of protein dynamics and conformational changes on femto- and pico-second time scales. The extreme intensity of X-ray pulses can potentially cause significant modifications to the sample structure during exposure. Successful time-resolved XFEL crystallography depends on the unambiguous interpretation of the protein dynamics of interest from the effects of radiation damage. Proteins containing relatively heavy elements, such as sulfur or metals, have a higher risk for radiation damage. In metaloenzymes, for example, the dynamics of interest usually occur at the metal centers, which are also hotspots for damage due to the higher atomic number of the elements they contain. An ongoing challenge with such local damage is to understand the residual bonding in these locally ionized systems and bond-breaking dynamics. Here, we present a perspective on radiation damage in XFEL experiments with a particular focus on the impacts for time-resolved protein crystallography. We discuss recent experimental and modelling results of bond-breaking and ion motion at disulfide bonding sites in protein crystals.

Tailoring the opto-electronic response of graphene nanoflakes by size and shape optimization

The long spin-diffusion length, spin-lifetime and excellent optical absorption coefficient of graphene provide an excellent platform for building opto-electronic devices and spin-based logic in a nanometer regime. In this study, by using density functional theory and its time-dependent version, we provide a detailed analysis of how the size and shape of graphene nanoflakes can be used to alter their magnetic structures and optical properties. As the edges of zigzag graphene nanoribbons are known to align anti-ferromagnetically and armchair nanoribbons are typically non-magnetic, a combination of both in a nanoflake geometry can be used to optimize the ground-state magnetic structure and tailor the exchange coupling decisive for ferro- or anti-ferromagnetic edge magnetism, thereby offering the possibility to optimize the external fields needed to switch magnetic ordering. Most importantly, we show that the magnetic state alters the optical response of the flake leading to the possibility of opto-spintronic applications.

Propagators for Quantum-Classical Models: Commutator-Free Magnus Methods

We consider the numerical propagation of models that combine both quantum and classical degrees of freedom, usually, electrons and nuclei, respectively. We focus, in our computational examples, on the case in which the quantum electrons are modeled with time-dependent density-functional theory, although the methods discussed below can be used with any other level of theory. Often, for these so-called quantum-classical molecular dynamics models, one uses some propagation technique to deal with the quantum part and a different one for the classical equations. While the resulting procedure may, in principle, be consistent, it can however spoil some of the properties of the methods, such as the accuracy order with respect to the time step or the preservation of the geometrical structure of the equations. Few methods have been developed specifically for hybrid quantum-classical models. We propose using the same method for both the quantum and classical particles, in particular, one family of techniques that proves to be very efficient for the propagation of Schrödinger-like equations: the (quasi)-commutator free Magnus expansions. These have been developed, however, for linear systems, yet our problem is nonlinear: formally, the full quantum-classical system can be rewritten as a nonlinear Schrödinger equation, i.e., one in which the Hamiltonian depends on the system itself. The Magnus expansion algorithms for linear systems require the application of the Hamiltonian at intermediate points in a given propagating interval. For nonlinear systems, this poses a problem as this Hamiltonian is unknown due to its dependence on the state. We approximate it by employing a higher order extrapolation using previous steps as input. The resulting technique can then be regarded as a multistep technique or, alternatively, as a predictor corrector formula.

Femtosecond bond breaking and charge dynamics in ultracharged amino acids

Historically, structure determination of nanocrystals, proteins, and macromolecules required the growth of high-quality crystals sufficiently large to diffract X-rays efficiently while withstanding radiation damage. The development of the X-ray free-electron laser has opened the path toward high resolution single particle imaging, and the extreme intensity of the X-rays ensures that enough diffraction statistics are collected before the sample is destroyed by radiation damage. Still, recovery of the structure is a challenge, in part due to the partial fragmentation of the sample during the diffraction event. In this study, we use first-principles based methods to study the impact of radiation induced ionization of six amino acids on the reconstruction process. In particular, we study the fragmentation and charge rearrangement to elucidate the time scales involved and the characteristic fragments occurring.

Suppression of Electron-Hole Recombination by Intrinsic Defects in 2D Monoelemental Material

The Shockley-Read-Hall (SRH) model, in which the deep trap defect states in the band gap are proposed as nonradiative electron-hole (e-h) recombination centers, has been widely used to describe the nonradiative e-h recombination through the defects in semiconductor. By using the ab initio nonadiabatic molecular dynamics method, we find that the SRH model fails to describe the e-h recombination behavior for defects in 2D monoelemental material such as monolayer black phosphorus (BP). Through the investigation of three intrinsic defects with shallow and deep defect states in monolayer BP, it is found that, surprisingly, none of these defects significantly accelerates the e-h recombination. Further analysis shows that because monolayer BP is a monoelemental material, the distinct impurity phonon, which often induces fast e-h recombination, is not formed. Moreover, because of the flexibility of 2D material, the defects scatter the phonons present in pristine BP, generating multiple modes with lower frequencies compared with the pristine BP, which further suppresses the e-h recombination. We propose that the conclusion can be extended to other monoelemental 2D materials, which is important guidance for the future design of functional semiconductors.

Imaginary-Time Time-Dependent Density Functional Theory and Its Application for Robust Convergence of Electronic States

Reliable and robust convergence to the electronic ground state within density functional theory (DFT) Kohn-Sham (KS) calculations remains a thorny issue in many systems of interest. In such cases, charge sloshing can delay or completely hinder the convergence. Here, we use an approach based on transforming the time-dependent DFT equations to imaginary time, followed by imaginary-time evolution, as a reliable alternative to the self-consistent field (SCF) procedure for determining the KS ground state. We discuss the theoretical and technical aspects of this approach and show that the KS ground state should be expected to be the long-imaginary-time output of the evolution, independent of the exchange-correlation functional or the level of theory used to simulate the system. By maintaining self-consistency between the single-particle wave functions (orbitals) and the electronic density throughout the determination of the stationary state, our method avoids the typical difficulties encountered in SCF. To demonstrate dependability of our approach, we apply it to selected systems which struggle to converge with SCF schemes. In addition, through the van Leeuwen theorem, we affirm the physical meaningfulness of imaginary-time TDDFT, justifying its use in certain topics of statistical mechanics such as in computing imaginary-time path integrals.

Photoexcitation Induced Quantum Dynamics of Charge Density Wave and Emergence of a Collective Mode in 1T-TaS2

Photoexcitation is a powerful means in distinguishing different interactions and manipulating the states of matter, especially in charge density wave (CDW) materials. The CDW state of 1T-TaS₂ has been widely studied experimentally mainly because of its intriguing laser-induced ultrafast responses of electronic and lattice subsystems. However, the microscopic atomic dynamics and underlying electronic mechanism upon photoexcitation remain unclear. Here, we demonstrate photoexcitation induced ultrafast dynamics of CDW in 1T-TaS₂ using time-dependent density functional theory molecular dynamics. We discover a novel collective oscillation mode between the CDW state and a transient state induced by photodoping, which is significantly different from thermally induced phonon mode and attributed to the modification of the potential energy surface from laser excitation. In addition, our finding validates nonthermal melting of CDW induced at low light intensities, supporting that conventional hot electron model is inadequate to explain photoinduced dynamics. Our results provide a deep insight into the coherent electron and lattice quantum dynamics during the formation and excitation of CDW in 1T-TaS₂.

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.

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.