304 Works

Relative Abundance of Z2 Topological Order in Exfoliable Two-Dimensional Insulators

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...

AENET-LAMMPS and AENET-TINKER: interfaces for accurate and efficient molecular dynamics simulations with machine learning potentials

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...

Randomly-displaced methane configurations

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...

Randomly-displaced methane configurations

Sergey Pozdnyakov, Michael Willat & 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 (7732489) 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...

Mail-order metal-organic frameworks (MOFs): designing isoreticular MOF-5 analogues comprising commercially available organic molecules

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...

In Silico Design of 2D and 3D Covalent Organic Frameworks for Methane Storage Applications

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...

In silico discovery of covalent organic frameworks for carbon capture

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...

Adatom-Induced Local Melting

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...

Local polarization in oxygen-deficient LaMnO3 induced by charge localization in the Jahn-Teller distorted structure

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...

Two-dimensional materials from high-throughput computational exfoliation of experimentally known compounds (Data download)

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...

Rare-earth magnetic nitride perovskites

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...

Vanadium is an optimal element for strengthening in both fcc and bcc high-entropy alloys

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...

Solvent-mediated morphology selection of the active pharmaceutical ingredient isoniazid: Experimental and simulation studies

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...

Mining the C-C Cross-Coupling Genome using Machine Learning

Boodsarin Sawatlon, Alberto Fabrizio, Benjamin Meyer, Stefan N. Heinen, Matthew D. Wodrich, O. Anatole Von Lilienfeld & 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,...

Termini effects on the optical properties of graphene nanoribbons

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...

Data-driven design of metal-organic frameworks for wet flue gas CO2 capture

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...

A Standard Solid State Pseudopotentials (SSSP) library optimized for accuracy and efficiency (Version 1.0, data download)

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...

Molecular Recognition and Specificity of Biomolecules to Titanium Dioxide from MD Simulations

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...

Applicability of tail-corrections in the molecular simulations of porous materials

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...

Applicability of tail-corrections in the molecular simulations of porous materials

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...

Tailoring Bond Topologies in Open-Shell Graphene Nanostructures

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...

Koopmans-Compliant Functionals and Potentials and Their Application to the GW100 Test Set

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,...

Generalized stacking fault energy curves for six body-centered cubic refractory metals

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.

High-throughput computational screening of nanoporous adsorbents for CO 2 capture from natural gas

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....

Capturing chemical intuition in synthesis of metal-organic frameworks

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...

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