koopmans: An Open-Source Package for Accurately and Efficiently Predicting Spectral Properties with Koopmans Functionals.

Over the past decade we have developed Koopmans functionals, a computationally efficient approach for predicting spectral properties with an orbital-density-dependent functional framework. These functionals impose a generalized piecewise linearity condition to the entire electronic manifold, ensuring that orbital energies match the corresponding electron removal/addition energy differences (in contrast to semilocal DFT, where a mismatch between the two lies at the heart of the band gap problem and, more generally, the unreliability of Kohn-Sham orbital energies). This strategy has proven to be very powerful, yielding molecular orbital energies and solid-state band structures with comparable accuracy to many-body perturbation theory but at greatly reduced computational cost while preserving a functional formulation. This paper reviews the theory of Koopmans functionals, discusses the algorithms necessary for their implementation, and introduces koopmans, an open-source package that contains all of the code and workflows needed to perform Koopmans functional calculations and obtain reliable spectral properties of molecules and materials.

Molecular Composition and Biological Activity of a Novel Acetonitrile-Water Extract of Lens Culinaris Medik in Murine Native Cells and Cell Lines Exposed to Different Chemotherapeutics Using Mass Spectrometry.

We evaluated the effects of a new extract (70% acetonitrile, 2E0217022196DIPFARMTDA) of Lens culinaris Medik (Terre di Altamura SRL, Altamura BA) to prevent cytotoxic damage from cisplatin, staurosporine, irinotecan, doxorubicin, and the glucocorticoid dexamethasone. The acetonitrile-water extract (range 0.1-5 mg/mL) was obtained by extracting 10 g of lentil flour with 50 milliliters of the acetonitrile-water extraction mixture in a 70:30 ratio, first for 3 h and then overnight in a shaker at room temperature. The next day, the extract was filtered and passed through a Rotavapor to obtain only the aqueous component and eliminate that with acetonitrile, and then freeze-dried to finally have the powdered extract. In vitro experiments showed that the extract prevented the cytotoxic damage induced by cisplatin, irinotecan, and doxorubicin on HEK293 and SHSY5Y cell lines after 24-96 h. In murine osteoblasts after 24-72 h of incubation time, the extract was cytoprotective against all chemicals. The extract was effective against dexamethasone, leading to synergic cell proliferation in all cell types. In bone marrow cells, the extract is cytoprotective after 72 h against doxorubicin, staurosporine, and dexamethasone. Instead, on muscle fibers, the extract has a synergic effect with chemotherapeutics, increasing cytotoxicity induced by doxorubicin and staurosporine. LC-MS attested to the existence of several phenolic structures in the extract. The most abundant families of compounds were flavonoids (25.7%) and mellitic acid (18%). Thus, the development of this extract could be implemented in the area of research related to the chemoprevention of damage to renal, neuronal, bone marrow cells, and osteoblasts by chemotherapeutics; moreover, it could be used as a reinforcer of cytotoxic action of chemotherapeutics on muscle fibers.

Charge fluctuations in the intermediate-valence ground state of SmCoIn5.

The microscopic mechanism of heavy band formation, relevant for unconventional superconductivity in CeCoIn5 and other Ce-based heavy fermion materials, depends strongly on the efficiency with which f electrons are delocalized from the rare earth sites and participate in a Kondo lattice. Replacing Ce3+ (4f1, J = 5/2) with Sm3+ (4f5, J = 5/2), we show that a combination of the crystal electric field and on-site Coulomb repulsion causes SmCoIn5 to exhibit a Γ7 ground state similar to CeCoIn5 with multiple f electrons. We show that with this single-ion ground state, SmCoIn5 exhibits a temperature-induced valence crossover consistent with a Kondo scenario, leading to increased delocalization of f holes below a temperature scale set by the crystal field, Tv ≈ 60 K. Our result provides evidence that in the case of many f electrons, the crystal field remains the dominant tuning knob in controlling the efficiency of delocalization near a heavy fermion quantum critical point, and additionally clarifies that charge fluctuations play a general role in the ground state of "115" materials.

Counteractions of a Novel Hydroalcoholic Extract from Lens Culinaria against the Dexamethasone-Induced Osteoblast Loss of Native Murine Cells.

The cytoprotective effects of a novel hydroalcoholic extract (0.01-5 mg/mL) from Lens culinaria (Terre di Altamura Srl) were investigated within murine native skeletal muscle fibers, bone marrow cells, and osteoblasts, and in cell lines treated with the apoptotic agent staurosporine (2.14 × 10-6 M), the alkylating drug cisplatin (10-4 M), the topoisomerase I inhibitor irinotecan (10-4 M), the antimitotic pro-oxidant doxorubicin (10-6 M), and the immunosuppressant dexamethasone (2 × 10-6 M). An amount of 10g of plant material was used to obtain a 70% ethanol/water product, following two-step extraction, evaporation, lyophilization, and storage at -20 °C. For the murine osteoblasts, doxorubicin reduced survival by -65%, dexamethasone by -32% and -60% after 24 and 48 h of incubation time, respectively. The extract was effective in preventing the osteoblast count-reduction induced by dexamethasone; it was also effective at preventing the inhibition of mineralization induced by dexamethasone. Doxorubicin and cisplatin caused a significant reduction in cell growth by -77% for bone marrow cells, -43% for irinotecan, and -60% for dexamethasone, but there was no evidence for the cytoprotective effects of the extract in these cells. Staurosporine and doxorubicin caused a fiber death rate of >-40% after 18 and 24 h of incubation, yet the extract was not effective at preventing these effects. The extract was effective in preventing the staurosporine-induced reduction of HEK293 proliferation and colony formation in the crystal violet DNA staining and the clonogenic assays. It was also effective for the cisplatin-induced reduction in HEK293 cell proliferation. The extract, however, failed to protect the SHSY5Y neurons against cisplatin and irinotecan-induced cytotoxicity. A UV/VIS spectroscopy analysis showed three peaks at the wavelengths of 350, 260, and 190 nm, which correspond to flavonoids, proanthocyanins, salicylates, and AA, constituting the extract. These data suggest the possible development of this extract for use against dexamethasone-induced bone loss and renal chemotherapy-induced damage.

Koopmans Spectral Functionals in Periodic Boundary Conditions.

Koopmans spectral functionals aim to describe simultaneously ground-state properties and charged excitations of atoms, molecules, nanostructures, and periodic crystals. This is achieved by augmenting standard density functionals with simple but physically motivated orbital-density-dependent corrections. These corrections act on a set of localized orbitals that, in periodic systems, resemble maximally localized Wannier functions. At variance with the original, direct supercell implementation (Phys. Rev. X 2018, 8, 021051), we discuss here (i) the complex but efficient formalism required for a periodic boundary code using explicit Brillouin zone sampling and (ii) the calculation of the screened Koopmans corrections with density functional perturbation theory. In addition to delivering improved scaling with system size, the present development makes the calculation of band structures with Koopmans functionals straightforward. The implementation in the open-source Quantum ESPRESSO distribution and the application to prototypical insulating and semiconducting systems are presented and discussed.

Atomic-Level Description of Thermal Fluctuations in Inorganic Lead Halide Perovskites.

A comprehensive microscopic description of thermally induced distortions in lead halide perovskites is crucial for their realistic applications, yet still unclear. Here, we quantify the effects of thermal activation in CsPbBr3 nanocrystals across length scales with atomic-level precision, and we provide a framework for the description of phase transitions therein, beyond the simplistic picture of unit-cell symmetry increase upon heating. The temperature increase significantly enhances the short-range structural distortions of the lead halide framework as a consequence of the phonon anharmonicity, which causes the excess free energy surface to change as a function of temperature. As a result, phase transitions can be rationalized via the soft-mode model, which also describes displacive thermal phase transitions in oxide perovskites. Our findings allow to reconcile temperature-dependent modifications of physical properties, such as changes in the optical band gap, that are incompatible with the perovskite time- and space-average structures.

Nanoscale-Resolved Surface-to-Bulk Electron Transport in CsPbBr3 Perovskite.

Describing the nanoscale charge carrier transport at surfaces and interfaces is fundamental for designing high-performance optoelectronic devices. To achieve this, we employ time- and angle-resolved photoelectron spectroscopy with ultraviolet pump and extreme ultraviolet probe pulses. The resulting high surface sensitivity reveals an ultrafast carrier population decay associated with surface-to-bulk transport, which was tracked with a sub-nanometer spatial resolution normal to the surface, and on a femtosecond time scale, in the case of the inorganic CsPbBr3 lead halide perovskite. The decay time exhibits a pronounced carrier density dependence, which is attributed via modeling to enhanced diffusive transport and concurrent recombination. The transport is found to approach an ordinary diffusive regime, limited by electron-hole scattering, at the highest excitation fluences. This approach constitutes an important milestone in our capability to probe hot-carrier transport at solid interfaces with sub-nanometer resolution in a theoretically and experimentally challenging, yet technologically relevant, high-carrier-density regime.

Quantifying Photoinduced Polaronic Distortions in Inorganic Lead Halide Perovskite Nanocrystals.

The development of next-generation perovskite-based optoelectronic devices relies critically on the understanding of the interaction between charge carriers and the polar lattice in out-of-equilibrium conditions. While it has become increasingly evident for CsPbBr3 perovskites that the Pb-Br framework flexibility plays a key role in their light-activated functionality, the corresponding local structural rearrangement has not yet been unambiguously identified. In this work, we demonstrate that the photoinduced lattice changes in the system are due to a specific polaronic distortion, associated with the activation of a longitudinal optical phonon mode at 18 meV by electron-phonon coupling, and we quantify the associated structural changes with atomic-level precision. Key to this achievement is the combination of time-resolved and temperature-dependent studies at Br K and Pb L3 X-ray absorption edges with refined ab initio simulations, which fully account for the screened core-hole final state effects on the X-ray absorption spectra. From the temporal kinetics, we show that carrier recombination reversibly unlocks the structural deformation at both Br and Pb sites. The comparison with the temperature-dependent XAS results rules out thermal effects as the primary source of distortion of the Pb-Br bonding motif during photoexcitation. Our work provides a comprehensive description of the CsPbBr3 perovskites' photophysics, offering novel insights on the light-induced response of the system and its exceptional optoelectronic properties.

Electronic Structure of Water from Koopmans-Compliant Functionals.

Obtaining a precise theoretical description of the spectral properties of liquid water poses challenges for both molecular dynamics (MD) and electronic structure methods. The lower computational cost of the Koopmans-compliant functionals with respect to Green's function methods allows the simulations of many MD trajectories, with a description close to the state-of-art quasi-particle self-consistent GW plus vertex corrections method (QSGW + fxc). Thus, we explore water spectral properties when different MD approaches are used, ranging from classical MD to first-principles MD, and including nuclear quantum effects. We have observed that different MD approaches lead to up to 1 eV change in the average band gap; thus, we focused on the band gap dependence with the geometrical properties of a system to explain such spread. We have evaluated the changes in the band gap due to variations in the intramolecular O-H bond distance and HOH angle, as well as the intermolecular hydrogen bond O···O distance and the OHO angles. We have observed that the dominant contribution comes from the O-H bond length; the O···O distance plays a secondary role, and the other geometrical properties do not significantly influence the gap. Furthermore, we analyze the electronic density of states (DOS), where the KIPZ functional shows good agreement with the DOS obtained with state-of-art approaches employing quasi-particle self-consistent GW plus vertex corrections. The O-H bond length also significantly influences the DOS. When nuclear quantum effects are considered, broadening of the peaks driven by the broader distribution of the O-H bond lengths is observed, leading to a closer agreement with the experimental photoemission spectra.

Koopmans Meets Bethe-Salpeter: Excitonic Optical Spectra without GW.

The Bethe-Salpeter equation (BSE) can be applied to compute from first-principles optical spectra that include the effects of screened electron-hole interactions. As input, BSE calculations require single-particle states, quasiparticle energy levels, and the screened Coulomb interaction, which are typically obtained with many-body perturbation theory, whose cost limits the scope of possible applications. This work tries to address this practical limitation, instead deriving spectral energies from Koopmans-compliant functionals and introducing a new methodology for handling the screened Coulomb interaction. The explicit calculation of the W matrix is bypassed via a direct minimization scheme applied on top of a maximally localized Wannier function basis. We validate and benchmark this approach by computing the low-lying excited states of the molecules in Thiel's set and the optical absorption spectrum of a C60 fullerene. The results show the same trends as quantum chemical methods and are in excellent agreement with previous simulations carried out at the time-dependent density functional theory or G0 W0-BSE level. Conveniently, the new framework reduces the parameter space controlling the accuracy of the calculation, thereby simplifying the simulation of charge-neutral excitations, offering the potential to expand the applicability of first-principles spectroscopies to larger systems of applied interest.

Koopmans-Compliant Functionals and Potentials and Their Application to the GW100 Test Set.

Koopmans-compliant (KC) functionals have been shown to provide accurate spectral properties through a generalized condition of piecewise linearity of the total energy as a function of the fractional addition/removal of an electron to/from any orbital. We analyze the performance of different KC functionals on a large and standardized set of 100 molecules, the GW100 test set, comparing vertical ionization potentials (taken as opposite of the orbital energies) to those obtained from accurate quantum chemistry methods, and to experimental results. We find excellent agreement, with a mean absolute error of 0.20 eV for the KIPZ functional on the first ionization potential, which is state-of-the-art for both density functional theory (DFT)-based calculations and many-body perturbation theory. We highlight similarities and differences between KC functionals and other electronic-structure approaches, such as dielectric-dependent hybrid functionals and Green's function methods, both from a theoretical and from a practical point of view, arguing that KC potentials can be considered as local and orbital-dependent approximations to the electronic self-energy, already including approximate vertex corrections.

Screening in Orbital-Density-Dependent Functionals.

Electronic-structure functionals that include screening effects, such as Hubbard or Koopmans' functionals, are required to describe the response of a system to the fractional addition or removal of an electron from an orbital or a manifold. Here, we present a general method to incorporate screening based on linear-response theory, and we apply it to the case of orbital-by-orbital screening of Koopmans' functionals. We illustrate the importance of such generalization when dealing with challenging systems containing orbitals with very different chemical character, also highlighting the simple dependence of the screening on the localization of the orbitals. We choose a set of 46 transition-metal complexes for which experimental data and accurate many-body perturbation theory calculations are available. When compared to experiment, results for ionization potentials show a very good performance, with a mean absolute error of 0.2 eV, comparable to the most accurate many-body perturbation theory approaches. These results reiterate the role of Koopmans-compliant functionals as simple and accurate quasiparticle approximations to the exact spectral functional, bypassing diagrammatic expansions and relying only on the physics of the local density or generalized-gradient approximation.