cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.24435/materialscloud:h5-wz
title: Reaction pathway of oxygen evolution on Pt(1 1 1) revealed through constant Fermi level molecular dynamics

description: The pathway of the oxygen evolution reaction at the Pt(1 1 1)/water interface is disclosed through constant Fermi level molecular dynamics. Upon the application of a positive bias potential H2O_ads and O_ads adsorbates are found to arrange in a hexagonal lattice with an irregular alternation. Increasing further the electrode potential then induces the oxygen evolution reaction, which is found to proceed through a hydrogen peroxide intermediate. Calculation of the associated overpotential shows a reduction of 0.2 eV compared to the associative mechanism. This result highlights the forcefullness of the applied scheme in exploring catalytic reactions in an unbiased way.
DOI: 10.24435/materialscloud:2020.0024/v1
title: Stable structures of exohedrally decorated C60-fullerenes

description: A good hydrogen storage material should adsorb hydrogen in high concentrations and with optimal binding energies. Exohedrally metal decorated carbon fullerene structures were proposed as a promising material in this context. We present a fully ab-initio, unbiased structure search of the configurational space of decorated C60 fullerenes and find that many of the hitherto postulated ground state structures are not ground states. We determine the energetically lowest configurations for decorations with a varying number of decorating atoms (2 ≤ n ≤ 32) for alkali metals, alkaline-earth metals as well as some other important elements and find that the dense uniform distribution of the decorating atoms over the surface of the C60 , desired for hydrogen storage, can be obtained only for a few elements. An understanding of the behavior of the decorating atoms can be obtained by analyzing their bonding characteristics via the electron localization function.
DOI: 10.24435/materialscloud:2020.0044/v1
title: Iterative unbiasing of quasi-equilibrium sampling

description: This repository contains the PLUMED-2 input files required to generate the data used in the ITRE publications. ITRE is a method to reweight Molecular Dynamics trajectory biased with a history-dependent potential (such as Metadynamics), and calculate unbiased thermodynamic observables. Since it uses the trajectory itself as a proxy of a grid, its scaling does not depend on the dimensionality of the space explored. In addition, thanks to its formulation, it is less affected by out-of-equilibrium points that characterize the early stages of a biased calculation and are usually discarded. Thanks to this feature, it can be used to increase the statistics when evaluating a thermodynamic observable from biased calculation.
DOI: 10.24435/materialscloud:p3-2k
title: Stable structures of exohedrally decorated C60-fullerenes

description: A good hydrogen storage material should adsorb hydrogen in high concentrations and with optimal binding energies. Exohedrally metal decorated carbon fullerene structures were proposed as a promising material in this context. We present a fully ab-initio, unbiased structure search of the configurational space of decorated C60 fullerenes and find that many of the hitherto postulated ground state structures are not ground states. We determine the energetically lowest configurations for decorations with a varying number of decorating atoms (2 ≤ n ≤ 32) for alkali metals, alkaline-earth metals as well as some other important elements and find that the dense uniform distribution of the decorating atoms over the surface of the C60 , desired for hydrogen storage, can be obtained only for a few elements. An understanding of the behavior of the decorating atoms can be obtained by analyzing their bonding characteristics via the electron localization function.
DOI: 10.24435/materialscloud:zt-39
title: Iterative unbiasing of quasi-equilibrium sampling

description: This repository contains the PLUMED-2 input files required to generate the data used in the ITRE publications. ITRE is a method to reweight Molecular Dynamics trajectory biased with a history-dependent potential (such as Metadynamics), and calculate unbiased thermodynamic observables. Since it uses the trajectory itself as a proxy of a grid, its scaling does not depend on the dimensionality of the space explored. In addition, thanks to its formulation, it is less affected by out-of-equilibrium points that characterize the early stages of a biased calculation and are usually discarded. Thanks to this feature, it can be used to increase the statistics when evaluating a thermodynamic observable from biased calculation.
DOI: 10.24435/materialscloud:87-wp
title: Property map collective variable as a useful tool for force field correction

description: Molecular mechanics potentials for small molecules suffer inaccuracies. To apply corrections we used a concept called property map to calculate corrections. It was calculated as a sum of [correction_i exp(-lambda D(x, x_i))] divided by the sum of [exp(-lambda D(x, x_i))], where correction_i is the difference between the accurate and inaccurate potential for i-th landmark structure x_i, lambda is a chosen prefactor, D is a distance (e.g. RMSD or MSD) and x are atomic coordinates. The concept was tested on alanine dipeptide (all combinations of 7 force fields, one used as a model of accurate and one as inaccurate). Next it was applied on an anticancer drug Imatinib (General AMBER Force Field corrected to DFT).
Simulations were carried out in Gromacs 2016.4. DFTB/MM simulation was carried out in CP2K 7.1. Correction was Implemented using Plumed 2.4. DFT energies were calculated by ORCA 4.0 at the BP86/def2-TZVP level of theory.
DOI: 10.24435/materialscloud:bx-gb
title: Property map collective variable as a useful tool for force field correction

description: Molecular mechanics potentials for small molecules suffer inaccuracies. To apply corrections we used a concept called property map to calculate corrections. It was calculated as a sum of [correction_i exp(-lambda D(x, x_i))] divided by the sum of [exp(-lambda D(x, x_i))], where correction_i is the difference between the accurate and inaccurate potential for i-th landmark structure x_i, lambda is a chosen prefactor, D is a distance (e.g. RMSD or MSD) and x are atomic coordinates. The concept was tested on alanine dipeptide (all combinations of 7 force fields, one used as a model of accurate and one as inaccurate). Next it was applied on an anticancer drug Imatinib (General AMBER Force Field corrected to DFT).
Simulations were carried out in Gromacs 2016.4. DFTB/MM simulation was carried out in CP2K 7.1. Correction was Implemented using Plumed 2.4. DFT energies were calculated by ORCA 4.0 at the BP86/def2-TZVP level of theory.
DOI: 10.24435/materialscloud:2019.0037/v1
title: On-surface light-induced generation of higher acenes and elucidation of their open-shell character

description: In this work we demonstrate the on surface synthesis of  nonacene and heptacene and we discuss their open shell character comparing experimental evidence to theoretical predictions. The record contains input files to reproduce the calculations discussed in the manuscript and the raw data of the experimental images discussed.
DOI: 10.24435/materialscloud:6m-mv
title: On-surface light-induced generation of higher acenes and elucidation of their open-shell character

description: In this work we demonstrate the on surface synthesis of  nonacene and heptacene and we discuss their open shell character comparing experimental evidence to theoretical predictions. The record contains input files to reproduce the calculations discussed in the manuscript and the raw data of the experimental images discussed.
DOI: 10.24435/materialscloud:2020.0045/v1
title: Origin of high strength in the CoCrFeNiPd high-entropy alloy

description: Recent experiments show that the CoCrFeNiPd high-entropy alloy (HEA) is significantly stronger than CoCrFeNi and with nanoscale composition fluctuations beyond those expected for random alloys. These fluctuations were suggested to be responsible for strengthening. Here, a recent parameter-free theory for initial yield strength in fcc random alloys is shown to predict the strength of CoCrFeNiPd in good agreement with experiments. The strengthening is due mainly to the large misfit volume of Pd in CoCrFeNi, indicating that the effects of the non-random composition fluctuations are secondary. Analyses of strength variations and strengthening-associated length scales help rationalize why dislocation motion is insensitive to such fluctuations. These findings point to the value of theory for understanding the mechanical behavior of HEAs.
DOI: 10.24435/materialscloud:ff-zb
title: Ab initio real-time quantum dynamics of charge carriers in momentum space

description: Application of the nonadiabatic molecular dynamics (NAMD) approach is severely limited to studying carrier dynamics in the momentum space, since a supercell is required to sample the phonon excitation and electron-phonon (e-ph) interaction at different momenta in a molecular dynamics simulation. Here, we develop an ab initio approach for the real-time quantum dynamics for charge carriers in the momentum space (NAMD_k) by directly introducing the e-ph coupling into the Hamiltonian based on the harmonic approximation. The NAMD_k approach maintains the quantum zero-point energy and proper phonon dispersion, and includes memory effects of phonon excitation. The application of NAMD_k to the hot carrier dynamics in graphene reveals the phonon-specific relaxation mechanism. An energy threshold of 0.2eV, defined by two optical phonon modes strongly coupled to the electrons, separates the hot electron relaxation into fast and slow regions with the lifetimes of pico- and nano-seconds, respectively. The NAMD_k approach provides a powerful tool to understand real-time carrier dynamics in the momentum space for different materials.
DOI: 10.24435/materialscloud:vr-3x
title: Origin of high strength in the CoCrFeNiPd high-entropy alloy

description: Recent experiments show that the CoCrFeNiPd high-entropy alloy (HEA) is significantly stronger than CoCrFeNi and with nanoscale composition fluctuations beyond those expected for random alloys. These fluctuations were suggested to be responsible for strengthening. Here, a recent parameter-free theory for initial yield strength in fcc random alloys is shown to predict the strength of CoCrFeNiPd in good agreement with experiments. The strengthening is due mainly to the large misfit volume of Pd in CoCrFeNi, indicating that the effects of the non-random composition fluctuations are secondary. Analyses of strength variations and strengthening-associated length scales help rationalize why dislocation motion is insensitive to such fluctuations. These findings point to the value of theory for understanding the mechanical behavior of HEAs.
DOI: 10.24435/materialscloud:2020.0029/v1
title: In silico discovery of covalent organic frameworks for carbon capture

description: We screen a database of more than 69,000 hypothetical covalent organic frameworks (COFs) for carbon capture, using parasitic energy as a metric. In order to compute CO2-framework interactions in molecular simulations, we develop a genetic algorithm to tune the charge equilibration method and derive accurate framework partial charges. Nearly 400 COFs are identified with parasitic energy lower than that of an amine scrubbing process using monoethanolamine; over 70 are better performers than the best experimental COFs; and several perform similarly to Mg-MOF-74. We analyze the effect of pore topology on carbon capture performance in order to guide development of improved carbon capture materials.
DOI: 10.24435/materialscloud:dz-84
title: In silico discovery of covalent organic frameworks for carbon capture

description: We screen a database of more than 69,000 hypothetical covalent organic frameworks (COFs) for carbon capture, using parasitic energy as a metric. In order to compute CO2-framework interactions in molecular simulations, we develop a genetic algorithm to tune the charge equilibration method and derive accurate framework partial charges. Nearly 400 COFs are identified with parasitic energy lower than that of an amine scrubbing process using monoethanolamine; over 70 are better performers than the best experimental COFs; and several perform similarly to Mg-MOF-74. We analyze the effect of pore topology on carbon capture performance in order to guide development of improved carbon capture materials.
DOI: 10.24435/materialscloud:vy-yg
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:2020.0036/v1
title: Vibrational hierarchy leads to dual-phonon transport in low thermal conductivity crystals

description: Many low-thermal-conductivity (κL) crystals show intriguing temperature (T) dependence of κL: κL∝T-1 (crystal-like) at intermediate temperatures whereas weak T-dependence (glass-like) at high temperatures. It has been in debate whether thermal transport can still be described by phonons at the Ioffe-Regel limit. In this work, we propose that most phonons are still well defined for thermal transport, whereas they carry heat via dual channels: "normal" phonons described by the Boltzmann transport equation theory and "diffuson-like" phonons described by the diffusion theory. Three physics-based criteria are incorporated into first-principles calculations to judge mode-by-mode between the two phonon channels. Case studies on La2Zr2O7 and Tl3VSe4 show that normal phonons dominate low temperatures while diffuson-like phonons dominate high temperatures. Our present dual-phonon theory enlightens the physics of hierarchical phonon transport as approaching the Ioffe-Regel limit, and provides a numerical method that should be practically applicable to many materials with vibrational hierarchy.
DOI: 10.24435/materialscloud:2020.0001/v1
title: Generalized stacking fault energy curves for six body-centered cubic refractory metals

description: Density functional theory calculations were used to obtain the generalized stacking fault energy curves in six BCC metals: Cr, Mo, Nb, Ta, V, and W. Among them, antiferromagnetism was considered only in Cr. Results based on non-magnetic Cr are denoted as Cr-NM.
DOI: 10.24435/materialscloud:9y-jp
title: Vibrational hierarchy leads to dual-phonon transport in low thermal conductivity crystals

description: Many low-thermal-conductivity (κL) crystals show intriguing temperature (T) dependence of κL: κL∝T-1 (crystal-like) at intermediate temperatures whereas weak T-dependence (glass-like) at high temperatures. It has been in debate whether thermal transport can still be described by phonons at the Ioffe-Regel limit. In this work, we propose that most phonons are still well defined for thermal transport, whereas they carry heat via dual channels: "normal" phonons described by the Boltzmann transport equation theory and "diffuson-like" phonons described by the diffusion theory. Three physics-based criteria are incorporated into first-principles calculations to judge mode-by-mode between the two phonon channels. Case studies on La2Zr2O7 and Tl3VSe4 show that normal phonons dominate low temperatures while diffuson-like phonons dominate high temperatures. Our present dual-phonon theory enlightens the physics of hierarchical phonon transport as approaching the Ioffe-Regel limit, and provides a numerical method that should be practically applicable to many materials with vibrational hierarchy.
DOI: 10.24435/materialscloud:b2-hw
title: Generalized stacking fault energy curves for six body-centered cubic refractory metals

description: Density functional theory calculations were used to obtain the generalized stacking fault energy curves in six BCC metals: Cr, Mo, Nb, Ta, V, and W. Among them, antiferromagnetism was considered only in Cr. Results based on non-magnetic Cr are denoted as Cr-NM.
DOI: 10.24435/materialscloud:2020.0014/v1
title: Solvent-mediated morphology selection of the active pharmaceutical ingredient isoniazid: Experimental and simulation studies

description: In solution crystallization, solvent has a profound effect on controlling crystal morphology. However, the role played by solvents in affecting crystal morphology remains elusive. Here, we accompany experiments with molecular dynamics simulations to investigate crystallization of an anti-tuberculosis drug, isoniazid, in different solvents. Experiments show that isoniazid grows as needle-like crystals in water, while in alcohols such as methanol, ethanol and isopropanol, it exhibits a rod-like crystal habit. The aspect ratio of isoniazid crystals decreases with the decrease in the relative solvent polarity. We modeled these experiments by performing molecular dynamics simulations of isoniazid crystallization in different solvents at constant chemical potential thus keeping the solution concentration constant. The simulation results reveal a rough growth mechanism for the fast growing (1 1 0) surface, and bulk transport of the solute from solution to the growing surface is the limiting-step. In accordance with experiments, the relative growth rate of this surface decreases from methanol, ethanol to isopropanol. On the other hand, the slow growing (0 0 2) surface appears to follow a stepwise growth mechanism, with a surface integration step chiefly controlling the growth. The relative growth rate of this surface increases from methanol to ethanol and isopropanol.
DOI: 10.24435/materialscloud:2020.0049/v1
title: Improving accuracy of biased Alchemistic simulations

description: Alchemistic simulations are versatile tools for prediction of relative free energy differences. Accuracy of these methods depends critically on sampling of orthogonal (non-Alchemistic) degrees of freedom. Here we apply flying Gaussian method to accelerate such orthogonal degree of freedom – peptide bond cis/trans iso-merisation.  The approach is demonstrated on prediction of pKa value of N-acetylproline. Isomerization of the amide bond was accelerated in this simulation by multiple orders of magnitude.  Alchemistic free energy was obtained by reweighting.  We also demonstrate that the accuracy of biased Alchemistic simulations can be significantly improved by a simple redefinition of the thermodynamic cycle using a flattening.  Such redefinition can be applied a posteriori to improve the accuracy of biased Alchemistic simulations.
DOI: 10.24435/materialscloud:2m-yp
title: Solvent-mediated morphology selection of the active pharmaceutical ingredient isoniazid: Experimental and simulation studies

description: In solution crystallization, solvent has a profound effect on controlling crystal morphology. However, the role played by solvents in affecting crystal morphology remains elusive. Here, we accompany experiments with molecular dynamics simulations to investigate crystallization of an anti-tuberculosis drug, isoniazid, in different solvents. Experiments show that isoniazid grows as needle-like crystals in water, while in alcohols such as methanol, ethanol and isopropanol, it exhibits a rod-like crystal habit. The aspect ratio of isoniazid crystals decreases with the decrease in the relative solvent polarity. We modeled these experiments by performing molecular dynamics simulations of isoniazid crystallization in different solvents at constant chemical potential thus keeping the solution concentration constant. The simulation results reveal a rough growth mechanism for the fast growing (1 1 0) surface, and bulk transport of the solute from solution to the growing surface is the limiting-step. In accordance with experiments, the relative growth rate of this surface decreases from methanol, ethanol to isopropanol. On the other hand, the slow growing (0 0 2) surface appears to follow a stepwise growth mechanism, with a surface integration step chiefly controlling the growth. The relative growth rate of this surface increases from methanol to ethanol and isopropanol.
DOI: 10.24435/materialscloud:v0-n3
title: Improving accuracy of biased Alchemistic simulations

description: Alchemistic simulations are versatile tools for prediction of relative free energy differences. Accuracy of these methods depends critically on sampling of orthogonal (non-Alchemistic) degrees of freedom. Here we apply flying Gaussian method to accelerate such orthogonal degree of freedom – peptide bond cis/trans iso-merisation.  The approach is demonstrated on prediction of pKa value of N-acetylproline. Isomerization of the amide bond was accelerated in this simulation by multiple orders of magnitude.  Alchemistic free energy was obtained by reweighting.  We also demonstrate that the accuracy of biased Alchemistic simulations can be significantly improved by a simple redefinition of the thermodynamic cycle using a flattening.  Such redefinition can be applied a posteriori to improve the accuracy of biased Alchemistic simulations.
DOI: 10.24435/materialscloud:2020.0033/v1
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).