We present a first-principles theoretical study of the atomistic footprints in the valence electron energy loss spectroscopy (EELS) of nanometer-size metallic particles.

When an organic molecule is placed inside a plasmonic cavity formed by two metallic nanoparticles (MNP) under illumination, the electronic excitations of the molecule couple to the plasmonic electromagnetic modes of the cavity, inducing new hybrid light–matter states called polaritons. Atomistic ab initio methods accurately describe the coupling between MNPs and molecules at the nanometer scale and allow us to analyze how atomistic features influence the interaction. In this work, we study the optical response of a porphine molecule coupled to a silver nanoparticle dimer from first principles, within the linear-response time-dependent density functional theory framework, using the recently developed Python Numeric Atomic Orbitals implementation to compute the optical excitations. The optical spectra show the splitting of the resonances of the plasmonic dimer and the molecule into two distinct polaritons, a characteristic feature of the strong light–matter coupling regime. Our results stress the importance of atomistic features, such as the gap configuration in determining the plasmon–exciton coupling strength and in the emergence of molecule-mediated charge-transfer plasmon (CTP) resonances at lower frequencies. Moreover, we show that the strength of the CTP resonance can be tuned by shifting the alignment of the molecular energy levels with respect to the Fermi level of the MNPs.

Moleculardoping provides a route toward designing new organiccompounds with improved performance for optoelectronics. Here, weinvestigate the p-type doping of crystalline diindenoperylene (DIP)with two recently proposed electron-accepting molecular dopants usingmany-body perturbation theory. For the pristine DIP crystal, the quasiparticleband structure and the optical absorption spectra are found in agreementwith the experimental data. Using the same methodology, we then characterizethe optical and electronic properties of the two doped DIP crystals.The bandgap of both doped crystals is narrowed considerably due tothe formation of hybridized states at the valence band edge. Moreover,a hybrid unoccupied mid-gap band is created with a host-dopantcharge-transfer characteristic, giving rise to broader absorptionspectra and a much lower absorption onset as compared to pristineDIP. Our results highlight that the interaction and hybridizationwith the host environment, including many-body effects, must be carefullyconsidered in order to identify appropriate molecular dopants fora given organic crystal.

The synthesis of novel organic prototypes combining different functionalities is key to achieve operational elements for applications in organic electronics. Here we set the stage towards individually addressable magneto-optical transducers by the on-surface synthesis of optically active manganese-phthalocyanine derivatives (MnPc) obtained directly on a metallic substrate. We created these 2D nanostructures under ultra-high vacuum conditions with atomic precision starting from a simple phthalonitrile precursor with reversible photo-induced reactivity in solution. These precursors maintain their integrity after powder sublimation and coordinate with the Mn ions into tetrameric complexes and then transform into MnPcs on Ag(111) after a cyclotetramerization reaction. Using scanning tunnelling microscopy and spectroscopy together with DFT calculations, we identify the isomeric configuration of two bi-stable structures and show that it is possible to switch them reversibly by mechanical manipulation. Moreover, the robust magnetic moment brought by the central Mn ion provides a feasible pathway towards magneto-optical transducer fabrication. This work should trigger further research confirming such magneto-optical effects in MnPcs both on surfaces and in liquid environments.

We evidence the possibility for coherent electrical manipulation of the spin orientation of topologically protected edge states in a low-symmetry quantum spin Hall insulator. By using a combination of ab initio simulations, symmetry-based modeling, and large-scale calculations of the spin Hall conductivity, it is shown that small electric fields can efficiently vary the spin textures of edge currents in monolayer 1T'-WTe2 by up to a 90-degree spin rotation, without jeopardizing their topological character. These findings suggest a new kind of gate-controllable spin-based device, topologically protected against disorder and of relevance for the development of topological spintronics.

Modelling the inelastic scattering of electrons in water is fundamental, given their crucial role in biological damage. In Monte Carlo track-structure (MC-TS) codes used to assess biological damage, the energy loss function (ELF), from which cross sections are extracted, is derived from different semi-empirical optical models. Only recently have first ab initio results for the ELF and cross sections in water become available. For benchmarking purpose, in this work, we present ab initio linear-response time-dependent density functional theory calculations of the ELF of liquid water. We calculated the inelastic scattering cross sections, inelastic mean free paths, and electronic stopping power and compared our results with recent calculations and experimental data showing a good agreement. In addition, we provide an in-depth analysis of the contributions of different molecular orbitals, species and orbital angular momenta to the total ELF. Moreover, we present single-differential cross sections computed for each molecular orbital channel, which should prove useful for MC-TS simulations.

PySCF is a Python-based general-purpose electronic structure platform that supports first-principles simulations of molecules and solids as well as accelerates the development of new methodology and complex computational workflows. This paper explains the design and philosophy behind PySCF that enables it to meet these twin objectives. With several case studies, we show how users can easily implement their own methods using PySCF as a development environment. We then summarize the capabilities of PySCF for molecular and solid-state simulations. Finally, we describe the growing ecosystem of projects that use PySCF across the domains of quantum chemistry, materials science, machine learning, and quantum information science.

The use of atomic orbitals in Hedin's GW approximation provides, in principle, an inexpensive alternative to plane-wave basis sets, especially when modeling large molecules. However, benchmarking of the algorithms and basis sets is essential for a careful balance between cost and accuracy. In this paper, we present an implementation of the GW approximation using numerical atomic orbitals and a pseudopotential treatment of core electrons. The combination of a contour deformation technique with a one-shot extraction of quasiparticle energies provides an efficient scheme for many applications. The performance of the implementation with respect to the basis set convergence and the effect of the use of pseudopotentials has been tested for the 117 closed-shell molecules from the G2/97 test set and 24 larger acceptor molecules from another recently proposed test set. Moreover, to demonstrate the potential of our method, we compute the thermally averaged GW density of states of a large photochromic compound by sampling ab initio molecular dynamics trajectories at different temperatures. The computed thermal line widths indicate approximately twice as large electron-phonon couplings with GW than with standard DFT-GGA calculations. This is further confirmed using frozen-phonon calculations.

A recent experimental study of the energy losses of various ions in titanium nitride, in the low-energy range [M. A. Sortica et al., Sci. Rep. 9, 176 (1)19)], showed a striking departure of the measured values from those predicted by density functional theory. They suggested electron promotion in atomic collisions between dressed atoms as an explanation. In this Rapid Communication, we investigate the process of energy loss of slow ions in TiN using theoretical formulations that are based, on one side, on self-consistent models of nonlinear screening and quantum scattering theory, and on the other, on ab initio computations of the electron-density profile of titanium nitride. Two theoretical approaches are considered to determine the average energy transfer: One is based on the local-density approximation for the inhomogeneous electron gas corresponding to the calculated density of TiN, and the other is based on the Penn model for the convolution of the inhomogeneous electron-gas response based on a measured electron-loss function. Both approaches produce very similar results and are in remarkable agreement with the experimental data, indicating that the observed enhancement in the energy-loss values is due to the contribution of a range of electron densities in the TiN compound.

We present an algorithm and its implementation to calculate the properties of electronic excitations in molecules and clusters from first principles, using time-dependent density functional theory (TDDFT). The algorithm assumes the use of some localized functions as a basis set to represent the spatial degrees of freedom. It relies on an iterative computation of the induced density according to the Dyson-like equation for the linear response function. The current implementation is built upon so-called numerical atomic orbitals. It is suitable for a wide variety of density functional theory (DFT) software. In this work, we demonstrate TDDFT calculations starting from preceding DFT runs with SIESTA, GPAW and PySCF packages, while a coupling with the other DFT packages such as Fireball and OpenMX is planned. The mentioned packages are capable of performing ab initio molecular dynamics simulations, and the speed of our TDDFT implementation makes feasible to perform a configuration average of the optical absorption spectra. Our code is written mostly in Python language allowing for a quick and compact implementation of most numerical methods and data-managing tasks with the help of NumPy/SciPy libraries and Python intrinsic constructs. Part of the code is written in C and Fortran to achieve a competitive speed in particular sections of the algorithm. Many parts of the current algorithm and implementation are useful in other ab initio methods for electronic excited states, such as Hedin's GW, Bethe-Salpeter equation and DFT with hybrid functionals. Corresponding proof-of-principles implementations are already part of the code. Program summary Program Title: PySCF-NAO Program Files doi: http://dx.doi.org/10.17632/9wgp6255hn.1 Licensing provisions: Apache License, Version 2.0 Programming language: Python (2 or 3), Fortran90 and C Supplementary material: We provide the source code and input files to organize example and benchmark calculations discussed in the paper. Nature of the problem: The study of the interaction of photons and charged particles with matter depends upon understanding of electronic excitations in matter. A description of the electronic excitations within time-dependent density functional theory (TDDFT) is popular due to the combination of its reasonable accuracy and its relatively low computational cost. Despite the relative simplicity of TDDFT, its application becomes difficult for quantum systems containing several hundreds of atoms. Such microscopically small systems are relevant in organic electronics, plasmonics and surface science. Therefore, much work has been devoted to the development of adequate electronic structure methods. Moreover, thermal motion of atoms and the presence of solvents affects the properties of electronic excited states in a decisive manner. Modeling of the electronic excited states including the system's dynamics within the Born-Oppenheimer approximation leads to even stronger efficiency requirements from the corresponding electronic structure methods. Solution method: We discretize the Kohn-Sham Hamiltonian using a basis of numerical atomic orbitals. The induced electronic density is determined in response to a dipolar external perturbation, according to linear response TDDFT, using an iterative algorithm. The method takes advantage of the sparsity generated by the finite support of the numerical atomic orbitals. This allows computing the dynamical polarizability of molecules and clusters containing up to several thousands of atoms. Additional comments including Restrictions and Unusual features: The current algorithm is formulated within the formalism of density response functions. Therefore, one needs to know explicitly an exchange correlation kernel (second-derivative of energy with respect to variation of the density). The exchange correlation kernel is analytically known for (semi-)local density functionals, but not for the hybrid density functionals. To date, we implemented only the local density approximation (LDA) for the exchange correlation kernel to be used with the iterative TDDFT in PySCF-NAO. Spin-restricted formalism for finite systems is covered in the current implementation. Moreover, although our code is prepared to compute the electronic response of all-electron systems, our current implementation of an auxiliary product basis (density-fitting basis) is working best in combination with the use of pseudopotentials. (C) 2018 Elsevier B.V. All rights reserved.

Plasmonic gaps are known to produce nanoscale localization and enhancement of optical fields, providing small effective mode volumes of about a few hundred nm3. Atomistic quantum calculations based on time-dependent density functional theory reveal the effect of subnanometric localization of electromagnetic fields due to the presence of atomic-scale features at the interfaces of plasmonic gaps. Using a classical model, we explain this as a nonresonant lightning rod effect at the atomic scale that produces an extra enhancement over that of the plasmonic background. The near-field distribution of atomic-scale hot spots around atomic features is robust against dynamical screening and spill-out effects and follows the potential landscape determined by the electron density around the atomic sites. A detailed comparison of the field distribution around atomic hot spots from full quantum atomistic calculations and from the local classical approach considering the geometrical profile of the atoms' electronic density validates the use of a classical framework to determine the effective mode volume in these extreme subnanometric optical cavities. This finding is of practical importance for the community of surface-enhanced molecular spectroscopy and quantum nanophotonics, as it provides an adequate description of the local electromagnetic fields around atomic-scale features with use of simplified classical methods.

Pentacenemolecules have recently been observed to form awell-orderedmonolayer on the (110) surface of rutile TiO2, with themolecules adsorbed lying flat, head to tail.With the geometry favorable for direct optical excitation and given its ordered character, this interface seems to provide an intriguingmodel to study charge-transfer excitationswhere the optically excited electrons and holes reside on different sides of the organic–inorganic interface. In this work, we theoretically investigate the structural and electronic properties of this systembymeans of ab initio calculations and compute its excitonic absorption spectrum.Molecular states appear in the band gap of the cleanTiO2 surface, which enables charge-transfer excitations directly from themolecularHOMO to the TiO2 conduction band. The calculated optical spectrum shows a strong polarization dependence and displays excitonic resonances corresponding to the charge-transfer states, which could stimulate new experimental work on the optical response of this interface.

Resumen del poster presentado a la NanoSpain Conference, celebrada en Logrono (Espana) del 15 al 18 de marzo de 2016.

We present a study of the optical response of compact and hollow icosahedral clusters containing up to 868 silver atoms by means of time-dependent density functional theory. We have studied the dependence on size and morphology of both the sharp plasmonic resonance at 3-4 eV (originated mainly from sp-electrons), and the less studied broader feature appearing in the 6-7 eV range (interband transitions). An analysis of the effect of structural relaxations, as well as the choice of exchange correlation functional (local density versus generalised gradient approximations) both in the ground state and optical response calculations is also presented. We have further analysed the role of the different atom layers (surface versus inner layers) and the different orbital symmetries on the absorption cross-section for energies up to 8 eV. We have also studied the dependence on the number of atom layers in hollow structures. Shells formed by a single layer of atoms show a pronounced red shift of the main plasmon resonances that, however, rapidly converge to those of the compact structures as the number of layers is increased. The methods used to obtain these results are also carefully discussed. Our methodology is based on the use of localised basis (atomic orbitals, and atom-centered and dominant-product functions), which bring several computational advantages related to their relatively small size and the sparsity of the resulting matrices. Furthermore, the use of basis sets of atomic orbitals also allows the possibility of extending some of the standard population analysis tools (e.g. Mulliken population analysis) to the realm of optical excitations. Some examples of these analyses are described in the present work.

The full monolayer of pentacene adsorbed on rutile TiO$_2$(110) provides an intriguing model to study charge-transfer excitations where the optically excited electrons and holes reside on different sides of the internal interface between the pentacene monolayer and the TiO$_2$ surface. In this work we investigate the electronic properties of this system with density functional theory, and compute its excitonic and optical properties making use of \emph{ab initio} matrix elements. The pentacene molecules are found to lie flat on the surface, head to tail, and slightly tilted towards the troughs of the oxygen rows of the surface --- in agreement with experiment. Molecular states appear in the band gap of the clean TiO$_2$ surface which enable charge transfer excitations directly from the molecular HOMO to the TiO$_2$ conduction band. The calculated optical spectrum shows a strong polarization dependence and displays excitonic resonances corresponding to the charge-transfer states. We characterize the computed excitons by their symmetry and location in k-space and use this information to explain the polarization dependence of the optical spectrum.

The correlation between transport properties across sub-nanometric metallic gaps and the optical response of the system is a complex effect which is determined by the fine atomic-scale details of the junction structure. As experimental advances are progressively accessing transport and optical characterization of smaller nanojunctions, a clear connection between the structural, electronic and optical properties in these nanocavities is needed. Using ab initio calculations, we present here a study of the simultaneous evolution of the structure and the optical response of a plasmonic junction as the particles forming the cavity, two Na$_{380}$ clusters, approach and retract. Atomic reorganizations are responsible for a large hysteresis of the plasmonic response of the system, that shows a jump-to-contact instability during the approach process and the formation of an atom-sized neck across the junction during retraction. Our calculations demonstrate that, due to the quantization of the conductance in metal nanocontacts, atomic-scale reconfigurations play a crucial role in determining the optical response of the whole system. We observe abrupt changes in the intensities and spectral positions of the dominating plasmon resonances, and find a one-to-one correspondence between these jumps and those of the quantized transport as the neck cross-section diminishes. These results point out to an unforeseen connection between transport and optics at the atomic scale, which is at the frontier of current optoelectronics and can drive new options in optical engineering of signals driven by the motion and manipulation of single atoms.

Trabajo presentado a la Conferencia Espanola de Nanofotonica (Spanish Nanophotonics Conference) celebrada en Valencia del 20 al 22 de junio de 2016.