Siesta: Recent developments and applications

Calculated vibration spectrum of calcium hexahydroxodizincate dihydrate (qatranaite)

On the basis of first-principles electronic structure calculations, crystallographic parameters have been refined for calcium hydroxozincate (Qatranaite mineral), and the vibration properties (frequencies and eigenvectors) calculated. A detailed analysis of vibration modes is done, in the context of comparison with infrared and Raman spectra previously available. Special attention is paid to a posteriori symmetry analysis of vibration modes, discussing the latters' attribution to four irreducible representations of the P21/c space group, and to identifying stretchings and bendings of particular chemical bonds, pronounced in different vibrations. It turns out that high-frequency (>700 cm-1) vibrations of hydroxyl groups bridging the Ca or Zn cations differ quite considerably for crystallographically distinct hydroxyl positions. It is shown that the vibrations involving hydroxyl groups and crystalline water typically come about in quadruplets at very close frequencies, whereby different irreducible representations reflect different combinations of similar "molecular" vibrations of four identical entities (of each hydroxyl or water) present in the unit cell. However, some vibrations show exceptions from this rule. In addition to interpretation of earlier experimental investigations, our study indicates that the low-frequency (<700 cm-1) vibrations within the cation-hydroxyl connected skeleton are of more "solid-state-like" character and cannot be reasonably interpreted in terms of "molecular" vibrations within ZnO4 or CaO6 units.

Minimum Tracking Linear Response Hubbard and Hund Corrected Density Functional Theory in CP2K

We present the implementation of the Hubbard (U) and Hund (J) corrected Density Functional Theory (DFT + U + J) functionality in the Quickstep program, which is part of the CP2K suite. The tensorial and Löwdin subspace representations are implemented and compared. Full analytical DFT + U + J forces are implemented and benchmarked for the tensorial and Löwdin representations. We also present the implementation of the recently proposed minimum-tracking linear-response method that enables the U and J parameters to be calculated on first-principles basis without reference to the Kohn-Sham eigensystem. These implementations are benchmarked against recent results for different materials properties including DFT + U band gap opening in NiO, the relative stability of various polaron distributions in TiO2, the dependence of the calculated TiO2 band gap on +J corrections, and, finally, the role of the +U and +J corrections for the computed properties of a series of the hexahydrated transition metals. Our implementation provides results consistent with those already reported in the literature from comparable methods. We conclude the contribution with tests on the influence of the Löwdin orthonormalization on the occupancies, calculated parameters, and derived properties.

Uncovering an Interfacial Band Resulting from Orbital Hybridization in Nickelate Heterostructures

The interaction of atomic orbitals at the interface of perovskite oxide heterostructures has been investigated for its profound impact on the band structures and electronic properties, giving rise to unique electronic states and a variety of tunable functionalities. In this study, we conducted an extensive investigation of the optical and electronic properties of epitaxial NdNiO3 synthesized on a series of single-crystal substrates. Unlike nanofilms synthesized on other substrates, NdNiO3 on SrTiO3 (NNO/STO) gives rise to a unique band structure featuring an additional unoccupied band situated above the Fermi level. Our comprehensive investigation, which incorporated a wide array of experimental techniques and density functional theory calculations, revealed that the emergence of the interfacial band structure is primarily driven by orbital hybridization between the Ti 3d orbitals of the STO substrate and the O 2p orbitals of the NNO thin film. Furthermore, exciton peaks have been detected in the optical spectra of the NNO/STO film, attributable to the pronounced electron-electron (e-e) and electron-hole (e-h) interactions propagating from the STO substrate into the NNO film. These findings underscore the substantial influence of interfacial orbital hybridization on the electronic structure of oxide thin films, thereby offering key insights into tuning their interfacial properties.

TPDH-Graphene as a New Anodic Material for Lithium Ion Battery: DFT-Based Investigations

The potential of tetra-penta-deca-hexagonal graphene (TPDH-gr), a recently proposed 2D carbon allotrope as an anodic material in lithium ion batteries (LIBs), was investigated through density functional theory calculations. The results indicate that Li-atom adsorption is moderate (around 0.70 eV), allowing for easy desorption. Moreover, energy barriers (0.08-0.20 eV), diffusion coefficient (>6 × 10-6 cm2/s), and open circuit voltage (0.29 V) calculations show rapid Li atom diffusion on the TPDH-gr surface, stable intercalation of lithium atoms, and good performance during the charge and discharge cycles of the LIB. These findings, combined with the intrinsic metallic nature of TPDH-gr, indicate that this new 2D carbon allotrope is a promising candidate for use as an anodic LIB material.

Atomic-Resolution Vibrational Mapping of Bilayer Borophene

The successful synthesis of borophene beyond the monolayer limit has expanded the family of two-dimensional boron nanomaterials. While atomic-resolution topographic imaging has been previously reported, vibrational mapping has the potential to reveal deeper insight into the chemical bonding and electronic properties of bilayer borophene. Herein, inelastic electron tunneling spectroscopy (IETS) is used to resolve the low-energy vibrational and electronic properties of bilayer-α (BL-α) borophene on Ag(111) at the atomic scale. Using a carbon monoxide (CO)-functionalized scanning tunneling microscopy tip, the BL-α borophene IETS spectra reveal unique features compared to single-layer borophene and typical CO vibrations on metal surfaces. Distinct vibrational spectra are further observed for hollow and filled boron hexagons within the BL-α borophene unit cell, providing evidence for interlayer bonding between the constituent borophene layers. These experimental results are compared with density functional theory calculations to elucidate the interplay between the vibrational modes and electronic states in bilayer borophene.

Effects of BPQ binding on the nonadiabatic dynamics of excited electrons in poly(dG)-poly(dC) DNA under proton irradiation

The interaction between DNA and small molecules is important for understanding the mechanisms of DNA-based multifunctional devices and has been extensively studied. However, there are few reports on such interactions in irradiation environments. Here, we investigate the nonadiabatic dynamic behaviors of excited electrons in double-stranded DNA bound to BPQ molecule upon proton irradiation, focusing on the energy deposition and electronic excitation dynamics as protons traverse the DNA along different channels. Our results reveal that the presence of BPQ significantly influences charge migration and DNA damage, with notable differences between CGvdW and CGcovalent adducts. The energy deposition process is highly dependent on charge density, and guanine exhibits higher excitation propensity than cytosine due to its structural characteristics. The BPQ molecule enhances DNA charge migration and promotes damage through secondary electron migration. These findings provide insights into the nonadiabatic dynamics of DNA under ionizing radiation and have implications for designing targeted electrophilic organics to improve radiotherapy efficacy.

Reversible hydrogen storage and release mechanism of a B2N monolayer: a first-principles insight

It was found the physical adsorption could be an efficient strategy for high capacity, high efficiency and high safety in hydrogen storage. In this research, a systematic investigation into the potential of the B2N monolayer as an excellent physical adsorption hydrogen storage material is conducted by utilizing the first-principles calculation method. The findings of the investigation demonstrate that the B2N monolayer has a planar lattice and excellent structural stability. It is possible for H2 molecules to adsorb onto the B2N monolayer spontaneously. Both the individual adsorption and saturation adsorption corresponded to average adsorption energies ranging from -0.221 to -0.194 eV, fulfilling the physical adsorption criteria. In the case of saturation adsorption, a 1 × 2 × 1 B2N supercell can store a total of 24 H2 molecules, with the hydrogen gravimetric density up to 14.511 wt% and volumetric density up to 138 g L-1. A semi-empirical calculation method is used to research the performance of the system in terms of adsorption and desorption with actual temperature and pressure conditions. Under the actual conditions with adsorption carried out at 30 atm/233 K and desorption carried out at 3 atm/358 K, the maximal reversible hydrogen storage capacity of the hydrogen storage system based on the B2N monolayer can still reach 12.157 wt%, which is superior to that of many other boron-nitrogen compounds and metal-free functionalized hydrogen storage materials. The findings of this work indicate that the pristine B2N monolayer is one of the promising physical adsorption materials which could achieve excellent reversible hydrogen storage under defined conditions.

Enabling Ab Initio Molecular Dynamics under Bias: The CP2K+SMEAGOL Interface for Integrating Density Functional Theory and Non-Equilibrium Green Functions

Density functional theory (DFT) combined with non-equilibrium Green's functions (NEGF) is a powerful approach to model quantum transport under external bias potentials at reasonable computational cost. In this work, we present a new interface between the popular mixed Gaussian/plane waves electronic structure package, CP2K, and the NEGF, code SMEAGOL, the most feature-rich implementation of DFT-NEGF available for CP2K to date. The CP2K+SMEAGOL interface includes the implementation of current induced forces. We verify this implementation for a variety of systems: an infinite 1D Au wire, a parallel-plate capacitor, and a Au-H2-Au junction. We find good agreement with SMEAGOL calculations performed with SIESTA for the same systems and with the example of a solvated Au wire demonstrating for the first time that DFT-NEGF can be used to perform molecular dynamics simulations under bias of large-scale condensed phase systems under realistic operating conditions.

Exploring Aromaticity Effects on Electronic Transport in Cyclo[n]carbon Single-Molecule Junctions

Cyclo[n]carbon (Cn) is one member of the all-carbon allotrope family with potential applications in next-generation electronic devices. By employing first-principles quantum transport calculations, we have investigated the electronic transport properties of single-molecule junctions of Cn, with n = 14, 16, 18, and 20, connected to two bulk gold electrodes, uncovering notable distinctions arising from the varying aromaticities. For the doubly aromatic C14 and C18 molecules, slightly deformed complexes at the singlet state arise after bonding with one Au atom at each side; in contrast, the reduced energy gaps between the highest occupied and the lowest unoccupied molecular orbitals due to the orbital reordering observed in the doubly anti-aromatic C16 and C20 molecules lead to heavily deformed asymmetric complexes at the triplet state. Consequently, spin-unpolarized transmission functions are obtained for the Au-C14/18-Au junctions, while spin-polarized transmission appears in the Au-C16/20-Au junctions. Furthermore, the asymmetric in-plane π-type hybrid molecular orbitals of the Au-C16/20-Au junctions contribute to two broad but low transmission peaks far away from the Fermi level (Ef), while the out-of-plane π-type hybrid molecular orbitals dominate two sharp transmission peaks that are adjacent to Ef, thus resulting in much lower transmission coefficients at Ef compared to those of the Au-C14/18-Au junctions. Our findings are helpful for the design and application of future cyclo[n]carbon-based molecular electronic devices.

Co-designing ab initio electronic structure methods on a RISC-V vector architecture

Ab initio electronic structure applications are among the most widely used in High-Performance Computing (HPC), and the eigenvalue problem is often their main computational bottleneck. This article presents our initial efforts in porting these codes to a RISC-V prototype platform leveraging a wide Vector Processing Unit (VPU). Our software tester is based on a mini-app extracted from the ELPA eigensolver library. The user-space Vehave and a RISC-V vector architecture implemented on an FPGA were tested. Metrics from both systems and different vectorisation strategies were extracted, ranging from the most simple and portable one (using autovectorisation and assisting this by fusing loops in the code) to the more complex one (using intrinsics). We observed a progressive reduction in the number of vectorial instructions, executed instructions and computing cycles with the different methodologies, which will lead to a substantial speed-up in the calculations. The obtained outcomes are crucial in advancing the porting of computational materials and molecular science codes to (post)-exascale architectures using RISC-V-based technologies fully developed within the EU. Our evaluation also provides valuable feedback for hardware designers, engineers and compiler developers, making this use case pivotal for co-design efforts.

Correlated electron-nuclear dynamics of photoinduced water dissociation on rutile TiO2

Elucidating the mechanism of photoinduced water splitting on TiO2 is important for advancing the understanding of photocatalysis and the ability to control photocatalytic surface reactions. However, incomplete experimental information and complex coupled electron-nuclear motion make the microscopic understanding challenging. Here we analyse the atomic-scale pathways of photogenerated charge carrier transport and photoinduced water dissociation at the prototypical water-rutile TiO2(110) interface using first-principles dynamics simulations. Two distinct mechanisms are observed. Field-initiated electron migration leads to adsorbed water dissociation via proton transfer to a surface bridging oxygen. In the other pathway, adsorbed water dissociation occurs via proton donation to a second-layer water molecule coupled to photoexcited-hole transfer promoted by in-plane surface lattice distortions. Two stages of non-adiabatic in-plane lattice motion-expansion and recovery-are observed, which are closely associated with population changes in Ti3d orbitals. Controlling such highly correlated electron-nuclear dynamics may provide opportunities for boosting the performance of photocatalytic materials.

Ab Initio Molecular Dynamics Insight to Structural Phase Transition and Thermal Decomposition of InN

Extensive ab initio density functional theory molecular dynamics calculations were used to evaluate stability conditions for relevant phases of InN. In particular, the p-T conditions of the thermal decomposition of InN and pressure-induced wurtzite-rocksalt solid-solid phase transition were established. The comparison of the simulation results with the available experimental data allowed for a critical evaluation of the capabilities and limitations of the proposed simulation method. It is shown that ab initio molecular dynamics can be used as an efficient tool for simulations of phase transformations of InN, including solid-solid structural transition and thermal decomposition with formation of N2 molecules. It is of high interest, because InN is an important component of epitaxial quantum structures, but it has not been obtained as a bulk single crystal. This makes it difficult to determine its basic physical properties to develop new applications.

Covalent surface modification of single-layer graphene-like BC6N nanosheets with reactive nitrenes for selective ammonia sensing via DFT modeling

Novel graphene-like nanomaterials with a non-zero bandgap are important for the design of gas sensors. The selectivity toward specific targets can be tuned by introducing appropriate functional groups on their surfaces. In this study, we use first-principles simulations, in the form of density functional theory (DFT), to investigate the covalent functionalization of a single-layer graphitized BC6N with azides to yield aziridine-functionalized adducts and explore their possible use to realize ammonia sensors. First, we determine the most favorable sites for physical adsorption and chemical reaction of methylnitrene, arising from the decomposition of methylazide, onto a BC6N monolayer. Then, we examine the thermodynamics of the [1 + 2]-cycloaddition reaction of various phenylnitrenes and perfluorinated phenylnitrenes para-substituted with (R = CO2H, SO3H) groups, demonstrating favorable energetics. We also monitor the effect of the functionalization on the electronic properties of the nanosheets via density of states and band structure analyses. Finally, we test four dBC6N to gBC6N substrates in the sensing of ammonia. We show that, thanks to their hydrogen bonding capabilities, the functionalized BC6N can selectively detect ammonia, with interaction energies varying from -0.54 eV to -1.37 eV, even in presence of competing gas such as CO2and H2O, as also confirmed by analyzing the change in the electronic properties and the values of recovery times near ambient temperature. Importantly, we model the conductance of a selected substrate alone and in presence of NH3to determine its effect on the integrated current, showing that humidity and coverage conditions should be properly tuned to use HO2C-functionalized BC6N-based nanomaterials to develop selective gas sensors for ammonia.

Exploring potential energy surfaces to reach saddle points above convex regions

Saddle points on high-dimensional potential energy surfaces (PES) play a determining role in the activated dynamics of molecules and materials. Building on approaches dating back more than 50 years, many open-ended transition-state search methods have been developed to follow the direction of negative curvature from a local minimum to an adjacent first-order saddle point. Despite the mathematical justification, these methods can display a high failure rate: using small deformation steps, up to 80% of the explorations can end up in a convex region of the PES, where all directions of negative curvature vanish, while if the deformation is aggressive, a similar fraction of attempts lead to saddle points that are not directly connected to the initial minimum. In high-dimension PES, these reproducible failures were thought to only increase the overall computational cost, without having any effect on the methods' capacity to find all saddle points surrounding a minimum. Using activation-relaxation technique nouveau (ARTn), we characterize the nature of the PES around minima, considerably expanding on previous knowledge. We show that convex regions can lie on activation pathways and that not exploring beyond them can introduce significant bias in the saddle-point search. We introduce an efficient approach for traversing the convex regions, almost eliminating exploration failures, while multiplying by almost 10 the number of identified unique and connected saddle points as compared to the standard ARTn, thus underlining the importance of correctly handling convex regions for completeness of saddle point explorations.

Predicting the One-Particle Density Matrix with Machine Learning

Two of the most widely used electronic-structure theory methods, namely, Hartree-Fock and Kohn-Sham density functional theory, require the iterative solution of a set of Schrödinger-like equations. The speed of convergence of such a process depends on the complexity of the system under investigation, the self-consistent-field algorithm employed, and the initial guess for the density matrix. An initial density matrix close to the ground-state matrix will effectively allow one to cut out many of the self-consistent steps necessary to achieve convergence. Here, we predict the density matrix of Kohn-Sham density functional theory by constructing a neural network that uses only the atomic positions as information. Such a neural network provides an initial guess for the density matrix far superior to that of any other recipes available. Furthermore, the quality of such a neural-network density matrix is good enough for the evaluation of interatomic forces. This allows us to run accelerated ab initio molecular dynamics with little to no self-consistent steps.

Charge-Controlled Energy Optimization of the Reconstruction of Semiconductor Surfaces: sp3-sp2 Transformation of Stoichiometric GaN(0001) Surface to (4 × 4) Pattern

It was demonstrated by ab initio calculations that energy optimization in the reconstruction of semiconductor surfaces is controlled by the global charge balance. The charge control was discovered during simulations of the influence of heavy doping in the GaN bulk, which changes sp3 to sp2 ratio in the reconstruction of stoichiometric GaN(0001), i.e., a Ga-polar surface. Thus, the reconstruction is not limited to the charge in the surface only; it can be affected by the charge in the bulk. The discovered new reconstruction of the GaN(0001) surface is (4 × 4), which is different from the previously reported (2 × 1) pattern. The undoped GaN reconstruction is surface charge controlled; accordingly, (3/8) top-layer Ga atoms remain in a standard position with sp3 hybridized bonding, while the remaining (5/8) top-layer Ga atoms are shifted into the plane of N atoms with sp2 hybridized bonding. The change in the charge balance caused by doping in the bulk leads to a change or disappearance of the reconstruction pattern.

A high density nanopore 3-triangulene kagome lattice

Nanopore-containing two-dimensional materials have been explored for a wide range of applications including filtration, sensing, catalysis, energy storage and conversion. Triangulenes have recently been experimentally synthesized in a variety of sizes. In this regard, using these systems as building blocks, we theoretically examined 3-triangulene kagome crystals with inherent holes of ∼12 Å diameter and a greater density array of nanopores (≥1013 cm-2) compared to conventional 2D systems. The energetic, electronic, and transport properties of pristine and B/N-doped 3-triangulene kagome crystals were evaluated through a combination of density functional theory and non-equilibrium Green's function method. The simulated scanning tunneling microscopy images clearly capture electronic perturbation around the doped sites, which can be used to distinguish the pristine system from the doped systems. The viability of precisely controlling the band structure and transport properties by changing the type and concentration of doping atoms is demonstrated. The findings presented herein can potentially widen the applicability of these systems that combine unique electronic properties and intrinsically high-density pores, which can pave the way for the next generation of nanopore-based devices.

Layer-dependent spin texture and origins of Rashba splitting quenching in the 2D CsPbI3 perovskite

The spin-orbit coupling in inorganic perovskite materials containing heavy elements causes interesting electronic characteristics such as Rashba and Dresselhaus effects. Several studies have reported significant band splitting in the presence of asymmetry, while the impacts of the external field strength, surface termination on the electronic structure still need to be resolved. In the current study, a systematic relation between the external parameters and the band splitting in CsPbI3 slabs is clarified through first-principles calculations. Here, we examine the band splitting and spin patterns of CsPbI3 slabs exposed to an external electric field ranging from zero to hundreds of kV cm-1. Our results indicate apparent non-linear behavior of the Rashba coefficient along with a turning point for the band splitting for a definite external field. Here, the origin of this quench in the band splitting is explained in terms of spatial localization of the wave functions and clear change in their center of charge going from low to high electric fields. The findings not only explain the origin of quenching band splitting but also reveal the external field's significance in the spin texture and recombination rate of 2D perovskites. The current research outcome paves the way for atomic scale engineering of perovskite materials for a wide range of applications.

Footprints of atomic-scale features in plasmonic nanoparticles as revealed by electron energy loss spectroscopy

We present a first-principles theoretical study of the atomistic footprints in the valence electron energy loss spectroscopy (EELS) of nanometer-size metallic particles. Charge density maps of excited plasmons and EEL spectra for specific electron paths through a nanoparticle (Na380 atom cluster) are modeled using ab initio calculations within time-dependent density functional theory. Our findings unveil the atomic-scale sensitivity of EELS within this low-energy spectral range. Whereas localized surface plasmons (LSPs) are particularly sensitive to the atomistic structure of the surface probed by the electron beam, confined bulk plasmons (CBPs) reveal quantum size effects within the nanoparticle's volume. Moreover, we prove that classical local dielectric theories mimicking the atomistic structure of the nanoparticles reproduce the LSP trends observed in quantum calculations, but fall short in describing the CBP behavior observed under different electron trajectories.

A chiral metal cluster triggers enantiospecific electronic transport

Chirality is a geometric property of matter that can be present at different scales, especially at the nanoscale. Here, we investigate the manifestation of chirality in electronic transport through a molecular junction. Spinless electronic transport through a chiral molecular junction is not enantiospecific. However, when a chiral metal cluster, C3-Au34, is attached to the source electrode, a different response is obtained in spinless electronic transport between R and L systems: this indicates the crucial role of chiral clusters in triggering enantiospecific spinless electronic transport. In contrast, when an achiral metal cluster, C3v-Au34, is attached, no change in conductance occurs between enantiomeric systems. Using the non-equilibrium green's function method, we characterized this phenomenon by calculating the transmission and conductance of spin-unpolarized electrons. Our theoretical results highlight the importance of metal clusters with specific sizes and chiral structures in electronic transport and support previously published experimental results that exhibited enantiospecific scanning tunneling measurements with intrinsically chiral tips.

Pyridinic-N Coordination Effect on the Adsorption and Activation of CO2 by Single Vacancy Iron-Doped Graphene

Graphene doped with different transition metals has been recently proposed to adsorb CO2 and help reduce the greenhouse effect. Iron-doped graphene is one of the most promising candidates for this task, but there is still a lack of full understanding of the adsorption mechanism. In this work, we analyze the electronic structure, geometry, and charge redistribution during adsorption of CO2 molecules by single vacancy iron-doped graphene by DFT calculations using the general gradient approximation of Perdew, Burke, and Ernzernhof functional (PBE) and the van der Waals density functional (vdW). To understand the impact of the pyridinic-N coordination of the iron atom, we gradually replaced the neighboring carbon atoms by nitrogen atoms. The analysis indicates that chemisorption and physisorption occur when the molecule is adsorbed in the side-on and end-on orientation, respectively. Adsorption is stronger when pyridinic-N coordination increases, and the vdW functional describes the chemical interactions and adsorption energy differently in relation to PBE without significant structural changes. The development of the chemical interactions with the change of coordination in the system is further investigated in this work with crystal overlap Hamilton population (COHP) analysis.

Three-Center Tight-Binding Together with Multipolar Auxiliary Functions

We present an ab initio tight-binding method that allows to improve on the effective potential and minimal basis approximations employed in semiempirical calculations. Three-center expansions are used to evaluate the zeroth-order Hamiltonian matrix elements and repulsive energy terms in the spirit of the Horsfield method. Self-consistency is handled by expanding atomic orbital products in an auxiliary basis following the work of Giese and York, combined with a two-center expansion of the exchange-correlation kernels. Together with nonminimal main basis sets (double-ζ plus polarization), we show that the resulting method trades a modest amount of accuracy for a significant gain in speed, compared to that of numerical atomic orbital density functional theory, in calculations on small molecules, bulk compounds, and metal nanoclusters.

GPAW: An open Python package for electronic structure calculations

We review the GPAW open-source Python package for electronic structure calculations. GPAW is based on the projector-augmented wave method and can solve the self-consistent density functional theory (DFT) equations using three different wave-function representations, namely real-space grids, plane waves, and numerical atomic orbitals. The three representations are complementary and mutually independent and can be connected by transformations via the real-space grid. This multi-basis feature renders GPAW highly versatile and unique among similar codes. By virtue of its modular structure, the GPAW code constitutes an ideal platform for the implementation of new features and methodologies. Moreover, it is well integrated with the Atomic Simulation Environment (ASE), providing a flexible and dynamic user interface. In addition to ground-state DFT calculations, GPAW supports many-body GW band structures, optical excitations from the Bethe-Salpeter Equation, variational calculations of excited states in molecules and solids via direct optimization, and real-time propagation of the Kohn-Sham equations within time-dependent DFT. A range of more advanced methods to describe magnetic excitations and non-collinear magnetism in solids are also now available. In addition, GPAW can calculate non-linear optical tensors of solids, charged crystal point defects, and much more. Recently, support for graphics processing unit (GPU) acceleration has been achieved with minor modifications to the GPAW code thanks to the CuPy library. We end the review with an outlook, describing some future plans for GPAW.

Asynchronous propagation of atomic force and excited electronic charge in GaAs under proton irradiation

The studies for the interaction of energetic particles with matter have greatly contributed to the exploration of material properties under irradiation conditions, such as nuclear safety, medical physics and aerospace applications. In this work, we theoretically simulate the non-adiabatic process for GaAs upon proton irradiation using time-dependent density functional theory, and find that the radial propagation of force on atoms and the excitation of electron in GaAs are non-synchronous process. We calculated the electronic stopping power on proton with the velocity of 0.1-0.6 a.u., agreement with the previous empirical results. After further analyzing the force on atoms and the population of excited electrons, we find that under proton irradiation, the electrons around the host atoms at different distances from the proton trajectories are excited almost simultaneously, especially those regions with relatively high charge density. However, the distant atoms have a significant hysteresis in force, which occurs after the surrounding electrons are excited. In addition, hysteresis in force and electron excitation behavior at different positions are closely related to the velocity of proton. This non-synchronous propagation reveals the microscopic dynamic mechanism of energy deposition into the target material under ion irradiation.

Characterization of iron(III) in aqueous and alkaline environments with ab initio and ReaxFF potentials

The iron(III) complexes [Fe(H2O)n(OH)m]3-m (n + m = 5, 6, m ≤ 3) and corresponding proton transfer reactions are studied with total energy calculations, the nudged elastic band (NEB) method, and molecular dynamics (MD) simulations using ab initio and a modification of reactive force field potentials, the ReaxFF-AQ potentials, based on the implementation according to Böhm et al. [J. Phys. Chem. C 120, 10849-10856 (2016)]. Applying ab initio potentials, the energies for the reactions [Fe(H2O)n(OH)m]3-m + H2O → [Fe(H2O)n-1(OH)m+1]2-m + H3O+ in a gaseous environment are in good agreement with comparable theoretical results. In an aqueous (aq) or alkaline environment, with the aid of NEB computations, respective minimum energy paths with energy barriers of up to 14.6 kcal/mol and a collective transfer of protons are modeled. Within MD simulations at room temperature, a permanent transfer of protons around the iron(III) ion is observed. The information gained concerning the geometrical and energetic properties of water and the [Fe(H2O)n(OH)m]3-m complexes from the ab initio computations has been used as reference data to optimize parameters for the O-H-Fe interaction within the ReaxFF-AQ approach. For the optimized ReaxFF-AQ parameter set, the statistical properties of the basic water model, such as the radial distribution functions and the proton hopping functions, are evaluated. For the [Fe(H2O)n(OH)m]3-m complexes, it was found that while geometrical and energetic properties are in good agreement with the ab initio data for gaseous environment, the statistical properties as obtained from the MD simulations are only partly in accordance with the ab initio results for the iron(III) complexes in aqueous or alkaline environments.

Positivity preserving density matrix minimization at finite temperatures via square root

We present a Wave Operator Minimization (WOM) method for calculating the Fermi-Dirac density matrix for electronic structure problems at finite temperature while preserving physicality by construction using the wave operator, i.e., the square root of the density matrix. WOM models cooling a state initially at infinite temperature down to the desired finite temperature. We consider both the grand canonical (constant chemical potential) and canonical (constant number of electrons) ensembles. Additionally, we show that the number of steps required for convergence is independent of the number of atoms in the system. We hope that the discussion and results presented in this article reinvigorate interest in density matrix minimization methods.

In silico approaches to investigate enzyme immobilization: a comprehensive systematic review

Enzymes are popular catalysts with many applications, especially in industry. Biocatalyst usage on a large scale is facing some limitations, such as low operational stability, low recyclability, and high enzyme cost. Enzyme immobilization is a beneficial strategy to solve these problems. Bioinformatics tools can often correctly predict immobilization outcomes, resulting in a cost-effective experimental phase with the least time consumed. This study provides an overview of in silico methods predicting immobilization processes via a comprehensive systematic review of published articles till 11 December 2022. It also mentions the strengths and weaknesses of the processes and explains the computational analyses in each method that are required for immobilization assessment. In this regard, Web of Science and Scopus databases were screened to gain relevant publications. After screening the gathered documents (n = 3873), 60 articles were selected for the review. The selected papers have applied in silico procedures including only molecular dynamics (MD) simulations (n = 20), parallel tempering Monte Carlo (PTMC) and MD simulations (n = 3), MD and docking (n = 1), density functional theory (DFT) and MD (n = 1), only docking (n = 11), metal ion binding site prediction (MIB) server and docking (n = 2), docking and DFT (n = 1), docking and analysis of enzyme surfaces (n = 1), only DFT (n = 1), only MIB server (n = 2), analysis of an enzyme structure and surface (n = 12), rational design of immobilized derivatives (RDID) software (n = 3), and dissipative particle dynamics (DPD; n = 2). In most included studies (n = 51), enzyme immobilization was investigated experimentally in addition to in silico evaluation.

Effectively Enhancing the Conductance of Asymmetric Molecular Wires by Aligning the Energy Level and Symmetrizing the Coupling

An asymmetric structure is an important strategy for designing highly conductive molecular wires for a gap-fixed molecular circuit. As the conductance enhancement in the current strategy is still limited to about 2 times, we inserted a methylene group as a spacer in a conjugated structure to modulate the structural symmetry. We found that the conductance drastically enhanced in the asymmetric molecular wire to 1.5 orders of magnitude as high as that in the symmetric molecular wire. First-principles quantum transport studies attributed the effective enhancement to the synchronization of improved energy alignment and nearly symmetric coupling between the frontier orbitals and the electrodes.

Deceptive orbital confinement at edges and pores of carbon-based 1D and 2D nanoarchitectures

The electronic structure defines the properties of graphene-based nanomaterials. Scanning tunneling microscopy/spectroscopy (STM/STS) experiments on graphene nanoribbons (GNRs), nanographenes, and nanoporous graphene (NPG) often determine an apparent electronic orbital confinement into the edges and nanopores, leading to dubious interpretations such as image potential states or super-atom molecular orbitals. We show that these measurements are subject to a wave function decay into the vacuum that masks the undisturbed electronic orbital shape. We use Au(111)-supported semiconducting gulf-type GNRs and NPGs as model systems fostering frontier orbitals that appear confined along the edges and nanopores in STS measurements. DFT calculations confirm that these states originate from valence and conduction bands. The deceptive electronic orbital confinement observed is caused by a loss of Fourier components, corresponding to states of high momentum. This effect can be generalized to other 1D and 2D carbon-based nanoarchitectures and is important for their use in catalysis and sensing applications.

Magnetostriction-Driven Muon Localization in an Antiferromagnetic Oxide

Magnetostriction results from the coupling between magnetic and elastic degrees of freedom. Though it is associated with a relatively small energy, we show that it plays an important role in determining the site of an implanted muon, so that the energetically favorable site can switch on crossing a magnetic phase transition. This surprising effect is demonstrated in the cubic rocksalt antiferromagnet MnO which undergoes a magnetostriction-driven rhombohedral distortion at the Néel temperature T_{N}=118  K. Above T_{N}, the muon becomes delocalized around a network of equivalent sites, but below T_{N} the distortion lifts the degeneracy between these equivalent sites. Our first-principles simulations based on Hubbard-corrected density-functional theory and molecular dynamics are consistent with the experimental data and help to resolve a long-standing puzzle regarding muon data on MnO, as well as having wider applicability to other magnetic oxides.

Crystal Growth, Structural and Electronic Characterizations of Zero-Dimensional Metal Halide (TEP)InBr4 Single Crystals for X-Ray Detection

Recently, metal halides have shown great potential for applications such as solar energy harvesting, light emission, and ionizing radiation detection. In this work, we report the preparation, structural, thermal, and electronic properties of a new zero-dimensional (0D) halide (TEP)InBr4 (where TEP is tetraethylphosphonium organic cation, C8H20P+). (TEP)InBr4 single crystals are obtained within a few days of continuous crystal growth time via a solution growth methodology. (TEP)InBr4 shows a relatively large optical bandgap energy of 4.32 eV and a low thermal conductivity between 0.33±0.05 and 0.45±0.07 W/m-K. Based on the density functional theory (DFT) calculations, the highest occupied molecular orbitals (HOMOs) of (TEP)InBr4 are dominated by the Br states, while the lowest unoccupied molecular orbitals (LUMOs) are constituted by both In and Br states. (TEP)InBr4 single crystals exhibit a semiconductor resistivity of 1.73×1013 Ω·cm and a mobility-lifetime (mu-tau) product of 2.07×10-5 cm2/V. Finally, a prototype (TEP)InBr4 single crystal-based X-ray detector with a detection sensitivity of 569.85 uCGy-1cm-2 (at electrical field E=100 V/mm) was fabricated, indicating the potential use of (TEP)InBr4 for radiation detection applications.

A Perspective on Sustainable Computational Chemistry Software Development and Integration

The power of quantum chemistry to predict the ground and excited state properties of complex chemical systems has driven the development of computational quantum chemistry software, integrating advances in theory, applied mathematics, and computer science. The emergence of new computational paradigms associated with exascale technologies also poses significant challenges that require a flexible forward strategy to take full advantage of existing and forthcoming computational resources. In this context, the sustainability and interoperability of computational chemistry software development are among the most pressing issues. In this perspective, we discuss software infrastructure needs and investments with an eye to fully utilize exascale resources and provide unique computational tools for next-generation science problems and scientific discoveries.

Quantum Transport in Large-Scale Patterned Nitrogen-Doped Graphene

It has recently been demonstrated how the nitrogen dopant concentration in graphene can be controlled spatially on the nano-meter scale using a molecular mask. This technique may be used to create ballistic electron optics-like structures of high/low doping regions; for example, to focus electron beams, harnessing the quantum wave nature of the electronic propagation. Here, we employ large-scale Greens function transport calculations based on a tight-binding approach. We first benchmark different tight-binding models of nitrogen in graphene with parameters based on density functional theory (DFT) and the virtual crystal approximation (VCA). Then, we study theoretically how the random distribution within the masked regions and the discreteness of the nitrogen scattering centers impact the transport behavior of sharp n-p and n-n' interfaces formed by different, realistic nitrogen concentrations. We investigate how constrictions for the current can be realized by patterned high/low doping regions with experimentally feasible nitrogen concentrations. The constrictions can guide the electronic current, while the quantized conductance is significantly washed out due to the nitrogen scattering. The implications for device design is that a p-n junction with nitrogen corrugation should still be viable for current focusing. Furthermore, a guiding channel with less nitrogen in the conducting canal preserves more features of quantized conductance and, therefore, its low-noise regime.

Vibrational-mechanical properties of the highly-mismatched Cd1-xBexTe semiconductor alloy: experiment and ab initio calculations

The emerging CdTe-BeTe semiconductor alloy that exhibits a dramatic mismatch in bond covalency and bond stiffness clarifying its vibrational-mechanical properties is used as a benchmark to test the limits of the percolation model (PM) worked out to explain the complex Raman spectra of the related but less contrasted Zn1-xBex-chalcogenides. The test is done by way of experiment ([Formula: see text]), combining Raman scattering with X-ray diffraction at high pressure, and ab initio calculations ([Formula: see text] ~ 0-0.5; [Formula: see text]~1). The (macroscopic) bulk modulus [Formula: see text] drops below the CdTe value on minor Be incorporation, at variance with a linear [Formula: see text] versus [Formula: see text] increase predicted ab initio, thus hinting at large anharmonic effects in the real crystal. Yet, no anomaly occurs at the (microscopic) bond scale as the regular bimodal PM-type Raman signal predicted ab initio for Be-Te in minority ([Formula: see text]~0, 0.5) is barely detected experimentally. At large Be content ([Formula: see text]~1), the same bimodal signal relaxes all the way down to inversion, an unprecedented case. However, specific pressure dependencies of the regular ([Formula: see text]~0, 0.5) and inverted ([Formula: see text]~1) Be-Te Raman doublets are in line with the predictions of the PM. Hence, the PM applies as such to Cd1-xBexTe without further refinement, albeit in a "relaxed" form. This enhances the model's validity as a generic descriptor of phonons in alloys.

Bright circularly polarized photoluminescence in chiral layered hybrid lead-halide perovskites

Hybrid perovskite semiconductor materials are predicted to lock chirality into place and encode asymmetry into their electronic states, while softness of their crystal lattice accommodates lattice strain to maintain high crystal quality with low defect densities, necessary for high luminescence yields. We report photoluminescence quantum efficiencies as high as 39% and degrees of circularly polarized photoluminescence of up to 52%, at room temperature, in the chiral layered hybrid lead-halide perovskites (R/S/Rac)-3BrMBA2PbI4 [3BrMBA = 1-(3-bromphenyl)-ethylamine]. Using transient chiroptical spectroscopy, we explain the excellent photoluminescence yields from suppression of nonradiative loss channels and high rates of radiative recombination. We further find that photoexcitations show polarization lifetimes that exceed the time scales of radiative decays, which rationalize the high degrees of polarized luminescence. Our findings pave the way toward high-performance solution-processed photonic systems for chiroptical applications and chiral-spintronic logic at room temperature.

Open-Source Machine Learning in Computational Chemistry

The field of computational chemistry has seen a significant increase in the integration of machine learning concepts and algorithms. In this Perspective, we surveyed 179 open-source software projects, with corresponding peer-reviewed papers published within the last 5 years, to better understand the topics within the field being investigated by machine learning approaches. For each project, we provide a short description, the link to the code, the accompanying license type, and whether the training data and resulting models are made publicly available. Based on those deposited in GitHub repositories, the most popular employed Python libraries are identified. We hope that this survey will serve as a resource to learn about machine learning or specific architectures thereof by identifying accessible codes with accompanying papers on a topic basis. To this end, we also include computational chemistry open-source software for generating training data and fundamental Python libraries for machine learning. Based on our observations and considering the three pillars of collaborative machine learning work, open data, open source (code), and open models, we provide some suggestions to the community.

Atomistic Study of the Bandgap Engineering of Two-Dimensional Silicon Carbide by Hydrogenation

This work studied hydrogen adsorption by a two-dimensional silicon carbide using a combined molecular dynamics and density functional theory approach. The geometrical properties of partially and fully hydrogenated structures were investigated, considering the effect of zero-point energy. The preferred hydrogen atom location is on top of silicon atoms. The hydrogen interaction energies were obtained for the first time as the attractive force. For fully hydrogenated 2D SiC, the chair-like conformer is the most stable configuration, and the next is the boat-like conformer, while the table-like structure is not stable. The coverage and arrangement of the adsorbed hydrogen atoms significantly influence the values of the direct/indirect bandgaps of the considered systems, increasing the bandgap to 4.07, 3.64, and 4.41 eV for chair-like, table-like, and boat-like, respectively. Their dynamical stability was investigated by phonon dispersion calculations. The obtained results can serve as a guide for the application of hydrogenated two-dimensional silicon carbide in optoelectronic applications in manufacturing innovation.

Evaluation interaction of graphene oxide with heparin for antiviral blockade: a study of ab initio simulations, molecular docking, and experimental analysis

CONTEXT

Heparin, one of the drugs reused in studies with antiviral activity, was chosen to investigate a possible blockade of the SARS-CoV-2 spike protein for viral entry through computational simulations and experimental analysis. Heparin was associated to graphene oxide to increase in the binding affinity in biological system. First, the electronic and chemical interaction between the molecules was analyzed through ab initio simulations. Later, we evaluate the biological compatibility of the nanosystems, in the target of the spike protein, through molecular docking. The results show that graphene oxide interacts with the heparin with an increase in the affinity energy with the spike protein, indicating a possible increment in the antiviral activity. Experimental analysis of synthesis and morphology of the nanostructures were carried out, indicating heparin absorption by graphene oxide, confirming the results of the first principle simulations. Experimental tests were conducted on the structure and surface of the nanomaterial, confirming the heparin aggregation on the synthesis with a size between the GO layers of 7.44 Å, indicating a C-O type bond, and exhibiting a hydrophilic surface characteristic (36.2°).

METHODS

Computational simulations of the ab initio with SIESTA code, LDA approximations, and an energy shift of 0.05 eV. Molecular docking simulations were performed in the AutoDock Vina software integrated with the AMDock Tools Software using the AMBER force field. GO, GO@2.5Heparin, and GO@5Heparin were synthesized by Hummers and impregnation methods, respectively, and characterized by X-ray diffraction and surface contact angle.

Drug Design in the Exascale Era: A Perspective from Massively Parallel QM/MM Simulations

The initial phases of drug discovery - in silico drug design - could benefit from first principle Quantum Mechanics/Molecular Mechanics (QM/MM) molecular dynamics (MD) simulations in explicit solvent, yet many applications are currently limited by the short time scales that this approach can cover. Developing scalable first principle QM/MM MD interfaces fully exploiting current exascale machines - so far an unmet and crucial goal - will help overcome this problem, opening the way to the study of the thermodynamics and kinetics of ligand binding to protein with first principle accuracy. Here, taking two relevant case studies involving the interactions of ligands with rather large enzymes, we showcase the use of our recently developed massively scalable Multiscale Modeling in Computational Chemistry (MiMiC) QM/MM framework (currently using DFT to describe the QM region) to investigate reactions and ligand binding in enzymes of pharmacological relevance. We also demonstrate for the first time strong scaling of MiMiC-QM/MM MD simulations with parallel efficiency of ∼70% up to >80,000 cores. Thus, among many others, the MiMiC interface represents a promising candidate toward exascale applications by combining machine learning with statistical mechanics based algorithms tailored for exascale supercomputers.

Zero-Dimensional Broadband Yellow Light Emitter (TMS)3Cu2I5 for Latent Fingerprint Detection and Solid-State Lighting

We report a new hybrid organic-inorganic Cu(I) halide, (TMS)₃Cu₂I₅ (TMS = trimethylsulfonium), which demonstrates high efficiency and stable yellow light emission with a photoluminescence quantum yield (PLQY) over 25%. The zero-dimensional crystal structure of the compound is comprised of isolated face-sharing photoactive [Cu₂I₅]^3- tetrahedral dimers surrounded by TMS⁺ cations. This promotes strong quantum confinement and electron-phonon coupling, leading to a highly efficient emission from self-trapped excitons. The hybrid structure ensures prolonged stability and nonblue emission compared to unstable blue emission from all-inorganic copper(I) halides. Substitution of Cu with Ag leads to (TMS)AgI₂, which has a one-dimensional chain structure made of edge-sharing tetrahedra, with weak light emission properties. Improved stability and highly efficient yellow emission of (TMS)₃Cu₂I₅ make it a candidate for practical applications. This has been demonstrated through utilization of (TMS)₃Cu₂I₅ in white light-emitting diode with a high Color Rendering Index value of 82 and its use as a new luminescent agent for visualization of in-depth latent fingerprint features. This work illuminates a new direction in designing multifunctional nontoxic hybrid metal halides.

Ferromagnetism in Defected TMD (MoX2, X = S, Se) Monolayer and Its Sustainability under O2, O3, and H2O Gas Exposure: DFT Study

Spin-polarized density-functional theory (DFT) has been employed to study the effects of atmospheric gases on the electronic and magnetic properties of a defective transition-metal dichalcogenide (TMD) monolayer, MoX₂ with X = S or Se. This study focuses on three single vacancies: (i) molybdenum "V_Mo"; (ii) chalcogenide "V_X"; and (iii) di-chalcogenide "V_X2". Five different samples of sizes ranging from 4 × 4 to 8 × 8 primitive cells (PCs) were considered in order to assess the effect of vacancy-vacancy interaction. The results showed that all defected samples were paramagnetic semiconductors, except in the case of V_Mo in MoSe₂, which yielded a magnetic moment of 3.99 μ_B that was independent of the sample size. Moreover, the samples of MoSe₂ with V_Mo and sizes of 4 × 4 and 5 × 5 PCs exhibited half-metallicity, where the spin-up state becomes conductive and is predominantly composed of dxy and dz2 orbital mixing attributed to Mo atoms located in the neighborhood of V_Mo. The requirement for the establishment of half-metallicity is confirmed to be the provision of ferromagnetic-coupling (FMC) interactions between localized magnetic moments (such as V_Mo). The critical distance for the existence of FMC is estimated to be dc≅ 16 Å, which allows small sample sizes in MoSe₂ to exhibit half-metallicity while the FMC represents the ground state. The adsorption of atmospheric gases (H₂O, O₂, O₃) can drastically change the electronic and magnetic properties, for instance, it can demolish the half-metallicity characteristics. Hence, the maintenance of half-metallicity requires keeping the samples isolated from the atmosphere. We benchmarked our theoretical results with the available data in the literature throughout our study. The conditions that govern the appearance/disappearance of half-metallicity are of great relevance for spintronic device applications.

Meta-GGA Density Functional Calculations on Atoms with Spherically Symmetric Densities in the Finite Element Formalism

Density functional calculations on atoms are often used for determining accurate initial guesses as well as generating various types of pseudopotential approximations and efficient atomic-orbital basis sets for polyatomic calculations. To reach the best accuracy for these purposes, the atomic calculations should employ the same density functional as the polyatomic calculation. Atomic density functional calculations are typically carried out employing spherically symmetric densities, corresponding to the use of fractional orbital occupations. We have described their implementation for density functional approximations (DFAs) belonging to the local density approximation (LDA) and generalized gradient approximation (GGA) levels of theory as well as Hartree-Fock (HF) and range-separated exact exchange [Lehtola, S. Phys. Rev. A 2020, 101, 012516]. In this work, we describe the extension to meta-GGA functionals using the generalized Kohn-Sham scheme, in which the energy is minimized with respect to the orbitals, which in turn are expanded in the finite element formalism with high-order numerical basis functions. Furnished with the new implementation, we continue our recent work on the numerical well-behavedness of recent meta-GGA functionals [Lehtola, S.; Marques, M. A. L. J. Chem. Phys. 2022, 157, 174114]. We pursue complete basis set (CBS) limit energies for recent density functionals and find many to be ill-behaved for the Li and Na atoms. We report basis set truncation errors (BSTEs) of some commonly used Gaussian basis sets for these density functionals and find the BSTEs to be strongly functional dependent. We also discuss the importance of density thresholding in DFAs and find that all of the functionals studied in this work yield total energies converged to 0.1 μEh when densities smaller than 10-11a0-3 are screened out.

Efficient calculation of derivatives of integrals in a basis of non-separable Gaussians

A computational procedure is developed for the efficient calculation of derivatives of integrals over non-separable Gaussian-type basis functions, used for the evaluation of gradients of the total energy in quantum-mechanical simulations. The approach, based on symbolic computation with computer algebra systems and automated generation of optimized subroutines, takes full advantage of sparsity and is here applied to first energy derivatives with respect to nuclear displacements and lattice parameters of molecules and materials. The implementation in the Crystal code is presented, and the considerably improved computational efficiency over the previous implementation is illustrated. For this purpose, three different tasks involving the use of analytical forces are considered: (i) geometry optimization; (ii) harmonic frequency calculation; and (iii) elastic tensor calculation. Three test case materials are selected as representatives of different classes: (i) a metallic 2D model of the Cu(111) surface; (ii) a wide-gap semiconductor ZnO crystal, with a wurtzite-type structure; and (iii) a porous metal-organic crystal, namely the ZIF-8 zinc-imidazolate framework. Finally, it is argued that the present symbolic approach is particularly amenable to generalizations, and its potential application to other derivatives is sketched.

Stretching effects on non-adiabatic electron dynamic behavior in poly(dG)-poly(dC) DNA upon the proton irradiation

The electronic excitations caused by DNA when exposed to ion radiation is essential to DNA damage. In this paper, we investigated the energy deposition and electron excitation process of DNA with reasonable stretching range upon proton irradiation based on time-dependent density functional theory. Stretching changes the strength of hydrogen bonding between the DNA base pairs, which in turn affects the Coulomb interaction between the projectile and DNA. As a semi-flexible molecule, the way of energy deposition is weakly sensitive to the stretching rate of DNA. However, the increase of stretching rate causes the increase of charge density along the trajectory channel, sequentially resulting in an increase in proton resistance along the intruding channel. The Mulliken charge analysis indicates that the guanine base and guanine ribose are ionized, meanwhile the cytosine base and cytosine ribose are reduced at all stretching rates. In a few femtoseconds, there exists an electron flow passing through the guanine ribose, guanine, cytosine base and the cytosine ribose in turn. This electron flow increases electron transfer and DNA ionization, promoting the side chain damage of the DNA upon ion irradiation. Our results provide a theoretical insight for deciphering the physical mechanism of the early stage of the irradiation process, and are also of great significance for the study of particle beam cancer therapy in different biological tissues.

Metastable Polymorphic Phases in Monolayer TaTe2

Polymorphic phases and collective phenomena-such as charge density waves (CDWs)-in transition metal dichalcogenides (TMDs) dictate the physical and electronic properties of the material. Most TMDs naturally occur in a single given phase, but the fine-tuning of growth conditions via methods such as molecular beam epitaxy (MBE) allows to unlock otherwise inaccessible polymorphic structures. Exploring and understanding the morphological and electronic properties of new phases of TMDs is an essential step to enable their exploitation in technological applications. Here, scanning tunneling microscopy (STM) is used to map MBE-grown monolayer (ML) TaTe₂ . This work reports the first observation of the 1H polymorphic phase, coexisting with the 1T, and demonstrates that their relative coverage can be controlled by adjusting synthesis parameters. Several superperiodic structures, compatible with CDWs, are observed to coexist on the 1T phase. Finally, this work provides theoretical insight on the delicate balance between Te…Te and Ta-Ta interactions that dictates the stability of the different phases. The findings demonstrate that TaTe₂ is an ideal platform to investigate competing interactions, and indicate that accurate tuning of growth conditions is key to accessing metastable states in TMDs.

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.

Enhancement of Graphene Phonon Excitation by a Chemically Engineered Molecular Resonance

The abstraction of pyrrolic hydrogen from a single phthalocyanine on graphene turns the molecule into a sensitive probe for graphene phonons. The inelastic electron transport measured with a scanning tunneling microscope across the molecular adsorbate and graphene becomes strongly enhanced for a graphene out-of-plane acoustic phonon mode. Supporting density functional and transport calculations elucidate the underlying physical mechanism. A molecular orbital resonance close to the Fermi energy controls the inelastic current while specific phonon modes of graphene are magnified due to their coupling to symmetry-equivalent vibrational quanta of the molecule.

Mixed-Valence Conductors from Ni Bis(diselenolene) Complexes with a Thiazoline Backbone

Highly conducting, mixed-valence, multi-component nickel bis(diselenolene) salts were obtained by electrocrystallization of the monoanionic species [Ni(Me-thiazds)₂]^-1 (Me-thiazds: N-methyl-1,3-thiazoline-2-thione-4,5-diselenolate), with 1:2 and 1:3 stoichiometries depending of the counter ion used (Et₄N⁺ and nBu₄N⁺ vs Ph₄P⁺, respectively). This behavior strongly differs from that of the corresponding monoanionic dithiolene complexes whose oxidation afforded the single component neutral species. This provides additional rare examples of mixed-valence conducting salts of nickel diselenolene complexes, only known in two examples with the dsit (1,3-dithiole-2-thione-4,5-diselenolate) and dsise (1,3-dithiole-2-selone-4,5-diselenolate) ligands. The mixed-valence salts form highly dimerized or trimerized bi- and trimetallic units, rarely seen with such nickel complexes. Transport measurements under a high pressure (up to 10 GPa) and band structure calculations confirm the semiconducting character of [Ph₄P][Ni(Me-thiazds)₂]₃ and the quasi metallic character of [Et₄N][Ni(Me-thiazds)₂]₂ and [NBu₄]_x[Ni(Me-thiazds)₂]₂ salts (0 < x < 1).

Bis(Vinylenedithio)-Tetrathiafulvalene-Based Coordination Networks

Novel coordination polymers embedding electroactive moieties present a high interest in the development of porous conducting materials. While tetrathiafulvalene (TTF) based metal-organic frameworks were reported to yield through-space conducting frameworks, the use of S-enriched scaffolds remains elusive in this field. Herein is reported the employment of bis(vinylenedithio)-tetrathiafulvalene (BVDT-TTF) functionalized with pyridine coordinating moieties in coordination polymers. Its combination with various transition metals yielded four isostructural networks, whose conductivity increased upon chemical oxidation with iodine. The oxidation was confirmed in a single-crystal to single-crystal X-ray diffraction experiment for the Cd(II) coordination polymer. Raman spectroscopy measurements and DFT calculations confirmed the oxidation state of the bulk materials, and band structure calculations assessed the ground state as an electronically localized antiferromagnetic state, while the conduction occurs in a 2D manner. These results are shedding light to comprehend how to improve through-space conductivity thanks to sulfur enriched ligands.

Thermal Treatment Impact on the Mechanical Properties of Mg3Si2O5(OH)4 Nanoscrolls

A group of phyllosilicate nanoscrolls conjoins several hydrosilicate layered compounds with a size mismatch between octahedral and tetrahedral sheets. Among them, synthetic Mg3Si2O5(OH)4 chrysotile nanoscrolls (obtained via the hydrothermal method) possess high thermal stability and mechanical properties, making them prospective composite materials fillers. However, accurate determination of these nano-objects with Young's modulus remains challenging. Here, we report on a study of the mechanical properties evolution of individual synthetic phyllosilicate nanoscrolls after a series of heat treatments, observed with an atomic force microscopy and calculated using the density functional theory. It appears that the Young's modulus, as well as shear deformation's contribution to the nanoscrolls mechanical behavior, can be controlled by heat treatment. The main reason for this is the heat-induced formation of covalent bonding between the adjacent layers, which complicate the shear deformation.