Data-driven approach for benchmarking DFTB-approximate excited state methods.

In this work we propose a chemically-informed data-driven approach to benchmark the approximate density-functional tight-binding (DFTB) excited state (ES) methods that are currently available within the DFTB+ suite. By taking advantage of the large volume of low-detail ES-data in the machine learning (ML) dataset, QM8, we were able to extract valuable insights regarding the limitations of the benchmarked methods in terms of the approximations made to the parent formalism, density-functional theory (DFT), while providing recommendations on how to overcome them. For this benchmark, we compared the first singlet-singlet vertical excitation energies (E1) predicted by the DFTB-approximate methods with predictions of less approximate methods from the reference ML-dataset. For the nearly 21800 organic molecules in the GDB-8 chemical space, we were able to identify clear trends in the E1 prediction error distributions, with respect to second-order approximate coupled cluster (CC2), showing a strong dependence on chemical identity.

Dynamical evolution of the Schottky barrier as a determinant contribution to electron-hole pair stabilization and photocatalysis of plasmon-induced hot carriers.

The harnessing of plasmon-induced hot carriers promises to open new avenues for the development of clean energies and chemical catalysis. The extraction of carriers before thermalization and recombination is of fundamental importance to obtain appealing conversion yields. Here, hot carrier injection in the paradigmatic Au-TiO2 system is studied by means of electronic and electron-ion dynamics. Our results show that pure electronic features (without considering many-body interactions or dissipation to the environment) contribute to the electron-hole separation stability. These results reveal the existence of a dynamic contribution to the interfacial potential barrier (Schottky barrier) that arises at the charge injection pace, impeding electronic back transfer. Furthermore, we show that this charge separation stabilization provides the time needed for the charge to leak to capping molecules placed over the TiO2 surface triggering a coherent bond oscillation that will lead to a photocatalytic dissociation. We expect that our results will add new perspectives to the interpretation of the already detected long-lived hot carrier lifetimes and their catalytical effect, and concomitantly to their technological applications.

QM/MM optimization with quantum coupling: Host-guest interactions in a pentacene-doped p-terphenyl crystal.

In this work, we present a novel force-based scheme to perform hybrid quantum mechanics/molecular mechanics (QM/MM) computations. The proposed scheme becomes especially relevant for the simulation of host-guest molecular systems, where the description of the explicit electronic interactions between a guest molecule and a classically described host is of key importance. To illustrate its advantages, we utilize the presented scheme in the geometry optimization of a technologically important host-guest molecular system: a pentacene-doped p-terphenyl crystal, a core component of a room-temperature MASER device. We show that, as opposed to the simpler and widely used hybrid scheme ONIOM, our Quantum-Coupling QM/MM scheme was able to reproduce explicit interactions in the minimum energy configuration for the host-guest complex. We also show that, as a result of these explicit interactions, the host-guest complex exhibits an oriented net electric dipole moment that is responsible for red-shifting the energy of the first singlet-singlet electronic excitation of pentacene.

Fano Resonance and Incoherent Interlayer Excitons in Molecular van der Waals Heterostructures.

Complex van der Waals heterostructures from layered molecular stacks are promising optoelectronic materials offering the means to efficient, modular charge separation and collection layers. The effect of stacking in the electrodynamics of such hybrid organic-inorganic two-dimensional materials remains largely unexplored, whereby molecular scale engineering could lead to advanced optical phenomena. For instance, tunable Fano engineering could make possible on-demand transparent conducting layers or photoactive elements, and passive cooling. We employ an adapted Gersten-Nitzan model and real time time-dependent density functional tight-binding to study the optoelectronics of self-assembled monolayers on graphene nanoribbons. We find Fano resonances that cause electromagnetic induced opacity and transparency and reveal an additional incoherent process leading to interlayer exciton formation with a characteristic charge transfer rate. These results showcase hybrid van der Waals heterostructures as paradigmatic 2D optoelectronic stacks, featuring tunable Fano optics and unconventional charge transfer channels.

A simple approximation to the electron-phonon interaction in population dynamics.

The modeling of coupled electron-ion dynamics including a quantum description of the nuclear degrees of freedom has remained a costly and technically difficult practice. The kinetic model for electron-phonon interaction provides an efficient approach to this problem, for systems evolving with low amplitude fluctuations, in a quasi-stationary state. In this work, we propose an extension of the kinetic model to include the effect of coherences, which are absent in the original approach. The new scheme, referred to as Liouville-von Neumann + Kinetic Equation (or LvN + KE), is implemented here in the context of a tight-binding Hamiltonian and employed to model the broadening, caused by the nuclear vibrations, of the electronic absorption bands of an atomic wire. The results, which show close agreement with the predictions given by Fermi's golden rule (FGR), serve as a validation of the methodology. Thereafter, the method is applied to the electron-phonon interaction in transport simulations, adopting to this end the driven Liouville-von Neumann equation to model open quantum boundaries. In this case, the LvN + KE model qualitatively captures the Joule heating effect and Ohm's law. It, however, exhibits numerical discrepancies with respect to the results based on FGR, attributable to the fact that the quasi-stationary state is defined taking into consideration the eigenstates of the closed system rather than those of the open boundary system. The simplicity and numerical efficiency of this approach and its ability to capture the essential physics of the electron-phonon coupling make it an attractive route to first-principles electron-ion dynamics.

A modelling study highlights the power of detecting and isolating asymptomatic or very mildly affected individuals for COVID-19 epidemic management.

BACKGROUND: Mathematical modelling of infectious diseases is a powerful tool for the design of management policies and a fundamental part of the arsenal currently deployed to deal with the COVID-19 pandemic. METHODS: We present a compartmental model for the disease where symptomatic and asymptomatic individuals move separately. We introduced healthcare burden parameters allowing to infer possible containment and suppression strategies. In addition, the model was scaled up to describe different interconnected areas, giving the possibility to trigger regionalized measures. It was specially adjusted to Mendoza-Argentina's parameters, but is easily adaptable for elsewhere. RESULTS: Overall, the simulations we carried out were notably more effective when mitigation measures were not relaxed in between the suppressive actions. Since asymptomatics or very mildly affected patients are the vast majority, we studied the impact of detecting and isolating them. The removal of asymptomatics from the infectious pool remarkably lowered the effective reproduction number, healthcare burden and overall fatality. Furthermore, different suppression triggers regarding ICU occupancy were attempted. The best scenario was found to be the combination of ICU occupancy triggers (on: 50%, off: 30%) with the detection and isolation of asymptomatic individuals. In the ideal assumption that 45% of the asymptomatics could be detected and isolated, there would be no need for complete lockdown, and Mendoza's healthcare system would not collapse. CONCLUSIONS: Our model and its analysis inform that the detection and isolation of all infected individuals, without leaving aside the asymptomatic group is the key to surpass this pandemic.

On the photophysics of electrochemically generated silver nanoclusters: spectroscopic and theoretical characterization.

Ligand-free atomic silver nanoclusters (AgNCs) were successfully synthesized following the electrochemical procedure developed by Lopez-Quintela and col. (D. Buceta, N. Busto, G. Barone, J. M. Leal, F. Domínguez, L. J. Giovanetti, F. G. Requejo, B. García and M. A. López-Quintela, Angew. Chem., Int. Ed., 2015, 54, 7612-7616), who have identified the presence of Ag2 and Ag3 AgNCs. The goal of this work was to get information on the photophysics of these AgNCs, which was achieved by combining information from excitation/emission matrix (EEM) and time resolved emission spectroscopy (TRES) along with DFT/TD-DFT calculations. This procedure allowed deconvolving the emission and excitation spectra of the AgNC mixture, with further assignment of each transition and lifetime associated to Ag2, Ag3+ and Ag42+ clusters. This deconvolution together with theoretical calculations allowed suggesting for the first time the radiative and non-radiative excited state deactivation mechanism for these clusters.

A Real-Time Time-Dependent Density Functional Tight-Binding Implementation for Semiclassical Excited State Electron-Nuclear Dynamics and Pump-Probe Spectroscopy Simulations.

The increasing need to simulate the dynamics of photoexcited molecular systems and nanosystems in the subpicosecond regime demands new efficient tools able to describe the quantum nature of matter at a low computational cost. By combining the power of the approximate DFTB method with the semiclassical Ehrenfest method for nuclear-electron dynamics, we have achieved a real-time time-dependent DFTB (TD-DFTB) implementation that fits such requirements. In addition to enabling the study of nuclear motion effects in photoinduced charge transfer processes, our code adds novel features to the realm of static and time-resolved computational spectroscopies. In particular, the optical properties of periodic materials such as graphene nanoribbons or the use of corrections such as the "LDA+U" and "pseudo SIC" methods to improve the optical properties in some systems can now be handled at the TD-DFTB level. Moreover, the simulation of fully atomistic time-resolved transient absorption spectra and impulsive vibrational spectra can now be achieved within reasonable computing time, owing to the good performance of the implementation and a parallel simulation protocol. Its application to the study of UV/visible light-induced vibrational coherences in molecules is demonstrated and opens a new door into the mechanisms of nonequilibrium ultrafast phenomena in countless materials with relevant applications.

Multiscale approach to electron transport dynamics.

Molecular simulations of transport dynamics in nanostructures usually require the implementation of open quantum boundary conditions. This can be instrumented in different frameworks including Green's functions, absorbing potentials, or the driven Liouville von Neumann equation, among others. In any case, the application of these approaches involves the use of large electrodes that introduce a high computational demand when dealing with first-principles calculations. Here, we propose a hybrid scheme where the electrodes are described at a semiempirical, tight binding level, coupled to a molecule or device represented with density functional theory (DFT). This strategy allows us to use massive electrodes at a negligible computational cost, preserving the accuracy of the DFT method in the modeling of the transport properties, provided that the electronic structure of every lead is properly defined to behave as a conducting fermionic reservoir. We study the nature of the multiscale coupling and validate the methodology through the computation of the tunneling decay constant in polyacetylene and of quantum interference effects in an aromatic ring. The present implementation is applied both in microcanonical and grand-canonical frameworks, in the last case using the Driven Liouville von Neumann equation, discussing the advantages of one or the other. Finally, this multiscale scheme is employed to investigate the role of an electric field applied normally to transport in the conductance of polyacetylene. It is shown that the magnitude and the incidence angle of the applied field have a considerable effect on the electron flow, hence constituting an interesting tool for current control in nanocircuits.

UV Photofragmentation of Cold Cytosine-M+ Complexes (M+: Na+, K+, Ag+).

The UV photofragmentation spectra of cold cytosine-M+ complexes (M+: Na+, K+, Ag+) were recorded and analyzed through comparison with geometry optimizations and frequency calculations of the ground and excited states at the SCS-CC2/Def2-SVPD level of theory. While in all complexes, the ground state minimum geometry is planar (Cs symmetry), the ππ* state minimum geometry has the NH2 group slightly twisted and an out-of-plane metal cation. This was confirmed by comparing the simulated ππ* Franck-Condon spectra with the vibrationally resolved photofragmentation spectra of CytNa+ and CytK+. Vertical excitation transitions were also calculated to evaluate the energies of the CT states involving the transfer of an electron from the Cyt moiety to M+. For both CytK+ and CytNa+ complexes, the first CT state corresponds to an electron transfer from the cytosine aromatic π ring to the antibonding σ* orbital centered on the alkali cation. This πσ* state is predicted to lie much higher in energy (>6 eV) than the band origin of the π-π* electronic transition (around 4.3 eV) unlike what is observed for the CytAg+ complex for which the first excited state has a nOσ* electronic configuration. This is the reason for the absence of the Cyt+ + M charge transfer fragmentation channel for CytK+ and CytNa+ complexes.

Plasmon-induced hot-carrier generation differences in gold and silver nanoclusters.

In the last thirty years, the study of plasmonic properties of noble metal nanostructures has become a very dynamic research area. The design and manipulation of matter in the nanometric scale demands a deep understanding of the underlying physico-chemical processes that operate in this size regimen. Here, a fully atomistic study of the spectroscopic and photodynamic properties of different icosahedral silver and gold nanoclusters has been carried out by using a Time-Dependent Density Functional Tight-Binding (TD-DFTB) model. The optical absorption spectra of different icosahedral silver and gold nanoclusters of diameters between 1 and 4 nanometers have been simulated. Furthermore, the energy absorption process has been quantified by means of calculating a fully quantum absorption cross-section using the information contained in the reduced single-electron density matrix. This approach allows us take into account the quantum confinement effects dominating in this size regime. Likewise, the plasmon-induced hot-carrier generation process under laser illumination has been explored from a fully dynamical perspective. We have found noticeable differences in the energy absorption mechanisms and the plasmon-induced hot-carrier generation process in both metals which can be explained by their respective electronic structures. These differences can be attributed to the existence of ultra-fast electronic dissipation channels in gold nanoclusters that are absent in silver nanoclusters. To the best of our knowledge, this is the first report that addresses this topic from a real time fully atomistic time-dependent approach.

Simulation of Impulsive Vibrational Spectroscopy.

In the present work we applied a fully atomistic electron-nuclear real-time propagation protocol to compute the impulsive vibrational spectroscopy of the five DNA/RNA nucleobases in order to study the very first steps (subpicosecond) of their energy distribution after UV excitation. We observed that after the pump pulse absorption the system is prepared in a coherent superposition of the ground and the pumped electronic excited states in the equilibrium geometry of the ground state. Furthermore, for relatively low fluency values of the pump pulse, the dominant contribution to the electronic wave function of the coherent state is of the ground state and the mean potential energy surface within the Ehrenfest approximation is similar to that of the ground state. As a consequence, the molecular displacements are better correlated with ground-state normal modes. On the other hand, when the pump fluency is increased the excited-state contribution to the electronic wave function becomes more important and the mean potential energy surface resembles more that of the excited state, producing a better correlation between the molecular displacements and the excited-state normal modes. Finally, it has been observed that the impulsive activation of several vibrational modes upon electronic excitation is triggered by the development of excited-state forces which accelerate the nuclei from their equilibrium positions causing a distribution of the absorbed electronic energy on the nuclear degrees of freedom and could be closely related to the driving force of the ultrafast nonradiative deactivation observed in these systems.

Quantum efficiency of the photo-induced electronic transfer in dye-TiO2 complexes.

We present a method based on a time-dependent self-consistent density functional tight-binding (TD-DFTB) approach, able to predict the quantum efficiency of the photoinjection process in a dye-TiO2 complex from a fully atomistic picture. We studied the process of charge transfer of three systems with different dyes: catechol (CAT), alizarin (ALZ) and FSD101. Each system was excited with lasers of different energies in the range of 300-2500 nm, studying the efficiency of the induced charge transfer process at the incident energies. We show that the perturbation can produce either hole transfer or electron transfer from the dye to the nanoparticle, therefore affecting the efficiency of the charge transfer in the solar cell when illuminated by broadband radiation.

Characterization of ZnO as substrate for DSSC.

We present a complete analysis of the photoinjection process in 3 nm spherical ZnO nanoparticles with different dyes attached to their surface. The study was carried using a TD-DFTB model to describe the quantum dynamics of charge transfer in the presence of an external time dependent electric field simulating resonant illumination. The ZnO + dye systems have been classified according to the injection process (type I and type II) that they present. In addition, the calculated charge transfer shows that many dyes present hole injection into the nanoparticle. We have classified the charge transfer into holes or electron and compare these results with the TiO2 + dye system obtained from the literature.

Optical properties and charge distribution in rod-shape DNA-silver cluster emitters.

While the atomic structure of DNA_Agn clusters remains unknown many efforts have been made to understand the photophysical properties of this type of systems. It is known that partial oxidation of the silver cluster is necessary for generation of fluorescent emitters. In this sense, the rod-shape model proposed by Gwinn and coworkers (D. Schultz, K. Gardner, S. S. R. Oemrawsingh, N. Markesevic, K. Olsson, M. Debord, D. Bouwmeester, and E. Gwinn, Adv. Mater., 2013, 25, 2797-2803), based on the idea that a neutral rod is generated with Ag+ acting as a "glue" in between the neutral rod and the DNA bases, is a good approximation in order to explain experimental results. With the aim to shed light towards the understanding of these systems, we explore the electronic dynamics and charge distribution in zigzag rod-shape DNA_Agn clusters, using the Ag0/Ag+ stoichiometry found experimentally.

Fully Atomistic Real-Time Simulations of Transient Absorption Spectroscopy.

We have implemented an electron-nuclear real-time propagation scheme for the calculation of transient absorption spectra. When this technique is applied to the study of ultrafast dynamics of Soret-excited zinc(II) tetraphenylporphyrin in the subpicosecond time scale, quantum beats in the transient absorption caused by impulsively excited molecular vibrations are observed. The launching mechanism of such vibrations can be regarded as a displacive excitation of the zinc-pyrrole and pyrrole C-C bonds.

Trap-Door-Like Irreversible Photoinduced Charge Transfer in a Donor-Acceptor Complex.

For efficient conversion of light into useful energy sources, it is very important to study and describe the first steps of primary charge-transfer process in natural structures and artificial devices. The time scale of these processes in artificial photosynthetic and photovoltaic devices is on the order of femto- to picoseconds and involves vibronic coupling of electrons and nuclei and also nuclear alleviation to enhance charge separation. Here we present an atomistic description of the photoexcited electron dynamics in a noncovalently bonded system formed by an hydrogenated nanodiamond as donor and a perylene diimide as an acceptor. The complex shows extremely fast charge transfer, separation, and stabilization within 90 fs. This stabilization is purely electronic in nature. To the best of our knowledge, these results show for the first time that it is possible to stabilize charge without polaron formation or nuclear relaxation, reaching a steady state enhanced by a pure electronic reorganization.

Plasmon-driven sub-picosecond breathing of metal nanoparticles.

We present the first real-time atomistic simulation on the quantum dynamics of icosahedral silver nanoparticles under strong laser pulses, using time dependent density functional theory (TDDFT) molecular dynamics. We identify the emergence of sub-picosecond breathing-like radial oscillations starting immediately after laser pulse excitation, with increasing amplitude as the field intensity increases. The ultrafast dynamic response of nanoparticles to laser excitation points to a new mechanism other than equilibrium electron-phonon scattering previously assumed, which takes a much longer timescale. A sharp weakening of all bonds during laser excitation is observed, thanks to plasmon damping into excited electrons in anti-bonding states. This sudden weakening of bonds leads to a uniform expansion of the nanoparticles and launches coherent breathing oscillations.

DNA-protected silver emitters: charge dependent switching of fluorescence.

The relationship between the state of charge and spectroscopy of DNA-protected silver emitters is not yet well understood. This remains one of the major issues to unveil in order to fully disentangle the spectroscopic features of these novel systems. It is a well known fact that a fluorescence response arises upon chemical reduction of silver cations attached to DNA, leading to neutral (or partially oxidized) "bright" clusters. It is important to note that the absence of fluorescence in completely ionic complexes is universal in the sense that it does not depend on any experimental variable. This suggests that its origin may be founded on the nature of the interaction between DNA bases and silver cations. Nevertheless, to the best of our knowledge, no explanation exists for this charge dependent switching between dark completely ionic complexes and bright (neutral or partially oxidized) clusters. In this brief report we address this experimental fact on the basis of the electronic structure of the complex as a function of its charge and quantum dynamical simulations of the processes following photoexcitation. These data provide a dynamical picture of the correlation between charge and fluorescence.

Optical properties of graphene nanoflakes: Shape matters.

In recent years there has been significant debate on whether the edge type of graphene nanoflakes (GNFs) or graphene quantum dots (GQDs) are relevant for their electronic structure, thermal stability, and optical properties. Using computer simulations, we have proven that there is a fundamental difference in the absorption spectra between samples of the same shape, similar size but different edge type, namely, armchair or zigzag edges. These can be explained by the presence of electronic structures near the Fermi level which are localized on the edges. These features are also evident from the dependence of band gap on the GNF size, which shows three very distinct trends for different shapes and edge geometries.