cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.24435/materialscloud:k0-7c
title: Scaling properties of RNA as a randomly branching polymer

description: Formation of base pairs between the nucleotides of a ribonucleic acid (RNA) sequence gives rise to a complex and often highly branched RNA structure. While numerous studies have demonstrated the functional importance of the high degree of RNA branching—for instance, for its spatial compactness or interaction with other biological macromolecules—RNA branching topology remains largely unexplored. Here, we use the theory of randomly branching polymers to explore the scaling properties of RNAs by mapping their secondary structures onto planar tree graphs. Focusing on random RNA sequences of varying lengths, we determine the two scaling exponents related to their topology of branching. Our results indicate that ensembles of RNA secondary structures are characterized by annealed random branching and scale similarly to self-avoiding trees in three dimensions. We further show that the obtained scaling exponents are robust upon changes in nucleotide composition, tree topology, and folding energy parameters. Finally, in order to apply the theory of branching polymers to biological RNAs, whose length cannot be arbitrarily varied, we demonstrate how both scaling exponents can be obtained from distributions of the related topological quantities of individual RNA molecules with fixed length. In this way, we establish a framework to study the branching properties of RNA and compare them to other known classes of branched polymers. By understanding the scaling properties of RNA related to its branching structure, we aim to improve our understanding of the underlying principles and open up the possibility to design RNA sequences with desired topological properties.
DOI: 10.24435/materialscloud:bk-y8
title: Time-resolved oxidation state changes are key to elucidating the bifunctionality of perovskite catalysts for oxygen evolution and reduction

description: In a unified regenerative fuel cell (URFC) or reversible fuel cell the oxygen bifunctional catalyst must switch reversibly between the oxygen reduction reaction (ORR), fuel cell mode, and the oxygen evolution reaction (OER), electrolyzer mode. However, it is often unclear what effect alternating between ORR and OER has on the electrochemical behavior and physiochemical properties of the catalyst. Herein, operando X-ray absorption spectroscopy (XAS) is utilized to monitor the continuous and dynamic evolution of the Co, Mn, and Fe oxidation states of perovskite catalysts Ba0.5Sr0.5Co0.8Fe0.2O3-δ (BSCF) and La0.4Sr0.6MnO3-δ (LSM), while the potential is oscillated between reducing and oxidizing potentials with cyclic voltammetry. The results reveal the importance of investigating bifunctional catalysts by alternating between fuel cell and electrolyzer operation and highlight the limitations and challenges of bifunctional catalysts. It is shown that the requirements for ORR and OER performance are divergent and that the oxidative potentials of OER are detrimental to ORR activity. These findings are used to give guidelines for future bifunctional catalyst design. Additionally, it is demonstrated how sunlight can be used to reactivate the ORR activity of LSM after rigorous cycling.
DOI: 10.24435/materialscloud:fp-1x
title: Time-resolved oxidation state changes are key to elucidating the bifunctionality of perovskite catalysts for oxygen evolution and reduction

description: In a unified regenerative fuel cell (URFC) or reversible fuel cell the oxygen bifunctional catalyst must switch reversibly between the oxygen reduction reaction (ORR), fuel cell mode, and the oxygen evolution reaction (OER), electrolyzer mode. However, it is often unclear what effect alternating between ORR and OER has on the electrochemical behavior and physiochemical properties of the catalyst. Herein, operando X-ray absorption spectroscopy (XAS) is utilized to monitor the continuous and dynamic evolution of the Co, Mn, and Fe oxidation states of perovskite catalysts Ba0.5Sr0.5Co0.8Fe0.2O3-δ (BSCF) and La0.4Sr0.6MnO3-δ (LSM), while the potential is oscillated between reducing and oxidizing potentials with cyclic voltammetry. The results reveal the importance of investigating bifunctional catalysts by alternating between fuel cell and electrolyzer operation and highlight the limitations and challenges of bifunctional catalysts. It is shown that the requirements for ORR and OER performance are divergent and that the oxidative potentials of OER are detrimental to ORR activity. These findings are used to give guidelines for future bifunctional catalyst design. Additionally, it is demonstrated how sunlight can be used to reactivate the ORR activity of LSM after rigorous cycling.
DOI: 10.24435/materialscloud:jx-fp
title: Extensive benchmarking of DFT+U calculations for predicting band gaps

description: Accurate computational predictions of band gaps are of practical importance to the modeling and development of semiconductor technologies, such as (opto)electronic devices and photoelectrochemical cells. Among available electronic-structure methods, density-functional theory (DFT) with the Hubbard U correction (DFT+U) applied to band edge states is a computationally tractable approach to improve the accuracy of band gap predictions beyond that of DFT calculations based on (semi)local functionals. At variance with DFT approximations, which are not intended to describe optical band gaps and other excited-state properties, DFT+U can be interpreted as an approximate spectral-potential method when U is determined by imposing the piecewise linearity of the total energy with respect to electronic occupations in the Hubbard manifold (thus removing self-interaction errors in this subspace), thereby providing a (heuristic) justification for using DFT+U to predict band gaps. However, it is still frequent in the literature to determine the Hubbard U parameters semiempirically by tuning their values to reproduce experimental band gaps, which ultimately alters the description of other total-energy characteristics. Here, we present an extensive assessment of DFT+U band gaps computed using self-consistent ab initio U parameters obtained from density-functional perturbation theory to impose the aforementioned piecewise linearity of the total energy. The study is carried out on 20 compounds containing transition-metal or p-block (group III-IV) elements, including oxides, nitrides, sulfides, oxynitrides, and oxysulfides. By comparing DFT+U results obtained using nonorthogonalized and orthogonalized atomic orbitals as Hubbard projectors, we find that the predicted band gaps are extremely sensitive to the type of projector functions and that the orthogonalized projectors give the most accurate band gaps, in satisfactory agreement with experimental data. This work demonstrates that DFT+U may serve as a useful method for high-throughput workflows that require reliable band gap predictions at moderate computational cost.
DOI: 10.24435/materialscloud:t6-fm
title: Extensive benchmarking of DFT+U calculations for predicting band gaps

description: Accurate computational predictions of band gaps are of practical importance to the modeling and development of semiconductor technologies, such as (opto)electronic devices and photoelectrochemical cells. Among available electronic-structure methods, density-functional theory (DFT) with the Hubbard U correction (DFT+U) applied to band edge states is a computationally tractable approach to improve the accuracy of band gap predictions beyond that of DFT calculations based on (semi)local functionals. At variance with DFT approximations, which are not intended to describe optical band gaps and other excited-state properties, DFT+U can be interpreted as an approximate spectral-potential method when U is determined by imposing the piecewise linearity of the total energy with respect to electronic occupations in the Hubbard manifold (thus removing self-interaction errors in this subspace), thereby providing a (heuristic) justification for using DFT+U to predict band gaps. However, it is still frequent in the literature to determine the Hubbard U parameters semiempirically by tuning their values to reproduce experimental band gaps, which ultimately alters the description of other total-energy characteristics. Here, we present an extensive assessment of DFT+U band gaps computed using self-consistent ab initio U parameters obtained from density-functional perturbation theory to impose the aforementioned piecewise linearity of the total energy. The study is carried out on 20 compounds containing transition-metal or p-block (group III-IV) elements, including oxides, nitrides, sulfides, oxynitrides, and oxysulfides. By comparing DFT+U results obtained using nonorthogonalized and orthogonalized atomic orbitals as Hubbard projectors, we find that the predicted band gaps are extremely sensitive to the type of projector functions and that the orthogonalized projectors give the most accurate band gaps, in satisfactory agreement with experimental data. This work demonstrates that DFT+U may serve as a useful method for high-throughput workflows that require reliable band gap predictions at moderate computational cost.
DOI: 10.24435/materialscloud:xy-j1
title: Interpretations of ground-state symmetry breaking and strong correlation in wavefunction and density functional theories

description: Strong correlations within a symmetry-unbroken ground-state wavefunction can show up in approximate density functional theory as symmetry-broken spin-densities or total densities, which are sometimes observable. They can arise from soft modes of fluctuations (sometimes collective excitations) such as spin-density or charge-density waves at non-zero wavevector. In this sense, an approximate density functional for exchange and correlation that breaks symmetry can be more revealing (albeit less accurate) than an exact functional that does not. The examples discussed here include the stretched H2 molecule, antiferromagnetic solids, and the static charge-density wave/Wigner crystal phase of a low-density jellium. Time-dependent density functional theory is used to show quantitatively that the static charge density wave is a soft plasmon. More precisely, the frequency of a related density fluctuation drops to zero, as found from the frequency moments of the spectral function, calculated from a recent constraint-based wavevector- and frequency-dependent jellium exchange-correlation kernel.

This record contains all raw data used in this project. The second version contains better-converged data for the frequency moments. The parameters used to generate this data are included in a text file.
DOI: 10.24435/materialscloud:6t-p9
title: Interpretations of ground-state symmetry breaking and strong correlation in wavefunction and density functional theories

description: Strong correlations within a symmetry-unbroken ground-state wavefunction can show up in approximate density functional theory as symmetry-broken spin-densities or total densities, which are sometimes observable. They can arise from soft modes of fluctuations (sometimes collective excitations) such as spin-density or charge-density waves at non-zero wavevector. In this sense, an approximate density functional for exchange and correlation that breaks symmetry can be more revealing (albeit less accurate) than an exact functional that does not. The examples discussed here include the stretched H2 molecule, antiferromagnetic solids, and the static charge-density wave/Wigner crystal phase of a low-density jellium. Time-dependent density functional theory is used to show quantitatively that the static charge density wave is a soft plasmon. More precisely, the frequency of a related density fluctuation drops to zero, as found from the frequency moments of the spectral function, calculated from a recent constraint-based wavevector- and frequency-dependent jellium exchange-correlation kernel.

This record contains all raw data used in this project.
DOI: 10.24435/materialscloud:9v-3q
title: On-the-fly assessment of diffusion barriers of disordered transition metal oxyfluorides using local descriptors

description: The dataset contains the result of 48 Nudged Elastic Band calculations of Li(2-x)VO2F diffusion barriers in the format of Atomic Simulation Environment (ASE) trajectories. The NEB was performed with VASP, using projector augmented-wave (PAW) method to describe electron-ion interaction. The disordered rock salt cells were created using a 3 x 4 x 4 supercell containing 96 atoms (in case of no vacancies). PBE is used as XC functional while a rotationally invariant Hubbard U correction was applied to the d orbital of V with a U value of 3.25 eV. See more details in the paper.
DOI: 10.24435/materialscloud:nb-4d
title: On-the-fly assessment of diffusion barriers of disordered transition metal oxyfluorides using local descriptors

description: The dataset contains the result of 48 Nudged Elastic Band calculations of Li(2-x)VO2F diffusion barriers in the format of Atomic Simulation Environment (ASE) trajectories. The NEB was performed with VASP, using projector augmented-wave (PAW) method to describe electron-ion interaction. The disordered rock salt cells were created using a 3 x 4 x 4 supercell containing 96 atoms (in case of no vacancies). PBE is used as XC functional while a rotationally invariant Hubbard U correction was applied to the d orbital of V with a U value of 3.25 eV. See more details in the paper.
DOI: 10.24435/materialscloud:vh-wc
title: Interpretations of ground-state symmetry breaking and strong correlation in wavefunction and density functional theories

description: Strong correlations within a symmetry-unbroken ground-state wavefunction can show up in approximate density functional theory as symmetry-broken spin-densities or total densities, which are sometimes observable. They can arise from soft modes of fluctuations (sometimes collective excitations) such as spin-density or charge-density waves at non-zero wavevector. In this sense, an approximate density functional for exchange and correlation that breaks symmetry can be more revealing (albeit less accurate) than an exact functional that does not. The examples discussed here include the stretched H2 molecule, antiferromagnetic solids, and the static charge-density wave/Wigner crystal phase of a low-density jellium. Time-dependent density functional theory is used to show quantitatively that the static charge density wave is a soft plasmon. More precisely, the frequency of a related density fluctuation drops to zero, as found from the frequency moments of the spectral function, calculated from a recent constraint-based wavevector- and frequency-dependent jellium exchange-correlation kernel.

This record contains all raw data used in this project. The second version contains better-converged data for the frequency moments. The parameters used to generate this data are included in a text file. The third version includes third moment sum rule data that is more stable (a typo in the spline interpolation was rectified, see the Gitlab commit record for more detailed information), as well as expanded correlation energy per electron data. The MCP07 analytic continuation to imaginary frequencies is also more correctly treated in this new data set.
DOI: 10.24435/materialscloud:x5-5r
title: Interpretations of ground-state symmetry breaking and strong correlation in wavefunction and density functional theories

description: Strong correlations within a symmetry-unbroken ground-state wavefunction can show up in approximate density functional theory as symmetry-broken spin-densities or total densities, which are sometimes observable. They can arise from soft modes of fluctuations (sometimes collective excitations) such as spin-density or charge-density waves at non-zero wavevector. In this sense, an approximate density functional for exchange and correlation that breaks symmetry can be more revealing (albeit less accurate) than an exact functional that does not. The examples discussed here include the stretched H2 molecule, antiferromagnetic solids, and the static charge-density wave/Wigner crystal phase of a low-density jellium. Time-dependent density functional theory is used to show quantitatively that the static charge density wave is a soft plasmon. More precisely, the frequency of a related density fluctuation drops to zero, as found from the frequency moments of the spectral function, calculated from a recent constraint-based wavevector- and frequency-dependent jellium exchange-correlation kernel.

This record contains all raw data used in this project. The second version contains better-converged data for the frequency moments. The parameters used to generate this data are included in a text file. The third version includes third moment sum rule data that is more stable (a typo in the spline interpolation was rectified, see the Gitlab commit record for more detailed information), as well as expanded correlation energy per electron data. The MCP07 analytic continuation to imaginary frequencies is also more correctly treated in this new data set.
DOI: 10.24435/materialscloud:xk-sn
title: Appraisal of calcium ferrites as cathodes for calcium rechargeable batteries: DFT, synthesis, characterization and electrochemistry of Ca4Fe9O17

description: Sustainability combined with high energy density prospects makes Fe-based oxides attractive as cathodes for calcium rechargeable batteries. This work presents a DFT evaluation of the CaFe2+nO4+n (0 < n < 3) family, for which both the average intercalation voltage and the theoretical specific capacity decrease with the increasing n value. The term n = 1/4, Ca4Fe9O17, meets the most appealing characteristics: a calculated average voltage of 4.16 V, a theoretical specific capacity of 230 mA h g−1 and the lowest energy barrier for Ca migration so far predicted for an existing oxide (0.72 eV). To overcome the previously reported synthesis difficulties, we employed a novel synthesis procedure in sealed quartz tubes followed by quenching in water. The XRD and SAED patterns of the prepared Ca4Fe9O17 powder reveal a certain degree of stacking defects along the c axis. Attempts to deinsert Ca ions from Ca4Fe9O17 by chemical means (NO2BF4 in ACN) and in electrochemical Ca cells were unsuccessful, although some hints of oxidation are observed in Li cells with the LP30 electrolyte. The suitability of Ca4Fe9O17 as a Ca cathode is pending further studies utilizing Ca-electrolytes with high anodic stability.
DOI: 10.24435/materialscloud:3t-8e
title: Appraisal of calcium ferrites as cathodes for calcium rechargeable batteries: DFT, synthesis, characterization and electrochemistry of Ca4Fe9O17

description: Sustainability combined with high energy density prospects makes Fe-based oxides attractive as cathodes for calcium rechargeable batteries. This work presents a DFT evaluation of the CaFe2+nO4+n (0 < n < 3) family, for which both the average intercalation voltage and the theoretical specific capacity decrease with the increasing n value. The term n = 1/4, Ca4Fe9O17, meets the most appealing characteristics: a calculated average voltage of 4.16 V, a theoretical specific capacity of 230 mA h g−1 and the lowest energy barrier for Ca migration so far predicted for an existing oxide (0.72 eV). To overcome the previously reported synthesis difficulties, we employed a novel synthesis procedure in sealed quartz tubes followed by quenching in water. The XRD and SAED patterns of the prepared Ca4Fe9O17 powder reveal a certain degree of stacking defects along the c axis. Attempts to deinsert Ca ions from Ca4Fe9O17 by chemical means (NO2BF4 in ACN) and in electrochemical Ca cells were unsuccessful, although some hints of oxidation are observed in Li cells with the LP30 electrolyte. The suitability of Ca4Fe9O17 as a Ca cathode is pending further studies utilizing Ca-electrolytes with high anodic stability.
DOI: 10.24435/materialscloud:2b-ht
title: SmB6 electron-phonon coupling constant from time- and angle-resolved photoelectron spectroscopy

description: This record contains the experimental results of the first ultrafast spectroscopic investigation of the electronic properties of SmB6, proposed to realize a Kondo topological insulator.  We employ a multi-temperature model to extract the electron-phonon coupling constant in the range 0.13-0.04, within the assumption of a strong coupling to the optical phonon modes in the range 10-19 meV.
DOI: 10.24435/materialscloud:qf-yq
title: SmB6 electron-phonon coupling constant from time- and angle-resolved photoelectron spectroscopy

description: This record contains the experimental results of the first ultrafast spectroscopic investigation of the electronic properties of SmB6, proposed to realize a Kondo topological insulator.  We employ a multi-temperature model to extract the electron-phonon coupling constant in the range 0.13-0.04, within the assumption of a strong coupling to the optical phonon modes in the range 10-19 meV.
DOI: 10.24435/materialscloud:j7-51
title: On-surface synthesis and characterization of super-nonazethrene

description: This record contains data to support the findings discussed in our recent work on the synthesis and characterization of super-nonazethrene. Beginning with the early work of Clar et al. in 1955, zethrenes and their laterally-extended homologues, super-zethrenes, have been intensively studied in the solution phase, and are widely investigated as optical and charge transport materials. Super-zethrenes are also considered to exhibit an open-shell ground state. Zethrenes may thus serve as model compounds to investigate nanoscale π-magnetism. However, their synthesis is extremely challenging due to their high reactivity. In the work we report here a combined in-solution and on-surface synthesis of the hitherto largest zethrene homologue – super-nonazethrene – on Au(111). Using single-molecule scanning tunneling microscopy and spectroscopy, we show that super-nonazethrene exhibits an open-shell singlet ground state featuring a large spin polarization-driven electronic gap of 1 eV. We obtain real-space maps of the frontier molecular orbitals, and find that they correspond to singly occupied molecular orbitals. In consistence with the emergence of an open-shell ground state, high-resolution tunneling spectroscopy reveals inelastic singlet-triplet spin excitations in super-nonazethrene, characterized by a strong intramolecular magnetic exchange coupling of 51 meV. Further insights are gained by mean-field and many-body perturbation theory calculations. Given the paucity of zethrene chemistry on surfaces, our results therefore provide unprecedented access to large open-shell zethrene compounds amenable to scanning probe measurements, with potential application in molecular spintronics.