On-Surface Synthesis and Characterization of a High-Spin Aza-[5]-Triangulene.

Triangulenes are a class of open-shell triangular graphene flakes with total spin increasing with their size. In the last years, on-surface-synthesis strategies have permitted fabricating and engineering triangulenes of various sizes and structures with atomic precision. However, direct proof of the increasing total spin with their size remains elusive. In this work, we report the combined in-solution and on-surface synthesis of a large nitrogen-doped triangulene (aza-[5]-triangulene) on a Au(111) surface, and the detection of its high-spin ground state. Bond-resolved scanning tunneling microscopy images uncovered radical states distributed along the zigzag edges, which were detected as weak zero-bias resonances in scanning tunneling spectra. These spectral features reveal the partial Kondo screening of a high-spin state. Through a combination of several simulation tools, we find that the observed distribution of radical states is explained by a quintet ground state (S=2), instead of the quartet state (S=3/2) expected for the neutral species. This confirms that electron transfer to the metal substrate raises the spin of the ground state. We further provide a qualitative description of the change of (anti)aromaticity introduced by N-substitution, and its role in the charge stabilization on a surface, resulting in an S=2 aza-triangulene on Au(111).

Modular implementation of the linear- and cubic-scaling orbital minimization methods in electronic structure codes using atomic orbitals.

We present a code modularization approach to design efficient and massively parallel cubic- and linear-scaling solvers for electronic structure calculations using atomic orbitals. The modular implementation of the orbital minimization method, in which linear algebra and parallelization issues are handled via external libraries, is demonstrated in the SIESTA code. The distributed block compressed sparse row (DBCSR) and scalable linear algebra package (ScaLAPACK) libraries are used for algebraic operations with sparse and dense matrices, respectively. The MatrixSwitch and libOMM libraries, recently developed within the Electronic Structure Library, facilitate switching between different matrix formats and implement the energy minimization. We show results comparing the performance of several cubic-scaling algorithms, and also demonstrate the parallel performance of the linear-scaling solvers, and their supremacy over the cubic-scaling solvers for insulating systems with sizes of several hundreds of atoms.

Inelastic scattering of electrons in water from first principles: cross sections and inelastic mean free path for use in Monte Carlo track-structure simulations of biological damage.

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.

Semi-empirical and linear-scaling DFT methods to characterize duplex DNA and G-quadruplexes in the presence of interacting small molecules.

The computational study of DNA and its interaction with ligands is a highly relevant area of research, with significant consequences for developing new therapeutic strategies. However, the computational description of such large and complex systems requires considering interactions of different types simultaneously in a balanced way, such as non-covalent weak interactions (namely hydrogen bonds and stacking), metal-ligand interactions, polarisation and charge transfer effects. All these considerations imply a real challenge for computational chemistry. The possibility of studying large biological systems using quantum methods for the entire system requires significant computational resources, with improvements in parallelisation and optimisation of theoretical strategies. Computational methods, such as Linear-Scaling Density Functional Theory (LS-DFT) and DLPNO-CCSD(T), may allow performing ab initio quantum mechanics calculations, including the electronic structure for large biological systems, in a reasonable computing time. In this work, we study the interaction of small molecules and cations with DNA (both duplex DNA and G-quadruplexes), comparing different computational methods: a LS-DFT method at the LMKLL/DZDP level of theory, semi-empirical methods (PM6-DH2 and PM7), mixed QM/MM, and DLPNO-CCSD(T). Our goal is to demonstrate the adequacy of LS-DFT to treat the different types of interactions present in DNA-dependent systems. We show that LMKLL/DZDP using SIESTA can yield very accurate geometries and energetics in all the different systems considered in this work: duplex DNA (dDNA), phenanthroline intercalating dDNA, G-quadruplexes, and metal-G-tetrads considering alkaline metals of different sizes. As far as we know, this is the first time that full G-quadruplex geometry optimisations have been carried out using a DFT method thanks to its linear-scaling capabilities. Moreover, we show that LS-DFT provides high-quality structures, and some semi-empirical Hamiltonians can also yield suitable geometries. However, DLPNO-CCSD(T) and LS-DFT are the only methods that accurately describe interaction energies for all the systems considered in our study.

Efficient ab initio calculation of electronic stopping in disordered systems via geometry pre-sampling: Application to liquid water.

Knowledge of the electronic stopping curve for swift ions, Se(v), particularly around the Bragg peak, is important for understanding radiation damage. Experimentally, however, the determination of such a feature for light ions is very challenging, especially in disordered systems such as liquid water and biological tissue. Recent developments in real-time time-dependent density functional theory (rt-TDDFT) have enabled the calculation of Se(v) along nm-sized trajectories. However, it is still a challenge to obtain a meaningful statistically averaged Se(v) that can be compared to observations. In this work, taking advantage of the correlation between the local electronic structure probed by the projectile and the distance from the projectile to the atoms in the target, we devise a trajectory pre-sampling scheme to select, geometrically, a small set of short trajectories to accelerate the convergence of the averaged Se(v) computed via rt-TDDFT. For protons in liquid water, we first calculate the reference probability distribution function (PDF) for the distance from the proton to the closest oxygen atom, ϕR(rp→O), for a trajectory of a length similar to those sampled experimentally. Then, short trajectories are sequentially selected so that the accumulated PDF reproduces ϕR(rp→O) to increasingly high accuracy. Using these pre-sampled trajectories, we demonstrate that the averaged Se(vp) converges in the whole velocity range with less than eight trajectories, while other averaging methods using randomly and uniformly distributed trajectories require approximately ten times the computational effort. This allows us to compare the Se(vp) curve to experimental data and assess widely used empirical tables based on Bragg's rule.

The CECAM electronic structure library and the modular software development paradigm.

First-principles electronic structure calculations are now accessible to a very large community of users across many disciplines, thanks to many successful software packages, some of which are described in this special issue. The traditional coding paradigm for such packages is monolithic, i.e., regardless of how modular its internal structure may be, the code is built independently from others, essentially from the compiler up, possibly with the exception of linear-algebra and message-passing libraries. This model has endured and been quite successful for decades. The successful evolution of the electronic structure methodology itself, however, has resulted in an increasing complexity and an ever longer list of features expected within all software packages, which implies a growing amount of replication between different packages, not only in the initial coding but, more importantly, every time a code needs to be re-engineered to adapt to the evolution of computer hardware architecture. The Electronic Structure Library (ESL) was initiated by CECAM (the European Centre for Atomic and Molecular Calculations) to catalyze a paradigm shift away from the monolithic model and promote modularization, with the ambition to extract common tasks from electronic structure codes and redesign them as open-source libraries available to everybody. Such libraries include "heavy-duty" ones that have the potential for a high degree of parallelization and adaptation to novel hardware within them, thereby separating the sophisticated computer science aspects of performance optimization and re-engineering from the computational science done by, e.g., physicists and chemists when implementing new ideas. We envisage that this modular paradigm will improve overall coding efficiency and enable specialists (whether they be computer scientists or computational scientists) to use their skills more effectively and will lead to a more dynamic evolution of software in the community as well as lower barriers to entry for new developers. The model comes with new challenges, though. The building and compilation of a code based on many interdependent libraries (and their versions) is a much more complex task than that of a code delivered in a single self-contained package. Here, we describe the state of the ESL, the different libraries it now contains, the short- and mid-term plans for further libraries, and the way the new challenges are faced. The ESL is a community initiative into which several pre-existing codes and their developers have contributed with their software and efforts, from which several codes are already benefiting, and which remains open to the community.

Siesta: Recent developments and applications.

A review of the present status, recent enhancements, and applicability of the Siesta program is presented. Since its debut in the mid-1990s, Siesta's flexibility, efficiency, and free distribution have given advanced materials simulation capabilities to many groups worldwide. The core methodological scheme of Siesta combines finite-support pseudo-atomic orbitals as basis sets, norm-conserving pseudopotentials, and a real-space grid for the representation of charge density and potentials and the computation of their associated matrix elements. Here, we describe the more recent implementations on top of that core scheme, which include full spin-orbit interaction, non-repeated and multiple-contact ballistic electron transport, density functional theory (DFT)+U and hybrid functionals, time-dependent DFT, novel reduced-scaling solvers, density-functional perturbation theory, efficient van der Waals non-local density functionals, and enhanced molecular-dynamics options. In addition, a substantial effort has been made in enhancing interoperability and interfacing with other codes and utilities, such as wannier90 and the second-principles modeling it can be used for, an AiiDA plugin for workflow automatization, interface to Lua for steering Siesta runs, and various post-processing utilities. Siesta has also been engaged in the Electronic Structure Library effort from its inception, which has allowed the sharing of various low-level libraries, as well as data standards and support for them, particularly the PSeudopotential Markup Language definition and library for transferable pseudopotentials, and the interface to the ELectronic Structure Infrastructure library of solvers. Code sharing is made easier by the new open-source licensing model of the program. This review also presents examples of application of the capabilities of the code, as well as a view of on-going and future developments.

Gap variability upon packing in organic photovoltaics.

The variation of the HOMO-LUMO band gap is explored for varying packing arrangements of the 4mod BT-4TIC donor-acceptor molecule pair, by means of a high-throughput ab-initio random structure search of packing possibilities. 350 arrangements of the dimer have been relaxed from initial random dispositions, using non-local density-functional theory. We find that the electronic band gap varies within 0.3 eV, and that this magnitude, the binding energy, and the geometry are not significantly correlated. A clearly favoured structure is found with a binding energy of 1.75±0.07 eV, with all but three other arrangements displaying values of less than one third of this highest binding one, which involves the aliphatic chain of 4TIC.

Entropic bonding of the type 1 pilus from experiment and simulation.

The type 1 pilus is a bacterial filament consisting of a long coiled proteic chain of subunits joined together by non-covalent bonding between complementing ß -strands. Its strength and structural stability are critical for its anchoring function in uropathogenic Escherichia coli bacteria. The pulling and unravelling of the FimG subunit of the pilus was recently studied by atomic force microscopy experiments and steered molecular dynamics simulations (Alonso-Caballero et al. 2018 Nat. Commun. 9, 2758. (doi:10.1038/s41467-018-05107-6)). In this work, we perform a quantitative comparison between experiment and simulation, showing a good agreement in the underlying work values for the unfolding. The simulation results are then used to estimate the free energy difference for the detachment of FimG from the complementing strand of the neighbouring subunit in the chain, FimF. Finally, we show that the large free energy difference for the unravelling and detachment of the subunits which leads to the high stability of the chain is entirely entropic in nature.

Ab initio electronic stopping power for protons in Ga0.5In0.5P/GaAs/Ge triple-junction solar cells for space applications.

Motivated by the radiation damage of solar panels in space, firstly, the results of Monte Carlo particle transport simulations are presented for proton impact on triple-junction Ga0.5In0.5P/GaAs/Ge solar cells, showing the proton projectile penetration in the cells as a function of energy. It is followed by a systematic ab initio investigation of the electronic stopping power (ESP) for protons in different layers of the cell at the relevant velocities via real-time time-dependent density functional theory calculations. The ESP is found to depend significantly on different channelling conditions, which should affect the low-velocity damage predictions, and which are understood in terms of impact parameter and electron density along the path. Additionally, we explore the effect of the interface between the layers of the multilayer structure on the energy loss of a proton, along with the effect of strain in the lattice-matched solar cell. Both effects are found to be small compared with the main bulk effect. The interface energy loss has been found to increase with decreasing proton velocity, and in one case, there is an effective interface energy gain.

Electrostatics and domains in ferroelectric superlattices.

The electrostatics arising in ferroelectric/dielectric two-dimensional heterostructures and superlattices is revisited within a Kittel model in order to define and complete a clear paradigmatic reference for domain formation. The screening of the depolarizing field in isolated ferroelectric or polar thin films via the formation of 180° domains is well understood, where the width of the domains w grows as the square-root of the film thickness d, following Kittel's Law for thick enough films (w ≪ d). For thinner films, a minimum is reached for w before diverging to a monodomain. Although this behaviour is known to be qualitatively unaltered when the dielectric environment of the film is modified, we consider the quantitative changes in that behaviour induced on the ferroelectric film by different dielectric settings: as deposited on a dielectric substrate, sandwiched between dielectrics, and in a superlattice of alternating ferroelectric/dielectric films. The model assumes infinitely thin domain walls, and therefore is not expected to be reliable for film thickness in the nanometre scale. The polarization field P(r) does vary in space, deviating from ±P S , following the depolarizing field in linear response, but the model does not include a polarization-gradient term as would appear in a Ginzburg-Landau free energy. The model is, however, worth characterizing, both as paradigmatic reference, and as applicable to not-so-thin films. The correct renormalization of parameters is obtained for the thick-film square-root behaviour in the mentioned settings, and the sub-Kittel regime is fully characterized. New results are presented alongside well-known ones for a comprehensive description. Among the former, a natural separation between strong and weak ferroelectric coupling in superlattices is found, which depends exclusively on the dielectric anisotropy of the ferroelectric layer.

Prediction of the near-IR spectra of ices by ab initio molecular dynamics.

A method to predict the near-infrared spectra of amorphous solids by means of ab initio molecular dynamics is presented. These solids can simulate molecular ices. To test the method, mixtures of methane, water and nitrogen are generated as amorphous samples of various concentrations. The full theoretical treatment includes as a first step, the optimization of their geometrical structure for a range of densities, after which, the most stable systems are taken as initial structures for molecular dynamics, performed at 200 K in trajectories of 4 ps duration with a 0.2 fs time step. All the dynamics are carried out using the first principles method, solving the quantum problem for the electrons using density-functional theory (DFT), and integrating the DFT forces, following the Born-Oppenheimer dynamics. After the dynamics, near-IR spectra are predicted by the Fourier transform of the macroscopic polarization autocorrelation function. The calculated spectra are compared with the experimental spectra of ice mixtures of CH4 and H2O recorded in our laboratory, and with some spectra recorded by the New Horizons mission on Pluto.

Core Electrons in the Electronic Stopping of Heavy Ions.

Electronic stopping power in the keV/Å range is accurately calculated from first principles for high atomic-number projectiles and the effect of core states is carefully assessed. The energy loss to electrons in self-irradiated nickel is studied using real-time time-dependent density functional theory. Different core states are explicitly included in the simulations to understand their involvement in the dissipation mechanism. The core electrons of the projectile are found to open additional dissipation channels as the projectile velocity increases. Almost all of the energy loss is accounted for, even for high projectile velocities, when core electrons as deep as 2s^{2}2p^{6} are explicitly treated. In addition to their expected excitation at high velocities, a flapping dynamical response of the projectile core electrons is observed at intermediate velocities. The empirical reference data are well reproduced in the projectile velocity range of 1.0-12.0 a.u. (1.5-210 MeV).

Mechanical architecture and folding of E. coli type 1 pilus domains.

Uropathogenic Escherichia coli attach to tissues using pili type 1. Each pilus is composed by thousands of coiled FimA domains followed by the domains of the tip fibrillum, FimF-FimG-FimH. The domains are linked by non-covalent ß-strands that must resist mechanical forces during attachment. Here, we use single-molecule force spectroscopy to measure the mechanical contribution of each domain to the stability of the pilus and monitor the oxidative folding mechanism of a single Fim domain assisted by periplasmic FimC and the oxidoreductase DsbA. We demonstrate that pilus domains bear high mechanical stability following a hierarchy by which domains close to the tip are weaker than those close to or at the pilus rod. During folding, this remarkable stability is achieved by the intervention of DsbA that not only forms strategic disulfide bonds but also serves as a chaperone assisting the folding of the domains.

Simulations of water nano-confined between corrugated planes.

Water confined to nanoscale widths in two dimensions between ideal planar walls has been the subject of ample study, aiming at understanding the intrinsic response of water to confinement, avoiding the consideration of the chemistry of actual confining materials. In this work, we study the response of such nanoconfined water to the imposition of a periodicity in the confinement by means of computer simulations, both using empirical potentials and from first-principles. For that we propose a periodic confining potential emulating the atomistic oscillation of the confining walls, which allows varying the lattice parameter and amplitude of the oscillation. We do it for a triangular lattice, with several values of the lattice parameter: one which is ideal for commensuration with layers of Ih ice and other values that would correspond to more realistic substrates. For the former, the phase diagram shows an overall rise of the melting temperature. The liquid maintains a bi-layer triangular structure, however, despite the fact that it is not favoured by the external periodicity. The first-principles liquid is significantly affected by the modulation in its layering and stacking even at relatively small amplitudes of the confinement modulation. Beyond some critical modulation amplitude, the hexatic phase present in flat confinement is replaced by a trilayer crystalline phase unlike any of the phases encountered for flat confinement. For more realistic lattice parameters, the liquid does not display higher tendency to freeze, but it clearly shows inhomogeneous behaviour as the strength of the rugosity increases. In spite of this expected inhomogeneity, the structural and dynamical response of the liquid is surprisingly insensitive to the external modulation. Although the first-principles calculations give a more triangular liquid than the one observed with empirical potentials (TIP4P/2005), both agree remarkably well for the main conclusions of the study.

Water radiolysis by low-energy carbon projectiles from first-principles molecular dynamics.

Water radiolysis by low-energy carbon projectiles is studied by first-principles molecular dynamics. Carbon projectiles of kinetic energies between 175 eV and 2.8 keV are shot across liquid water. Apart from translational, rotational and vibrational excitation, they produce water dissociation. The most abundant products are H and OH fragments. We find that the maximum spatial production of radiolysis products, not only occurs at low velocities, but also well below the maximum of energy deposition, reaching one H every 5 Å at the lowest speed studied (1 Bohr/fs), dissociative collisions being more significant at low velocity while the amount of energy required to dissociate water is constant and much smaller than the projectile's energy. A substantial fraction of the energy transferred to fragments, especially for high velocity projectiles, is in the form of kinetic energy, such fragments becoming secondary projectiles themselves. High velocity projectiles give rise to well-defined binary collisions, which should be amenable to binary approximations. This is not the case for lower velocities, where multiple collision events are observed. H secondary projectiles tend to move as radicals at high velocity, as cations when slower. We observe the generation of new species such as hydrogen peroxide and formic acid. The former occurs when an O radical created in the collision process attacks a water molecule at the O site. The latter when the C projectile is completely stopped and reacts with two water molecules.

Simulations and spectra of water in CO matrices.

Models for the inclusion of water molecules in carbon monoxide matrices are developed using density functional theory applied to amorphous solid systems. The models cover a large range of systems for smaller or larger CO matrices with different water content, consisting of either individual H2O molecules or small clusters linked by H-bonds. The vibrational spectra of the samples are predicted at the minimum of their potential energy surface. The spectra allow instances where the water molecules remain isolated or form aggregates to be discerned, and they also provide an indication of the strength of the H-bonding, when present. The calculations support recent experimental observations that linked IR bands at 3707 cm-1 and 3617 cm-1 to the presence of unbound water molecules in water-poor CO/H2O mixed ices. Assignment of some observed bands to water dimers or trimers is suggested as well. The residual static pressure in fixed-volume simulation cells is also calculated.

Continuous melting through a hexatic phase in confined bilayer water.

Liquid water is not only of obvious importance but also extremely intriguing, displaying many anomalies that still challenge our understanding of such an a priori simple system. The same is true when looking at nanoconfined water: The liquid between constituents in a cell is confined to such dimensions, and there is already evidence that such water can behave very differently from its bulk counterpart. A striking finding has been reported from computer simulations for two-dimensionally confined water: The liquid displays continuous or discontinuous melting depending on its density. In order to understand this behavior, we have analyzed the melting exhibited by a bilayer of nanoconfined water by means of molecular dynamics simulations. At high density we observe the continuous melting to be related to the phase change of the oxygens only, with the hydrogens remaining liquidlike throughout. Moreover, we find an intermediate hexatic phase for the oxygens between the liquid and a triangular solid ice phase, following the Kosterlitz-Thouless-Halperin-Nelson-Young theory for two-dimensional melting. The liquid itself tends to maintain the local structure of the triangular ice, with its two layers being strongly correlated yet with very slow exchange of matter. The decoupling in the behavior of the oxygens and hydrogens gives rise to a regime in which the complexity of water seems to disappear, resulting in what resembles a simple monoatomic liquid. This intrinsic tendency of our simulated water may be useful for understanding novel behaviors in other confined and interfacial water systems.

Electronic and magnetic properties of superconducting LnO1-x F x BiS2 (Ln = La, Ce, Pr, and Nd) from first principles.

A density functional theory study of the BiS2 superconductors containing rare-earths: LnO1-x F x BiS2 (Ln = La, Ce, Pr, and Nd) is presented. We find that CeO0.5F0.5BiS2 has competing ferromagnetic and weak antiferromagnetic tendencies, the first one corresponding to experimental results. We show that PrO0.5F0.5BiS2 has a strong tendency for magnetic order, which can be ferromagnetic or antiferromagnetic depending on subtle differences in 4f orbital occupations. We demonstrate that NdO0.5F0.5BiS2 has a stable magnetic ground state with weak tendency to order. Finally, we show that the change of rare earth does not affect the Fermi surface, and predict that CeOBiS2 should display a pressure induced phase transition to a metallic, if not superconducting, phase under pressure.

Enhanced Configurational Entropy in High-Density Nanoconfined Bilayer Ice.

A novel kind of crystal order in high-density nanoconfined bilayer ice is proposed from molecular dynamics and density-functional theory simulations. A first-order transition is observed between a low-temperature proton-ordered solid and a high-temperature proton-disordered solid. The latter is shown to possess crystalline order for the oxygen positions, arranged on a close-packed triangular lattice with AA stacking. Uniquely among the ice phases, the triangular bilayer is characterized by two levels of disorder (for the bonding network and for the protons) which results in a configurational entropy twice that of bulk ice.