cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.24435/materialscloud:x4-wy
title: Structural transitions of calcium carbonate by molecular dynamics simulation

description: Calcium carbonate (CaCO₃) plays a crucial role in the global carbon cycle, and its phase diagram is of significant scientific interest. We used molecular dynamics to investigate selected structural phase transitions of calcium carbonate. Using the Raiteri potential, we explored the structural transitions occurring at the constant pressure of 1 bar, with temperatures ranging from 300 to 2500 K, and at the constant temperature of 1600 K, with pressures ranging from 0 to 13 GPa. With increasing temperature, the transitions between calcite, CaCO₃-IV, and CaCO₃-V were characterized. In the calcite structure, the carbonate ions are ordered in a planar triangular arrangement, alternating with layers of calcium ions. As the temperature increases, the transition from calcite to CaCO₃-IV occurs, leading to partial disordering of the carbonate ions. At higher temperatures, CaCO₃-IV transforms into CaCO₃-V. Through free energy analysis, we classified the latter transition as a continuous phase transition. At a temperature of 2000 K, a 'disordered CaCO₃' structure appears, characterized by low order within the calcium and carbonate sublattices and the free rotation of the carbonate ions. With increasing pressure, two calcium carbonate transformations were observed. At P = 2 GPa, the CaCO₃-V phase undergoes a phase transition into CaCO₃-IV, demonstrating that the model can describe the transition between these two phases as pressure- and temperature-driven. At P = 4.25 GPa, CaCO₃-IV undergoes a phase transition into the CaCO₃-Vb phase. This transition is classified as first-order based on free energy calculations.
DOI: 10.24435/materialscloud:a8-4c
title: Understanding the role of oxygen-vacancy defects in Cu₂O(111) from first-principle calculations

description: The presence of defects, such as copper and oxygen vacancies, in cuprous oxide films determines their characteristic carrier conductivity and consequently their application as semiconducting systems. There are still open questions on the induced electronic re-distribution, including the formation of polarons. Indeed, to accurately reproduce the structural and electronic properties at the cuprous oxide surface, very large slab models and theoretical approaches that go beyond the standard generalized gradient corrected density functional theory are needed. In this work we investigate oxygen vacancies formed in proximity of a reconstructed Cu₂O(111) surface, where the outermost unsaturated copper atoms are removed, thus forming non-stoichiometric surface layers with copper vacancies. We address simultaneously surface and bulk properties by modelling a thick and symmetric slab, to find that hybrid exchange-correlation functionals are needed to describe the oxygen vacancy in this system. Our simulations show that the formation of oxygen vacancies is favoured in the sub-surface layer. Moreover, the oxygen vacancy leads to a splitting and left-shift of the shallow hole states in the gap, which are associated with the deficiency of copper at the surface. These findings suggest that surface electronic structure and reactivity are sensitive to the presence of oxygen vacancies, also when the latter are formed deeper within the film.
DOI: 10.24435/materialscloud:z6-gb
title: Understanding the role of oxygen-vacancy defects in Cu₂O(111) from first-principle calculations

description: The presence of defects, such as copper and oxygen vacancies, in cuprous oxide films determines their characteristic carrier conductivity and consequently their application as semiconducting systems. There are still open questions on the induced electronic re-distribution, including the formation of polarons. Indeed, to accurately reproduce the structural and electronic properties at the cuprous oxide surface, very large slab models and theoretical approaches that go beyond the standard generalized gradient corrected density functional theory are needed. In this work we investigate oxygen vacancies formed in proximity of a reconstructed Cu₂O(111) surface, where the outermost unsaturated copper atoms are removed, thus forming non-stoichiometric surface layers with copper vacancies. We address simultaneously surface and bulk properties by modelling a thick and symmetric slab, to find that hybrid exchange-correlation functionals are needed to describe the oxygen vacancy in this system. Our simulations show that the formation of oxygen vacancies is favoured in the sub-surface layer. Moreover, the oxygen vacancy leads to a splitting and left-shift of the shallow hole states in the gap, which are associated with the deficiency of copper at the surface. These findings suggest that surface electronic structure and reactivity are sensitive to the presence of oxygen vacancies, also when the latter are formed deeper within the film.
DOI: 10.24435/materialscloud:vs-79
title: Switching p-type to high-performance n-type organic electrochemical transistors via doped state engineering

description: High-performance n-type organic electrochemical transistors (OECTs) are essential for logic circuits and sensors. However, the performances of n-type OECTs lag far behind that of p-type ones. Conventional wisdom posits that the LUMO energy level dictates the n-type performance. Herein, we show that engineering the doped state is more critical for n-type OECT polymers. By balancing more charges to the donor moiety, we could effectively switch a p-type polymer to high-performance n-type material. Based on this concept, the polymer, P(gTDPP2FT), exhibits a record high n-type OECT performance with μC* of 54.8 F cm⁻¹ V⁻¹ s⁻¹, mobility of 0.35 cm² V⁻¹ s⁻¹, and response speed of τon/τoff = 1.75/0.15 ms. Calculations and comparison studies show that the conversion is primarily due to the more uniform charges, stabilized negative polaron, enhanced conformation, and backbone planarity at negatively charged states. Our work highlights the critical role of understanding and engineering polymers' doped states.
DOI: 10.24435/materialscloud:ch-6s
title: Switching p-type to high-performance n-type organic electrochemical transistors via doped state engineering

description: High-performance n-type organic electrochemical transistors (OECTs) are essential for logic circuits and sensors. However, the performances of n-type OECTs lag far behind that of p-type ones. Conventional wisdom posits that the LUMO energy level dictates the n-type performance. Herein, we show that engineering the doped state is more critical for n-type OECT polymers. By balancing more charges to the donor moiety, we could effectively switch a p-type polymer to high-performance n-type material. Based on this concept, the polymer, P(gTDPP2FT), exhibits a record high n-type OECT performance with μC* of 54.8 F cm⁻¹ V⁻¹ s⁻¹, mobility of 0.35 cm² V⁻¹ s⁻¹, and response speed of τon/τoff = 1.75/0.15 ms. Calculations and comparison studies show that the conversion is primarily due to the more uniform charges, stabilized negative polaron, enhanced conformation, and backbone planarity at negatively charged states. Our work highlights the critical role of understanding and engineering polymers' doped states.
DOI: 10.24435/materialscloud:xc-5e
title: Bayesian hierarchical models for quantitative estimates for performance metrics applied to saddle search algorithms

description: The increasing use of high-throughput computational chemistry demands rigorous methods for evaluating algorithm performance. We present a Bayesian hierarchical modeling paradigm (brms/Stan) for analyzing key performance metrics: function evaluations, computation time, and success/failure. This framework accounts for variability across different systems and functionals, providing reliable uncertainty estimates beyond subjective visual assessments or frequentist limitations. We applied this to compare conjugate gradient (CG) and L-BFGS algorithms for the Dimer method's rotation phase (in EON, with/without removal of external rotations) on a benchmark of 500 initial saddle search approximations, analyzing over 2000 runs. Our results show CG rotations generally outperform L-BFGS, exhibiting a statistically credible, small reduction in PES calls and significantly higher odds of successful convergence. Conversely, enabling rotation removal incurred a substantial PES call penalty without a corresponding credible improvement in success odds in the implementation studied. These findings, from our novel Bayesian hierarchical modeling application, suggest CG may be preferable for Dimer rotational optimization in similar contexts. This robust statistical framework highlights benefits for revisiting optimization strategies, quantifying uncertainty, and facilitating improved high-throughput computational chemistry methods. This record contains the saddle search output logs for EON with NWChem across four settings, with/without external rotation and the use of CG/LBFGS for the rotational phase of the dimer. The record also includes fitted Bayesian Hierarchical models for performance and success analysis. These models and data are used to generate the figures and validate the analysis in the manuscript. For details, refer to the code in the associated GitHub repository.
DOI: 10.24435/materialscloud:zt-0k
title: Bayesian hierarchical models for quantitative estimates for performance metrics applied to saddle search algorithms

description: The increasing use of high-throughput computational chemistry demands rigorous methods for evaluating algorithm performance. We present a Bayesian hierarchical modeling paradigm (brms/Stan) for analyzing key performance metrics: function evaluations, computation time, and success/failure. This framework accounts for variability across different systems and functionals, providing reliable uncertainty estimates beyond subjective visual assessments or frequentist limitations. We applied this to compare conjugate gradient (CG) and L-BFGS algorithms for the Dimer method's rotation phase (in EON, with/without removal of external rotations) on a benchmark of 500 initial saddle search approximations, analyzing over 2000 runs. Our results show CG rotations generally outperform L-BFGS, exhibiting a statistically credible, small reduction in PES calls and significantly higher odds of successful convergence. Conversely, enabling rotation removal incurred a substantial PES call penalty without a corresponding credible improvement in success odds in the implementation studied. These findings, from our novel Bayesian hierarchical modeling application, suggest CG may be preferable for Dimer rotational optimization in similar contexts. This robust statistical framework highlights benefits for revisiting optimization strategies, quantifying uncertainty, and facilitating improved high-throughput computational chemistry methods. This record contains the saddle search output logs for EON with NWChem across four settings, with/without external rotation and the use of CG/LBFGS for the rotational phase of the dimer. The record also includes fitted Bayesian Hierarchical models for performance and success analysis. These models and data are used to generate the figures and validate the analysis in the manuscript. For details, refer to the code in the associated GitHub repository.
DOI: 10.24435/materialscloud:gn-qs
title: Density functional perturbation theory for one-dimensional systems: implementation and relevance for phonons and electron-phonon interactions

description: The electronic and vibrational properties and electron-phonon couplings of one-dimensional materials will be key to many prospective applications in nanotechnology. Dimensionality strongly affects these properties and has to be correctly accounted for in first-principles calculations. Here we develop and implement a formulation of density-functional and density-functional perturbation theory that is tailored for one-dimensional systems. A key ingredient is the inclusion of a Coulomb cutoff, a reciprocal-space technique designed to correct for the spurious interactions between periodic images in periodic-boundary conditions. This restores the proper one-dimensional open-boundary conditions, letting the true response of the isolated one-dimensional system emerge. In addition to total energies, forces and stress tensors, phonons and electron-phonon interactions are also properly accounted for. We demonstrate the relevance of the present method on a portfolio of realistic systems: BN atomic chains, BN armchair nanotubes, and GaAs nanowires. Notably, we highlight the critical role of the Coulomb cutoff by studying previously inaccessible polar-optical phonons and Fröhlich electron-phonon couplings. We also develop and apply analytical models to support the physical insights derived from the calculations and we discuss their consequences on electronic lifetimes. The present work unlocks the possibility to accurately simulate the linear response properties of one-dimensional systems, sheds light on the transition between dimensionalities and paves the way for further studies in several fields, including charge transport, optical coupling and polaritronics.
DOI: 10.24435/materialscloud:46-31
title: High-throughput screening of nano-hybrid metal–organic-frameworks for photocatalytic CO₂ reduction

description: Photocatalytic conversion of CO₂ into fuel feed stocks is a promising method for sustainable fuel production. A highly attractive class of materials, inorganic-core@metal–organic-framework heterogeneous catalysts, boasts a significant increase in catalytic performance when compared to the individual materials. However, due to the ever-expanding chemical space of inorganic-core catalysts and metal–organic frameworks (MOFs), identification of these optimal heterojunctions is difficult without appropriate computational screening. In this work, a novel high-throughput screening method of nano-hybrid photocatalysts is presented by screening 65'784 inorganic-core materials and 20'375 MOF-shells for their ability to reduce CO₂ based on their synthesizability, aqueous stability, visible light absorption, and electronic structure; the passing materials were then paired based on their electronic structure to create novel heterojunctions. The results showed 58 suitable inorganic-core materials and 204 suitable MOFs ranging from never-beforesynthesized catalysts to catalysts that have been overlooked for their photocatalytic ability. These materials lay a new foundation of photocatalysts that have passed theoretical requirements and can significantly increase the rate of catalyst discovery.
DOI: 10.24435/materialscloud:fx-hx
title: Density functional perturbation theory for one-dimensional systems: implementation and relevance for phonons and electron-phonon interactions

description: The electronic and vibrational properties and electron-phonon couplings of one-dimensional materials will be key to many prospective applications in nanotechnology. Dimensionality strongly affects these properties and has to be correctly accounted for in first-principles calculations. Here we develop and implement a formulation of density-functional and density-functional perturbation theory that is tailored for one-dimensional systems. A key ingredient is the inclusion of a Coulomb cutoff, a reciprocal-space technique designed to correct for the spurious interactions between periodic images in periodic-boundary conditions. This restores the proper one-dimensional open-boundary conditions, letting the true response of the isolated one-dimensional system emerge. In addition to total energies, forces and stress tensors, phonons and electron-phonon interactions are also properly accounted for. We demonstrate the relevance of the present method on a portfolio of realistic systems: BN atomic chains, BN armchair nanotubes, and GaAs nanowires. Notably, we highlight the critical role of the Coulomb cutoff by studying previously inaccessible polar-optical phonons and Fröhlich electron-phonon couplings. We also develop and apply analytical models to support the physical insights derived from the calculations and we discuss their consequences on electronic lifetimes. The present work unlocks the possibility to accurately simulate the linear response properties of one-dimensional systems, sheds light on the transition between dimensionalities and paves the way for further studies in several fields, including charge transport, optical coupling and polaritronics.
DOI: 10.24435/materialscloud:fj-db
title: High-throughput screening of nano-hybrid metal–organic-frameworks for photocatalytic CO₂ reduction

description: Photocatalytic conversion of CO₂ into fuel feed stocks is a promising method for sustainable fuel production. A highly attractive class of materials, inorganic-core@metal–organic-framework heterogeneous catalysts, boasts a significant increase in catalytic performance when compared to the individual materials. However, due to the ever-expanding chemical space of inorganic-core catalysts and metal–organic frameworks (MOFs), identification of these optimal heterojunctions is difficult without appropriate computational screening. In this work, a novel high-throughput screening method of nano-hybrid photocatalysts is presented by screening 65'784 inorganic-core materials and 20'375 MOF-shells for their ability to reduce CO₂ based on their synthesizability, aqueous stability, visible light absorption, and electronic structure; the passing materials were then paired based on their electronic structure to create novel heterojunctions. The results showed 58 suitable inorganic-core materials and 204 suitable MOFs ranging from never-beforesynthesized catalysts to catalysts that have been overlooked for their photocatalytic ability. These materials lay a new foundation of photocatalysts that have passed theoretical requirements and can significantly increase the rate of catalyst discovery.
DOI: 10.7910/dvn/0gxeis
title: gaze_dev

description: Files Associated with ROS gaze detection
DOI: 10.24435/materialscloud:2k-pr
title: Incorporating static intersite correlation effects in vanadium dioxide through DFT+V

description: We analyze the effects on the structural and electronic properties of vanadium dioxide (VO₂) of adding an empirical inter-atomic potential within the density-functional theory+V (DFT+V) framework. We use the DFT+V machinery founded on the extended Hubbard model to apply an empirical self-energy correction between nearest-neighbor vanadium atoms in both rutile and monoclinic phases, and for a set of structures interpolating between these two cases. We observe that imposing an explicit intersite interaction V along the vanadium-vanadium chains enhances the characteristic bonding-antibonding splitting of the relevant bands in the monoclinic phase, thus favoring electronic dimerization and the formation of a band gap. We then explore the effect of V on the structural properties and the relative energies of the two phases, finding an insulating global energy minimum for the monoclinic phase, consistent with experimental observations. With increasing V, this minimum becomes deeper relative to the rutile structure, and the transition from the metallic to the insulating state becomes sharper. We also analyze the effect of applying the +V correction either to all or only to selected vanadium-vanadium pairs, and both in the monoclinic as well as in the metallic rutile phase. Our results suggest that  DFT+V can indeed serve as a computationally inexpensive unbiased way of modeling VO₂ which is well suited for studies that, e.g., require large system sizes.
DOI: 10.24435/materialscloud:8e-5d
title: Incorporating static intersite correlation effects in vanadium dioxide through DFT+V

description: We analyze the effects on the structural and electronic properties of vanadium dioxide (VO₂) of adding an empirical inter-atomic potential within the density-functional theory+V (DFT+V) framework. We use the DFT+V machinery founded on the extended Hubbard model to apply an empirical self-energy correction between nearest-neighbor vanadium atoms in both rutile and monoclinic phases, and for a set of structures interpolating between these two cases. We observe that imposing an explicit intersite interaction V along the vanadium-vanadium chains enhances the characteristic bonding-antibonding splitting of the relevant bands in the monoclinic phase, thus favoring electronic dimerization and the formation of a band gap. We then explore the effect of V on the structural properties and the relative energies of the two phases, finding an insulating global energy minimum for the monoclinic phase, consistent with experimental observations. With increasing V, this minimum becomes deeper relative to the rutile structure, and the transition from the metallic to the insulating state becomes sharper. We also analyze the effect of applying the +V correction either to all or only to selected vanadium-vanadium pairs, and both in the monoclinic as well as in the metallic rutile phase. Our results suggest that  DFT+V can indeed serve as a computationally inexpensive unbiased way of modeling VO₂ which is well suited for studies that, e.g., require large system sizes.
DOI: 10.24435/materialscloud:c9-9x
title: High-throughput magnetic co-doping and design of exchange interactions in a topological insulator

description: Using high-throughput automation of ab-initio impurity-embedding simulations we created a database of 3d and 4d transition metal defects embedded into the prototypical topological insulator (TI) Bi₂Te₃. We simulate both single impurities as well as impurity dimers at different impurity-impurity distances inside the topological insulator matrix. We extract changes to magnetic moments, analyze the polarizability of non-magnetic impurity atoms via nearby magnetic impurity atoms and calculate the exchange coupling constants for a Heisenberg Hamiltonian. 
We uncover chemical trends in the exchange coupling constants and discuss the impurities' potential with respect to magnetic order in the fields of quantum anomalous Hall insulators. In particular, we predict that co-doping of different magnetic dopants is a viable strategy to engineer the magnetic ground state in magnetic TIs.
DOI: 10.24435/materialscloud:66-am
title: Dislocation-grain boundary interaction dataset for FCC Cu

description: Dislocation-grain boundary play a major role in the strength and ductility of structural materials. An understanding of governing parameters such as grain boundary local atomic structures on the outcome of this interaction can accelerate new alloy design strategies that tailors materials' microstructures. Previous studies have focused only on the subset of minimum-energy grain boundary structures. We present a comprehensive database of dislocation-grain boundary interaction for edge, screw, and 60o mixed dislocation with 449 < 110 > and < 112 > symmetric tilt grain boundary in FCC Cu consisting of 67 minimum-energy grain boundary structures and 389 metastable ones. The dataset contains the outcomes for 5593 unique interactions with a particular dislocation type, grain boundary structure, and applied shear stress.
DOI: 10.24435/materialscloud:cw-ct
title: 2D pentagonal-graphene and pentagonal-silicene sheets engineered for the detection of DNA nucleobases for genetic biomarker: A DFT study

description: The deposited structure models of DNA adsorbed on prisitne PG/p-Si and metal (Au/W) doped PG/p-Si sheets, have been subjected to first principles calculations  based on DFT (PBE+vdW). The calculated binding affinity on PG and p-Si surface by M062X/6-31G* level of theory and adsorption energies by DFT predicts that PG has higher sensitivity towards DNA nucleic bases compared to p-Si with evident changes in their band structure properties.