cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.24435/materialscloud:vn-8p
title: Hamiltonian-Reservoir Replica Exchange and Machine Learning Potentials for Computational Organic Chemistry

description: This work combines a machine learning potential energy function with a modular enhanced sampling scheme to obtain statistically converged thermodynamical properties of flexible medium size organic molecules at high ab initio level. We offer a modular environment in the python package MORESIM that allows custom design of  replica exchange simulations with any level of theory including ML-based potentials. Our specific combination of Hamiltonian and reservoir replica exchange is shown to be a powerful technique to accelerate enhanced sampling simulations and explore free energy landscapes with a quantum chemical accuracy unattainable otherwise (e.g., DLPNO-CCSD(T)/CBS quality). This engine is used to demonstrate the relevance of accessing the ab initio free energy landscapes of molecules whose stability is determined by a subtle interplay between variations in the underlying potential energy and conformational entropy (i.e., a bridged asymmetrically polarized dithiacyclophane and a widely used organocatalyst) both in the gas phase and in solution (implicit solvent).
DOI: 10.24435/materialscloud:2020.0011/v1
title: Self-consistent DFT+U+V study of oxygen vacancies in SrTiO3

description: Contradictory theoretical results for oxygen vacancies (VO) in SrTiO3 (STO) were often related to the peculiar properties of STO, which is a d0 transition metal oxide with mixed ionic-covalent bonding. Here, we apply, for the first time, density functional theory (DFT) within the extended Hubbard DFT+U+V approach, including on-site as well as inter-site electronic interactions, to study oxygen-deficient STO with Hubbard U and V parameters computed self-consistently (SC) via density-functional perturbation theory. Our results demonstrate that the extended Hubbard functional is a promising approach to study defects in materials with electronic properties similar to STO. Indeed, DFT+U+V provides a better description of stoichiometric STO compared to standard DFT or DFT+U, the band gap and crystal field splitting being in good agreement with experiments.
In turn, also the description of the electronic properties of oxygen vacancies in STO is improved, with formation energies in excellent agreement with experiments as well as results obtained with the most frequently used hybrid functionals, however at a fraction of the computational cost. While our results do not fully resolve the contradictory findings reported in literature, our systematic approach leads to a deeper understanding of their origin, which stems from different cell sizes, STO phases, the exchange-correlation functional, and the treatment of structural relaxations and spin-polarization.
DOI: 10.24435/materialscloud:2020.0016/v1
title: Hubbard-corrected density functional perturbation theory with ultrasoft pseudopotentials

description: We present in full detail a newly developed formalism enabling density functional perturbation theory (DFPT) calculations from a DFT+U ground state. The implementation includes ultrasoft pseudopotentials and is valid for both insulating and metallic systems. It aims at fully exploiting the versatility of DFPT combined with the low-cost DFT+U functional. This allows to avoid computationally intensive frozen-phonon calculations when DFT+U is used to eliminate the residual electronic self-interaction from approximate functionals and to capture the localization of valence electrons e.g. on d or f states. In this way, the effects of electronic localization (possibly due to correlations) are consistently taken into account in the calculation of specific phonon modes, Born effective charges, dielectric tensors and in quantities requiring well converged sums over many phonon frequencies, as phonon density of states and free energies. The new computational tool is applied to two representative systems, namely CoO, a prototypical transition metal monoxide and LiCoO2, a material employed for the cathode of Li-ion batteries. The results show the effectiveness of our formalism to capture in a quantitatively reliable way the vibrational properties of systems with localized valence electrons.
DOI: 10.24435/materialscloud:bg-7c
title: Hubbard-corrected density functional perturbation theory with ultrasoft pseudopotentials

description: We present in full detail a newly developed formalism enabling density functional perturbation theory (DFPT) calculations from a DFT+U ground state. The implementation includes ultrasoft pseudopotentials and is valid for both insulating and metallic systems. It aims at fully exploiting the versatility of DFPT combined with the low-cost DFT+U functional. This allows to avoid computationally intensive frozen-phonon calculations when DFT+U is used to eliminate the residual electronic self-interaction from approximate functionals and to capture the localization of valence electrons e.g. on d or f states. In this way, the effects of electronic localization (possibly due to correlations) are consistently taken into account in the calculation of specific phonon modes, Born effective charges, dielectric tensors and in quantities requiring well converged sums over many phonon frequencies, as phonon density of states and free energies. The new computational tool is applied to two representative systems, namely CoO, a prototypical transition metal monoxide and LiCoO2, a material employed for the cathode of Li-ion batteries. The results show the effectiveness of our formalism to capture in a quantitatively reliable way the vibrational properties of systems with localized valence electrons.
DOI: 10.24435/materialscloud:2019.0042/v1
title: Atomistic simulation of carbohydrate-protein complex formation: Hevein-32 domain

description: Unbiased molecular dynamics simulation was used to simulate systems containing hevein (HEV32) domain and mono-, di- or trisaccharide of GlcNAc. Carbohydrate molecules were placed outside the binding site. Three of six simulations led to formation of a carbohydrate-protein complex. Trajectories are available without water and are sampled every 100 ps. This study is one of the first application of docking by dynamics concept on carbohydrate-protein interactions.
DOI: 10.24435/materialscloud:sf-4r
title: Self-consistent DFT+U+V study of oxygen vacancies in SrTiO3

description: Contradictory theoretical results for oxygen vacancies (VO) in SrTiO3 (STO) were often related to the peculiar properties of STO, which is a d0 transition metal oxide with mixed ionic-covalent bonding. Here, we apply, for the first time, density functional theory (DFT) within the extended Hubbard DFT+U+V approach, including on-site as well as inter-site electronic interactions, to study oxygen-deficient STO with Hubbard U and V parameters computed self-consistently (SC) via density-functional perturbation theory. Our results demonstrate that the extended Hubbard functional is a promising approach to study defects in materials with electronic properties similar to STO. Indeed, DFT+U+V provides a better description of stoichiometric STO compared to standard DFT or DFT+U, the band gap and crystal field splitting being in good agreement with experiments.
In turn, also the description of the electronic properties of oxygen vacancies in STO is improved, with formation energies in excellent agreement with experiments as well as results obtained with the most frequently used hybrid functionals, however at a fraction of the computational cost. While our results do not fully resolve the contradictory findings reported in literature, our systematic approach leads to a deeper understanding of their origin, which stems from different cell sizes, STO phases, the exchange-correlation functional, and the treatment of structural relaxations and spin-polarization.
DOI: 10.24435/materialscloud:g5-9z
title: Band alignment at β-Ga2O3/III-N (III=Al, Ga) interfaces through hybrid functional calculations

description: The band alignment and the chemical bonding at the β-Ga2O3/AlN and β-Ga2O3/GaN interfaces are studied through hybrid functional calculations. We construct realistic slab models with III-O (III=Al, Ga) bonds dominating the chemical bonding at both interfaces. The epitaxial relationships between β-Ga2O3 and wurtzite AlN and GaN determined from experiments are adopted in our slab models. These models satisfy electron counting rules and all the dangling bonds are saturated at the interfaces. β-Ga2O3 is found to form type II heterojunctions with both wurtzite AlN and GaN. For the interfaces with AlN and GaN substrates, the calculated valence band offsets are 0.74 and 0.90 eV, respectively. These are in good agreement with experimental values. The obtained band alignments are useful for designing optical and electronic devices based on β-Ga2O3 and group III nitrides.
DOI: 10.24435/materialscloud:m5-54
title: Self-consistent DFT+U+V study of oxygen vacancies in SrTiO3

description: Contradictory theoretical results for oxygen vacancies (VO) in SrTiO3 (STO) were often related to the peculiar properties of STO, which is a d0 transition metal oxide with mixed ionic-covalent bonding. Here, we apply, for the first time, density functional theory (DFT) within the extended Hubbard DFT+U+V approach, including on-site as well as inter-site electronic interactions, to study oxygen-deficient STO with Hubbard U and V parameters computed self-consistently (SC) via density-functional perturbation theory. Our results demonstrate that the extended Hubbard functional is a promising approach to study defects in materials with electronic properties similar to STO. Indeed, DFT+U+V provides a better description of stoichiometric STO compared to standard DFT or DFT+U, the band gap and crystal field splitting being in good agreement with experiments.
In turn, also the description of the electronic properties of oxygen vacancies in STO is improved, with formation energies in excellent agreement with experiments as well as results obtained with the most frequently used hybrid functionals, however at a fraction of the computational cost. While our results do not fully resolve the contradictory findings reported in literature, our systematic approach leads to a deeper understanding of their origin, which stems from different cell sizes, STO phases, the exchange-correlation functional, and the treatment of structural relaxations and spin-polarization.
DOI: 10.24435/materialscloud:st-mz
title: Band alignment at β-Ga2O3/III-N (III=Al, Ga) interfaces through hybrid functional calculations

description: The band alignment and the chemical bonding at the β-Ga2O3/AlN and β-Ga2O3/GaN interfaces are studied through hybrid functional calculations. We construct realistic slab models with III-O (III=Al, Ga) bonds dominating the chemical bonding at both interfaces. The epitaxial relationships between β-Ga2O3 and wurtzite AlN and GaN determined from experiments are adopted in our slab models. These models satisfy electron counting rules and all the dangling bonds are saturated at the interfaces. β-Ga2O3 is found to form type II heterojunctions with both wurtzite AlN and GaN. For the interfaces with AlN and GaN substrates, the calculated valence band offsets are 0.74 and 0.90 eV, respectively. These are in good agreement with experimental values. The obtained band alignments are useful for designing optical and electronic devices based on β-Ga2O3 and group III nitrides.
DOI: 10.24435/materialscloud:2019.0042/v2
title: Atomistic simulation of carbohydrate-protein complex formation: Hevein-32 domain

description: Unbiased molecular dynamics simulation was used to simulate systems containing hevein (HEV32) domain and mono-, di- or trisaccharide of GlcNAc. Carbohydrate molecules were placed outside the binding site. Three of six simulations led to formation of a carbohydrate-protein complex. Trajectories are available without water and are sampled every 100 ps. This study is one of the first application of docking by dynamics concept on carbohydrate-protein interactions.
DOI: 10.24435/materialscloud:2019.0050/v1
title: Exploring chemical space in the search for improved Azoheteroarene-based photoswitches

description: In the quest for improved photo switches, azoheteroarenes have emerged as a potential alternative to azobenzene. However, to date the number and types of these species that have subjected to study is insufficient to provide an in-depth understanding of the photochemical effects brought about by different substituents. Here, we computationally screen the optical properties and thermal stabilities of 512 azoheteroarenes that consist of eight different N-containing heteroarenes combined with 64 substitution patterns. The most promising compounds are identified and their properties rationalized based on the nature of the azoheteroarene core and the location and type of substitution patterns.
DOI: 10.24435/materialscloud:7a-1k
title: Atomistic simulation of carbohydrate-protein complex formation: Hevein-32 domain

description: Unbiased molecular dynamics simulation was used to simulate systems containing hevein (HEV32) domain and mono-, di- or trisaccharide of GlcNAc. Carbohydrate molecules were placed outside the binding site. Three of six simulations led to formation of a carbohydrate-protein complex. Trajectories are available without water and are sampled every 100 ps. This study is one of the first application of docking by dynamics concept on carbohydrate-protein interactions.
DOI: 10.24435/materialscloud:2020.0039/v1
title: Ab-initio phase diagram and nucleation of gallium

description: Elemental gallium possesses several intriguing properties such as a low melting point, a density anomaly and an electronic structure in which covalent and metallic features coexist. In order to simulate this complex system, we construct an ab-initio quality interaction potential by training a neural network on a set of density functional theory calculations performed on configurations generated in multithermal-multibaric simulations. Here we show that the relative equilibrium between liquid gallium, alpha-Ga, beta-Ga, and Ga-II is well described. The resulting phase diagram is in agreement with the experimental findings. The local structure of liquid gallium and its nucleation into alpha-Ga and beta-Ga are studied. We find that the formation of metastable beta-Ga is kinetically favored over the thermodinamically stable alpha-Ga. Finally, we provide insight into the experimental observations of extreme undercooling of liquid Ga.
DOI: 10.24435/materialscloud:3h-yx
title: Exploring chemical space in the search for improved Azoheteroarene-based photoswitches

description: In the quest for improved photo switches, azoheteroarenes have emerged as a potential alternative to azobenzene. However, to date the number and types of these species that have subjected to study is insufficient to provide an in-depth understanding of the photochemical effects brought about by different substituents. Here, we computationally screen the optical properties and thermal stabilities of 512 azoheteroarenes that consist of eight different N-containing heteroarenes combined with 64 substitution patterns. The most promising compounds are identified and their properties rationalized based on the nature of the azoheteroarene core and the location and type of substitution patterns.
DOI: 10.24435/materialscloud:hm-kt
title: Ab-initio phase diagram and nucleation of gallium

description: Elemental gallium possesses several intriguing properties such as a low melting point, a density anomaly and an electronic structure in which covalent and metallic features coexist. In order to simulate this complex system, we construct an ab-initio quality interaction potential by training a neural network on a set of density functional theory calculations performed on configurations generated in multithermal-multibaric simulations. Here we show that the relative equilibrium between liquid gallium, alpha-Ga, beta-Ga, and Ga-II is well described. The resulting phase diagram is in agreement with the experimental findings. The local structure of liquid gallium and its nucleation into alpha-Ga and beta-Ga are studied. We find that the formation of metastable beta-Ga is kinetically favored over the thermodinamically stable alpha-Ga. Finally, we provide insight into the experimental observations of extreme undercooling of liquid Ga.
DOI: 10.24435/materialscloud:2020.0012/v1
title: Balancing DFT Interaction Energies in Charged Dimers Precursors to Organic Semiconductors

description: Accurately describing intermolecular interactions within the framework of Kohn-Sham density functional theory (KS-DFT) has resulted in numerous benchmark databases over the past two decades. By far, the largest efforts have been spent on closed-shell, neutral dimers for which today, the interaction energies and geometries can be accurately reproduced by various combinations of dispersion-corrected density functional approximations (DFAs). In sharp contrast, charged, open-shell dimers remain a challenge as illustrated by the analysis of the OREL26rad benchmark set consisting of pi-dimer radical cations. Aside from the methodological aspect, achieving a proper description of radical cationic complexes is appealing due to their role as models for charge carriers in organic semiconductors. In the interest of providing an assessment of more realistic dimer systems, we construct a dataset of large radical cationic dimers (CryOrel) and jointly train the 19 parameters of a dispersion corrected, range-separated hybrid density functional (wB97X-dDsC), with the objective of providing the maximum balance between the treatment of long-range London dispersion and reduction of the delocalization error. These conditions are essential to obtain accurate energy profiles and binding energies of charged, open-shell dimers. Comparisons with the performance of the parent wB97X functional series and state-of-the-art wavefunction based methods are provided.
DOI: 10.24435/materialscloud:2020.0034/v1
title: Helicity-dependent photocurrents in the chiral Weyl semimetal RhSi

description: Weyl semimetals are crystals in which electron bands cross at isolated points in momentum space. Associated with each crossing point (or Weyl node) is an integer topological invariant known as the Berry monopole charge. The discovery of new classes of Weyl materials is driving the search for novel properties that derive directly from the Berry charge. The circular photogalvanic effect (CPGE), whereby circular polarized light generates a current whose direction depends on the helicity of the absorbed photons, is a striking example of a macroscopic property that emerges from Weyl topology. Recently, it was predicted that the rate of current generation associated with optical transitions near a Weyl node is proportional to its monopole charge. In Weyl semimetals that retain mirror symmetry the current is strongly suppressed by contributions from energy equivalent nodes of opposite charge. However, when all mirror symmetries are broken, as in chiral Weyl systems, nodes with opposite topological charge are no longer degenerate, opening a window of photon energies where the CPGE derived from the topological band structure can emerge. In this work we report the photon-energy dependence of the CPGE in the chiral Weyl semimetal RhSi. The spectrum reveals a helicity-sensitive response in a low-energy window that closes at 0.65 eV, in quantitative agreement with the bandstucture recently predicted from DFT calculations.
DOI: 10.24435/materialscloud:dq-h8
title: Balancing DFT Interaction Energies in Charged Dimers Precursors to Organic Semiconductors

description: Accurately describing intermolecular interactions within the framework of Kohn-Sham density functional theory (KS-DFT) has resulted in numerous benchmark databases over the past two decades. By far, the largest efforts have been spent on closed-shell, neutral dimers for which today, the interaction energies and geometries can be accurately reproduced by various combinations of dispersion-corrected density functional approximations (DFAs). In sharp contrast, charged, open-shell dimers remain a challenge as illustrated by the analysis of the OREL26rad benchmark set consisting of pi-dimer radical cations. Aside from the methodological aspect, achieving a proper description of radical cationic complexes is appealing due to their role as models for charge carriers in organic semiconductors. In the interest of providing an assessment of more realistic dimer systems, we construct a dataset of large radical cationic dimers (CryOrel) and jointly train the 19 parameters of a dispersion corrected, range-separated hybrid density functional (wB97X-dDsC), with the objective of providing the maximum balance between the treatment of long-range London dispersion and reduction of the delocalization error. These conditions are essential to obtain accurate energy profiles and binding energies of charged, open-shell dimers. Comparisons with the performance of the parent wB97X functional series and state-of-the-art wavefunction based methods are provided.
DOI: 10.24435/materialscloud:c9-6m
title: Helicity-dependent photocurrents in the chiral Weyl semimetal RhSi

description: Weyl semimetals are crystals in which electron bands cross at isolated points in momentum space. Associated with each crossing point (or Weyl node) is an integer topological invariant known as the Berry monopole charge. The discovery of new classes of Weyl materials is driving the search for novel properties that derive directly from the Berry charge. The circular photogalvanic effect (CPGE), whereby circular polarized light generates a current whose direction depends on the helicity of the absorbed photons, is a striking example of a macroscopic property that emerges from Weyl topology. Recently, it was predicted that the rate of current generation associated with optical transitions near a Weyl node is proportional to its monopole charge. In Weyl semimetals that retain mirror symmetry the current is strongly suppressed by contributions from energy equivalent nodes of opposite charge. However, when all mirror symmetries are broken, as in chiral Weyl systems, nodes with opposite topological charge are no longer degenerate, opening a window of photon energies where the CPGE derived from the topological band structure can emerge. In this work we report the photon-energy dependence of the CPGE in the chiral Weyl semimetal RhSi. The spectrum reveals a helicity-sensitive response in a low-energy window that closes at 0.65 eV, in quantitative agreement with the bandstucture recently predicted from DFT calculations.
DOI: 10.24435/materialscloud:2020.0028/v1
title: Motif based high-throughput structure prediction of superconducting monolayer titanium boride

description: Two-dimensional boron structures, due to the diversity of properties, attract great attention because of their potential applications in nanoelectronic devices. A series of TiB_x (4≤x≤11) monolayers are efficiently constructed through our motif based method and theoretically investigated through high-throughput first-principles calculations. The configurations are generated based on motifs of boron triangular/quadrilateral fragments and multicoordinate titanium-centered boron molecular wheels. Besides priviously reported TiB4 which was discovered by global search method, we predict that high symmetry monolayers TiB7 (Cmmm) and TiB9 (P31m) which are octa-coordinate and nona-coordinate titanium boride are thermodynamic stable. The TiB7 monolayer is a BCS superconductor with the transition temperature Tc up to 8K. The motif based approach is proved to be efficient in searching stable structures with a prior knowledge so that the potentially stable transition metal monolayers can be quickly constructed by using basic cluster motifs. As an efficient way of discovering materials, the method is easily extended to predict other type of materials which have common characteristic pattern in the structure.