cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.24435/materialscloud:w8-cg
title: Improving the silicon interactions of GFN-xTB

description: This record addresses inaccuracies in the widely-used GFN-xTB model when it comes to the description of organosilicon compounds. Here, an ab initio reference data set of 10000 compounds is provided alongside files needed to execute a parameter fitting scheme that improves geometries, nuclear gradients and energies predicted by the GFN-xTB Hamiltonian.
DOI: 10.24435/materialscloud:zp-xj
title: Assessment of approximate methods for anharmonic free energies

description: Quantitative evaluation of the thermodynamic properties of materials—most notably their stability, as measured by the free energy—must take into account the role of thermal and zero-point energy fluctuations. While these effects can easily be estimated within a harmonic approximation, corrections arising from the anharmonic nature of the interatomic potential are often crucial and require computationally costly path integral simulations to obtain results that are essentially exact for a given potential. Consequently, different approximate frameworks for computing affordable estimates of the anharmonic free energies have been developed over the years. Understanding which of the approximations involved are justified for a given system, and therefore choosing the most suitable method, is complicated by the lack of comparative benchmarks. To facilitate this choice we assess the accuracy and efficiency of some of the most commonly used approximate methods: the independent mode framework, the vibrational self-consistent field, and self-consistent phonons. We compare the anharmonic correction to the Helmholtz free energy against reference path integral calculations. These benchmarks are performed for a diverse set of systems, ranging from simple weakly anharmonic solids to flexible molecular crystals with freely rotating units. The results suggest that, for simple solids such as allotropes of carbon, these methods yield results that are in excellent agreement with the reference calculations, at a considerably lower computational cost. For more complex molecular systems such as polymorphs of ice and paracetamol the methods do not consistently provide a reliable approximation of the anharmonic correction. Despite substantial cancellation of errors when comparing the stability of different phases, we do not observe a systematic improvement over the harmonic approximation even for relative free energies. We conclude that, at least for the classes of materials considered here, efforts toward obtaining computationally feasible anharmonic free energies should therefore be directed toward reducing the expense of path integral methods.
DOI: 10.24435/materialscloud:48-qs
title: Zeo-1: A computational data set of zeolite structures

description: Fast, empirical potentials are gaining increased popularity in the computational fields of materials science, physics and chemistry. With it, there is a rising demand for high-quality reference data for the training and validation of such models. In contrast to research that is mainly focused on small organic molecules, this work presents a data set of geometry-optimized bulk phase zeolite structures. Covering a majority of framework types from the Database of Zeolite Structures, this set includes over thirty thousand geometries. Calculated properties include system energies, nuclear gradients and stress tensors at each point, making the data suitable for model development, validation or referencing applications focused on periodic silica systems.
DOI: 10.24435/materialscloud:3k-9k
title: Data and analyses for first proton-coupled electron transfer of water oxidation at the BiVO₄-water interface

description: This entry provides original trajectories of on-the-fly probability enhanced sampling (OPES) and of molecular dynamics simulations and images of nudged-elastic band (NEB) calculation. Jupyter notebooks are provided for a NEB profile, NEB collective variables, free energy surface of the OPES simulations, hole transfer of the OPES simulations, proton transfer mechanisms of of the OPES simulations, water density profiles of MD simulations, radial distribution functions of MD simulations, reweight of Bi-O bonds of OPES simulations, coordination numbers of surface Bi atoms and hydrogen-bond analysis of proton transfer.
DOI: 10.24435/materialscloud:ct-c6
title: Reaction pathway for coke-free methane steam reforming on a Ni/CeO2 catalyst: Active sites and role of metal-support interactions

description: Methane steam reforming (MSR) plays a key role in the production of syngas and hydrogen from natural gas. The increasing interest in the use of hydrogen for fuel cell applications demands the development of catalysts with high activity at reduced operating temperatures. Ni-based catalysts are promising systems because of their high activity and low cost, but coke formation generally poses a severe problem. Studies of ambient-pressure X-ray photoelectron spectroscopy (AP-XPS) indicate that CH4/H2O gas mixtures react with Ni/CeO2(111) surfaces to form OH, CHx and CHxO at 300 K. All these species are easy to form and desorb at temperatures below 700 K when the rate of the MSR process accelerates. Density functional theory (DFT) modeling of the reaction over ceria-supported small Ni nanoparticles predicts relatively low activation barriers between 0.3–0.7 eV for the complete dehydrogenation of methane to carbon and the barrierless activation of water at interfacial Ni sites. Hydroxyls resulting from water activation allow CO formation via a COH intermediate with a barrier of about 0.9 eV, which is much lower than that through a pathway involving lattice oxygen from ceria. Neither methane nor water activation are rate-determining steps, and the OH-assisted CO formation through the COH intermediate constitutes a low-barrier pathway that prevents carbon accumulation. The interaction between Ni and the ceria support and the low metal loading are crucial for the reaction to proceed in a coke-free and efficient way. These results could pave the way for further advances in the design of stable and highly active Ni-based catalysts for hydrogen production.
DOI: 10.24435/materialscloud:3t-b1
title: Impact of glutamate carboxylation in the adsorption of the alpha-1 domain of osteocalcin to hydroxyapatite and titania

description: This record contains files necessary to reproduce enhanced sampling well-tempered metadynamics (wtMTD) and parallel tempering metadynamics in the well-tempered ensemble (PT-MetaD-WTE) simulations in PLUMED using GROMACS 2018.3.
DOI: 10.24435/materialscloud:6c-hk
title: Exploding and weeping ceramics

description: The systematic tuning of the lattice parameters to achieve improved kinematic compatibility between phases is a broadly effective strategy for improving the reversibility, and lowering the hysteresis, of solid-solid phase transformations. Here, "kinematic compatibility" refers to the fitting together of the phases. We present an apparently paradoxical example in which tuning to near perfect compatibility in (Zr/Hf)O2-(YNb)O4 results in a high degree of irreversibility, as manifested in explosive or "weeping" behavior on cooling through the tetragonal-to-monoclinic phase transformation. In the case of weeping the polycrystal slowly and steadily falls apart at the grain boundaries. These effects occur without chemical change. Finally, tuning to satisfy a condition we term the equidistance condition results in reversible behavior with the lowest hysteresis in this system. We give evidence that all these observations are explained by a more careful analysis of compatibility of the polycrystal, accounting for sample shape. These results show that an extreme diversity of behaviors, from reversible to explosive, is possible in a chemically homogeneous system by manipulating conditions of compatibility in unexpected ways. They provide critical concepts underlying the current search for a shape memory oxide ceramic.
DOI: 10.24435/materialscloud:kh-b3
title: Exploding and weeping ceramics

description: The systematic tuning of the lattice parameters to achieve improved kinematic compatibility between phases is a broadly effective strategy for improving the reversibility, and lowering the hysteresis, of solid-solid phase transformations. Here, "kinematic compatibility" refers to the fitting together of the phases. We present an apparently paradoxical example in which tuning to near perfect compatibility in (Zr/Hf)O2-(YNb)O4 results in a high degree of irreversibility, as manifested in explosive or "weeping" behavior on cooling through the tetragonal-to-monoclinic phase transformation. In the case of weeping the polycrystal slowly and steadily falls apart at the grain boundaries. These effects occur without chemical change. Finally, tuning to satisfy a condition we term the equidistance condition results in reversible behavior with the lowest hysteresis in this system. We give evidence that all these observations are explained by a more careful analysis of compatibility of the polycrystal, accounting for sample shape. These results show that an extreme diversity of behaviors, from reversible to explosive, is possible in a chemically homogeneous system by manipulating conditions of compatibility in unexpected ways. They provide critical concepts underlying the current search for a shape memory oxide ceramic.
DOI: 10.24435/materialscloud:m4-b5
title: DFT calculations of the electronic structure of CoPt in L1₁ and A1 structures

description: Spintronics applications for high-density non-volatile memories require simultaneous optimization of the perpendicular magnetic anisotropy (PMA) and current-induced magnetization switching. These properties determine, respectively, the thermal stability of a ferromagnetic memory cell and a low operation power consumption, which are mutually incompatible with the spin transfer torque as the driving force for the switching. Here, we demonstrate a strategy of alloy engineering to overcome this obstacle by using electrically induced orbital currents instead of spin currents. A non-equilibrium orbital density generated in paramagnetic γ-FeMn flows into CoPt coupled to the magnetization through spin-orbit interaction, ultimately creating an orbital torque. Controlling the atomic arrangement of Pt and Co by structural phase transition, we show that the propagation length of the transferred angular momentum can be modified concurrently with the PMA strength. We find a strong correlation to the phase transition-induced changes of d orbitals with mₗ = ±1 and mₗ = ±2 character. The close link of orbital hybridization to the dynamic orbital response and magnetic properties offers new possibilities to realize optimally designed orbitronics memory and logic applications.
This dataset contains the DFT calculations for the electronic structure of CoPt in L1₁ and A1 structures that are discussed the corresponding publication.
DOI: 10.24435/materialscloud:xn-v7
title: DFT calculations of the electronic structure of CoPt in L1₁ and A1 structures

description: Spintronics applications for high-density non-volatile memories require simultaneous optimization of the perpendicular magnetic anisotropy (PMA) and current-induced magnetization switching. These properties determine, respectively, the thermal stability of a ferromagnetic memory cell and a low operation power consumption, which are mutually incompatible with the spin transfer torque as the driving force for the switching. Here, we demonstrate a strategy of alloy engineering to overcome this obstacle by using electrically induced orbital currents instead of spin currents. A non-equilibrium orbital density generated in paramagnetic γ-FeMn flows into CoPt coupled to the magnetization through spin-orbit interaction, ultimately creating an orbital torque. Controlling the atomic arrangement of Pt and Co by structural phase transition, we show that the propagation length of the transferred angular momentum can be modified concurrently with the PMA strength. We find a strong correlation to the phase transition-induced changes of d orbitals with mₗ = ±1 and mₗ = ±2 character. The close link of orbital hybridization to the dynamic orbital response and magnetic properties offers new possibilities to realize optimally designed orbitronics memory and logic applications.
This dataset contains the DFT calculations for the electronic structure of CoPt in L1₁ and A1 structures that are discussed the corresponding publication.
DOI: 10.24435/materialscloud:ha-t5
title: Topological frustration induces unconventional magnetism in a nanographene

description: The chemical versatility of carbon imparts manifold properties to organic compounds, where magnetism remains one of the most desirable but elusive. Polycyclic aromatic hydrocarbons, also referred to as nanographenes, show a critical dependence of electronic structure on the topologies of the edges and the π-electron network, which makes them model systems with which to engineer unconventional properties including magnetism. In 1972, Erich Clar envisioned a bow-tie-shaped nanographene, C38H18, where topological frustration in the π-electron network renders it impossible to assign a classical Kekulé structure without leaving unpaired electrons, driving the system into a magnetically non-trivial ground state. In this record we include data needed to support our recent work where we demonstrate the experimental realization and in-depth characterization of this emblematic nanographene, known as Clar's goblet. Scanning tunnelling microscopy and spin excitation spectroscopy of individual molecules on a gold surface reveal a robust antiferromagnetic order with an exchange-coupling strength of 23 meV, exceeding the Landauer limit of minimum energy dissipation at room temperature. Through atomic manipulation, we realize switching of magnetic ground states in molecules with quenched spins. Our results provide direct evidence of carbon magnetism in a hitherto unrealized class of nanographenes, and prove a long-predicted paradigm where topological frustration entails unconventional magnetism, with implications for room-temperature carbon-based spintronics.
DOI: 10.24435/materialscloud:av-24
title: Tight-Binding Electronic Transport Application (TBETA) for graphene nanoribbon junctions

description: TBETA provides a simple graphical interface for building structures of two-terminal junctions of graphene nanoribbons (GNRs) at angles 60°, 120° and 180°. The electronic structure and transport properties of the constructed junctions are calculated using the nearest-neighbour tight-binding model in combination with the Landauer-Büttiker formalism and Green's function techniques.
DOI: 10.24435/materialscloud:yb-5v
title: Topological frustration induces unconventional magnetism in a nanographene

description: The chemical versatility of carbon imparts manifold properties to organic compounds, where magnetism remains one of the most desirable but elusive. Polycyclic aromatic hydrocarbons, also referred to as nanographenes, show a critical dependence of electronic structure on the topologies of the edges and the π-electron network, which makes them model systems with which to engineer unconventional properties including magnetism. In 1972, Erich Clar envisioned a bow-tie-shaped nanographene, C38H18, where topological frustration in the π-electron network renders it impossible to assign a classical Kekulé structure without leaving unpaired electrons, driving the system into a magnetically non-trivial ground state. In this record we include data needed to support our recent work where we demonstrate the experimental realization and in-depth characterization of this emblematic nanographene, known as Clar's goblet. Scanning tunnelling microscopy and spin excitation spectroscopy of individual molecules on a gold surface reveal a robust antiferromagnetic order with an exchange-coupling strength of 23 meV, exceeding the Landauer limit of minimum energy dissipation at room temperature. Through atomic manipulation, we realize switching of magnetic ground states in molecules with quenched spins. Our results provide direct evidence of carbon magnetism in a hitherto unrealized class of nanographenes, and prove a long-predicted paradigm where topological frustration entails unconventional magnetism, with implications for room-temperature carbon-based spintronics.
DOI: 10.24435/materialscloud:br-eg
title: Tight-Binding Electronic Transport Application (TBETA) for graphene nanoribbon junctions

description: TBETA provides a simple graphical interface for building structures of two-terminal junctions of graphene nanoribbons (GNRs) at angles 60°, 120° and 180°. The electronic structure and transport properties of the constructed junctions are calculated using the nearest-neighbour tight-binding model in combination with the Landauer-Büttiker formalism and Green's function techniques.
DOI: 10.24435/materialscloud:x5-bb
title: Optical absorption properties of metal-organic frameworks: solid state versus molecular perspective

description: The vast chemical space of metal and ligand combinations in Transition Metal Complexes (TMCs) gives rise to a rich variety of electronic excited states with local and non-local character such as intra-ligand (IL), metal-centered (MC), metal-to-ligand (MLCT) or ligand-to-metal charge-transfer (LMCT) states. Those features are equally found in Metal Organic Frameworks (MOFs), defined as modular materials built from metal-nodes connected through organic-ligands. Because of the electronic and structural complexity of MOFs, the computational description of their excited states is a formidable challenge for which two different approaches have been usually followed: the solid state and the molecular perspective. The first consists in analysing the frontier electronic bands and crystal orbitals of the electronic ground state (GS) in periodic boundary conditions, while the latter points to an accurate computation of the excited states in representative clusters at the molecular level. Herein, we apply both approaches to evaluate the optical absorption properties of three experimentally reported Ti(IV) mononuclear MOFs with in silico metal substitutions with Zn(II), Cd(II), Fe(II), Ru(II) and Zr(IV) ions, thus covering d10, d6 and d0 electronic configurations of 1st and 2nd row TMCs in MOFs. Our analysis captures the main electronic features attributed to these systems while we discuss the main advantages and drawbacks of both approximations.
DOI: 10.24435/materialscloud:ad-z1
title: Impact of glutamate carboxylation in the adsorption of the alpha-1 domain of osteocalcin to hydroxyapatite and titania

description: One proposed mechanism of implant fouling is attributed to the nonspecific adsorption of non-collagenous bone matrix proteins (NCPs) onto a newly implanted interface. With the goal of capturing the fundamental mechanistic and thermodynamic forces that govern changes in these NCP recognition domains as a function of γ-carboxyglutamic acid (Gla) post-translational modification and surface chemistry, we probe the adsorption process of the most commonly occurring NCP, osteocalcin, onto a mineral and metal oxide surface. Here, we apply two enhanced sampling methods to independently probe the effects of post-translational modification and peptide structure on adsorption. First, well-tempered metadynamics was used to capture the binding of acetyl and N-methylamide capped glutamic acid and Gla single amino acids onto crystalline hydroxyapatite and titania model surfaces at physiological pH. Following this, parallel tempering metadynamics in the well-tempered ensemble (PTMetaD-WTE) was used to study adsorption of the α-1 domain of osteocalcin onto hydroxyapatite and titania. Simulations were performed for the α-1 domain of osteocalcin in both its fully decarboxylated (dOC) and fully carboxylated (OC) form. Our simulations find that increased charge density due to carboxylation results in increased interactions at the interface, and stronger adsorption of the single amino acids to both surfaces. Interestingly, the role of Gla in promoting compact and helical structure in the α-1 domain resulted in disparate binding modes at the two surfaces, which is attributed to differences in interfacial water behavior. Overall, this work provides a benchmark for understanding the mechanisms that drive adsorption of Gla-containing mineralizing proteins onto different surface chemistries.

This record contains files necessary to reproduce enhanced sampling well-tempered metadynamics (wtMTD) and parallel tempering metadynamics in the well-tempered ensemble (PT-MetaD-WTE) simulations in PLUMED using GROMACS 2018.3.
DOI: 10.24435/materialscloud:xq-0t
title: Optical absorption properties of metal-organic frameworks: solid state versus molecular perspective

description: The vast chemical space of metal and ligand combinations in Transition Metal Complexes (TMCs) gives rise to a rich variety of electronic excited states with local and non-local character such as intra-ligand (IL), metal-centered (MC), metal-to-ligand (MLCT) or ligand-to-metal charge-transfer (LMCT) states. Those features are equally found in Metal Organic Frameworks (MOFs), defined as modular materials built from metal-nodes connected through organic-ligands. Because of the electronic and structural complexity of MOFs, the computational description of their excited states is a formidable challenge for which two different approaches have been usually followed: the solid state and the molecular perspective. The first consists in analysing the frontier electronic bands and crystal orbitals of the electronic ground state (GS) in periodic boundary conditions, while the latter points to an accurate computation of the excited states in representative clusters at the molecular level. Herein, we apply both approaches to evaluate the optical absorption properties of three experimentally reported Ti(IV) mononuclear MOFs with in silico metal substitutions with Zn(II), Cd(II), Fe(II), Ru(II) and Zr(IV) ions, thus covering d10, d6 and d0 electronic configurations of 1st and 2nd row TMCs in MOFs. Our analysis captures the main electronic features attributed to these systems while we discuss the main advantages and drawbacks of both approximations.