Sergey Pozdnyakov,
Michael Willatt,
Michele Ceriotti
- Most of the datasets to benchmark machine-learning models contain minimum-energy structures, or small fluctuations around stable geometries, and focus on the diversity of chemical compositions, or the presence of different phases. This dataset provides a large number (7732488) configurations for a simple CH4 composition, that are generated in an almost completely unbiased fashion. Hydrogen atoms are randomly distributed in a 3A sphere centered around the carbon atom, and the only structures that are discarded are those with atoms that are closer than 0.5A, or such that the reference DFT calculation does not converge.
This dataset is ideal to benchmark structural representations and regression algorithms, verifying whether they allow reaching arbitrary accuracy in the data rich regime.
Latest version: v2
Publication date: Sep 18, 2020
Maria Fumanal,
Andres Ortega-Guerrero,
Kevin Maik Jablonka,
Berend Smit,
Ivano Tavernelli
- Metal-Organic Frameworks (MOFs) are highly versatile materials owing to their vast structural and chemical tunability. These hybrid inorganic-organic crystalline materials offer an ideal platform to incorporate light-harvesting and catalytic centers and thus, exhibit a great potential to be exploited in solar-driven photocatalytic processes such as H2 production and CO2 reduction. To be photocatalytically active, UV-visible optical absorption and appropriate band alignment with respect to the target redox potential is required. Despite fulfilling these criteria, the photocatalytic performance of MOFs is still limited by their ability to produce long-lived electron-hole pairs and long-range charge transport. In this work, we present a computational strategy to address these two descriptors in MOF structures and translate them into charge transfer numbers and effective mass values. We apply our approach to 15 MOF structures from the literature that encompass the main strategies used ...
Latest version: v1
Publication date: Sep 17, 2020
Alexey Tal,
Peitao Liu,
Georg Kresse,
Alfredo Pasquarello
- We investigate optical absorption spectra obtained through time-dependent density functional theory (TD-DFT) based on nonempirical hybrid functionals that are designed to correctly reproduce the dielectric function. The comparison with state-of-the-art GW calculations followed by the solution of the Bethe-Salpeter equation (BSE-GW) shows close agreement for both the transition energies and the main features of the spectra. We confront TD-DFT with BSE-GW by focusing on the model dielectric function and the local exchange-correlation kernel. The present TD-DFT approach achieves the accuracy of BSE-GW at a fraction of the computational cost.
Latest version: v1
Publication date: Sep 11, 2020
Daniele Ongari,
Aliaksandr V. Yakutovich,
Leopold Talirz,
Berend Smit
- We present a workflow that traces the path from the bulk structure of a crystalline material to assessing its performance in carbon capture from coal’s postcombustion flue gases. This workflow is applied to a database of 324 covalent−organic frameworks (COFs) reported in the literature, to characterize their CO2 adsorption properties using the following steps:
(1) optimization of the crystal structure (atomic positions and unit cell) using density functional theory,
(2) fitting atomic point charges based on the electron density,
(3) characterizing the pore geometry of the structures before and after optimization,
(4) computing carbon dioxide and nitrogen isotherms using grand canonical Monte Carlo simulations with an empirical interaction potential, and finally,
(5) assessing the CO2 parasitic energy via process modeling.
The full workflow has been encoded in the Automated Interactive Infrastructure and Database for Computational Science (AiiDA). Both the workflow and the ...
Latest version: v6
Publication date: Sep 09, 2020
Jiawei Zhou,
Te-Huan Liu,
Qichen Song,
Qian Xu,
Zhiwei Ding,
Bolin Liao,
Gang Chen
- We publish our code for electron transport and thermoelectric property calculations in solid state materials. This code is modified based on the EPW v4 code, originally from the open-source Quantum ESPRESSO suite (version 5.4.0), and is released under GNU General Public License. The original EPW v4 is developed by S. Poncé, E.R. Margine, C. Verdi, and, F. Giustino, initially released inside Quantum ESPRESSO in 2016. This modified version is dedicated to the simulation of electron-phonon transport properties in quantum materials. Specifically, it calculates the electron-phonon and electron-defect scattering rates and uses them as inputs in Boltzmann transport equation to obtain transport properties (e.g. electrical conductivity, mobility, Seebeck coefficient, thermoelectric power factor, and electronic thermal conductivity).
Latest version: v1
Publication date: Sep 08, 2020
Michael A. Hope,
Bowen Zhang,
Bonan Zhu,
David M. Halat,
Judith L. MacManus-Driscoll,
Clare P. Gray
- Vertically aligned nanocomposite (VAN) films, comprising nanopillars of one phase embedded in a matrix of another, have shown great promise for a range of applications due to their high interfacial areas oriented perpendicular to the substrate. In particular, oxide VANs show enhanced oxide-ion conductivity in directions that are orthogonal to those found in more conventional thin-film heterostructures, however the structure of the interfaces and its influence on conductivity remain unclear. In this work 17O NMR spectroscopy is used to study CeO2–SrTiO3 VAN thin films: selective isotopic enrichment is combined with a lift-off technique to remove the substrate, facilitating detection of the 17O NMR signal from single atomic layer interfaces. By performing the isotopic enrichment at variable temperatures, the superior oxide-ion conductivity of the VAN films compared to the bulk materials is shown to arise from enhanced oxygen mobility at this interface; oxygen motion at the interface ...
Latest version: v1
Publication date: Sep 04, 2020
Kevin Maik Jablonka,
Daniele Ongari,
Seyed Mohamad Moosavi,
Berend Smit
- Knowledge of the oxidation state of a metal centre in a material is essential to understand its properties. Chemists have developed theories to predict the oxidation state based on counting rules, which can fail to describe the oxidation states of systems such as metal-organic frameworks.
Here we present a data-driven approach to automatically assign oxidation states, using a machine learning model trained on assignments by chemists encoded in the chemical names in the Cambridge Crystallographic Database.
Our approach only considers the immediate local environment around a metal centre, and is robust to experimental uncertainties (like incorrect protonation, unbound solvents, or changes in bondlength).
We find such excellent accuracy in our predictions that we can use our method to detect incorrect assignments.
This work nicely illustrates how powerful the collective knowledge of chemists is. Machine learning can harvest this knowledge and convert it into a useful tool for chemists.
Latest version: v2
Publication date: Sep 03, 2020
Ethan Berger,
Julia Wiktor,
Alfredo Pasquarello
- The dielectric properties of tetragonal hybrid perovskite CH3NH3PbI3 are studied through molecular dynamics at a temperature of 300 K in the presence of a finite electric field. The high-frequency dielectric constant ε∞ is found to be 4.5 along the a axis and 4.7 along the c axis. The values of the respective static dielectric constants ε0 are 43 ± 1 and 53 ± 3, much larger than the value of ∼25 pertaining to the orthorhombic phase, in which the organic cations cannot rotate. At frequencies below 3 cm–1, we observe a significant increase in ε0 by ∼23 (a axis) and ∼30 (c axis) compared to a vibrational approach, which does not account for the reorientation of the molecular units. The decomposition shows that the reorientation of the organic cations accounts for an increase of only ∼10. An increase of similar size results from the displacement of the cations within the cages of the lattice. The dominant contribution is found to arise from lattice vibrations coupled to the motion of the organic cations.
Latest version: v1
Publication date: Sep 02, 2020
Ting-Hang Pei
- The superconductor theory based on the electron pair is reviewed and several viewpoints are proposed. A demonstrated case reveals the speed of each electron in the electron pair at Fermi level about 1.82x10^6 m/s in Pb. However, the fastest longitudinal and transverse speeds of crystal waves in Pb at 0 K are 2.18x10^3 m/s and 1.29x10^3 m/s in [100] direction, respectively. It seems to be very hard even impossible that the mediated phonon can real-time transfer momentum and energy between two so high-speed and antiparallel-momentum electrons in the superconducting state. In this research, we focus on single electron based on the experiments of Transmission Electron Microscopy. The new fitting temperature-dependent model for the London penetration depth is proposed. This model is much better than the one- and two-gap models and matches three experimental data much well. Then it further gives the temperature-dependent effective electron mass for the Nb superconductor film. Finally, ...
Latest version: v2
Publication date: Sep 02, 2020
Pablo G. Lustemberg,
Philipp Pleßow,
Yuemin Wang,
Chengwu Yang,
Alexei Nefedov,
Felix Studt,
Christof Wöll,
M. Verónica Ganduglia-Pirovano
- In ceria-based catalysis, the shape of the catalyst particle, which determines the exposed crystal facets, profoundly affects its reactivity. The vibrational frequency of adsorbed carbon monoxide (CO) can be used as a sensitive probe to identify the exposed surface facets, provided reference data on well-defined single crystal surfaces together with a definitive theoretical assignment exist. We investigate the adsorption of CO on the CeO2 (110) and (111) surfaces and show that the commonly applied DFT(PBE)+U method does not provide reliable CO vibrational frequencies by comparing with state-of-the-art infrared spectroscopy experiments for monocrystalline CeO2 surfaces. Good agreement requires the hybrid DFT approach with the HSE06 functional. The failure of conventional DFT is explained in terms of its inability to accurately describe the facet- and configuration-specific donation and backdonation effects that control the changes in the C-O bond length upon CO adsorption and the ...
Latest version: v1
Publication date: Aug 27, 2020
Yu Xie,
Jonathan Vandermause,
Lixin Sun,
Andrea Cepellotti,
Boris Kozinsky
- Gaussian process (GP) regression is one promising technique of constructing machine learning force fields with built-in uncertainty quantification, which can be used to monitor the quality of model predictions. A current limitation of existing GP force fields is that the prediction cost grows linearly with the size of the training data set, making accurate GP predictions slow.
In this work, we exploit the special structure of the kernel function to construct a mapping of the trained Gaussian process model, including both forces and their uncertainty predictions, onto spline functions of low-dimensional structural features. This method is incorporated in the Bayesian active learning workflow for training of Bayesian force fields.
To demonstrate the capabilities of this method, we construct a force field for stanene and perform large scale dynamics simulation of its structural evolution.
We provide a fully open-source implementation of our method, as well as the training and testing examples with the stanene dataset.
Latest version: v2
Publication date: Aug 24, 2020
Maria Fumanal,
Clémence Corminboeuf,
Berend Smit,
Ivano Tavernelli
- The vast chemical space of metal and ligand combinations in Transition Metal Complexes (TMCs) gives rise to a rich variety of electronic excited states with local and non-local character such as intra-ligand (IL), metal-centered (MC), metal-to-ligand (MLCT) or ligand-to-metal charge-transfer (LMCT) states. Those features are equally found in Metal Organic Frameworks (MOFs), defined as modular materials built from metal-nodes connected through organic-ligands. Because of the electronic and structural complexity of MOFs, the computational description of their excited states is a formidable challenge for which two different approaches have been usually followed: the solid state and the molecular perspective. The first consists in analysing the frontier electronic bands and crystal orbitals of the electronic ground state (GS) in periodic boundary conditions, while the latter points to an accurate computation of the excited states in representative clusters at the molecular level. ...
Latest version: v1
Publication date: Aug 24, 2020
Francesco Libbi,
Nicola Bonini,
Nicola Marzari
- Lattice dynamics in low-dimensional materials and, in particular, the quadratic behaviour of the flexural acoustic modes play a fundamental role in their thermomechanical and thermal transport properties. A first-principles evaluation of these can be computationally very demanding, and can be affected by numerical noise which breaks translational and/or rotational invariance. In order to overcome these challenges in honeycomb lattices, we consider the Gartstein internal-coordinate potential where we tune its 13 parameters on first-principles calculations of the interatomic force constants for graphene. We show that the resulting potential not only reproduces very well the phonon dispersions of graphene, but that it can also describe the vibrational properties of carbon nanotubes of any diameter and chirality, without any additional modifications to its analytic expression or parametrization. In addition, one can augment its functional form with a single cubic term that allows also ...
Latest version: v1
Publication date: Aug 24, 2020
Hossein Ghorbanfekr,
Jörg Behler,
François M. Peeters
- Water permeation between stacked layers of hBN sheets forming 2D nanochannels is investigated using large-scale ab initio-quality molecular dynamics simulations. A high-dimensional neural network potential trained on density functional theory calculations is employed. We simulate water in van der Waals nanocapillaries and study the impact of nanometric confinement on the structure and dynamics of water using both equilibrium and nonequilibrium methods. At an interlayer distance of 10.2 Å confinement induces a first-order phase transition resulting in a well-defined AA-stacked bilayer of hexagonal ice. In contrast, for h < 9 Å, the 2D water monolayer consists of a mixture of different locally ordered patterns of squares, pentagons, and hexagons. We found a significant change in the transport properties of confined water, particularly for monolayer water where the water−solid friction coefficient decreases to half and the diffusion coefficient increases by a factor of 4 as compared ...
Latest version: v1
Publication date: Aug 16, 2020
Philipp Rüßmann,
Fabian Bertoldo,
Stefan Blügel
- We present JuDiT (Jülich Database of impurities embedded into a Topological insulator) which collects first principles calculation of impurities embedded into the prototypical topological insulator Sb2Te3. The density functional calculations of this work were performed with the JuKKR package [1], which allows to embed translational invariance breaking impurities into a crystalline host system based on the Korringa-Kohn-Rostoker Green function method, and were performed with the AiiDA-KKR package [2]. Our database collects, among others, predicted impurity properties like charge doping introduced by the defects, magnetic moments of the impurities and impurity density of states calculations. We include calculations for the intrinsic Fermi level in the middle of the bulk band gap as well as for shifted Fermi level into valence and conduction band which models different experimental conditions. The impurities were embedded into different layers throughout a 6 quintuple layer thick ...
Latest version: v2
Publication date: Aug 14, 2020
Sai Lyu,
Alfredo Pasquarello
- 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.
Latest version: v1
Publication date: Aug 14, 2020
Michael S. Chen,
Tobias Morawietz,
Thomas E. Markland,
Nongnuch Artrith
- This data set contains atomic structures of liquid water and amorphous Li(x)Si in the XCrySDen structure format (XSF) [1]. Total energies are included as additional meta information. The extended XSF format is compatible with the Atomic Energy Network (ænet) package [2,3] for artificial neural network (ANN) potential construction and application.
Liquid water: The liquid water data set comprises energies and forces of 9,189 condensed-phase structures. The data was obtained in an iterative procedure described in detail in Ref. [4]. The final ANN potential was employed in Refs. [4,5].
Initial structures (iteration 0) were obtained from classical and path integral AIMD simulations of bulk liquid water in a cubic box containing 64 water molecules at 300 K as reported in Ref. [6]. Distorted configurations with higher forces were added by randomly displacing the Cartesian coordinates. Iteration 1 contains 500 configurations from MD simulations with the fully flexible SPC/E flex water ...
Latest version: v1
Publication date: Aug 13, 2020
Matthew D. Wodrich,
Alberto Fabrizio,
Benjamin Meyer,
Clemence Corminboeuf
- Transitioning from small-scale to big-data studies has the potential to reveal new layers of intricacy that better facilitate and rationalize catalytic behavior. Given the computational resources available today, data-driven approaches can propel the next leap forward in catalyst design. Using a data-driven inspired workflow consisting of data generation, statistical analysis, and dimensionality reduction algorithms we explore trends surrounding the thermodynamics of a model hydroformylation reaction catalyzed by group 9 metals bearing phosphine ligands. Specifically, we introduce a type of “augmented” volcano plot, the energetic profile similarity (EPSim) map, as a means to easily visualize the similarity of each catalyst’s complete catalytic cycle energy profile to that of a hypothetical ideal reference profile without relying upon linear scaling relationships. In addition to quickly identifying catalysts that most closely match the ideal thermodynamic catalytic cycle energy ...
Latest version: v1
Publication date: Aug 13, 2020
Wenwen Li,
Yasunodu Ando,
Satoshi Watanabe
- Amorphous alumina (a-AlOx), which plays important roles in several technological fields, shows wide variation of the density and composition. However, their influences on the properties of a-AlOx have rarely been investigated from a theoretical perspective. In this study, high dimensional neural network (NN) potentials were constructed to generate a series of atomic structures of a-AlOx with different densities (2.6–3.3 g/cm3) and O/Al ratios (1.0–1.75). The structural, vibrational, mechanical, and thermal properties of the a-AlOx models were investigated, as well as the Li and Cu diffusion behaviour in the models. The results showed that the density and composition had different degrees of effects on the different properties. The structural and vibrational properties were strongly affected by the composition, whereas the mechanical properties were mainly determined by the density. The thermal conductivity was affected by both the density and composition of a-AlOx. However, the ...
Latest version: v1
Publication date: Aug 03, 2020
Daniel Marchand,
Abhinav Jain,
Albert Glensk,
W. A. Curtin
- High-strength metal alloys achieve their performance via careful control of precipitates and solutes. The nucleation, growth, and kinetics of precipitation, and the resulting mechanical properties, are inherently atomic-scale phenomena, particularly during early-stage nucleation and growth. Atomistic modeling using interatomic potentials is a desirable tool for understanding the detailed phenomena involved in precipitation and strengthening, which requires length and time scales far larger than those accessible by first-principles methods. Current interatomic potentials for alloys are not, however, sufficiently accurate for such studies. Here, a family of neural-network potentials (NNPs) for the Al-Cu system is presented as a first example of a machine-learning potential that can achieve near-first-principles accuracy for many different metallurgically-important aspects of this alloy. High fidelity predictions of intermetallic compounds, elastic constants, dilute ...
Latest version: v2
Publication date: Aug 03, 2020
Thibault Sohier,
Marco Gibertini,
Nicola Marzari
- When complex mechanisms are involved, pinpointing high-performance materials within large databases is a major challenge in materials discovery. We focus here on phonon-limited conductivities, and study 2D semiconductors doped by field effects. Using state-of-the-art density-functional perturbation theory and Boltzmann transport equation, we discuss 11 monolayers with outstanding transport properties.
These materials are selected from a computational database of exfoliable materials providing monolayers that are dynamically stable and that do not have more than 6 atoms per unit cell. We first analyze electron-phonon scattering in two well-known systems: electron-doped InSe and hole-doped phosphorene. Both are single-valley systems with weak electron-phonon interactions, but they represent two distinct pathways to fast transport: a steep and deep isotropic valley for the former and strongly anisotropic electron-phonon physics for the latter.
We identify similar features in the ...
Latest version: v1
Publication date: Jul 31, 2020
Antimo Marrazzo,
Marco Gibertini,
Davide Campi,
Nicolas Mounet,
Nicola Marzari
- Quantum spin Hall insulators (QSHIs) make up a class of two-dimensional materials with a finite electronic band gap in the bulk and gapless helical edge states. Some of the phenomena that can be hosted in these materials, from one-dimensional low-dissipation electronic transport to spin filtering, could be promising for many technological applications in the fields of electronics, spintronics, and topological quantum computing. Nevertheless, the rarity of two-dimensional materials that can exhibit nontrivial topological order at room temperature hinders development. In the publication, we report on our screening of a comprehensive database we recently identified of 1825 monolayers that can be exfoliated from experimentally known compounds to search for novel quantum spin Hall insulators. In this entry we provide the AiiDA database with the calculations of the DFT band structures (both with and without spin-orbit coupling) and the DFPT phonon dispersions for the QSHI candidates ...
Latest version: v2
Publication date: Jul 31, 2020
Zoran Bjelobrk,
Pablo M. Piaggi,
Thilo Weber,
Tarak Karmakar,
Marco Mazzotti,
Michele Parrinello
- We used molecular dynamics simulations to predict the steady state crystal shape of naphthalene grown from ethanol solution. The simulations were performed at constant supersaturation by utilizing a recently proposed algorithm [Perego et al., J. Chem. Phys., 2015, 142, 144113]. To bring the crystal growth within the timescale of a molecular dynamics simulation we applied well-tempered Metadynamics with a spatially constrained collective variable, which focuses the sampling on the growing layer. We estimated that the resulting steady state crystal shape corresponds to a rhombic prism, which is in line with experiments. Further, we observed that at the investigated supersaturations, the {00-1} face grows in a two step two dimensional nucleation mechanism while the considerably faster growing faces {1-10} and {20-1} grow new layers with a one step two dimensional nucleation mechanism.
Latest version: v1
Publication date: Jul 30, 2020
Shantanu Mishra,
Jason Melidonie,
Kristjan Eimre,
Sebastian Obermann,
Oliver Gröning,
Carlo A. Pignedoli,
Pascal Ruffieux,
Xinliang Feng,
Roman Fasel
- Zethrenes are model diradicaloids with potential applications in spintronics and optoelectronics. Despite a rich chemistry in solution, on-surface synthesis of zethrenes has never been demonstrated. This record contains data to support our recent publication where we report the on-surface synthesis of super-heptazethrene on Au(111). Scanning tunneling spectroscopy investigations reveal that super-heptazethrene exhibits an exceedingly low HOMO–LUMO gap of 230 meV and, in contrast to its open-shell singlet ground state in the solution phase and in the solid-state, likely adopts a closed-shell ground state on Au(111).
Latest version: v1
Publication date: Jul 29, 2020
Marco Di Giovannantonio,
Xuelin Yao,
Kristjan Eimre,
José I. Urgel,
Pascal Ruffieux,
Carlo A. Pignedoli,
Klaus Müllen,
Roman Fasel,
Akimitsu Narita
- Coronoids, polycyclic aromatic hydrocarbons with geometrically defined cavities, are promising model structures of porous graphene. This record contains data to support our recent research where we report the on-surface synthesis of C168 and C140 coronoids, referred to as [6]- and [5]coronoid, respectively, using 5,9-dibromo-14-phenylbenzo[m]tetraphene as the precursor. These coronoids entail large cavities (>1 nm) with inner zigzag edges, distinct from their outer armchair edges. While [6]coronoid is planar, [5]coronoid is not. Low-temperature scanning tunneling microscopy/spectroscopy and noncontact atomic force microscopy unveil structural and electronic properties in accordance with those obtained from density functional theory calculations. Detailed analysis of ring current effects identifies the rings with the highest aromaticity of these coronoids, whose pattern matches their Clar structure. The pores of the obtained coronoids offer intriguing possibilities of further functionalization toward advanced host–guest applications.
Latest version: v1
Publication date: Jul 29, 2020
Anders Christensen,
O. Anatole von Lilienfeld
- The original MD17 dataset (http://quantum-machine.org/datasets/#md-datasets) [Chemiela et al. Sci. Adv. 3(5), e1603015, 2017] contains numerical noise. Thus, any numbers presented from benchmarks on this data are likely flawed. Here, we present a new dataset with negligible numerical noise for benchmarking of forces and energy predictions for molecular dynamics simulations. As the structures are taken from a molecular dynamics simulation (i.e. time series data), they are not guaranteed to be independent samples. This is easily evident from the autocorrelation function for the original MD17 dataset. In short: DO NOT train a model on more than 1000 samples from the revised dataset, and do not train models for more than 50 samples from the original MD17 dataset. Data already published with 50K samples on the original MD17 dataset should be considered meaningless due to this fact and due to the noise in the original data.
Latest version: v1
Publication date: Jul 23, 2020
Michele Invernizzi,
Pablo Miguel Piaggi,
Michele Parrinello
- The sampling problem lies at the heart of atomistic simulations and over the years many different enhanced sampling methods have been suggested towards its solution. These methods are often grouped into two broad families. On the one hand methods such as umbrella sampling and metadynamics that build a bias potential based on few order parameters or collective variables. On the other hand tempering methods such as replica exchange that combine different thermodynamic ensembles in one single expanded ensemble. We adopt instead a unifying perspective, focusing on the target probability distribution sampled by the different methods. This allows us to introduce a new method that can sample any of the ensembles normally sampled via replica exchange, but does so in a collective-variables-based scheme. This method is an extension of the recently developed on-the-fly probability enhanced sampling method [Invernizzi and Parrinello, J. Phys. Chem. Lett. 11.7 (2020)] that has been previously ...
Latest version: v1
Publication date: Jul 20, 2020
Benjamin A. Helfrecht,
Rose K. Cersonsky,
Guillaume Fraux,
Michele Ceriotti
- Data analyses based on linear methods constitute the simplest, most robust, and transparent approaches to the automatic processing of large amounts of data for building supervised or unsupervised machine learning models. Principal covariates regression (PCovR) is an underappreciated method that interpolates between principal component analysis and linear regression, and can be used to conveniently reveal structure-property relations in terms of simple-to-interpret, low-dimensional maps. Here we introduce a kernelized version of PCovR and a sparsified extension, and demonstrate the performance of this approach in revealing and predicting structure-property relations in chemistry and materials science, showing a variety of examples including elemental carbon, porous silicate frameworks, organic molecules, amino acid conformers, and molecular materials.
Latest version: v1
Publication date: Jul 16, 2020
Shantanu Mishra,
Doreen Beyer,
Kristjan Eimre,
Shawulienu Kezilebieke,
Reinhard Berger,
Oliver Gröning,
Carlo A. Pignedoli,
Klaus Müllen,
Peter Liljeroth,
Pascal Ruffieux,
Xinliang Feng,
Roman Fasel
- The chemical versatility of carbon imparts manifold properties to organic compounds, where magnetism remains one of the most desirable but elusive. Polycyclic aromatic hydrocarbons, also referred to as nanographenes, show a critical dependence of electronic structure on the topologies of the edges and the π-electron network, which makes them model systems with which to engineer unconventional properties including magnetism. In 1972, Erich Clar envisioned a bow-tie-shaped nanographene, C38H18, where topological frustration in the π-electron network renders it impossible to assign a classical Kekulé structure without leaving unpaired electrons, driving the system into a magnetically non-trivial ground state. In this record we include data needed to support our recent work where we demonstrate the experimental realization and in-depth characterization of this emblematic nanographene, known as Clar’s goblet. Scanning tunnelling microscopy and spin excitation spectroscopy of individual ...
Latest version: v1
Publication date: Jul 15, 2020
Qiang Sun,
Oliver Gröning,
Jan Overbeck,
Oliver Braun,
Mickael L. Perrin,
Gabriela Borin Barin,
Maria El Abbassi,
Kristjan Eimre,
Edward Ditler,
Colin Daniels,
Vincent Meunier,
Carlo A. Pignedoli,
Michel Calame,
Roman Fasel,
Pascal Ruffieux
- Graphene nanoribbons (GNRs) have attracted much interest due to their largely modifiable electronic properties. Manifestation of these properties requires atomically precise GNRs which can be achieved through a bottom–up synthesis approach. This has recently been applied to the synthesis of width‐modulated GNRs hosting topological electronic quantum phases, with valence electronic properties that are well captured by the Su–Schrieffer–Heeger (SSH) model describing a 1D chain of interacting dimers. In this record we provide data to support our recent publication where we demonstrate that ultralow bandgap GNRs with charge carriers behaving as massive Dirac fermions can be realized when their valence electrons represent an SSH chain close to the topological phase boundary, i.e., when the intra‐ and interdimer coupling become approximately equal. Such a system has been achieved via on‐surface synthesis based on readily available pyrene‐based precursors and the resulting GNRs are ...
Latest version: v1
Publication date: Jul 15, 2020
Luis M. Mateo,
Qiang Sun,
Shi‐Xia Liu,
Jesse J. Bergkamp,
Kristjan Eimre,
Carlo A. Pignedoli,
Pascal Ruffieux,
Silvio Decurtins,
Giovanni Bottari,
Roman Fasel,
Tomas Torres
- On‐surface synthesis offers a versatile approach to prepare novel carbon‐based nanostructures that cannot be obtained by conventional solution chemistry. Graphene nanoribbons (GNRs) have potential for a variety of applications. A key issue for their application in molecular electronics is in the fine‐tuning of their electronic properties through structural modifications, such as heteroatom doping or the incorporation of non‐benzenoid rings.
In this record we provide data to support our recent publication that reports the covalent fusion of grapnene nanoribbons (GNRs) and porphyrins (Pors). We demonstrated selective on‐surface synthesis of a Por–GNR hybrid, which consists of two Pors connected by a short GNR segment. The atomically precise structure of the Por–GNR hybrid has been characterized by bond‐resolved scanning tunneling microscopy and noncontact atomic force microscopy. The electronic properties have been investigated by scanning tunneling spectroscopy, in combination with ...
Latest version: v1
Publication date: Jul 15, 2020
Qiang Sun,
Ian Cheng-Yi Hou,
Kristjan Eimre,
Carlo A. Pignedoli,
Pascal Ruffieux,
Akimitsu Narita,
Roman Fasel
- Azulene, the smallest neutral nonalternant aromatic hydrocarbon, serves not only as a prototype for fundamental studies but also as a versatile building block for functional materials because of its unique opto(electronic) properties. The record contains data to support our recent work where we report the on-surface synthesis and characterization of the homopolymer of azulene connected exclusively at the 2,6-positions using 2,6-diiodoazulene as the monomer precursor. Properties of carbon-based aromatic systems are sensitively determined by their bond topologies. So far, much attention has been paid to the design and synthesis of aromatic materials like conjugated polymers and nanographenes constituted by alternant hydrocarbons, which do not possess odd-membered rings. In contrast, incorporation of non-alternant hydrocarbons has only rarely been explored.
Latest version: v1
Publication date: Jul 15, 2020
J. Terence Blaskovits,
Maria Fumanal,
Sergi Vela,
Clémence Corminboeuf
- Singlet Fission (SF) has demonstrated significant promise for boosting the power conversion efficiency (PCE) of solar cells. Traditionally, SF is targeted as an intermolecular process, however its dependence on crystal packing makes molecular design difficult. In contrast, intramolecular SF (iSF) enables the exploration of tunable bi-chromophoric systems following well-defined structure-property relationships. In this work, we propose a set of parameters to screen conjugated donor-acceptor copolymer candidates with potential iSF behaviour. We focus our analysis on the E(S1)>2E(T1) thermodynamic condition and on the appropriate charge transfer (CT) character of S1. We map the CT character with respect to the frontier molecular orbital (FMO) energies of the constituent monomers, providing a cost-effective protocol for an accelerated screening of promising iSF donor-acceptor pairs, while minimizing the number of computations. These parameters are applied to a chemically diverse, ...
Latest version: v1
Publication date: Jul 13, 2020
Thomas Bischoff,
Igor Reshetnyak,
Alfredo Pasquarello
- We determine the band alignment at the CaF2/Si(111) interface through various advanced electronic-structure methods. This interface is experimentally well-studied and serves as an ideal test case to examine the accuracy of theoretical schemes. We use both global and range-separated hybrid functionals as well as GW calculations including self-consistency and vertex corrections. Our calculation procedure accounts for residual strain resulting from the small mismatch in the lateral lattice constants at the interface to minimize the systematic error in the comparison with experiment. Both the hybrid-functional and the GW schemes give band alignments in overall good agreement with the experimental characterization. However, the considered methods yield sizable variations in the calculated band offsets, which do not originate from incorrect evaluations of the band gaps but rather from different inherent relative positions of the band edges. The comparison with experiment reveals that ...
Latest version: v1
Publication date: Jul 13, 2020
Federico Grasselli,
Lars Stixrude,
Stefano Baroni
- The impact of the inner structure and thermal history of planets on their observable features, such as luminosity or magnetic field, crucially depends on the poorly known heat and charge transport properties of their internal layers. The thermal and electric conductivities of different phases of water (liquid, solid, and super-ionic) occurring in the interior of ice giant planets, such as Uranus or Neptune, are evaluated from equilibrium ab initio molecular dynamics, leveraging recent progresses in the theory and data analysis of transport in extended systems. In this record we collect the ab-initio time series of the energy flux and of the electronic and ionic charge fluxes for H2O at different planetary conditions, from which the related transport coefficients are extracted according to the Green-Kubo theory of linear response.
Latest version: v1
Publication date: Jul 13, 2020
Shujing Jia,
Min Zhu,
Huanglong Li,
Tamihiro Gotoh,
Christophe Longeaud,
Bin Zhang,
Juan Lyu,
Shilong Lv,
Zhitang Song,
Qi Liu,
John Robertson,
Ming Liu
- Selector devices are indispensable components of large-scale nonvolatile memory and neuromorphic array systems. Besides the conventional silicon transistor, two-terminal ovonic threshold switching (OTS) devices with much higher scalability are currently the most industrially favored selector technology. Despite industrial confidence in OTS selectors, current devices rely heavily on intricate control of material stoichiometry and generally suffer from toxic and complex dopants to remedy the intrinsic demerits of the principal functioning materials. Here, we report on a selector with a large drive current density of 34 MA/cm2 and a ~106 high nonlinearity, realized in an environment-friendly and earth-abundant sulfide binary semiconductor, GeS. Both experiments and first-principles calculations have revealed Ge pyramid-dominated network and high density of near-valence band trap states in amorphous GeS. The high drive current capacity is associated with the strong Ge-S covalency and ...
Latest version: v1
Publication date: Jul 10, 2020
Oleksandr Motornyi,
Nathalie Vast,
Iurii Timrov,
Oscar Baseggio,
Stefano Baroni,
Andrea Dal Corso
- The implementation of ultrasoft pseudopotentials into time-dependent density-functional perturbation theory is detailed for both the Sternheimer approach and the Liouville-Lanczos (LL) method, and equations are presented in the scalar relativistic approximation for periodic solids with finite momentum transfer q. The LL method is applied to calculations of the electron energy loss (EEL) spectrum of face-centered cubic bulk Au both at vanishing and finite q. Our study reveals the richness of the physics underlying the various contributions to the density fluctuation in gold. In particular, our calculations suggest the existence in gold of two quasiseparate 5d and 6s electron gasses, each one oscillating with its own frequency at, respectively, 5.1 eV and 10.2 eV. We find that the contribution near 2.2 eV comes from 5d to 6s interband transitions modified by the intraband contribution to the real part of the dielectric function, which we call a mixed excitation.
Latest version: v1
Publication date: Jul 07, 2020
Stefano Falletta,
Julia Wiktor,
Alfredo Pasquarello
- We develop a scheme for finite-size corrections of vertical transition energies and single-particle energy levels involving defect states with built-in ionic polarization in supercell calculations.The method accounts on an equal footing for the screening of the electrons and of the ionic polarization charge arising from the lattice distortions. We demonstrate the accuracy of our corrections for various defects in MgO and in water by comparing with the dilute limit achieved through the scaling of the system size. The general validity of our formulation is also confirmed through a sum rule that connects vertical transition energies with formation energies of structurally relaxed defects.
Latest version: v1
Publication date: Jul 07, 2020
Chiara Ricca,
Nicolas Niederhauser,
Ulrich Aschauer
- The functional properties of transition metal perovskite oxides are known to result from a complex interplay of magnetism, polarization, strain, and stoichiometry. Here, we show that for materials with a cooperative Jahn-Teller distortion, such as LaMnO3 (LMO), the orbital order can also couple to the defect chemistry and induce novel material properties. At low temperatures, LMO exhibits a strong Jahn-Teller distortion that splits the eg orbitals of the high-spin Mn3+ ions and leads to alternating long, short, and intermediate Mn-O bonds. Our DFT+U calculations show that, as a result of this orbital order, the charge localization in LMO upon oxygen vacancy formation differs from other manganites, like SrMnO3, where the two extra electrons reduce the two Mn sites adjacent to the vacancy. In LMO, relaxations around the defect depend on which type of Mn-O bond is broken, affecting the d-orbital energies and leading to asymmetric and hence polar excess electron localization with ...
Latest version: v1
Publication date: Jul 01, 2020
Seyed Mohamad Moosavi,
Aditya Nandy,
Kevin Maik Jablonka,
Daniele Ongari,
Jon Paul Janet,
Peter G. Boyd,
Yongjin Lee,
Berend Smit,
Heather J. Kulik
- By combining metal nodes and organic linkers one can make millions of different metal-organic frameworks (MOFs). At present over 90,000 MOFs have been synthesized and there are databases with over 500,000 predicted structures. This raises the question of whether a new experimental or predicted structure adds new information. For MOF-chemists the chemical design space is a combination of pore geometry, metal nodes, organic linkers, and functional groups, but at present we do not have a formalism to quantify optimal coverage of chemical design space. In this work, we show how machine learning can be used to quantify similarities of MOFs. This quantification allows us to use techniques from ecology to analyse the chemical diversity of these materials in terms of diversity metrics. In particular, we show that this diversity analysis can identify biases in the databases, and how such bias can lead to incorrect conclusions. This formalism provides us with a simple and powerful practical ...
Latest version: v1
Publication date: Jun 26, 2020
Kristiāns Čerņevičs,
Valeria Granata,
Oleg V. Yazyev
- TBETA provides a simple graphical interface for building structures of two-terminal junctions of graphene nanoribbons (GNRs) at angles 60°, 120° and 180°. The electronic structure and transport properties of the constructed junctions are calculated using the nearest-neighbour tight-binding model in combination with the Landauer-Büttiker formalism and Green's function techniques.
Latest version: v1
Publication date: Jun 23, 2020
Sarah Alamdari,
Jim Pfaendtner
- This record contains files necessary to reproduce enhanced sampling well-tempered metadynamics (wtMTD) and parallel tempering metadynamics in the well-tempered ensemble (PT-MetaD-WTE) simulations in PLUMED using GROMACS 2018.3.
Latest version: v1
Publication date: Jun 22, 2020
Kevin Rossi,
Veronika Juraskova,
Raphael Wischert,
Laurent Garel,
Clemence Corminboeuf,
Michele Ceriotti
- Set of inputs to perform the calculations reported in the paper.
The i-pi input enables to perform molecular dynamics / metadynamics / REMD / PIMD simulations, with adequate thermostats.
The DFTB and LAMMPS input respectively enable to calculate force and energies within the DFTB and Neural Network Forcefield frameworks.
The CP2K input files enable to calculate force and energies at PBE and PBE0 level. The latter is used as the reference to train the neural network correction on top of DFTB.
Brief description of the work: We present a generally-applicable computational framework for the efficient and accurate characterization of molecular structural patterns and acid properties in explicit solvent using H₂O₂ and CH₃SO₃H in phenol as an example. In order to address the challenges posed by the complexity of the problem, we resort to a set of data-driven methods and enhanced sampling algorithms. The synergistic application of these techniques makes the first-principle estimation of ...
Latest version: v1
Publication date: Jun 22, 2020
Chiara Ricca,
Iurii Timrov,
Matteo Cococcioni,
Nicola Marzari,
Ulrich Aschauer
- 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 ...
Latest version: v2
Publication date: Jun 22, 2020
Iurii Timrov,
Piyush Agrawal,
Xinyu Zhang,
Selma Erat,
Riping Liu,
Artur Braun,
Matteo Cococcioni,
Matteo Calandra,
Nicola Marzari,
Daniele Passerone
- We present a joint theoretical and experimental study of the oxygen K-edge spectra for LaFeO₃ and homovalent Ni-substituted LaFeO₃ (LaFe₀.₇₅Ni₀.₂₅O₃), using first-principles simulations based on density-functional theory with extended Hubbard functionals and x-ray absorption near edge structure (XANES) measurements. Ground-state and excited-state XANES calculations employ Hubbard on-site U and inter-site V parameters determined from first principles and the Lanczos recursive method to obtain absorption cross sections, which allows for a reliable description of XANES spectra in transition-metal compounds in a very broad energy range, with an accuracy comparable to that of hybrid functionals but at a substantially lower cost. We show that standard gradient-corrected exchange-correlation functionals fail in capturing accurately the electronic properties of both materials. In particular, for LaFe₀.₇₅Ni₀.₂₅O₃ they do not reproduce its semiconducting behaviour and provide a poor ...
Latest version: v1
Publication date: Jun 22, 2020
Valerio Vitale,
Giovanni Pizzi,
Antimo Marrazzo,
Jonathan R. Yates,
Nicola Marzari,
Arash A. Mostofi
- Maximally-localised Wannier functions (MLWFs) are routinely used to compute from first-principles advanced materials properties that require very dense Brillouin zone integration and to build accurate tight-binding models for scale-bridging simulations. At the same time, high-throughput (HT) computational materials design is an emergent field that promises to accelerate the reliable and cost-effective design and optimisation of new materials with target properties. The use of MLWFs in HT workflows has been hampered by the fact that generating MLWFs automatically and robustly without any user intervention and for arbitrary materials is, in general, very challenging. We address this problem directly by proposing a procedure for automatically generating MLWFs for HT frameworks. Our approach is based on the selected columns of the density matrix method (SCDM) and we present the details of its implementation in an AiiDA workflow. We apply our approach to a dataset of 200 bulk ...
Latest version: v3
Publication date: Jun 21, 2020
Samuel Poncé,
Elena Roxana Margine,
Feliciano Giustino
- We probe the accuracy limit of ab initio calculations of carrier mobilities in semiconductors, within the framework of the Boltzmann transport equation. By focusing on the paradigmatic case of silicon, we show
that fully predictive calculations of electron and hole mobilities require many-body quasiparticle corrections to band structures and electron-phonon matrix elements, the inclusion of spin-orbit coupling, and an extremely fine sampling of inelastic scattering processes in momentum space. By considering all these factors we obtain excellent agreement with experiment, and we identify the band effective masses as the most critical parameters to achieve predictive accuracy. Our findings set a blueprint for future calculations of carrier mobilities, and pave the way to engineering transport properties in semiconductors by design.
Latest version: v1
Publication date: Jun 21, 2020
Samuel Poncé,
Elena Roxana Margine,
Carla Verdi,
Feliciano Giustino
- The EPW (Electron-Phonon coupling using Wannier functions) software is a Fortran90 code that uses density-functional perturbation theory and maximally localized Wannier functions for computing
electron-phonon couplings and related properties in solids accurately and efficiently. The EPW v4 program can be used to compute electron and phonon self-energies, linewidths, electron-phonon scattering
rates, electron-phonon coupling strengths, transport spectral functions, electronic velocities, resistivity, anisotropic superconducting gaps and spectral functions within the Migdal-Eliashberg theory. The
code now supports spin-orbit coupling, time-reversal symmetry in non-centrosymmetric crystals, polar materials, and k and q-point parallelization. Considerable effort was dedicated to optimization and
parallelization, achieving almost a ten times speedup with respect to previous releases. A computer test farm was implemented to ensure stability and portability of the code on the most ...
Latest version: v1
Publication date: Jun 21, 2020
Rahul Bhowmik
- We have developed a polymer descriptor data set from the existing data. The data set has 188 descriptors which describe polymer atomic and molecular behavior. The descriptors are mapped to the specific heat of polymers using supervised and unsupervised machine learning approaches. The mapping helps predict the specific heat of polymers at room temperature. The descriptor data set is useful in synthesizing novel polymers with desired heat capacities.
Latest version: v1
Publication date: Jun 19, 2020
Max Veit,
David M. Wilkins,
Yang Yang,
Robert A. DiStasio Jr.,
Michele Ceriotti
- Molecular dipole moments of the QM7b dataset, a random sample of 21'000 molecules from the QM9 dataset, and the MuML showcase set (including the four challenge series) described in the linked publication.
Latest version: v1
Publication date: Jun 10, 2020
Guido Falk von Rudorff,
Stefan N. Heinen,
Marco Bragato,
O. Anatole von Lilienfeld
- For competing E2 and SN2 reactions, we report 4'400 validated transition state geometries and 143'200 reactant complex geometries including conformers obtained at MP2/6-311G(d) and DF-LCCSD/cc-pVTZ//MP2/6-311G(d) level of theory. The data covers the chemical compound space spanned by the substituents NO2, CN, CH3, and NH2 and early halogens (F, Cl, Br) as nucleophiles and leaving groups based on an ethane skeleton. Ready-to-use activation energies are given for the different levels of theory where in some cases relaxation effects have been treated with machine learning surrogate models.
Latest version: v1
Publication date: Jun 09, 2020
Adrien Bouhon,
QuanSheng Wu,
Robert-Jan Slager,
Hongming Weng,
Oleg V. Yazyev,
Tomáš Bzdušek
- Weyl semimetals in three-dimensional crystals provide the paradigm example of topologically protected band nodes. It is usually taken for granted that a pair of colliding Weyl points annihilate whenever they carry opposite chiral charges. In stark contrast, here we report that Weyl points in systems symmetric under the composition of time-reversal with a π-rotation are characterized by a non-Abelian topological invariant. The topological charges of the Weyl points are transformed via braid phase factors which arise upon exchange inside symmetric planes of the reciprocal momentum space. We elucidate this process with an elementary two-dimensional tight-binding model implementable in cold-atoms setups and in photonic systems. In three dimensions, interplay of the non-Abelian topology with point-group symmetry is shown to enable topological phase transitions in which pairs of Weyl points may scatter or convert into nodal-line rings. By combining our theoretical arguments with ...
Latest version: v1
Publication date: Jun 09, 2020
Edward Linscott,
Daniel Cole,
Nicholas Hine,
Michael Payne,
Cédric Weber
- We introduce the unification of dynamical mean field theory (DMFT) and linear-scaling density functional theory (DFT), as recently implemented in ONETEP, a linear-scaling DFT package, and TOSCAM, a DMFT toolbox. This code can account for strongly correlated electronic behavior while simultaneously including the effects of the environment, making it ideally suited for studying complex and heterogeneous systems that contain transition metals and lanthanides, such as metalloproteins. We systematically introduce the necessary formalism, which must account for the non-orthogonal basis set used by ONETEP. In order to demonstrate the capabilities of this code, we apply it to carbon monoxide-ligated iron porphyrin and explore the distinctly quantum-mechanical character of the iron 3d electrons during the process of photodissociation.
This archive record contains example input and output files for the DFT, DFT+U, and DFT+DMFT calculations presented in the associated journal article.
Latest version: v1
Publication date: May 28, 2020
Julia Vecchietti,
Pablo Lustemberg,
Esteban L. Fornero,
Mónica Calatayud,
Sebastián E. Collins,
Susanne Mohr,
M. Verónica Ganduglia-Pirovano,
Jörg Libuda,
Adrian L. Bonivardi
- The ethanol steam reforming reaction, together with the adsorption and decomposition of ethanol was studied on CeO2 and gallium-doped ceria (CeGaOx) by a combined experimental and theoretical approach using infrared spectroscopy (IR), mass spectrometry (MS) and density functional theory (DFT) calculations. At 100 °C, different types of monodentate ethoxy species were identified as standing-up (SU) on Ce4+ and lying-down (LD) on Ce4+ and Ga3+, with the alkyl chain more perpendicular or parallel to the surface, respectively. It is suggested that the incorporation of Ga into the ceria lattice changes the decomposition pathway of LD species, which converts to acetate instead of ethylene, attributed to the increased lattice oxygen lability in the Ce―O―Ga interface upon doping and the propensity to form Ga―H surface species. Under ethanol steam reforming conditions, Ga doping of ceria-based materials has a drastic effect by improving the H2:CO2 ratio, changing the product distribution and reducing coke formation.
Latest version: v1
Publication date: May 28, 2020
Max Schwilk,
Diana N. Tahchieva,
O. Anatole von Lilienfeld
- High-quality data sets of free carbenes have remained unavailable in the scientific literature so far. We provide approximately 5k and 8k verified carbene structures in their respective singlet or triplet state. Vertical spin gaps have been computed at higher order multireference level of theory (MRCISD+Q-F12/cc-pVDZ-F12). The carbenes presented are all derived through double hydrogen abstraction from saturated carbon centers of a subset obtained by randomly sampling the chemical space of approximately 300k carbene candidates possible within closed shell organic molecules in the QM9 data set.
Latest version: v1
Publication date: May 08, 2020
Tomáš Vašíček,
Vojtěch Spiwok,
Jakub Červený,
Lucie Petrásková,
Ladislav Bumba,
David Vrbata,
Helena Pelantová,
Vladimír Křen,
Pavla Bojarová
- Regioselective derivatization of oligosaccharides is a challenging issue in carbohydrate chemistry. A commonly required series of (de)protection steps substantially lowers synthetic yields and increases time demands. We present here a regioselective one-step introduction of benzylic substituents at 3-hydroxy moieties of beta-D-galactopyranosyl-(1<->1)-thio-beta-D-galactopyranoside (TDG) employing tin butyl oxide in fair isolated yields. These glycomimetics act as inhibitors of galectins - human lectins, which are biomedically attractive targets for therapeutic inhibition. The affinity of prepared glycomimetics to recombinant galectin-1 and galectin-3 was studied in ELISA-type assay and their inhibitory potential was also demonstrated on the surface of a model HEK293 cell line. The results of biological experiments were correlated with data from molecular modelling with both galectins. The present work reveals a facile and elegant synthetic route for the preparation of ...
Latest version: v3
Publication date: May 05, 2020
Georgios A. Tritsaris,
Stephen Carr,
Ziyan Zhu,
Yiqi Xie,
Steven B. Torrisi,
Jing Tang,
Marios Mattheakis,
Daniel Larson,
Efthimios Kaxiras
- Quantum confinement endows two-dimensional (2D) layered materials with exceptional physics and novel properties compared to their bulk counterparts. Although certain two- and few-layer configurations of graphene have been realized and studied, a systematic investigation of the properties of arbitrarily layered graphene assemblies is still lacking. We introduce theoretical concepts and methods for the processing of materials information, and as a case study, apply them to investigate the electronic structure of multi-layer graphene-based assemblies in a high-throughput fashion. We provide a critical discussion of patterns and trends in tight binding band structures and we identify specific layered assemblies using low-dispersion electronic bands as indicators of potentially interesting physics like strongly correlated behavior. A combination of data-driven models for visualization and prediction is used to intelligently explore the materials space. This work more generally aims to ...
Latest version: v1
Publication date: May 04, 2020
Dalibor Trapl,
Carmen Cuerdo del Río,
Pavel Kříž,
Vojtěch Spiwok
- 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.
Latest version: v1
Publication date: May 03, 2020
Gianluca Prandini,
Antimo Marrazzo,
Ivano E. Castelli,
Nicolas Mounet,
Nicola Marzari
- Despite the enormous success and popularity of density functional theory, systematic verification and validation studies are still very limited both in number and scope. Here, we propose a universal standard protocol to verify publicly available pseudopotential libraries, based on several independent criteria including verification against all-electron equations of state and plane-wave convergence tests for phonon frequencies, band structure, cohesive energy and pressure. Adopting these criteria we obtain two optimal pseudopotential sets, namely the Standard Solid State Pseudopotential (SSSP) efficiency and precision libraries, tailored for high-throughput materials screening and high-precision materials modelling. As of today, the SSSP precision library is the most accurate open-source pseudopotential library available. This archive entry contains the database of calculations (phonons, cohesive energy, equation of state, band structure, pressure, etc.) together with the ...
Latest version: v4
Publication date: Apr 30, 2020
Janani Sampath,
Jim Pfaendtner
- Titania (TiO2) is used extensively in biomedical applications; efforts to boost the biocompatibility of TiO2 include coating it with the titania binding hexamer, RKLPDA. To understand the binding mechanism of this peptide, we employ molecular dynamics simulations enhanced by metadynamics to study three amino acids present in the peptide – arginine (R), lysine (K), and aspartate (D), on four TiO2 variants that have different degrees of surface hydroxyl groups. We find that binding is a function of both sidechain charge and structure, with R binding to all four surfaces, whereas the affinity of K and D is dependent on the distribution of hydroxyl groups. Informed by this, we study the binding of the titania binding hexamer and 12mer (RKLPDAPGMHTW) on two of the four surfaces, and we see strong correlations between the binding free energy and the primary binding residues, in agreement with prior experiments and simulations. We propose that the discrepancies observed in prior work ...
Latest version: v1
Publication date: Apr 30, 2020
Fatemeh Haddadi,
QuanSheng Wu,
Alex J. Kruchkov,
Oleg V. Yazyev
- We investigate twisted double bilayer graphene (TDBG), a four-layer system composed of two AB-stacked graphene bilayers rotated with respect to each other by a small angle. Our ab-initio band structure calculations reveal a considerable energy gap at the charge point neutrality that we assign to the intrinsic symmetric polarization (ISP). We then introduce the ISP effect into the tight-binding parameterization and perform calculations on TDBG models that include lattice relaxation effects down to very small twist angles. We identify a narrow region around the magic angle θ*= 1.3° characterized by a manifold of remarkably flat bands gapped out from other states even without external electric fields. To understand the fundamental origin of the magic angle in TDBG, we construct a continuum model that points to a hidden mathematical link to the twisted bilayer graphene (TBG) model, thus indicating that the band flattening is a fundamental feature of TDBG, and is not a result of external fields.
Latest version: v1
Publication date: Apr 29, 2020
Diego Pasquier,
Oleg V. Yazyev
- Two-dimensional (2D) transition metal dichalcogenides (TMDs) exist in two polymorphs, referred to as 1T and 1H, depending on the coordination sphere of the transition metal atom. The broken octahedral and trigonal prismatic symmetries lead to different crystal and ligand field splittings of the d electron states, resulting in distinct electronic properties. In this work, we quantify the crystal and ligand field parameters of 2D TMDs using a Wannier-function approach. We adopt the methodology proposed by Scaramucci et al (2015 J. Phys.: Condens. Matter 27 175503) that allows to separate various contributions to the ligand field by choosing different manifolds in the construction of the Wannier functions. We discuss the relevance of the crystal and ligand fields in determining the relative stability of the two polymorphs as a function of the filling of the d-shell. Based on the calculated parameters, we conclude that the ligand field, while leading to a small stabilizing factor for ...
Latest version: v1
Publication date: Apr 28, 2020
Diego Pasquier,
Oleg V. Yazyev
- Transition metal dichalcogenides (TMDs) in the 1T polymorph are subject to a rich variety of periodic lattice distortions, often referred to as charge-density waves (CDWs) when not too strong. We study from first principles the fermiology and phonon dispersion of three representative single-layer transition metal disulfides with different occupation of the t2g subshell: TaS2 (t1 2g), WS2 (t2 2g), and ReS2 (t3 2g) across a broad range of doping levels. While strong electron-phonon interactions are at the heart of these instabilities, we argue that away from half-filling of the t2g subshell, the doping dependence of the calculated CDW wave vector can be explained from simple fermiology arguments, so that a weak-coupling nesting picture is a useful starting point for understanding. On the other hand, when the t2g subshell is closer to half-filling, we show that nesting is irrelevant, while a real-space strong-coupling picture of bonding Wannier functions is more appropriate and ...
Latest version: v1
Publication date: Apr 28, 2020
Binglun Yin,
W. A. Curtin
- 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.
Latest version: v1
Publication date: Apr 27, 2020
Federico Giberti,
Bingqing Cheng,
Gareth Tribello,
Michele Ceriotti
- 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.
Latest version: v1
Publication date: Apr 27, 2020
Francesco Petocchi,
Sophie Beck,
Claude Ederer,
Philipp Werner
- We study the dynamics of photoinduced charge carriers in semirealistic models of LaVO3 and YTiO3 polar heterostructures. It is shown that two types of impact ionization processes contribute to the carrier multiplication in these strongly correlated multiorbital systems: The first mechanism involves local spin state transitions, while the second mechanism involves the scattering of high-kinetic-energy carriers. Both processes act on the 10-fs timescale and play an important role in the harvesting of high-energy photons in solar cell applications. As a consequence, the optimal gap size for Mott solar cells is substantially smaller than for semiconductor devices.
Latest version: v1
Publication date: Apr 27, 2020
Binglun Yin,
Markus Stricker,
W.A. Curtin
- This dataset provides DFT (density functional theory as implemented in VASP, Vienna Ab Initio Simulation Package) calculations for pure Magnesium. It was designed by Binglun Yin, Markus Stricker and William A. Curtin for fitting a neural network potential with Behler-Parrinello symmetry functions. Binglun Yin carried out the calculation.
Latest version: v1
Publication date: Apr 27, 2020
Deborah Prezzi,
Guillaume Schull,
Michael C. Chong,
Nasima Afshar-Imani,
Fabrice Scheurer,
Claudia Cardoso,
Andrea Ferretti
- This record refers to a study on the electroluminescence of individual GNRs suspended between the tip of a scanning tunneling microscope (STM) and a Au(111) substrate. Emission spectra of such GNR junctions reveal a bright and narrow band emission of red light, whose energy can be tuned with the bias voltage applied to the junction, but always lying below the gap of infinite GNRs. Comparison with ab initio calculations indicates that the emission involves electronic states localized at the GNR termini. The results shed light on unpredicted optical transitions in GNRs.
The record includes the computational data that allows to reproduce the published results.
Latest version: v1
Publication date: Apr 26, 2020
Haiyang Niu,
Luigi Bonati,
Pablo M. Piaggi,
Michele Parrinello
- 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.
Latest version: v1
Publication date: Apr 20, 2020
Patrick Gono,
Alfredo Pasquarello
- The bifunctional mechanism for the oxygen evolution reaction (OER) involving two distinct reaction sites is studied through the computational hydrogen electrode method for a set of catalyst materials including rutile TiO2(110), anatase TiO2(101), SnO2(110), RuO2(110), IrO2(110), Ni2P(0001), and BiVO4(001). The calculations are performed both at the semilocal level and at the hybrid functional level. Moreover, anodic conditions are modeled and their effect on the OER free energy steps is evaluated. The free energies of the reaction steps indicate that for specific combinations of catalysts, the limitations due to the linear scaling relationship can be overcome, leading to smaller overpotentials for the overall OER. At the same time, a detailed analysis of the results reveals a strong dependence on the adopted functional. For both functionals, it is shown that the energy level of the highest occupied electronic state can serve as a descriptor to guide the search for the optimal ...
Latest version: v1
Publication date: Apr 18, 2020
April Cooper,
Johannes Kästner,
Alexander Urban,
Nongnuch Artrith
- This data set contains atomic structures of water clusters, bulk water and rock-salt Li8Mo2Ni7Ti7O32 in the XCrySDen [1] structure format (XSF), and total energies are included as additional meta information. The extended XSF format is compatible with the atomic energy network (aenet) package [2,3] for artificial neural network potential construction and application. The structures were generated using ab initio molecular dynamics (AIMD) simulations performed with the Vienna Ab Initio Simulation Package (VASP) [4,5] and projector-augmented wave (PAW) [6] pseudopontentials.
For the bulk water system the revised Perdew-Burke-Ernzerhof density functional [7] with the Grimme D3 van-der-Waals correction [8] (revPBE+D3) was used. The AIMD simulations of the Li-Mo-Ni-Ti-O system employed the strongly constrained and appropriately normed (SCAN) semilocal density functional [9]. For both periodic systems, the plane-wave cutoff was 400 eV, and Gamma-point only k-point meshes were ...
Latest version: v1
Publication date: Apr 14, 2020
Yixiu Luo,
Xiaolong Yang,
Tianli Feng,
Jingyang Wang,
Xiulin Ruan
- 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 ...
Latest version: v1
Publication date: Apr 11, 2020
Luigi Bonati,
Valerio Rizzi,
Michele Parrinello
- Designing an appropriate set of collective variables is crucial to the success of several enhanced sampling methods. Here we focus on how to obtain such variables from information limited to the metastable states. We characterize these states by a large set of descriptors and employ neural networks to compress this information in a lower-dimensional space, using Fisher's linear discriminant as an objective function to maximize the discriminative power of the network. We test this method on alanine dipeptide, using the non-linearly separable dataset composed by atomic distances. We then study an intermolecular aldol reaction characterized by a concerted mechanism. The resulting variables are able to promote sampling by drawing non-linear paths in the physical space connecting the fluctuations between metastable basins. Lastly, we interpret the behavior of the neural network by studying its relation to the physical variables. Through the identification of its most relevant features, we are able to gain chemical insight into the process.
Latest version: v1
Publication date: Apr 06, 2020
Raimon Fabregat,
Alberto Fabrizio,
Benjamin Meyer,
Daniel Hollas,
Clémence Corminboeuf
- 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 ...
Latest version: v1
Publication date: Apr 02, 2020
Dylan Rees,
Kaustuv Manna,
Baozhu Lu,
Takahiro Morimoto,
Horst Borrmann,
Claudia Felser,
Joel Moore,
Darius Torchinsky,
Joseph Orenstein
- 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 ...
Latest version: v1
Publication date: Mar 26, 2020
Alberto Fabrizio,
Benjamin Meyer,
Clemence Corminboeuf
- The average energy curvature as a function of the particle number is a molecule-specific quantity, which measures the deviation of a given functional from the exact conditions of density functional theory (DFT). Related to the lack of derivative discontinuity in approximate exchange-correlation potentials, the information about the curvature has been successfully used to restore the physical meaning of Kohn-Sham orbital eigenvalues and to develop non-empirical tuning and correction schemes for density functional approximations. In this work, we propose the construction of a machine-learning framework targeting the average energy curvature between the neutral and the radical cation state of thousands of small organic molecules (QM7 database). The applicability of the model is demonstrated in the context of system-specific gamma-tuning of the LC-ωPBE functional and validated against the molecular first ionization potentials at equation-of-motion (EOM) coupled-cluster references. In ...
Latest version: v1
Publication date: Mar 25, 2020
Michele Invernizzi,
Michele Parrinello
- Metadynamics is an enhanced sampling method of great popularity, based on the on-the-fly construction of a bias potential that is a function of a selected number of collective variables. We propose here a change in perspective that shifts the focus from the bias to the probability distribution reconstruction while retaining some of the key characteristics of metadynamics, such as flexible on-the-fly adjustments to the free energy estimate. The result is an enhanced sampling method that presents a drastic improvement in convergence speed, especially when dealing with suboptimal and/or multidimensional sets of collective variables. The method is especially robust and easy to use and in fact requires only a few simple parameters to be set, and it has a straightforward reweighting scheme to recover the statistics of the unbiased ensemble. Furthermore, it gives more control of the desired exploration of the phase space since the deposited bias is not allowed to grow indefinitely and it ...
Latest version: v2
Publication date: Mar 24, 2020
Kathryn S. Deeg,
Daiane Damasceno Borges,
Daniele Ongari,
Nakul Rampal,
Leopold Talirz,
Aliaksandr V. Yakutovich,
Johanna M. Huck,
Berend Smit
- 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.
Latest version: v1
Publication date: Mar 24, 2020
Zhongtian Mao,
Pablo G. Lustemberg,
John R. Rumptz,
M. Veronica Ganduglia-Pirovano,
Charles T. Campbell
- The morphology, interfacial bonding energetics and charge transfer of Ni clusters and nanoparticles on slightly-reduced CeO2-x(111) surfaces at 100 to 300 K have been studied using single crystal adsorption calorimetry (SCAC), low-energy ion scattering spectroscopy (LEIS), X-ray photoelectron spectroscopy (XPS), low energy electron diffraction (LEED) and density functional theory (DFT). The initial heat of adsorption of Ni vapor decreased with the extent of pre-reduction (x) of the CeO2-x(111), showing that stoichiometric ceria adsorbs Ni more strongly than oxygen vacancies. On CeO1.95(111) at 300 K, the heat dropped quickly with coverage in the first 0.1 ML, attributed to nucleation of Ni clusters on stoichiometric steps, followed by the Ni particles spreading onto less favorable terrace sites. At 100 K, the clusters nucleate on terraces due to slower diffusion. Adsorbed Ni monomers are in the +2 oxidation state, and they bind by ~45 kJ/mol more strongly to step sites than ...
Latest version: v1
Publication date: Mar 23, 2020
Sebastiaan P. Huber,
Spyros Zoupanos,
Martin Uhrin,
Leopold Talirz,
Leonid Kahle,
Rico Häuselmann,
Dominik Gresch,
Tiziano Müller,
Aliaksandr V. Yakutovich,
Casper W. Andersen,
Francisco F. Ramirez,
Carl S. Adorf,
Fernando Gargiulo,
Snehal Kumbhar,
Elsa Passaro,
Conrad Johnston,
Andrius Merkys,
Andrea Cepellotti,
Nicolas Mounet,
Nicola Marzari,
Boris Kozinsky,
Giovanni Pizzi
- The ever-growing availability of computing power and sustained development of advanced computational methods have contributed much to recent scientific progress.
These developments present new challenges driven by the sheer amount of calculations and data to manage. Next-generation exascale supercomputers will harden these challenges, such that automated and scalable solutions become crucial. In recent years, we have been developing AiiDA (http://www.aiida.net), a robust open-source high-throughput infrastructure addressing the challenges arising from the needs of automated workflow management and data provenance recording. Here, we introduce developments and capabilities required to reach sustained performance, with AiiDA supporting throughputs of tens of thousands processes/hour, while automatically preserving and storing the full data provenance in a relational database making it queryable and traversable, thus enabling high-performance data analytics. AiiDA's workflow ...
Latest version: v1
Publication date: Mar 23, 2020
Jason Yu,
Jihai Liao,
Yujun Zhao,
Xiaobao Yang,
Yinchang Zhao
- 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 ...
Latest version: v1
Publication date: Mar 18, 2020
Chris J. Pickard
- Ab initio random structure searching (AIRSS) has been performed for carbon at 10GPa, a pressure at which diamond is expected to be the thermodynamic ground state. A small (~10K structures) and larger (~100K structures) set are provided. To demonstrate a search in a ternary composition space ~100K AIRSS structures for the C+N+H+O system are provided. All structures are generated at random using the buildcell tool of the AIRSS suite, and relaxed to a nearby local minimum in the DFT-PBE total energy using the CASTEP code. Computational details are provided in the REM block of the .res structure files.
Latest version: v1
Publication date: Mar 02, 2020
Maria Fumanal,
Gloria Capano,
Senja Barthel,
Berend Smit,
Ivano Tavernelli
- Metal-organic frameworks (MOFs) consist of metal nodes that are connected by organic linkers. They are thus highly chemically tunable materials given the broad range of potential linkers and nodes that can be chosen for their synthesis. Their tunability has recently sparked interest for the development of new MOF photo-catalysts for energy-related applications such as hydrogen (H2) evolution and CO2 reduction. The sheer amount of potentially synthesizable MOFs requires to define descriptors that allow to predict their performance with this aim. Herein we propose a systematic computational protocol to determine two energy-based descriptors that are directly related to the performance of a MOF as a photocatalyst. These descriptors assess the UV-vis light absorption capability and the band energy alignment with respect to redox processes and/or co-catalysts energy levels. High-throughput screening based on cost-effective computations of these features is envisioned to aid the discovery of new promising photoactive systems.
Latest version: v1
Publication date: Feb 24, 2020
Dipanwita Dutta,
Deb Sankar De,
Daniel Fan,
Shantanu Roy,
Giovanni Alfieri,
Massimo Camarda,
Maximilian Amsler,
Joerg Lehmann,
Holger Bartolf,
Stefan Goedecker,
Thomas Andreas Jung
- High power SiC MOSFET technologies are critical for energy saving in, e.g., distribution of electrical power. They suffer, however, from low near-interface mobility, the origin of which has not yet been conclusively determined. Here, we present unique concerting evidence for the presence of interface defects in the form of carbon clusters at native thermally processed oxides of SiC. These clusters, with a diameter of 2–5 nm, are HF-etch resistant and possess a mixture of graphitic (sp2) and amorphous (sp3 mixed in sp2) carbon bonds different from the normal sp3 carbon present in 4H-SiC. The nucleation of such defects during thermal oxidation as well as their atomic structure is elucidated by state-of-the-art atomistic and electronic structure calculations. In addition, our property prediction techniques show the impact of the simulated carbon accumulates on the electronic structure at the interface.
Latest version: v1
Publication date: Feb 20, 2020
Paolo Giannozzi,
Oscar Baseggio,
Pietro Bonfà,
Davide Brunato,
Roberto Car,
Ivan Carnimeo,
Carlo Cavazzoni,
Stefano de Gironcoli,
Pietro Delugas,
Fabrizio Ferrari Ruffino,
Andrea Ferretti,
Nicola Marzari,
Iurii Timrov,
Andrea Urru,
Stefano Baroni
- Quantum ESPRESSO is an open-source distribution of computer codes for quantum-mechanical materials modeling, based on density-functional theory, pseudo-potentials, and plane waves, and renowned for its performance on a wide range of hardware architectures, from laptops to massively parallel computers, as well as for the breadth of its applications. In this paper we present a motivation and brief review of the ongoing effort to port Quantum ESPRESSO onto heterogeneous architectures based on hardware accelerators, which will overcome the energy constraints that are currently hindering the way towards exascale computing.
Latest version: v1
Publication date: Feb 17, 2020
Georges Hattab,
Tilman Ahlfeld,
Anna Klimova,
Alexander Koepp,
Michael Schuerer,
Stefanie Speidel
- Anatomically realistic organ replicas or phantoms allow for accurate studies and reproducible research. To recreate a human kidney, mimicry of the viscoelastic properties of the human kidney is crucial. However, none of the related work addressed the design and development of a kidney phantom using only silicone as material. In contrast to paraffin and hydrogel, silicone is an ideal variant for its extended shelf life, soft-tissue-like feeling, and viscoelastic modularity. To this end, we conducted uniaxial compression testing and Cauchy stress modeling. Results indicate that none of the available manufacturer silicone brands are suitable for the task of creating a realistic kidney phantom. Indeed, the tested silicone mixtures in low and high strain do not fall within the required approximate target compressive moduli of 20 kPa and 500 kPa, respectively. This work provides a frame of reference for future work by avoiding the pitfalls of the selected ready-made silicones and ...
Latest version: v2
Publication date: Feb 17, 2020
Jayashrita Debnath,
Michele Parrinello,
Michele Invernizzi
- The free energy landscapes of several fundamental processes are characterized by high barriers separating long-lived metastable states. In order to explore these type of landscapes enhanced sampling methods are used. While many such methods are able to obtain sufficient sampling in order to draw the free energy, the transition states are often sparsely sampled. We propose an approach based on the Variationally Enhanced Sampling Method to enhance sampling in the transition region. To this effect, we introduce a dynamic target distribution which uses the derivative of the instantaneous free energy surface to locate the transition regions on the fly and modulate the probability of sampling different regions. Finally, we exemplify the effectiveness of this approach in enriching the number of configurations in the transition state region in the cases of a chemical reaction and of a nucleation process.
Latest version: v2
Publication date: Feb 14, 2020
Binglun Yin,
Francesco Maresca,
W. A. Curtin
- The element Vanadium (V) appears unique among alloying elements for providing high strengthening in both the fcc Co-Cr-Fe-Mn-Ni-V and bcc Cr-Mo-Nb-Ta-V-W-Hf-Ti-Zr high-entropy alloy families. The origin of Vanadium’s special role is its atomic volume: large in the fcc alloys and small in the bcc alloys, and thus having a large misfit volume in both crystalline structures. A parameter-free theory applicable to both fcc and bcc HEAs rationalizes this finding, with predictions of strength across a range of fcc and bcc alloys in quantitative and qualitative agreement with experiments. In the fcc class, the analysis demonstrates why the newly-discovered NiCoV and Ni0.632V0.368 alloys have far higher strength than any other fcc alloy and are predicted to be the highest attainable. In the bcc class, the analysis demonstrates that the addition of V always increases the strength relative to the same alloys without V. The optimization of complex alloys for high strength should thus center ...
Latest version: v1
Publication date: Feb 12, 2020
Deb Sankar De,
Santanu Saha,
Luigi Genovese,
Stefan Goedecker
- We present a fully ab-initio, unbiased structure search of the configurational space of decorated C60 fullerenes in the presence of an electric field. We observed that the potential energy surface (PES) is significantly perturbed by an external electric field and that the energetic ordering of low energy isomers differs with and without electric field. We identify the energetically lowest configuration for a varying number of decorating atoms (1 ≤ n ≤ 12) for Li and (1 ≤ n ≤ 6) for K on the C60 surface at different electric field strengths. Using the correct geometric ground state in the electric field for the calculation of the dipole we obtain better agreement with the experimentally measured values than previous calculations based on the ground state in absence of an electric field. Since the lowest energy structures are typically nearly degenerate in energy, a combination of different structures is expected to be found at room temperature. The experimentally measured dipole is ...
Latest version: v1
Publication date: Feb 02, 2020
Deb Sankar De,
José A. Flores-Livas,
Santanu Saha,
Luigi Genovese,
Stefan Goedecker
- 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.
Latest version: v1
Publication date: Feb 02, 2020
Somayeh Faraji,
S. Alireza Ghasemi,
Behnam Parsaeifard,
Stefan Goedecker
- In this work, surface reconstructions on the (100) surface of CaF2 are comprehensively investigated. The configurations were explored by employing the Minima Hopping Method (MHM) coupled to a machine-learning interatomic potential, that is based on a charge equilibration scheme steered by a neural network (CENT). The combination of these powerful methods revealed about 80 different morphologies for the (100) surface with very similar surface formation energies differing by not more than 0.3 J m−2. To take into account the effect of temperature on the dynamics of this surface as well as to study the solid–liquid transformation, molecular dynamics simulations were carried out in the canonical (NVT) ensemble. By analyzing the atomic mean-square displacements (MSD) of the surface layer in the temperature range of 300–1200 K, it was found that in the surface region the F sublattice is less stable and more diffusive than the Ca sublattice. Based on these results we demonstrate that not ...
Latest version: v1
Publication date: Jan 31, 2020
Jonathan Vandermause,
Steven B. Torrisi,
Simon Batzner,
Yu Xie,
Lixin Sun,
Alexie M. Kolpak,
Boris Kozinsky
- Machine learned force fields typically require manual construction of training sets consisting of thousands of first principles calculations, which can result in low training efficiency and unpredictable errors when applied to structures not represented in the training set of the model. This severely limits the practical application of these models in systems with dynamics governed by important rare events, such as chemical reactions and diffusion. We present an adaptive Bayesian inference method for automating the training of interpretable, low-dimensional, and multi-element interatomic force fields using structures drawn on the fly from molecular dynamics simulations. Within an active learning framework, the internal uncertainty of a Gaussian process regression model is used to decide whether to accept the model prediction or to perform a first principles calculation to augment the training set of the model. The method is applied to a range of single- and multi-element systems ...
Latest version: v1
Publication date: Jan 28, 2020
Andrea Floris,
Iurii Timrov,
Burak Himmetoglu,
Nicola Marzari,
Stefano de Gironcoli,
Matteo Cococcioni
- 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 ...
Latest version: v1
Publication date: Jan 28, 2020
Dandan Han,
Tarak Karmakar,
Zoran Bjelobrk,
Junbo Gong,
Michele Parrinello
- 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 ...
Latest version: v1
Publication date: Jan 28, 2020
Tarak Karmakar,
Pablo M. Piaggi,
Claudio Perego,
Michele Parrinello
- Canonical molecular dynamics simulations of crystal growth from solution suffer from severe finite-size effects. As the crystal grows, the solute molecules are drawn from the solution to the crystal, leading to a continuous drop in the solution concentration. This is in contrast to experiments in which the crystal grows at an approximately constant supersaturation of a bulk solution. Recently, Perego et al. [J. Chem. Phys.2015, 142, 144113] showed that in a periodic setup in which the crystal is represented as a slab, the concentration in the vicinity of the two surfaces can be kept constant while the molecules are drawn from a part of the solution that acts as a molecular reservoir. This method is quite effective in studying crystallization under controlled supersaturation conditions. However, once the reservoir is depleted, the constant supersaturation conditions cannot be maintained. We propose a variant of this method to tackle this depletion problem by simultaneously ...
Latest version: v1
Publication date: Jan 28, 2020
Tarak Karmakar,
Pablo M. Piaggi,
Michele Parrinello
- A widespread method of crystal preparation is to precipitate it from a supersaturated solution. In such a process, control of solution concentration is of paramount importance. The nucleation process, polymorph selection, and crystal habits depend crucially on this thermodynamic parameter. When performing molecular dynamics simulations with a fixed number of molecules in the canonical ensemble, crystal growth is accompanied by a decrease in the solution concentration. This modification of the thermodynamic condition leads to significant artifacts. Inspired by the recent development of the constant chemical potential molecular dynamics simulation method by Perego et al. [J. Chem. Phys. 2015, 142, 144113], we develop a spherical variant of it to study nucleation from solution. Our method allows determining the crystal nucleus size and nucleation rates at constant supersaturation. As an example, we study the homogeneous nucleation of sodium chloride from its supersaturated aqueous solution.
Latest version: v1
Publication date: Jan 28, 2020
Alberto Fabrizio,
Riccardo Petraglia,
Clemence Corminboeuf
- 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 ...
Latest version: v1
Publication date: Jan 24, 2020
Jingyu Qu,
Qiang Zhu
- The development of new high dielectric materials is essential for advancement in modern electronics. Oxides are generally regarded as the most promising class of high dielectric materials for industrial applications as they possess both high dielectric constants and large band gaps. Most previous researches on high dielectrics were limited to already known materials. In this study, we conducted an extensive search for high dielectrics over a set of ternary oxides by combining crystal structure prediction and density functional perturbation theory calculations. From this search, we adopted multiple stage screening to identify 441 new low-energy high dielectric materials. Among these materials, 33 were identified as potential high dielectrics favorable for modern device applications. Our research has opened an avenue to explore novel high dielectric materials by combining crystal structure prediction and high throughput screening
Latest version: v1
Publication date: Jan 23, 2020
José A. Flores-Livas,
Rafael Sarmiento-Pérez,
Silvana Botti,
Stefan Goedecker,
Miguel A. L. Marques
- We propose perovskite nitrides with magnetic rare-earth metals as novel materials with a range of technological applications. These materials appear to be thermodynamically stable and, in spite of possessing different crystal structures and different atomic environments, they retain the magnetic moment of the corresponding elemental rare-earth metal. We find both magnetic metals and semiconductors, with a wide range of magnetic moments and some systems posses record-high magnetic anisotropy energies. Further tuning of the electronic and magnetic properties can also be expected by doping with other rare-earths or by creating solid solutions. The synthesis of these exotic materials with unusual compositions would extend not only the accepted stability domain of perovskites but also open the way for a series of applications enabled by their rich physics.
Latest version: v1
Publication date: Jan 20, 2020
Migle Grauzinyte,
Daniele Tomerini,
Stefan Goedecker,
José A. Flores-Livas
- The role of the divalent nature of tin is explored in tin monoxide, revealing a novel path for enhancing p-type conductivity. The consequences of oxygen off-stoichiometry indicate that a defect complex formed by a tin vacancy (VSn) and an impurity interstitial (Di) leads to an increased number of free carriers as well as improved acceptor state stability when compared with the isolated VSn. In this study, we identify several elements that are able to stabilize such a defect complex configuration. The enhanced ionization of the resulting complex arises from the divalent nature of Sn, which allows Sn(II) and Sn(IV) oxidation states to form. Such a novel doping mechanism not only offers a path for creating a high-performance p-type transparent SnO, but reveals an as-of-yet unexplored route to improve conductivity in other compounds formed by multivalent elements, for example, Sn(II)-based thermoelectrics.
Latest version: v1
Publication date: Jan 20, 2020
Gerald Bauer,
Daniele Ongari,
Davide Tiana,
Patrick Gäumann,
Thomas Rohrbach,
Gerard Pareras,
Mohamed Tarik,
Berend Smit,
Marco Ranocchiari
- Finding heterogeneous catalysts that are superior to homogeneous ones for selective organic transformation is a major challenge in catalysis. Here we show how micropores in metal-organic frameworks (MOFs) push homogeneous catalytic reactions into kinetic regimes inaccessible under standard conditions. Such property allows branched selectivity up to 90% in the Co-catalysed hydroformylation of olefins without directing groups, not achievable with existing catalysts. This finding has a big potential in the production of aldehydes for the fine chemical industry. Monte Carlo and density functional theory simulations combined with kinetic models show that the micropores of MOFs with UMCM-1 and MOF-74 topologies increase the olefins density beyond neat conditions while partially preventing the adsorption of syngas leading to high branched selectivity. The easy experimental protocol and the chemical and structural flexibility of MOFs will attract the interest of the fine chemical ...
Latest version: v1
Publication date: Jan 16, 2020
Haiyang Niu,
Yi Isaac Yang,
Michele Parrinello
- Ice nucleation is a process of great relevance in physics, chemistry, technology, and environmental sciences; much theoretical effort has been devoted to its understanding, but it still remains a topic of intense research. We shed light on this phenomenon by performing atomistic based simulations. Using metadynamics and a carefully designed set of collective variables, reversible transitions between water and ice are able to be simulated. We find that water freezes into a stacking disordered structure with the all-atom transferable intermolecular potential with 4 points/ice (TIP4P/ice) model, and the features of the critical nucleus of nucleation at the microscopic level are revealed. We have also estimated the ice nucleation rates along with other nucleation parameters at different undercoolings. Our results are in agreement with recent experimental and other theoretical works, and they confirm that nucleation is preceded by a large increase in tetrahedrally coordinated water molecules.
Latest version: v1
Publication date: Jan 14, 2020
Tina Chen,
Dong-hwa Seo
- Fast-charging batteries typically employ electrodes capable of accommodating lithium continuously via solid-solution transformation because they have few kinetic barriers apart from Li+ diffusion. One exception is lithium titanate, an anode that exhibits extraordinary rate capability seemingly inconsistent with its two-phase reaction and slow diffusion within the two phases. Through real-time tracking of Li+ migration using operando electron energy-loss spectroscopy (EELS) along with simulation of the EELS spectra, we observe that the kinetic pathway that enables facile ionic transport in lithium titanate consists of distorted Li polyhedra in metastable intermediate states. Thus, fast-charging electrodes may not be controlled solely by the intrinsic ionic diffusivity of macroscopic phases, but also by the transport via kinetically accessible low-energy landscapes.
In order to understand the origin of various EELS spectra features, we simulate EELS spectra using the Vienna Ab ...
Latest version: v1
Publication date: Jan 14, 2020
Nicola Colonna,
Ngoc Linh Nguyen,
Andrea Ferretti,
Nicola Marzari
- Koopmans-compliant (KC) functionals have been shown to provide accurate spectral properties through a generalized condition of piecewise linearity of the total energy as a function of the fractional addition/removal of an electron to/from any orbital. We analyze the performance of different KC functionals on a large and standardized set of 100 molecules, the GW100 test set, comparing vertical ionization potentials (taken as opposite of the orbital energies) to those obtained from accurate quantum chemistry methods, and to experimental results. We find excellent agreement, with a mean absolute error of 0.20 eV for the KIPZ functional on the first ionization potential, which is state-of-the-art for both density functional theory (DFT)-based calculations and many-body perturbation theory. We highlight similarities and differences between KC functionals and other electronic-structure approaches, such as dielectric-dependent hybrid functionals and Green’s function methods, both from a ...
Latest version: v1
Publication date: Jan 09, 2020
Thomas Bischoff,
Julia Wiktor,
Wei Chen,
Alfredo Pasquarello
- Nonempirical hybrid functionals are investigated for band-gap predictions of inorganic metal-halide perovskites belonging to the class CsBX3 , with B = Ge, Sn, Pb and X = Cl, Br, I. We consider both global and range-separated hybrid functionals and determine the parameters through two different schemes. The first scheme is based on the static screening response of the material and thus yields dielectric-dependent hybrid functionals. The second scheme defines the hybrid functionals through the enforcement of Koopmans’ condition for localized defect states. We also carry out quasiparticle self-consistent GW calculations with vertex corrections to establish state-of-the-art references. For the investigated class of materials, dielectric-dependent functionals and those fulfilling Koopmans’ condition yield band gaps of comparable accuracy (∼0.2 eV), but the former only require calculations for the primitive unit cell and are less subject to the specifics of the material.
Latest version: v1
Publication date: Jan 07, 2020
Shuozhi Xu,
Yanqing Su,
Lauren Smith,
Irene Beyerlein
- 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.
Latest version: v1
Publication date: Jan 06, 2020
M.-Y Yao,
N. Xu,
Q.S. Wu,
O.V. Yazyev,
M. Shi
- Distinct to type-I Weyl semimetals (WSMs) that host quasiparticles described by the Weyl equation, the energy dispersion of quasiparticles in type-II WSMs violates Lorentz invariance and the Weyl cones in the momentum space are tilted. Since it was proposed that type-II Weyl fermions could emerge from WTe2, MoTe2, WP2 and MoP2 families of materials, a large number of experiments have been dedicated to unveiling the possible manifestation of type-II WSMs, e.g., surface-state Fermi arcs. However, the interpretations of the experimental results are very controversial. Here, using angle-resolved photoemission spectroscopy supported by the first-principles calculations, we probe the tilted Weyl cone bands in the bulk electronic structure of WP2 directly, which are at the origin of Fermi arcs at the surfaces and transport properties related to the chiral anomaly in type-II WSMs. Our results ascertain that, due to the spin-orbit coupling, the Weyl nodes originate from the splitting of ...
Latest version: v1
Publication date: Dec 19, 2019
Andrea Grisafi,
Michele Ceriotti
- The most successful and popular machine learning models of atomic-scale properties derive their transferability from a locality ansatz. The properties of a large molecule or a bulk material are written as a sum over contributions that depend on the configurations within finite atom-centered environments. The obvious downside of this approach is that it cannot capture nonlocal, nonadditive effects such as those arising due to long-range electrostatics or quantum interference. We propose a solution to this problem by introducing nonlocal representations of the system, which are remapped as feature vectors that are defined locally and are equivariant in O(3). We consider, in particular, one form that has the same asymptotic behavior as the electrostatic potential. We demonstrate that this framework can capture nonlocal, long-range physics by building a model for the electrostatic energy of randomly distributed point-charges, for the unrelaxed binding curves of charged organic ...
Latest version: v1
Publication date: Dec 18, 2019
Binglun Yin,
Predrag Andric,
W. A. Curtin
- Generalized stacking fault energy (GSFE) is a crucial material property for describing nanoscale plasticity in crystalline materials, such as dislocation dissociation, nucleation, and twinning. The dependence of the GSFE on applied stress normal to the stacking fault (SF) plane has been suggested to influence such phenomena. Here, the SF stress dependence is analyzed through (i) the generalized stacking fault potential energy (GSFE) and (ii) the generalized stacking fault enthalpy (GSFH). Our DFT calculations reveal that the GSFE is almost independent of the applied normal stress, which contradicts the long-standing wisdom and previous studies. We also reveal the inelastic inter-planar normal displacement associated with the SF. The coupling between the positive inelastic normal displacement and the applied normal stress decreases the GSFH.
Latest version: v1
Publication date: Dec 17, 2019
Dariusz J. Gawryluk,
Y. Maximilian Klein,
Tian Shang,
Denis Sheptyakov,
Lukas Keller,
Nicola Casati,
Philippe Lacorre,
Maria Teresa Fernandez-Diaz,
Juan Rodriguez-Carvajal,
Marisa Medarde
- The origin of the metal-to-insulator transition (MIT) in RNiO3 perovskites with R = trivalent 4 f ion has challenged the condensed matter research community for almost three decades. A drawback for progress in this direction has been the lack of studies combining physical properties and accurate structural data covering the full nickelate phase diagram. Here we focus on a small region close to the itinerant limit (R = Pr, 1.5 K < T < 300 K), where we investigate the gap opening and the simultaneous emergence of charge order in PrNiO3. We combine electrical resistivity, magnetization, and heat capacity measurements with high-resolution neutron and synchrotron x-ray powder diffraction data that, in contrast to previous studies, we analyze in terms of symmetry-adapted distortion modes. Such analysis allow us to identify the contribution of the different modes to the global distortion in a broad temperature range. Moreover, it shows that the structural changes at the MIT, ...
Latest version: v2
Publication date: Dec 14, 2019
Guadalupe S. Otero,
Pablo G. Lustemberg,
Fernando Prado,
M. Veronica Ganduglia-Pirovano
- The effects of Zr doping on the stability of the CeO2(111) surface as a function of the dopant concentration and distribution, as well as on the relative stability of surface and subsurface oxygen vacancies, were studied by means of density functional theory (DFT+U) calculations. For a given Zr content, the more stable structures do not correspond to those configurations with Zr located in the topmost O-Ce-O trilayer (TL1), but in inner layers, and the stability decreases with increasing Zr concentration. For the undoped CeO2(111) surface, the preference of subsurface vacancies with next-nearest neighbor (NNN) Ce3+ configuration has earlier been predicted. For the Zr-doped surface, the formation of vacancies was studied using a surface unit cell with 2x2 periodicity, and it was found that the most stable configuration corresponds to the Zr atom located in the surface layer (TL1) neighboring a subsurface oxygen vacancy with NNN Ce3+, being the formation energy equal to 1.16 eV. ...
Latest version: v2
Publication date: Dec 12, 2019
Yue-Yu Zhang,
Haiyang Niu,
GiovanniMaria Piccini,
Dan Mendels,
Michele Parrinello
- Several enhanced sampling methods, such as umbrella sampling or metadynamics, rely on the identification of an appropriate set of collective variables. Recently two methods have been proposed to alleviate the task of determining efficient collective variables. One is based on linear discriminant analysis; the other is based on a variational approach to conformational dynamics and uses time-lagged independent component analysis. In this paper, we compare the performance of these two approaches in the study of the homogeneous crystallization of two simple metals. We focus on Na and Al and search for the most efficient collective variables that can be expressed as a linear combination of X-ray diffraction peak intensities. We find that the performances of the two methods are very similar. Wherever the different metastable states are well-separated, the method based on linear discriminant analysis, based on its harmonic version, is to be preferred because simpler to implement and less ...
Latest version: v1
Publication date: Dec 12, 2019
Pablo M. Piaggi,
Michele Parrinello
- From the Ising model and the Lennard-Jones fluid to water and the iron-carbon system, phase diagrams are an indispensable tool to understand phase equilibria. Despite the effort of the simulation community, the calculation of a large portion of a phase diagram using computer simulation is still today a significant challenge. Here, we propose a method to calculate phase diagrams involving liquid and solid phases by the reversible transformation of the liquid and the solid. To this end, we introduce an order parameter that breaks the rotational symmetry and we leverage our recently introduced method to sample the multithermal-multibaric ensemble. In this way, in a single molecular dynamics simulation, we are able to compute the liquid-solid coexistence line for entire regions of the temperature and pressure phase diagram. We apply our approach to the bcc-liquid phase diagram of sodium and the fcc-bcc-liquid phase diagram of aluminum.
This repository contains the input files to ...
Latest version: v1
Publication date: Dec 11, 2019
Luigi Giacomazzi,
Paolo Umari,
Alfredo Pasquarello
- Using a density-functional framework, we investigate the vibrational spectra of vitreous SiO2 to determine to what extent these spectra provide information about the medium-range structure of the oxide network. We carry out a comparative study involving three model structures, which all feature a nondefective network of corner-sharing tetrahedra but differ through their Si-O-Si bond-angle distributions and ring statistics. We first address the results of typical diffraction probes. Fair agreement with experiment is achieved for the total neutron and total x-ray structure factors of all models, indicating limited sensitivity of these structure factors to the medium-range structure. The same consideration also applies to the Si-O and O-O partial structure factors. At variance, the Si-Si partial structure factor is found to be highly sensitive to the Si-O-Si bond-angle distribution. We then address typical vibrational spectra, such as the inelastic neutron spectrum, the infrared ...
Latest version: v1
Publication date: Dec 11, 2019
Seyed Mohamad Moosavi,
Henglu Xu,
Linjiang Chen,
Andrew I. Cooper,
Berend Smit
- Porous molecular crystals are an emerging class of porous materials formed by crystallisation of molecules with weak intermolecular interactions, which distinguishes them from extended nanoporous materials like metal-organic frameworks (MOFs). To aid discovery of porous molecular crystals for desired applications, energy-structure-function (ESF) maps were developed that combine a priori prediction of both the crystal structure and its functional properties. However, it is a challenge to represent the high-dimensional structural and functional landscapes of an ESF map and to identify energetically favourable and functionally interesting polymorphs among the 1,000s-10,000s of structures typically on a single ESF map. Here, we introduce geometric landscapes, a representation for ESF maps based on geometric similarity, quantified by persistent homology. We show that this representation allows the exploration of complex ESF maps, automatically pinpointing interesting crystalline phases ...
Latest version: v1
Publication date: Dec 03, 2019
Junzhang Ma,
Simin Nie,
Changjiang Yi,
Jasmin Jandke,
Tian Shang,
Mengyu Yao,
Muntaser Naamneh,
Liqin Yan,
Young Sun,
Alla Chikina,
Vladimir Strocov,
Marisa Medarde,
Meng Song,
Yimin Xiong,
Gang Xu,
Wulf Wulfhekel,
Joël Mesot,
Michele Reticcioli,
Cesare Franchini,
Christopher Mudry,
Markus Müller,
Youguo Shi,
Tian Qian,
Hong Ding,
Ming Shi
- This record mainly upload all the raw experimental data related to the manuscript. Fig1 include the transport data, magnetotransport data, AHE data, ESR data, uSR data. These data related to the conclusion that spin fluctuation established in the paramagnetic phase. Fig2 contains in-plane and out-of-plane 3D photoemission spectra, and high resolution cuts on top and side surface. Fig3 contains band electronic structure along high symmetry lines with spin along all kinds of typical directions. Fig4 contains 3-D in-plane and out-of-plane Fermi surfaces on the 101 cleavage, high resolution cuts, STM/STS data. The proved the observation of Weyl points.
Latest version: v1
Publication date: Nov 11, 2019
Benjamin A. Helfrecht,
Rocio Semino,
Giovanni Pireddu,
Scott M. Auerbach,
Michele Ceriotti
- We have analyzed structural motifs in the Deem database of hypothetical zeolites to investigate whether the structural diversity found in this database can be well-represented by classical descriptors, such as distances, angles, and ring sizes, or whether a more general representation of the atomic structure, furnished by the smooth overlap of atomic position (SOAP) method, is required to capture accurately structure–property relations. We assessed the quality of each descriptor by machine-learning the molar energy and volume for each hypothetical framework in the dataset. We have found that a SOAP representation with a cutoff length of 6 Å, which goes beyond near-neighbor tetrahedra, best describes the structural diversity in the Deem database by capturing relevant interatomic correlations. Kernel principal component analysis shows that SOAP maintains its superior performance even when reducing its dimensionality to those of the classical descriptors and that the first three ...
Latest version: v1
Publication date: Nov 06, 2019
Thibault Sohier,
Marco Gibertini,
Davide Campi,
Giovanni Pizzi,
Nicola Marzari
- Two-dimensional materials are emerging as a promising platform for ultrathin channels in field-effect transistors. To this aim, novel high-mobility semiconductors need to be found or engineered. Although extrinsic mechanisms can in general be minimized by improving fabrication processes, the suppression of intrinsic scattering (driven, for example, by electron–phonon interactions) requires modification of the electronic or vibrational properties of the material. Because intervalley scattering critically affects mobilities, a powerful approach to enhance transport performance relies on engineering the valley structure. We show here the power of this strategy using uniaxial strain to lift degeneracies and suppress scattering into entire valleys, dramatically improving performance. This is shown in detail for arsenene, where a 2% strain stops scattering into four of the six valleys and leads to a 600% increase in mobility. The mechanism is general and can be applied to many other ...
Latest version: v2
Publication date: Nov 04, 2019
Shengnan Zhang,
Quansheng Wu,
Yi Liu,
Oleg V. Yazyev
- In this work, we investigate the transverse magnetoresistance of materials by combining the Fermi surfaces calculated from first principles with the Boltzmann transport theory approach relying on the semiclassical model and the relaxation time approximation. We first consider a series of simple model Fermi surfaces to provide a didactic introduction into the charge-carrier compensation and open-orbit mechanisms leading to nonsaturating magnetoresistance. We then address in detail magnetotransport in three representative materials: (i) copper, (ii) bismuth, and (iii) tungsten diphosphide. Furthermore, the calculations allow for a full interpretation of the observed features in terms of the Fermi surface topology. Our study thus establishes guidelines to clarifying the physical mechanisms underlying the magnetotransport properties in a broad range of materials.
Latest version: v1
Publication date: Oct 29, 2019
Shengnan Zhang,
Quansheng Wu,
Oleg V. Yazyev
- In this work, we investigate the angle-dependent magnetoresistance (AMR) of the layered nodal-line Dirac semimetal ZrSiS for the in-plane and out-of-plane current directions. Combining the Fermi surfaces calculated from first principles with the Boltzmann’s semiclassical transport theory, we reproduce all the prominent features of the unusual behavior of the in-plane and out-of-plane AMR.We can conclude that the dominant contribution the cusplike AMR lies in open orbits of the hole pocket and, in general, AMR is strongly influenced by charge compensation effect and the off-diagonal conductivity tensor elements, which give rise to peculiar butterfly-shaped AMR.
Latest version: v1
Publication date: Oct 29, 2019
Doreen Beyer,
Shiyong Wang,
Carlo A. Pignedoli,
Jason Melidonie,
Bingkai Yuan,
Can Li,
Jan Wilhelm,
Pascal Ruffieux,
Reinhard Berger,
Klaus Müllen,
Roman Fasel,
Xinliang Feng
- In a recent work, we demonstrated the bottom-up on-surface synthesis of poly(para-dibenzo[bc,kl]-coronenylene) , a zigzag edge-encased analog of poly(para-phenylene), and its lateral fusion into zigzag edge-extended graphene nanoribbons.
The record contains data to reproduce the calculations that were performed at Empa to support the findings discussed in the manuscript.
Latest version: v1
Publication date: Oct 29, 2019
Andrea Grisafi,
Alberto Fabrizio,
Benjamin Meyer,
David Wilkins,
Clemence Corminboeuf,
Michele Ceriotti
- The electronic charge density plays a central role in determining the behavior of matter at the atomic scale, but its computational evaluation requires demanding electronic-structure calculations. We introduce an atom-centered, symmetry-adapted framework to machine-learn the valence charge density based on a small number of reference calculations. The model is highly transferable, meaning it can be trained on electronic-structure data of small molecules and used to predict the charge density of larger compounds with low, linear-scaling cost. Applications are shown for various hydrocarbon molecules of increasing complexity and flexibility, and demonstrate the accuracy of the model when predicting the density on octane and octatetraene after training exclusively on butane and butadiene. This transferable, data-driven model can be used to interpret experiments, accelerate electronic structure calculations, and compute electrostatic interactions in molecules and condensed-phase systems.
Latest version: v1
Publication date: Oct 28, 2019
Alberto Fabrizio,
Andrea Grisafi,
Benjamin Meyer,
Michele Ceriotti,
Clemence Corminboeuf
- Chemists continuously harvest the power of non-covalent interactions to control phenomena in both the micro- and macroscopic worlds. From the quantum chemical perspective, the strategies essentially rely upon an in-depth understanding of the physical origin of these interactions, the quantification of their magnitude and their visualization in real-space. The total electron density ρ(r) represents the simplest yet most comprehensive piece of information available for fully characterizing bonding patterns and non-covalent interactions. The charge density of a molecule can be computed by solving the Schrödinger equation, but this approach becomes rapidly demanding if the electron density has to be evaluated for thousands of different molecules or very large chemical systems, such as peptides and proteins. Here we present a transferable and scalable machine-learning model capable of predicting the total electron density directly from the atomic coordinates. The regression model is ...
Latest version: v1
Publication date: Oct 28, 2019
Leopold Talirz,
Hajo Söde,
Shigeki Kawai,
Pascal Ruffieux,
Ernst Meyer,
Xinliang Feng,
Klaus Müllen,
Roman Fasel,
Carlo A. Pignedoli,
Daniele Passerone
- The record contains the theoretical data supporting a recent publication where we discuss the band gap of finite armchair graphene nanoribbons with a width of seven rows of carbon atoms (7‐AGNRs) on Au(111) through scanning tunneling microscopy/spectroscopy combined with density functional theory calculations.
Latest version: v1
Publication date: Oct 28, 2019
Leonid Kahle,
Aris Marcolongo,
Nicola Marzari
- We present a computational screening of experimental structural repositories for fast Li-ion conductors, with the goal of finding new candidate materials for application as solid-state electrolytes in next-generation batteries. We start from ~1400 unique Li-containing materials, of which ~900 are insulators at the level of density-functional theory. For those, we calculate the diffusion coefficient in a highly automated fashion, using extensive molecular dynamics simulations on a potential energy surface (the recently published pinball model) fitted on first-principles forces. The ~130 most promising candidates are studied with full first-principles molecular dynamics, first at high temperature and then more extensively for the 78 most promising candidates. The results of the first-principles simulations of the candidate solid-state electrolytes found are discussed in detail.
Latest version: v1
Publication date: Oct 28, 2019
Aris Marcolongo,
Tobias Binninger,
Federico Zipoli,
Teodoro Laino
- The recently published DeePMD model, based on a deep neural network architecture, brings the hope of solving the time-scale issue which often prevents the application of first principle molecular dynamics to physical systems. With this contribution we assess the performance of the DeePMD potential on a real-life application and model diffusion of ions in solid-state electrolytes. We consider as test cases the well known Li10GeP2S12, Li7La3Zr2O12 and Na3Zr2Si2PO12. We develop and test a training protocol suitable for the computation of diffusion coefficients, which is one of the key properties to be optimized for battery applications, and we find good agreement with previous computations. Our results show that the DeePMD model may be a successful component of a framework to identify novel solid-state electrolytes.
Latest version: v1
Publication date: Oct 25, 2019
Junzhi Liu,
Shantanu Mishra,
Carlo A. Pignedoli,
Daniele Passerone,
José I. Urgel,
Alberto Fabrizio,
Thorsten G. Lohr,
Ji Ma,
Hartmut Komber,
Martin Baumgarten,
Clemence Corminboeuf,
Reinhard Berger,
Pascal Ruffieux,
Klaus Müllen,
Roman Fasel,
Xinliang Feng
- Nonbenzenoid carbocyclic rings are postulated to serve as important structural elements toward tuning the chemical and electronic properties of extended polycyclic aromatic hydrocarbons (PAHs, or namely nanographenes), necessitating a rational and atomically precise synthetic approach toward their fabrication. This record contains data supporting a recent work where, using a combined bottom-up in-solution and on-surface synthetic approach, we report the synthesis of nonbenzenoid open-shell nanographenes containing two pairs of embedded pentagonal and heptagonal rings.
Latest version: v1
Publication date: Oct 25, 2019
Tobias Binninger,
Aris Marcolongo,
Matthieu Mottet,
Valéry Weber,
Teodoro Laino
- Superior stability and safety are key promises attributed to all-solid-state batteries (ASSBs) containing solid-state electrolyte (SSE) in comparison to their conventional counterparts utilizing liquid electrolyte. To unfold the full potential of ASSBs, SSE materials are desirable that are stable in contact with both the low and the high potential electrode. The electrochemical stability window is conveniently used to assess the SSE--electrode interface stability. In the present work, we review the most important methods to compute the SSE stability window. We find that the stoichiometry stability method represents a bridge between HOMO--LUMO method and phase stability method (grand canonical phase diagram). We further provide implementations of these methods for SSE material screening and we compare their results for the relevant Li- and Na-SSE materials LGPS, LIPON, LLZO, LLTO, LATP, LISICON, and NASICON.
Latest version: v1
Publication date: Oct 25, 2019
Leonid Kahle,
Xi Cheng,
Tobias Binninger,
Steven D. Lacey,
Aris Marcolongo,
Federico Zipoli,
Elisa Gilardi,
Claire Villevieille,
Mario El Kazzi,
Nicola Marzari,
Daniele Pergolesi
- We study the oxo-hexametallate Li7TaO6 with first-principles and classical molecular dynamics simulations, obtaining a low activation barrier for diffusion of ∼0.29 eV and a high ionic conductivity of 5.7×10−4 S cm−1 at room temperature (300 K). We find evidence for a wide electrochemical stability window from both calculations and experiments, suggesting its viable use as a solid-state electrolyte in next-generation solid-state Li-ion batteries. To assess its applicability in an electrochemical energy storage system, we performed electrochemical impedance spectroscopy measurements on multicrystalline pellets, finding substantial ionic conductivity, if below the values predicted from simulation. We further elucidate the relationship between synthesis conditions and the observed ionic conductivity using X-ray diffraction, inductively coupled plasma optical emission spectrometry, and X-ray photoelectron spectroscopy, and study the effects of Zr and Mo doping.
Latest version: v1
Publication date: Oct 25, 2019
Jaime Souto-Casares,
Nicola A. Spaldin,
Claude Ederer
- Oxygen vacancies are a common source of excess electrons in complex oxides. In Mott insulators, these additional electrons can induce a metal-insulator transition (MIT), fundamentally altering the electronic properties of the system. Here we study the effect of oxygen vacancies in LaTiO3, a prototypical Mott insulator close to the MIT. We show that the introduction of oxygen vacancies creates a vacancy-related band immediately below the partially filled Ti-t 2g bands. We study the effect of this additional band on the Mott MIT using a combination of density functional theory and dynamical mean-field theory (DFT+DMFT), employing a minimal correlated subspace consisting of effective Ti-t 2g orbitals plus an additional Wannier function centered on the vacancy site. We find that the Mott insulating state in LaTiO3 is robust to the presence of the vacancy band, which remains fully occupied even in the presence of a local Coulomb repulsion, and therefore does not cause a doping of the Mott insulator
Latest version: v1
Publication date: Oct 24, 2019
Kun Xu,
José I. Urgel,
Kristjan Eimre,
Marco Di Giovannantonio,
Ashok Keerthi,
Hartmut Komber,
Shiyong Wang,
Akimitsu Narita,
Reinhard Berger,
Pascal Ruffieux,
Carlo A. Pignedoli,
Junzhi Liu,
Klaus Müllen,
Roman Fasel,
Xinliang Feng
- In a recent publication we demonstrated the on surface synthesis of a porous nanographene and we characterized its electronic properties combining spectroscopy experiments to ab-initio simulations. In this record we provide experimental and computational data that support the results discussed in the manuscript.
Latest version: v1
Publication date: Oct 23, 2019
Oleg E. Peil,
Alexander Hampel,
Claude Ederer,
Antoine Georges
- Rare-earth nickelates exhibit a remarkable metal-insulator transition accompanied by a symmetry-lowering structural distortion. Using model considerations and first-principles calculations, we present a theory of this phase transition which reveals the key role of the coupling between electronic and lattice instabilities. We show that the transition is driven by the proximity to an instability towards electronic disproportionation which couples to a specific structural distortion mode, cooperatively driving the system into the insulating state. This allows us to identify two key control parameters of the transition: the susceptibility to electronic disproportionation and the stiffness of the lattice mode. We show that our findings can be rationalized in terms of a Landau theory involving two coupled order parameters, with general implications for transition-metal oxides.
Latest version: v1
Publication date: Oct 22, 2019
Luigi Bonati,
Yue-Yu Zhang,
Michele Parrinello
- Sampling complex free-energy surfaces is one of the main challenges of modern atomistic simulation methods. The presence of kinetic bottlenecks in such surfaces often renders a direct approach useless. A popular strategy is to identify a small number of key collective variables and to introduce a bias potential that is able to favor their fluctuations in order to accelerate sampling. Here, we propose to use machine-learning techniques in conjunction with the recent variationally enhanced sampling method [O. Valsson, M. Parrinello, Phys. Rev. Lett. 113, 090601 (2014)] in order to determine such potential. This is achieved by expressing the bias as a neural network. The parameters are determined in a variational learning scheme aimed at minimizing an appropriate functional. This required the development of a more efficient minimization technique. The expressivity of neural networks allows representing rapidly varying free-energy surfaces, removes boundary effects artifacts, and allows several collective variables to be handled.
Latest version: v1
Publication date: Oct 22, 2019
Michele Ceriotti,
Lyndon Emsley,
Federico Paruzzo,
Albert Hofstetter,
Félix Musil,
Sandip De,
Edgar A. Engel,
Andrea Anelli
- We present a database of energy and NMR chemical shifts DFT calculations of 4150 crystal organic solids. The structures contain only H/C/N/O/S atoms and were subject to all-atoms geometry optimisation. Calculations were carried out using Quantum Espresso and GIPAW.
Latest version: v2
Publication date: Oct 22, 2019
Shantanu Mishra,
Doreen Beyer,
Kristjan Eimre,
Junzhi Liu,
Reinhard Berger,
Oliver Gröning,
Carlo A. Pignedoli,
Klaus Müllen,
Roman Fasel,
Xinliang Feng,
Pascal Ruffieux
- In a recent work, we reported a combined in-solution and on-surface synthesis of π-extended triangulene, a non-Kekulé nanographene with the structural formula C33H15, consisting of ten benzene rings fused in a triangular fashion. The distinctive topology of the molecule entails the presence of three unpaired electrons that couple to form a spin quartet ground state. In this record we include experimental and computational data that support the findings of the manuscript.
Latest version: v1
Publication date: Oct 21, 2019
Vojtěch Spiwok,
Charles Oluremi Solanke,
Dalibor Trapl,
Zoran Šućur,
Václav Mareška,
Igor Tvaroška
- 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.
Latest version: v2
Publication date: Oct 21, 2019
Sophie Beck,
Claude Ederer
- We use density-functional theory plus dynamical mean-field theory to demonstrate the emergence of a metallic layer at the interface between the two Mott insulators LaTiO3 and LaVO3. The metallic layer is due to charge transfer across the interface, which alters the valence state of the transition-metal cations close to the interface. Somewhat counterintuitively, the charge is transferred from the Ti cations with formal d1 electron configuration to the the V cations with formal d2 configuration, thereby increasing the occupation difference of the t2g states. This can be understood as a result of a gradual transition of the charge-transfer energy, or electronegativity, across the interface. The spatial extension of the metallic layer, in particular toward the LaTiO3 side, can be controlled by epitaxial strain, with tensile strain leading to a localization within a thickness of only two unit cells. Our results open up a route for creating a tunable quasi-two-dimensional electron gas in materials with strong electronic correlations.
Latest version: v1
Publication date: Oct 17, 2019
Mathieu Luisier,
Aron Szabo,
Achint Jain,
Markus Parzefall,
Lukas Novotny
- In ultra-thin two-dimensional (2-D) materials, the formation of ohmic contacts with top metallic layers is a challenging task that involves different processes than in bulk-like structures. Besides the Schottky barrier height, the transfer length of electrons between metals and 2-D monolayers is a highly relevant parameter. For MoS2, both short (≤30 nm) and long (≥0.5 μm) values have been reported, corresponding to either an abrupt carrier injection at the contact edge or a more gradual transfer of electrons over a large contact area. Here we use ab initio quantum transport simulations to demonstrate that the presence of an oxide layer between a metallic contact and a MoS2 monolayer, for example TiO2 in case of titanium electrodes, favors an area-dependent process with a long transfer length, while a perfectly clean metal-semiconductor interface would lead to an edge process. These findings reconcile several theories that have been postulated about the physics of metal/MoS2 ...
Latest version: v1
Publication date: Oct 14, 2019
Mathieu Luisier,
Aron Szabo,
Cedric Klinkert,
Davide Campi,
Christian Stieger,
Nicola Marzari
- Full-band atomistic quantum transport simulations based on first principles are employed to assess the potential of band-to-band tunneling field-effect-transistors (TFETs) with a 2-D channel material as future electronic circuit components. We demonstrate that single layer transition metal dichalcogenides (TMDs) are not well-suited for TFET applications. There might, however, exist a great variety of 2-D semiconductors that have not even been exfoliated yet: this work pinpoints some of the most promising candidates among them to realize highly efficient TFETs. Single-layer SnTe, As, TiNBr, and Bi are all found to ideally deliver ON-currents larger than 100 μA/μm at 0.5 V supply voltage and 0.1 nA/μm OFF current value. We show that going from single to multiple layers can boost the TFET performance as long as the gain from a narrowing band gap exceeds the loss from the deteriorating gate control. Finally, a 2-D van der Waals heterojunction TFET is revealed to perform almost as well ...
Latest version: v1
Publication date: Oct 11, 2019
José I. Urgel,
Marco Di Giovannantonio,
Guido Gandus,
Qiang Chen,
Xunshan Liu,
Hironobu Hayashi,
Pascal Ruffieux,
Silvio Decurtins,
Akimitsu Narita,
Daniele Passerone,
Hiroko Yamada,
Shi‐Xia Liu,
Klaus Müllen,
Carlo A. Pignedoli,
Roman Fasel
- On‐surface synthesis is a unique tool for growing low‐dimensional carbon nanomaterials with precise structural control down to the atomic level.
One of the most applied reactions to covalently interlink molecular precursors is dehalogenative aryl‐aryl coupling.
Failures in this process are often related to the steric hindrance between reactants, which may arise due to their coplanarity upon adsorption on a surface. In a recent work we proposed a copolymerization approach to overcome the limitations that prevent intermolecular homocoupling. We used suitable linkers as additional reactants to demonstrate formation of fully conjugated polycyclic nanowires incorporating non‐benzenoid rings. This record contains data to support the experimental and theoretical evidences discussed in the manuscript.
Latest version: v1
Publication date: Oct 10, 2019
Martina Danese,
Marta Bon,
GiovanniMaria Piccini,
Daniele Passerone
- In a recent publication we inspected the mechanism of the azide–alkyne Huisgen cycloaddition. We studied the dynamical aspects of the process using metadynamics computer simulations. We focused on the conformational aspects that determine the course of the reaction and characterize its free energy landscape. This record contains data related to the calculations discussed in the publication.
Latest version: v1
Publication date: Oct 09, 2019
Claudia Cardoso,
Andrea Ferretti,
Deborah Prezzi
- First principles the optical response of finite-length armchair-edged graphene nanoribbons (AGNRs) within the framework of many-body perturbation theory. As a result of the explicit inclusion of zigzag extremities, we identify low-energy and low-intensity excitations that are expected to be almost independent of the GNR length. These excitations coexist with bulk-like excitations, which have the same origin as the ones characterizing infinite AGNRs. Our results are used to rationalize termini effects on the optical response of GNRs and to shed light on recent photoluminescence data.
Latest version: v1
Publication date: Oct 03, 2019
Peter G. Boyd,
Arunraj Chidambaram,
Enrique García-Díez,
Christopher P. Ireland,
Thomas D. Daff,
Richard Bounds,
Andrzej Gładysiak,
Pascal Schouwink,
Seyed Mohamad Moosavi,
M. Mercedes Maroto-Valer,
Jeffrey A. Reimer,
Jorge A. R. Navarro,
Tom K. Woo,
Susana Garcia,
Kyriakos C. Stylianou,
Berend Smit
- In this entry is a database of 324,426 hypothetical Metal-Organic Frameworks (MOFs) that were used in a study to screen potential carbon dioxide scrubbers. Using a method to assemble these materials with topological blueprints, we only selected materials that could be accurately represented with the MEPO-QEq charge generation method. By ensuring that the electrostatic potential is accurately represented in these materials, screening for CO2 adsorption properties would result very few false positives/negatives. The atom-centered charges reported in the CIF file for each MOF were derived from the MEPO-QEq method, which can be found under the '_atom_type_partial_charge' column in each CIF file.
The relevant data for each MOF is reported in accompanying .csv files. Post-combustion flue gas was simulated at a temperature of both 298K and 0.15 bar CO2, and 313K and 0.15 bar CO2. Mixture adsorption was simulated with the conditions 298K and 0.15:0.85 CO2/N2 with a total pressure of 1 ...
Latest version: v3
Publication date: Oct 02, 2019
Ulrich Aschauer,
Chiara Ricca,
Iurii Timrov,
Matteo Cococcioni,
Nicola Marzari
- We propose a self-consistent site-dependent Hubbard U approach for density functional theory (DFT)+U calculations of defects in complex transition metal oxides, using Hubbard parameters computed via linear response theory. The formation of a defect locally perturbs the chemical environment of Hubbard sites in its vicinity, resulting in different Hubbard U parameters for different sites. Using oxygen vacancies in SrMnO3 as a model system, we investigate the dependence of U on the chemical environment and study its influence on the structural, electronic, and magnetic properties of defective bulk and strained thin-film structures. Our results show that a self-consistent U improves the description of stoichiometric bulk SrMnO3 with respect to generalized gradient approximation (GGA) or GGA+U calculations using an empirical U. For defective systems, U changes as a function of the distance of the Hubbard site from the defect, its oxidation state, and the magnetic phase of the bulk ...
Latest version: v1
Publication date: Sep 25, 2019
Marco Di Giovannantonio,
Kristjan Eimre,
Aliaksandr V. Yakutovich,
Qiang Chen,
Shantanu Mishra,
José I. Urgel,
Carlo A. Pignedoli,
Pascal Ruffieux,
Klaus Müllen,
Akimitsu Narita,
Roman Fasel
- This record contains the experimental and computational data needed to support the work done on on-surface synthesis of conjugated polymers consisting of indeno[2,1-b]fluorene units, which are antiaromatic and open-shell biradicaloids. The observed reaction products have been characterized via low-temperature scanning tunneling microscopy/spectroscopy and noncontact atomic force microscopy, complemented by density-functional theory calculations. These polymers present a low band gap when adsorbed on Au(111). Moreover, their pronounced antiaromaticity and radical character, elucidated by ab initio calculations, make them promising candidates for applications in electronics and spintronics. Further, they provide a rich playground to explore magnetism in low-dimensional organic nanomaterials.
Latest version: v1
Publication date: Sep 23, 2019
Michele Invernizzi,
Michele Parrinello
- Many enhanced sampling techniques rely on the identification of a number of collective variables that describe all the slow modes of the system. By constructing a bias potential in this reduced space one is then able to sample efficiently and reconstruct the free energy landscape. In methods like metadynamics, the quality of these collective variables plays a key role in convergence efficiency. Unfortunately in many systems of interest it is not possible to identify an optimal collective variable, and one must deal with the non-ideal situation of a system in which some slow modes are not accelerated.
We propose a two-step approach in which, by taking into account the residual multiscale nature of the problem, one is able to significantly speed up convergence. To do so, we combine an exploratory metadynamics run with an optimization of the free energy difference between metastable states, based on the recently proposed variationally enhanced sampling method. This new method is ...
Latest version: v4
Publication date: Sep 17, 2019
Soumyadipta Maiti,
Walter Steurer
- This is a LAMMPS readable EAM type potential file for Hf-Nb-Ta-Zr based high-entropy alloys (HEAs). In this potential file the elements are sequenced as Hf, Nb, Ta and Zr, respectively. This potential was previously used to model the HEA for the local lattice distortions due to short-range order clustering found in the alloy after long-term annealing at high-temperature. The input to build this potential is based on the physical properties of pure elements such as the lattice parameter, cohesive energy, elastic constants etc and the details are discussed in the associated reference. Units used are in eV/atom for energy and Angstrom for distance.
Latest version: v1
Publication date: Sep 14, 2019
Migle Grauzinyte,
Stefan Goedecker,
Silvana Botti,
Miguel Marques,
Jose Flores-Livas
- Computational data to support an extensive study of prospective dopants in the zinc blende (gamma) phase of cuprous iodide. This phase of CuI holds the current record hole conductivity for intrinsic transparent p-type semiconductors. In the corresponding scientific article, a high-throughput approach was employed to systematically explore strategies for enhancing CuI further by impurity incorporation. Our objectives were to identify a practical approach for increasing hole conductivity in CuI thin films and to explore the possibility for ambivalent doping. A total of 64 chemical elements was investigated. This materials cloud record contains all optimized defective structures for Cu and I substitutional sites, calculation settings and some of the output (LOCPOT files, required for electrostatic correction calculations are not included due to their large size). Chalcogen elements were found to display acceptor character when substituting iodine. Further eight impurities suitable ...
Latest version: v1
Publication date: Sep 11, 2019
Sergi Vela,
Clémence Corminboeuf,
Constantin Krüger
- 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.
Latest version: v1
Publication date: Sep 10, 2019
Haruhiko Dekura,
Taku Tsuchiya
- This database includes Isotropic lattice thermal conductivities of MgSiO3 post-perovskite under the lowermost mantle conditions. The conductivity was calculated based on the ab initio anharmonic lattice dynamics with solving the linearized phonon Boltzmann transport equation.
Latest version: v1
Publication date: Sep 10, 2019
Assil Bouzid,
Alfredo Pasquarello
- We investigate formation energies of C, Si, and Ge defects in β-Ga2O3 through hybrid functional calculations. We find that the interstitial defects of these elements generally occur at higher energies than their substitutional counterparts, while they are more stable at low Fermi energies in Ga-rich conditions. In n-type and Ga-rich conditions, interstitials of Si and Ge show significantly higher formation energies than their substitutional form, but this difference is less pronounced for C. Charge transition levels of interstitial defects lie in the upper part of the band-gap, and account for several measured levels in unintentionally doped and Ge-doped samples of β-Ga2O3.
Latest version: v1
Publication date: Sep 09, 2019
Yong-Ji Hu,
Ge Zhao,
Baiyu Zhang,
Chaoming Yang,
Mingfei Zhang,
Zi-Kui Liu,
Xiaofeng Qian,
Liang Qi
- The interactions between solute atoms and crystalline defects such as vacancies, dislocations, and grain boundaries are essential in determining alloy properties. Here we present a general linear correlation between two descriptors of local electronic structures and the solute-defect interaction energies in binary alloys of body-centered-cubic (bcc) refractory metals (such as W and Ta) with transition-metal substitutional solutes. One electronic descriptor is the bimodality of the d-orbital local density of states for a matrix atom at the substitutional site, and the other is related to the hybridization strength between the valance sp- and d-bands for the same matrix atom. For a particular pair of solute-matrix elements, this linear correlation is valid independent of types of defects and the locations of substitutional sites. These results provide the possibility to apply local electronic descriptors for quantitative and efficient predictions on the solute-defect interactions and defect properties in alloys.
Latest version: v1
Publication date: Sep 02, 2019
Daniele Ongari,
Yifei Michelle Liu,
Berend Smit
- ∆9-tetrahydrocannabinol (THC) is the principal psychoactive component of cannabis, and there is an urgent need to build low-cost and portable devices that can detect its presence from breath. Similarly to alcohol detectors, these tools can be used by law enforcement to determine driver intoxication and enforce safer and more regulated use of cannabis. In this work, we propose to use a class of microporous crystals, metal–organic frameworks (MOFs), to selectively adsorb THC that can be later detected using optical, electrochemical, or fluorescence-based sensing methods. We screened computationally more than 5000 MOFs, highlighting the materials that have the largest affinity with THC, as well as the highest selectivity against water, showing that it is thermodynamically feasible for MOFs to adsorb THC from humid breath. We propose and compare different models for THC and different computational protocols to rank the promising materials, also presenting a novel approach to assess ...
Latest version: v1
Publication date: Sep 02, 2019
José I. Urgel,
Carlo A. Pignedoli,
Roman Fasel
- In this work we characterize a conjugated polycyclic hydrocarbon containing multiple nonbenzenoid rings and exhibiting negative curvature—the warped nanographene C80H30. The record contains input files to reproduce the calculations discussed in the manuscript and the raw data of the experimental images discussed.
Latest version: v1
Publication date: Aug 27, 2019
Janani Sampath,
Jim Pfaendtner
- The leucine-lysine amphiphilic peptide LKα14 has been used to study fundamental driving forces in processes such as peptide-surface binding and biomineralization. Here, we employ molecular dynamics (MD) simulations in tandem with replica exchange metadynamics to probe the binding mechanism and thermodynamics of LKα14 on silica. We also investigate the effect that the nature of the silica surface – crystalline vs. amorphous, has on the binding properties and peptide-surface conformations. We find that water adsorbs differently on both surfaces; it forms a denser interfacial layer on the crystalline surface, compared to the amorphous surface. This causes the peptide to bind more strongly on the amorphous surface than the crystalline surface. Cluster analysis shows that the peptide adopts a helical conformation at both surfaces, with a greater distribution of states on the crystalline surface. Peptide binding is primarily through lysine interactions, in line with prior experimental results.
Latest version: v1
Publication date: Aug 26, 2019
Kevin Maik Jablonka,
Daniele Ongari,
Berend Smit
- Molecular simulations with periodic boundary conditions require to define a certain cutoff distance beyond which pairwise dispersion interactions are neglected. For the simulation of homogeneous phases it is well-established to use tail-corrections, that can remedy this truncation of the potential. These corrections are built under the assumption that beyond the cutoff the radial distribution function is equal to one. In this work we shed some light on the discussion whether or not tail corrections should be used in the modelling of heterogeneous systems. We show that for the adsorption of gasses in a diverse set nanoporous crystalline materials (zeolites, Covalent Organic Frameworks (COFs), and Metal Organic Frameworks (MOFs)), tail-corrections are an appropriate choice with which the results are much less sensitive to the details of the truncation.
Latest version: v3
Publication date: Aug 21, 2019
Yang Yang,
Ka Un Lao,
David M. Wilkins,
Andrea Grisafi,
Michele Ceriotti,
Robert A. DiStasio Jr.
- Dipole polarizabilities (and other molecular properties) computed using linear response coupled cluster theory (LR-CCSD/d-aug-cc-pVDZ) and hybrid density functional theory (B3LYP/d-aug-cc-pVDZ, SCAN0/d-aug-cc-pVDZ, and B3LYP/d-aug-cc-pVTZ) for the 7,211 molecules in the QM7b database and the 52 molecules in the AlphaML showcase database.
Latest version: v3
Publication date: Aug 13, 2019
Yanqing Su,
Shuozhi Xu,
Irene Beyerlein
- Density functional theory calculations were used to obtain the generalized stacking fault energy surfaces in eight FCC metals: Ag, Au, Cu, Ir, Ni, Pd, Pt, and Rh. Among them, ferromagnetism was considered only in Ni. Results based on non-magnetic Ni are denoted as Ni-NM.
Latest version: v1
Publication date: Aug 13, 2019
QuanSheng Wu,
Alexey A. Soluyanov,
Tomáš Bzdušek
- Electron energy bands, which are studied to explain electronic and optical properties of crystalline solids, often exhibit degeneracies called band-structure nodes. Here, we introduce non-Abelian topological charges that characterize line nodes inside the momentum space of -symmetric crystalline metals with weak spin-orbit coupling. We show that these are quaternion charges, similar to those describing disclinations in biaxial nematics. Starting from two-band considerations, we develop the complete many-band description of nodes in the presence of and mirror symmetries, which allows us to investigate the topological stability of nodal chains in metals. The non-Abelian charges put strict constraints on the possible nodal line configurations. Our analysis goes beyond the standard approach to band topology and implies the existence of 1D topological phases not present in existing classifications.
Latest version: v1
Publication date: Aug 09, 2019
Thomas Bischoff,
Igor Reshetnyak,
Alfredo Pasquarello
- We describe a nonempirical procedure for achieving accurate band gaps of extended systems through the insertion of suitably defined potential probes. By enforcing Koopmans' condition on the resulting localized electronic states, we determine the optimal fraction of Fock exchange to be used in the adopted hybrid functional. As potential probes, we consider point defects, the hydrogen interstitial, and various adjustable potentials that allow us to vary the energy level of the localized state in the band gap. By monitoring the delocalized screening charge, we achieve a measure of the degree of hybridization with the band states, which can be used to improve the band-gap estimate. Application of this methodology to AlP, C, and MgO yields band gaps differing by less than 0.2 eV from experiment.
Latest version: v1
Publication date: Aug 08, 2019
Patrick Gono,
Francesco Amborsio,
Alfredo Pasquarello
- We investigate the solvation effect of water on the overpotentials of the oxygen evolution reaction on rutile TiO2 by applying the thermodynamic integration method on atomistic model interfaces with and without the water molecules. We compare the results at the vacuum interface with the commonly used computational hydrogen electrode method, finding overall good agreement. The effect of the solvent is found to be twofold. First, the explicit treatment of the solvent can lead to equilibrium configurations differing from the relaxed structures without solvent. Second, the overpotentials can be affected by up to 0.5 eV. The energetics are subject to electrostatic effects at the interface rather than to modifications in the hydrogen bond network. These results provide a promising perspective for treating the solvent with implicit models.
Latest version: v2
Publication date: Aug 02, 2019
José I. Urgel,
Carlo Antonio Pignedoli,
Roman Fasel
- 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.
Latest version: v1
Publication date: Jul 15, 2019
Yue-Wen Fang,
Hanghui Chen
- Project abstract: Frustrated magnets are one class of fascinating materials that host many intriguing phases such as spin ice, spin liquid and complex long-range magnetic orderings at low temperatures. In this work we use first-principles calculations to find that in a wide range of magnetically frustrated oxides, at zero temperature a number of non-collinear magnetic orderings are more stable than the type-I collinear ordering that is observed at finite temperatures. The emergence of non-collinear orderings in those complex oxides is due to higher-order exchange interactions that originate from second-row and third-row transition metal elements. This implies a collinear-to-noncollinear spin transition at sufficiently low temperatures in those frustrated complex oxides. Furthermore, we find that in a particular oxide Ba2YOsO6, experimentally feasible uniaxial strain can tune the material between two different non-collinear magnetic orderings. Our work predicts new non- collinear ...
Latest version: v1
Publication date: Jul 02, 2019
Julia Wiktor,
Alfredo Pasquarello
- We determine the transition levels of electron and hole polarons at the BiVO4–water interface through thermodynamic integration within a hybrid functional scheme, thereby accounting for the liquid nature of the water component. The electron polaron is found to be less stable at the interface than in the bulk by 0.18 eV, while for the hole polaron the binding energy increases by 0.20 eV when the charge localizes in the surface layer of BiVO4. These results indicate that interfacial effects on the polaron binding energy and charge distribution are sizeable and cannot trivially be inferred from bulk calculations.
Latest version: v1
Publication date: Jul 01, 2019
Michele Pizzochero,
Francesco Ambrosio,
Alfredo Pasquarello
- A transient state of the excess electron in liquid water preceding the development of the solvation shell, the so-called wet electron, has been invoked to explain spectroscopic observations, but its binding energy and atomic structure have remained highly elusive. Here, we carry out hybrid functional molecular dynamics to unveil the ultrafast solvation mechanism leading to the hydrated electron. In the pre-hydrated regime, the electron is found to repeatedly switch between a quasi-free electron state in the conduction band and a localized state with a binding energy of 0.26 eV, which we assign to the wet electron. This transient state self-traps in a region of the liquid which extends up to ∼4.5 Å and involves a severe disruption of the hydrogen-bond network. Our picture provides an unprecedented view on the nature of the wet electron, which is instrumental to understand the properties of this fundamental species in liquid water.
Latest version: v1
Publication date: Jun 20, 2019
Assil Bouzid,
Patrick Gono,
Alfredo Pasquarello
- 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.
Latest version: v1
Publication date: Jun 18, 2019
Vojtech Spiwok,
Zoran Sucur
- Molecular simulations are computationally expensive, especially in systems with multiple free energy minima. To address this problem many enhanced sampling techniques have been developed. Metadynamics uses a bias potential defined as a sum of Gaussian hills in space of few (one or two) collective variables. This bias potential disfavors states that have been visited since the beginning of the simulation. Multiple walker metadynamics simulates the system in multiple parallel replicas. The bias potential disfavors states that have been visited since the beginning of the simulation in any replica. Flying Gaussian method presented here also simulates the system in multiple parallel replicas. It disfavors states that are, at certain moment, similar in two or more replicas. It was demonstrated on Alanine Dipeptide in vacuum and water, cis/trans-isomerisation of Proline-containing peptides and Met-enkephalin.
Latest version: v1
Publication date: Jun 18, 2019
Jana Hozzova,
Ales Krenek,
Maria Simkova,
Vojtech Spiwok
- Biomolecular simulations are computationally expensive. This limits their application in protein folding simulations, protein engineering, drug design and related fields. Enhanced sampling techniques such as metadynamics accelerates slow events in molecular simulation. This and other method apply artificial forces in directions of collective degrees of freedom (aka collective variables). Path collective variables and Property Map collective variables are defined using a series of reference structures of the studied molecular system. They require a huge number of mean square deviation calculations along the simulation. Close Structure algorithm reduces the number of these operations.
Latest version: v2
Publication date: Jun 17, 2019
Pablo M. Piaggi,
Michele Parrinello
- We present a method for performing multithermal-multibaric molecular dynamics simulations that sample entire regions of the temperature-pressure (TP) phase diagram. The method uses a variational principle [Valsson and Parrinello, Phys. Rev. Lett. 113, 090601 (2014)] in order to construct a bias that leads to a uniform sampling in energy and volume. The intervals of temperature and pressure are taken as inputs and the relevant energy and volume regions are determined on the fly. In this way the method guarantees adequate statistics for the chosen TP region. We show that our multithermal-multibaric simulations can be used to calculate all static physical quantities for all temperatures and pressures in the targeted region of the TP plane. We illustrate our approach by studying the density anomaly of TIP4P/Ice water.
This record includes input and output files, and Jupyter Notebooks describing the analysis of the simulations and the creation of the figures for the paper.
Latest version: v3
Publication date: Jun 12, 2019
Zhendong Guo,
Francesco Ambrosio,
Wei Chen,
Patrick Gono,
Alfredo Pasquarello
- This entry includes the MD trajectories of several semiconductor-water interfaces generated with ab initio molecular dynamics using the rVV10 density functional at the temperature of 350 K. Eight semiconductor surfaces are considered, namely GaAs(110), GaP(110), GaN(10-10), CdS(10-10), ZnO(10-10), SnO2(110), rutile TiO2(110) and anatase TiO2(101). For GaAs, GaP and anatase TiO2, the trajectories for the interfaces with both the molecular and the dissociative adsorption mode of water are provided. In addition, the relaxed atomic structures of the semiconductor surfaces used to calculate the ionization potential (IP) reported in [Chem. Mater. 2018, 30, 94−111] are added.
Latest version: v1
Publication date: Jun 02, 2019
Zhendong Guo,
Francesco Ambrosio,
Alfredo Pasquarello
- This entry provides MD trajectories for bulk water and the water-vacuum interface generated with ab initio molecular dynamics using rVV10 density functional at the temperature of 350 K. In the rVV10 functional, the parameter b is set to 9.3.
Latest version: v1
Publication date: Jun 01, 2019
Bonan Zhu,
Georg Schusteritsch,
Ping Lu,
Judith L. MacManus-Driscoll,
Chris J. Pickard
- Vertically aligned nanocomposites (VANs) films have self-assembled pillar-matrix nanostructures. Owing to their large area-to-volume ratios, interfaces in VAN films are expected to play key roles in inducing functional properties, but our understanding is hindered by limited knowledge about their structures. Motivated by the lack of definitive explanation for the experimentally-found enhanced ionic conductivity in Sm-doped-CeO2/SrTiO3 VAN films, we determine the structure at vertical interfaces using random structure searching and explore how it can affect ionic conduction. This record contains the candidate structures and provenance of the DFT validation calculations. Previously unknown interface structures are found, with lower energy than that of an optimized hand-built model. We find a strongly distorted oxygen sub-lattice which gives a complex landscape of vacancy energies. The cation lattice remains similar to the bulk phase but has a localized strain field. The excess ...
Latest version: v1
Publication date: May 31, 2019
Zhendong Guo,
Francesco Ambrosio,
Alfredo Pasquarello
- This entry provides the most stable defect configurations of hydrogen, carbon, and nitrogen impurities in alumina, which are identified through ab initio molecular dynamics in various charge states and structural relaxations with the PBE functional. The structural configurations related to carbon and nitrogen impurities are found to depend on the total charge set in the simulation cell.
Latest version: v1
Publication date: May 30, 2019
Zhendong Guo,
Francesco Ambrosio,
Alfredo Pasquarello
- The electronic properties of the oxygen vacancy and interstitial in amorphous Al2O3 are studied via ab initio molecular dynamics simulations and hybrid functional calculations. Our results indicate that these defects do not occur in amorphous Al2O3, due to structural rearrangements which assimilate the defect structure and cause a delocalization of the associated defect levels. The imbalance of oxygen leads to a nonstoichiometric compound in which the oxygen occurs in the form of O2– ions. Intrinsic oxygen defects are found to be unable to trap excess electrons. For low Fermi energies, the formation of peroxy linkages is found to be favored leading to the capture of holes. The relative +2/0 defect levels occur at 2.5 eV from the valence band.
Latest version: v1
Publication date: May 30, 2019
Zhendong Guo,
Francesco Ambrosio,
Alfredo Pasquarello
- This entry provides the atomic structures of three bulk amorphous TiO2 models generated through the melt-and-quench method with different cooling rates and of ten O-O peroxy linkages obtained by adding two holes to the bulk model constructed with the lowest cooling rate.
Latest version: v1
Publication date: May 30, 2019
Vladimir Rybkin
- Trajectories and spin densities for the bulk hydrated electron at the MP2 level of theory. The data represent the first ab initio molecular dynamics study of the hydrated electron in the bulk using many-body wave function theory.
Latest version: v1
Publication date: May 27, 2019
Gabriel Autes,
QuanSheng Wu,
Nicolas Mounet,
Oleg V. Yazyev
- We present a database of topological materials predicted from high-throughput first-principles calculations. The database contains electronic band structures and topological indices of 13628 materials calculated on experimental crystal structures taken from the Inorganic Crystal Structure Database (ICSD) and the Crystallography Open Database (COD). The calculations have been performed on non-magnetic phases taking into account the spin-orbit interactions using the Quantum ESPRESSO package. The Fu-Kane method and the Wannier charge center method implemented in the Z2pack code have been utilized to calculate the Z2 topological numbers of centrosymmetric and non-centrosymmetric materials, respectively. Over 4000 topologically non-trivial materials have been identified.
Latest version: v2
Publication date: May 21, 2019
Trevor David Rhone,
Wei Chen,
Shaan Desai,
Amir Yacoby,
Efthimios Kaxiras
- We use a data-driven approach to study the magnetic and thermodynamic properties of van der Waals (vdW) layered materials. We investigate monolayers of the form A2B2X6, based on the known material Cr2Ge2Te6, using density functional theory (DFT) calculations and determine their magnetic properties, such as magnetic order and magnetic moment. We also examine formation energies and use them as a proxy for chemical stability.
Latest version: v1
Publication date: May 20, 2019
QuanSheng Wu,
Christophe Piveteau,
Zhida Song,
Oleg V. Yazyev
- MgTa2N3 is predicted to host the topological Dirac semimetal phase. This archive includes input data necessary for reproducing first-principles calculation described in the publication.
Latest version: v1
Publication date: May 13, 2019
Tian Xie,
Arthur France-Lanord,
Yanming Wang,
Yang Shao-Horn,
Jeffrey Grossman
- Understanding the dynamical processes that govern the performance of functional materials is essential for the design of next generation materials to tackle global energy and environmental challenges. Many of these processes involve the dynamics of individual atoms or small molecules in condensed phases, e.g. lithium ions in electrolytes, water molecules in membranes, molten atoms at interfaces, etc., which are difficult to understand due to the complexity of local environments. We develop graph dynamical networks, an unsupervised learning approach for understanding atomic scale dynamics in arbitrary phases and environments from molecular dynamics simulations. We show that important dynamical information can be learned for various multi-component amorphous material systems, which is difficult to obtain otherwise. We develop a software package "gdynet" at https://github.com/txie-93/gdynet which implements the graph dynamical networks algorithm. This record contains the MD ...
Latest version: v1
Publication date: May 09, 2019
Osman Mamun,
Kirsten Winther,
Jacob Boes,
Thomas Bligaard
- We present a large dataset of adsorption of H, C, N, O and S onto more than 2,000 metallic and bimetallic alloy surfaces, consisting of approximately 90,000 DFT calculations performed in Quantum Espresso. The alloys are constructed from all possible combinations of 37 metals into AB and A3B stoichiometries, in the L1_0 and L1_2 structures respectively, where the 37 metals in the A1 structure are included as well. Slabs are cleaved along the 111 facet for A1 and L1_2 and along the 101 facet for L1_0, and all possible adsorption sites are sampled. In addition to the monoatomic adsorbates, adsorption of CH, CH2, CH3, NH, NH2, OH, H2O and SH is sampled for a smaller subset of alloys.
Latest version: v1
Publication date: May 01, 2019
Dalibor Trapl,
Izabela Horvacanin,
Vaclav Mareska,
Furkan Ozcelik,
Gozde Unal,
Vojtech Spiwok
- Biomolecular simulations are computationally expensive. This limits their application in drug or protein design and related fields. Several methods have been developed to address this problem. These methods often use an artificial force or potential acting on selected degrees of freedom known as collective variables. This requires explicit calculation of a collective variable (and its derivatives) from molecular structure. For collective variables that cannot be calculated explicitly or such calculations is slow we developed anncolvar package (https://github.com/spiwokv/anncolvar). This package approximates collective variables using artificial neural networks. It was tested on Isomap low dimensional representation of cyclooctane derivative or solvent-accessible surface area of Trp-cage miniprotein.
Latest version: v1
Publication date: Apr 23, 2019
Vojtech Spiwok,
Zoran Šućur,
Pavel Kříž
- Biomolecular simulations have a great potential in protein engineering, drug discovery and many other fields. Unfortunately, this method is computationally expensive, so many interesting processes cannot be routinely studied. In order to address this problem we developed Flying Gaussian method [Journal of Chemical Theory and Computation 12, 4644-4650 (2016)]. This method simultaneously simulates multiple replicas of the studied system and disfavor replicas with similar structures by artificial bias potential. The question arises how to calculate an unbiased free energy surface from a biased simulation. This dataset demonstrates together with mathematical arguments supports application of Umbrella Sampling reweighing method, despite the fact that this method is designed for methods with a time-independent bias potential.
Latest version: v1
Publication date: Apr 17, 2019
Michele Simoncelli,
Nicola Marzari,
Francesco Mauri
- Crystals and glasses exhibit fundamentally different heat conduction mechanisms: the periodicity of crystals allows for the excitation of propagating vibrational waves that carry heat, as first discussed by Peierls; in glasses, the lack of periodicity breaks Peierls' picture and heat is mainly carried by the coupling of vibrational modes, often described by a harmonic theory introduced by Allen and Feldman. Anharmonicity or disorder are thus the limiting factors for thermal conductivity in crystals or glasses; hitherto, no transport equation has been able to account for both. In the paper https://arxiv.org/abs/1901.01964, we derive such equation, resulting in a thermal conductivity that reduces to the Peierls and Allen-Feldman limits, respectively, in anharmonic-and-ordered or harmonic-and-disordered solids, while also covering the intermediate regimes where both effects are relevant. This approach also solves the long-standing problem of accurately predicting the thermal ...
Latest version: v2
Publication date: Apr 08, 2019
Shantanu Mishra,
Carlo Antonio Pignedoli,
Roman Fasel
- The data contained in this record, raw data of images and input files to reproduce calculations, support our recent report for the on-surface synthesis and characterization of two ultralow-gap open-shell molecules, namely peri-tetracene, a benzenoid graphene fragment with zigzag edge topology, and dibenzo[a,m]dicyclohepta[bcde,nopq]rubicene, a nonbenzenoid nonalternant structural isomer of peri-tetracene with two embedded azulene units. Our results provide an understanding of the ramifications of altered bond topologies at the single-molecule scale, with the prospect of designing functionalities in carbon-based nanostructures via engineering of bond topology
Latest version: v1
Publication date: Apr 07, 2019
Nicolas Mounet,
Marco Gibertini,
Philippe Schwaller,
Davide Campi,
Andrius Merkys,
Antimo Marrazzo,
Thibault Sohier,
Ivano E. Castelli,
Andrea Cepellotti,
Giovanni Pizzi,
Nicola Marzari
- Two-dimensional (2D) materials have emerged as promising candidates for next-generation electronic and optoelectronic applications. Yet, only a few dozens of 2D materials have been successfully synthesized or exfoliated. Here, we search for novel 2D materials that can be easily exfoliated from their parent compounds. Starting from 108423 unique, experimentally known three-dimensional compounds we identify a subset of 5619 that appear layered according to robust geometric and bonding criteria. High-throughput calculations using van-der-Waals density-functional theory, validated against experimental structural data and calculated random-phase-approximation binding energies, allow to identify 1825 compounds that are either easily or potentially exfoliable. In particular, the subset of 1036 easily exfoliable cases provides novel structural prototypes and simple ternary compounds as well as a large portfolio of materials to search from for optimal properties. For a subset of 258 ...
Latest version: v3
Publication date: Apr 03, 2019
Amber Mace,
Senja Barthel,
Berend Smit
- Data for the case study of TuTraSt on methane diffusion in zeolites, using a standard kinetic Monte Carlo simulation based on the output of our grid analysis. We find that it is accurate, fast, and rigorous without limitations to the geometries of the diffusion tunnels or transition states.
Latest version: v1
Publication date: Mar 11, 2019
Seyed Mohamad Moosavi,
Arunraj Chidambaram,
Leopold Talirz,
Maciej Haranczyk,
Kyriakos C. Stylianou,
Berend Smit
- We report a methodology using machine learning to capture chemical intuition from a set of (partially) failed attempts to synthesize a metal organic framework. We define chemical intuition as the collection of unwritten guidelines used by synthetic chemists to find the right synthesis conditions. As (partially) failed experiments usually remain unreported, we have reconstructed a typical track of failed experiments in a successful search for finding the optimal synthesis conditions that yields HKUST-1 with the highest surface area reported to date. We illustrate the importance of quantifying this chemical intuition for the synthesis of novel materials.
Latest version: v4
Publication date: Mar 03, 2019
Boodsarin Sawatlon,
Alberto Fabrizio,
Benjamin Meyer,
Matthew D. Wodrich,
Clémence Corminboeuf
- Applications of machine-learning (ML) techniques to the study of catalytic processes have begun to appear in the literature with increasing frequency. The computational speed up provided by ML allows the properties and energetics of thousands of prospective catalysts to be rapidly assessed. These results, once compiled into a database containing different properties, can be mined with the goal of establishing relationships between the intrinsic chemical properties of different catalysts and their overall catalytic performance. Previously, we applied ML models to predict the performance of 18,000 prospective catalysts for a Suzuki coupling reaction using molecular volcano plots. Here, we expand on our earlier work by examining a larger section of the C-C cross-coupling genome by using a dimensionality-reducing data-clustering algorithms (i.e., sketch-map) to, first, identify the compatibility of each catalyst with different C-C cross-coupling variants (e.g., Suzuki, Kumada, ...
Latest version: v3
Publication date: Feb 23, 2019
Alexander Hampel,
Claude Ederer,
Peitao Liu,
Cesare Franchini
- Rare-earth nickelates exhibit a metal–insulator transition accompanied by a structural distortion that breaks the symmetry between formerly equivalent Ni sites. The quantitative theoretical description of this coupled electronic–structural instability is extremely challenging. Here, we address this issue by simultaneously taking into account both structural and electronic degrees of freedom using a charge self-consistent combination of density functional theory and dynamical mean-field theory, together with screened interaction parameters obtained from the constrained random phase approximation. Our total energy calculations show that the coupling to an electronic instability toward a charge disproportionated insulating state is crucial to stabilize the structural distortion, leading to a clear first order character of the coupled transition. The decreasing octahedral rotations across the series suppress this electronic instability and simultaneously increase the screening of the ...
Latest version: v1
Publication date: Feb 21, 2019
Leonid Kahle,
Albert Musaelian,
Nicola Marzari,
Boris Kozinsky
- Molecular dynamics is a versatile and powerful method to study diffusion in solid-state ionic conductors, requiring minimal prior knowledge of equilibrium or transition states of the system's free energy surface. However, the analysis of trajectories for relevant but rare events, such as a jump of the diffusing mobile ion, is still rather cumbersome, requiring prior knowledge of the diffusive process in order to get meaningful results. In this work we present a novel approach to detect the relevant events in a diffusive system without assuming prior information regarding the underlying process. We start from a projection of the atomic coordinates into a landmark basis to identify the dominant features in a mobile ion's environment. Subsequent clustering in landmark space enables a discretization of any trajectory into a sequence of distinct states. As a final step, the use of the Smooth Overlap of Atomic Positions descriptor allows distinguishing between different environments in ...
Latest version: v1
Publication date: Feb 12, 2019
Benjamin Meyer,
Senja Barthel,
Amber Mace,
Laurent Vannay,
Benoit Guillot,
Berend Smit,
Clémence Corminboeuf
- The study of organic molecular crystals under high pressure provides fundamental insight into crystal packing distortions and reveals mechanisms of phase transitions and the crystallization of polymorphs. These solid state transformations can be monitored directly by analyzing electron charge densities that are experimentally obtained at high pressure. However, restricting the analysis to the featureless electron density does not reveal the chemical bonding nature and the existence of intermolecular interactions. This shortcoming can be resolved by the use of the DORI (Density Overlap Region Indicator) descriptor, which is capable of detecting simultaneously both covalent patterns and non-covalent interactions from electron density and its derivatives. Using the biscarbonyl[14]annulene crystal under pressure as an example, we demonstrate how DORI can be exploited on experimental electron densities to reveal and monitor changes in electronic structure patterns resulting from ...
Latest version: v1
Publication date: Feb 06, 2019
Louis Madsen,
Ying Wang,
Yadong He,
Zhou Yu,
Jianwei Gao,
Stephanie Brinck,
Carla Slebodnick,
Gregory Fahs,
Curt Zanelotti,
Maruti Hegde,
Robert Moore,
Bernd Ensing,
Theo Dingemans,
Rui Qiao
- We describe a double helical conformation in the densely charged aromatic polyamide poly(2,2’- disulfonyl-4,4’-benzidine terephthalamide) or PBDT. This double helix macromolecule represents one of the most rigid simple molecular structures known, exhibiting an extremely high axial persistence length (~ 1 micrometer).
Latest version: v1
Publication date: Feb 03, 2019
José A. Flores-Livas,
Daniele Tomerini,
Maximilian Amsler,
Ariadni Boziki,
Ursula Rothlisberger,
Stefan Goedecker
- We perform a thorough structural search with the minima hopping method (MHM) to explore low-energy structures of methylammonium lead iodide. By combining the MHM with a forcefield, we efficiently screen vast portions of the configurational space with large simulation cells containing up to 96 atoms. Our search reveals two structures of methylammonium iodide perovskite (MAPI) that are substantially lower in energy than the well-studied experimentally observed low-temperature orthorhombic phase. The data set containing approximately ~180,000 crystal structures is provided.
Latest version: v1
Publication date: Jan 23, 2019
Vicent Lloret,
Miguel Ángel Rivero–Crespo,
José Alejandro Vidal–Moya,
Stefan Wild,
Antonio Doménech–Carbó,
Bettina S. J. Heller,
Sunghwan Shin,
Hans-Peter Steinrück,
Florian Maier,
Frank Hauke,
Maria Varela,
Andreas Hirsch,
Antonio Leyva–Pérez,
Gonzalo Abellán
- Group 15 elements in zero oxidation state (P, As, Sb and Bi), also called pnictogens, are rarely used in catalysis due to the difficulties associated in preparing well–structured and stable materials. Here, we report on the synthesis of highly exfoliated, few layer 2D phosphorene and antimonene in zero oxidation state, suspended in an ionic liquid, with the native atoms ready to interact with external reagents while avoiding aerobic or aqueous decomposition pathways, and on their use as efficient catalysts for the alkylation of nucleophiles with esters. The few layer pnictogen material circumvents the extremely harsh reaction conditions associated to previous superacid–catalyzed alkylations, by enabling an alternative mechanism on surface, protected from the water and air by the ionic liquid. These 2D catalysts allow the alkylation of a variety of acid–sensitive organic molecules and giving synthetic relevancy to the use of simple esters as alkylating agents.
Latest version: v2
Publication date: Jan 14, 2019
Wei Chen,
Alfredo Pasquarello
- This entry includes the surface structures of some prototypical semiconductors obtained via structural optimizations using the PBE density functional. The structures were initially used for benchmarking ionization potentials calculated with hybrid density functionals and GW approximation.
Seven semiconductor surfaces are provided in the form of Quantum ESPRESSO input: Si(111), C(111), GaAs(110), GaP(110), ZnSe(110), ZnO(10-10), and TiO2(110).
Latest version: v1
Publication date: Dec 10, 2018
Wei Chen,
Francesco Ambrosio,
Giacomo Miceli,
Alfredo Pasquarello
- This entry provides the snapshots of liquid water generated with ab initio molecular dynamics using rVV10 density functional at room temperature. Nuclear quantum effects are taken into account through path-integral molecular dynamics simulations.
Latest version: v1
Publication date: Dec 10, 2018
Bingqing Cheng,
Edgar Engel,
Jörg Behler,
Christoph Dellago,
Michele Ceriotti
- Thermodynamic properties of liquid water as well as hexagonal (Ih) and cubic (Ic) ice are predicted based on density functional theory at the hybrid-functional level, rigorously taking into account quantum nuclear motion, anharmonic fluctuations and proton disorder. This is made possible by combining advanced free energy methods and state-of-the-art machine learning techniques. The ab initio description leads to structural properties in excellent agreement with experiments, and reliable estimates of the melting points of light and heavy water. We observe that nuclear quantum effects contribute a crucial 0.2 meV/H2O to the stability of ice Ih, making it more stable than ice Ic. Our computational approach is general and transferable, providing a comprehensive framework for quantitative predictions of ab initio thermodynamic properties using machine learning potentials as an intermediate step.
In this set of supplemental materials, we have included the neural network potential for ...
Latest version: v1
Publication date: Dec 04, 2018
Binglun Yin,
William Curtin
- We propose a general method to calculate the average misfit volumes of atoms in any random alloy via DFT calculations. The method is validated with an example of a 6-component equi-composition high entropy alloy. The special quasi-random structures (SQSs) used in our work are reported here.
Latest version: v1
Publication date: Dec 03, 2018
Daniele Ongari,
Peter G. Boyd,
Ozge Kadioglu,
Amber K. Mace,
Seda Keskin,
Berend Smit
- Charge equilibration (Qeq) methods can estimate the electrostatic potential of molecules and periodic frameworks by assigning point charges to each atom, using only a small fraction of the resources needed to compute density functional (DFT)-derived charges. This makes possible, for example, the computational screening of thousands of microporous structures to assess their performance for the adsorption of polar molecules. Recently, different variants of the original Qeq scheme were proposed to improve the quality of the computed point charges. One focus of this research was to improve the gas adsorption predictions in Metal Organic Frameworks (MOFs), for which many different structures are available. In this work, we review the evolution of the method from the original Qeq scheme, understanding the role of the different modifications on the final output. We evaluated the result of combining different protocols and set of parameters, by comparing the Qeq charges with high quality ...
Latest version: v2
Publication date: Nov 29, 2018
Aliaksandr V. Yakutovich,
Johannes Hoja,
Daniele Passerone,
Alexandre Tkatchenko,
Carlo A. Pignedoli
- We provide the input files to reproduce the data presented in the work:
Hidden Beneath the Surface: Origin of the Observed Enantioselective Adsorption on PdGa(111)
The files are subdivided in directories named after the figures/table of the manuscript
A. V. Yakutovich, J. Hoja, D. Passerone, Alexandre Tkatchenko, C. A. Pignedoli
J. Am. Chem. Soc., 140, 1401-1408 (2018) DOI: 10.1021/jacs.7b10980
In the work, we unravel the origin of the recently observed striking enantioselectivity of the PdGa(111) surface with respect to the adsorption of a small organic molecule, 9-ethynylphenanthrene, using first-principles calculations. It turns out that the key ingredient to understand the experimental evidence is the appropriate description of van der Waals interactions beyond the widely employed atomic pairwise approximation. A recently developed van der Waals-inclusive density functional method, which encompasses dielectric screening effects, reveals the origin of the experimentally ...
Latest version: v1
Publication date: Nov 23, 2018
Richard L. Martin,
Li-Chiang Lin,
Kuldeep Jariwala,
Berend Smit,
Maciej Haranczyk
- Metal–organic frameworks (MOFs), a class of porous materials, are of particular interest in gas storage and separation applications due largely to their high internal surface areas and tunable structures. MOF-5 is perhaps the archetypal MOF; in particular, many isoreticular analogues of MOF-5 have been synthesized, comprising alternative dicarboxylic acid ligands. In this contribution we introduce a new set of hypothesized MOF-5 analogues, constructed from commercially available organic molecules. We describe our automated procedure for hypothetical MOF design, comprising selection of appropriate ligands, construction of 3D structure models, and structure relaxation methods. 116 MOF-5 analogues were designed and characterized in terms of geometric properties and simulated methane uptake at conditions relevant to vehicular storage applications. A strength of the presented approach is that all of the hypothesized MOFs are designed to be synthesizable utilizing ligands purchasable online.
Version 2 includes the structures in CIF format.
Latest version: v2
Publication date: Nov 14, 2018
Efrem Braun,
Alexander F. Zurhelle,
Wouter Thijssen,
Sondre Schnell,
Li-Chiang Lin,
Jihan Kim,
Joshua A. Thompson,
Berend Smit
- With the growth of natural gas as an energy source, upgrading CO2-contaminated supplies has become increasingly important. Here we develop a single metric that captures how well an adsorbent performs the separation of CH4 and CO2, and we then use this metric to computationally screen tens of thousands of all-silica zeolites. We show that the most important predictors of separation performance are the CO2 heat of adsorption (Qst, CO2) and the CO2 saturation loading capacity. We find that a higher-performing material results when the absolute value of the CH4 heat of adsorption (Qst, CH4) is decreased independently of Qst, CO2, but a correlation that exists between Qst, CH4 and Qst, CO2 in all-silica zeolites leads to incongruity between the objectives of optimizing Qst, CO2 and minimizing Qst, CH4, rendering Qst, CH4 nonpredictive of separation performance. We also conduct a large-scale analysis of ideal adsorbed solution theory (IAST) by comparing results obtained using ...
Latest version: v2
Publication date: Nov 14, 2018
Matthew Witman,
Sanliang Ling,
Sudi Jawahery,
Peter G. Boyd,
Maciej Haranczyk,
Ben Slater,
Berend Smit
- Project Abstract: For applications of metal-organic frameworks (MOFs) such as gas storage and separation, flexibility is often seen as a parameter that can tune material performance. In this work we aim to determine the optimal flexibility for the shape selective separation of similarly sized molecules (e.g., Xe/Kr mixtures). To obtain systematic insight into how the flexibility impacts this type of separation we develop a simple analytical model that predicts a material's Henry regime adsorption and selectivity as a function of flexibility. We elucidate the complex dependence of selectivity on a framework's intrinsic flexibility whereby performance is either improved or reduced with increasing flexibility, depending on the material's pore size characteristics. However, the selectivity of a material with the pore size and chemistry that already maximizes selectivity in the rigid approximation is continuously diminished with increasing flexibility, demonstrating that the globally ...
Latest version: v2
Publication date: Nov 10, 2018
Rocio Mercado,
Rueih-Sheng Fu,
Aliaksandr V. Yakutovich,
Leopold Talirz,
Maciej Haranczyk,
Berend Smit
- Here we present 69,840 covalent organic frameworks (COFs) assembled in silico from a set of 666 distinct organic linkers into 2D-layered and 3D configurations. We investigate the feasibility of using these frameworks for methane storage by using grand-canonical Monte Carlo (GCMC) simulations to calculate their deliverable capacities (DCs). From these calculations, we predict that the best structure in the database is linker91_C_linker91_C_tbd, a structure composed of carbon-carbon bonded triazine linkers in the tbd topology. This structure has a predicted 65-bar DC of 216 v STP/v, greater than that of the best current methane storage material. We also predict other top performing materials, with 305 structures having DCs of over 190 v STP/v, and 34 of these having DCs of over 200 v STP/v.
This archive entry contains the database of assembled COF structures (in CIF file format) together with all of their properties, which can be explored using interactive figures. Among the ...
Latest version: v3
Publication date: Oct 05, 2018
Jan Wilhelm,
Dorothea Golze,
Leopold Talirz,
Jürg Hutter,
Carlo Antonio Pignedoli
- We provide the input files needed to reproduce the results of the article
Toward GW Calculations on Thousands of Atoms
J. Wilhelm, D. Golze, L. Talirz, J. Hutter, C. A. Pignedoli
J. Phys. Chem. Lett. 9, 306–312 (2018) DOI:10.1021/acs.jpclett.7b02740
The GW approximation of many-body perturbation theory is an accurate method
for computing electron addition and removal energies of molecules and solids.
In a canonical implementation, however, its computational cost is in the
system size N, which prohibits its application to many systems of interest.
We present a full-frequency GW algorithm in a Gaussian-type basis,
whose computational cost scales with N2 to N3.
The implementation is optimized for massively parallel execution on
state-of-the-art supercomputers and is suitable for nanostructures and molecules in the gas,
liquid or condensed phase, using either pseudopotentials or all electrons.
We validate the accuracy of the algorithm on the GW100 molecular test ...
Latest version: v1
Publication date: Sep 28, 2018
Marina R. Filip,
Feliciano Giustino
- Perovskite minerals form an essential component of the Earth’s mantle, and synthetic crystals are ubiquitous in electronics, photonics, and energy technology. The extraordinary chemical diversity of these crystals raises the question of how many and which perovskites are yet to be discovered. Here we show that the “no-rattling” principle postulated by Goldschmidt in 1926, describing the geometric conditions under which a perovskite can form, is much more effective than previously thought and allows us to predict perovskites with a fidelity of 80%. By supplementing this principle with inferential statistics and internet data mining we establish that currently known perovskites are only the tip of the iceberg, and we enumerate 90,000 hitherto-unknown compounds awaiting to be studied. Our results suggest that geometric blueprints may enable the systematic screening of millions of compounds and offer untapped opportunities in structure prediction and materials design.
Latest version: v1
Publication date: Sep 03, 2018
Benjamin Meyer,
Boodsarin Sawatlon,
Stefan Niklaus Heinen,
O. Anatole von Lilienfeld,
Clémence Corminboeuf
- The application of modern machine learning to challenges in atomistic simulation is gaining attraction. We present new machine learning models that can predict the energy of the oxidative addition process between a transition metal complex and a substrate for C-C cross-coupling reaction. In turn, this quantity can be used as a descriptor to estimate the activity of homogeneous catalysts using molecular volcano plots. The versatility of this approach is illustrated for vast libraries of organometallic catalysts based on Pt, Pd, Ni, Cu, Ag, and Au combined with 91 ligands. Out-of-sample machine learning predictions were made on a total of 18,062 compounds leading to 557 catalyst candidates falling into the ideal thermodynamic window. This number was further refined by searching for candidates with an estimated price lower than 10 US$/mmol. The 37 catalyst finalists are dominated by palladium phosphine ligand combinations but also include earth abundant (Cu) transition metal with ...
Latest version: v1
Publication date: Aug 01, 2018
Efrem Braun,
Yongjin Lee,
Seyed Mohamad Moosavi,
Senja Barthel,
Rocio Mercado,
Igor A. Baburin,
Davide M. Proserpio,
Berend Smit
- Zeolite-templated carbons (ZTCs) comprise a relatively recent material class synthesized via the chemical vapor deposition of a carbon-containing precursor on a zeolite template, followed by the removal of the template. We have developed a theoretical framework to generate a ZTC model from any given zeolite structure, which we show can successfully predict the structure of known ZTCs. We use our method to generate a library of ZTCs from all known zeolites, to establish criteria for which zeolites can produce experimentally accessible ZTCs, and to identify over 10 ZTCs that have never before been synthesized. We show that ZTCs partition space into two disjoint labyrinths that can be described by a pair of interpenetrating nets. Since such a pair of nets also describes a triply periodic minimal surface (TPMS), our results establish the relationship between ZTCs and schwarzites—carbon materials with negative Gaussian curvature that resemble TPMSs—linking the research topics and ...
Latest version: v1
Publication date: Jul 31, 2018
Edgar A. Engel,
Andrea Anelli,
Michele Ceriotti,
Chris J. Pickard,
Richard J. Needs
- We report a large-scale density-functional-theory study of the configuration space of water ice. We geometry optimise 74,963 ice structures, which are selected and constructed from over five million tetrahedral networks listed in the databases of Treacy and Deem, and the International Zeolite Association database. All prior knowledge of ice is set aside and we introduce generalised convex hulls to identify configurations stabilised by appropriate thermodynamic constraints. We thereby rediscover all known phases (I to XVII, i, 0 and the quartz phase) except the metastable ice IV. Crucially, we also find promising candidates for ices XVIII through LI. Using the sketch-map dimensionality-reduction algorithm we construct an a priori, navigable map of configuration space, which reproduces similarity relations between structures and highlights the novel candidates. By relating the known phases to the tractably small, yet structurally diverse set of synthesisable candidate structures, we ...
Latest version: v1
Publication date: May 19, 2018
Andrea Grisafi,
David M. Wilkins,
Gabor Csányi,
Michele Ceriotti
- Here we present 1,000 structures each of a water monomer, water dimer, Zundel cation and bulk water used to train tensorial machine-learning models in Phys. Rev. Lett. 120, 036002 (2018). The archive entry contains files in extended-XYZ format including the structures and several tensorial properties: for the monomer, dimer and Zundel cation, the dipole moment, polarizability and first hyperpolarizability are included, and for bulk water the dipole moment, polarizability and dielectric tensor are given.
Latest version: v1
Publication date: May 19, 2018
Richard L. Martin,
Cory M. Simon,
Berend Smit,
Maciej Haranczyk
- Porous polymer networks (PPNs) are a class of advanced porous materials that combine the advantages of cheap and stable polymers with the high surface areas and tunable chemistry of metal–organic frameworks. They are of particular interest for gas separation or storage applications, for instance, as methane adsorbents for a vehicular natural gas tank or other portable applications. PPNs are self-assembled from distinct building units; here, we utilize commercially available chemical fragments and two experimentally known synthetic routes to design in silico a large database of synthetically realistic PPN materials. All structures from our database of 18,000 materials have been relaxed with semiempirical electronic structure methods and characterized with Grand-canonical Monte Carlo simulations for methane uptake and deliverable (working) capacity. A number of novel structure–property relationships that govern methane storage performance were identified. The relationships are ...
Latest version: v1
Publication date: May 15, 2018
Richard L. Martin,
Cory M. Simon,
Bharat Medasani,
David K. Britt,
Berend Smit,
Maciej Haranczyk
- Covalent organic frameworks (COFs) are a class of advanced nanoporous polymeric materials which combine the crystallinity of metal–organic frameworks (MOFs) with the stability and potentially low-cost organic chemistry of porous polymer networks (PPNs). Like other advanced porous materials, COFs can potentially be designed to meet the needs of a variety of applications, from energy, to security, to human health. In this work, we construct in silico a database of hypothetical three-dimensional, crystalline COFs. In constructing this library we generate novel COFs using only established synthetic routes, previously utilized tetrahedral building units, and commercially available bridging “linker” molecules. This ensures that there are no known chemical barriers to synthesizing all materials in our database. We relaxed all materials in our database through semiempirical electronic structure calculations. In addition, for those structures that allow interpenetration, we designed ...
Latest version: v1
Publication date: May 15, 2018
Seyed Mohamad Moosavi,
Peter G. Boyd,
Lev Sarkisov,
Berend Smit
- Metal-organic frameworks (MOFs) have emerged as versatile materials for applications ranging from gas separation and storage, catalysis, and sensing. The attractive feature of MOFs is that by changing the ligand and/or metal, they can be chemically tuned to perform optimally for a given application. In most, if not all, of these applications one also needs a material that has a sufficient mechanical stability, but our understanding of how changes in the chemical structure influence mechanical stability is limited. In this work, we rationalize how the mechanical properties of MOFs are related to framework bonding topology and ligand structure. We illustrate that the functional groups on the organic ligands can either enhance the mechanical stability through formation of a secondary network of non-bonded interactions, or soften the material by destabilizing the bonded network of a MOF. In addition, we show that synergistic effect of the bonding network of the material and the ...
Latest version: v1
Publication date: Apr 17, 2018
Ngoc Linh Nguyen,
Francesca Baletto,
Nicola Marzari
- We introduce and discuss the phenomenon of adatom-induced surface local melting, using extensive first-principles molecular dynamics simulations of Al(100) taken as a paradigmatic case of a non-premelting surface that nevertheless displays facile adatom diffusion with single and multiple exchange pathways. Here, a single adatom deposited on the surface is sufficient to nucleate a localized and diffusing liquid-like region that remains confined to the surface layer, but with an area that increases with temperature; in the absence of the adatom, the surface instead remains crystalline until reaching the bulk melting temperature.
Latest version: v1
Publication date: Feb 11, 2018
Mauro Del Ben,
Joost VandeVondele,
Juerg Hutter
- Methods based on the second order Møller–Plesset perturbation theory (MP2) and the Random Phase Approximation (RPA) have emerged as practicable and reliable approaches to improve the accuracy of density functional approximations for first principle atomistic simulations. Such approaches are in fact capable to account ab-initio for non-local dynamical electron correlation effects, which play a fundamental role, for example, in the description of non-bonded interactions. To assess the performance of MP2 and RPA for real applications, isobaric-isothermal Monte Carlo simulations have been performed to study the structural properties of bulk liquid water under ambient conditions. The choice of bulk liquid water as benchmark system is motivated by the complicated nature of the intermolecular interactions, where repulsion, polarization, hydrogen bonding and van der Waals forces play an important role and are particularly difficult to reproduce accurately in atomistic models. The results ...
Latest version: v1
Publication date: Nov 28, 2017
Daniele Dragoni,
Tom Daff,
Gabor Csanyi,
Nicola Marzari
- Interatomic potentials are often necessary to describe complex realistic systems that would be too costly to study from first-principles. Commonly, interatomic potentials are designed using functional forms driven by physical intuition and fitted to experimental or computational data. The moderate flexibility of these functional forms limits their ability to be systematically improved by increasing the fitting datasets; on the other hand, their qualitative description of the essential physical interactions ensures a modicum degree of transferability. Recently, a novel trend has emerged where potential-energy surfaces are represented by neural networks fitted on large numbers of first-principles calculations, thus maximizing flexibility but requiring extensive datasets to ensure transferability. Gaussian Approximation Potentials in particular are a novel class of potentials based on non-linear, non-parametric Gaussian-process regression. Here we generate a Gaussian Approximation ...
Latest version: v2
Publication date: Nov 06, 2017
Daniele Ongari,
Peter G. Boyd,
Senja Barthel,
Matthew Witman,
Maciej Haranczyk,
Berend Smit
- Project Abstract: Pore volume is one of the main properties for the characterization of microporous crystals. It is experimentally measurable and it can also be obtained from the refined unit cell by a number of computational techniques. In this work we assess the accuracy and the discrepancies between the different computational methods which are commonly used for this purpose, i.e, geometric, helium and probe center pore volume, by studying a database of more than 5000 frameworks. We developed a new technique to fully characterize the internal void of a microporous material and to compute the probe accessible and occupiable pore volume. We show that unlike the other definitions of pore volume, the occupiable pore volume can be directly related to the experimentally measured pore volumes from nitrogen isotherms.
Latest version: v1
Publication date: May 18, 2017
Yifei Michelle Liu,
Berend Smit
- Project abstract: In this work, a theoretical framework is developed to explain and predict changes in the product distribution of the propene dimerization reaction, which yields a mixture of C6 olefin isomers, resulting from the use of different porous materials as catalysts. The MOF-74 class of materials has shown promise in catalyzing the dimerization of propene with high selectivity for valuable linear olefin products. We show that experimentally observed changes in the product distribution can be explained in terms of the contribution of the pores to the free energy of formation, which are directly computed using molecular simulation. Our model is used to screen a library of 118 existing and hypothetical MOF and zeolite structures to study how product distribution can be tuned by changing pore size, shape, and composition of porous materials. Using these molecular descriptors, catalyst properties are identified that increase the selective reaction of linear olefin ...
Latest version: v1
Publication date: May 05, 2017
Yongjin Lee,
Senja D. Barthel,
Paweł Dłotko,
S. Mohamad Moosavi,
Kathryn Hess,
Berend Smit
- In most applications of nanoporous materials the pore structure is as important as the chemical composition as a determinant of performance. For example, one can alter performance in applications like carbon capture or methane storage by orders of magnitude by only modifying the pore structure. For these applications it is therefore important to identify the optimal pore geometry and use this information to find similar materials. However, the mathematical language and tools to identify materials with similar pore structures, but different composition, has been lacking. Recently, we developed a pore recognition approach to quantify similarity of pore structures using topological data analysis. Barcodes generated with using this approach allow us to identify materials with similar pore geometries, and to screen for materials that are similar to given top-performing structures. This database has barcodes for zeolites, metal organic frameworks, and zeolitic imidazolate frameworks.
Latest version: v1
Publication date: Mar 14, 2017
