49 Works

Symmetry-Adapted Machine Learning for Tensorial Properties of Atomistic Systems

Michele Ceriotti, Gabor Csányi, Andrea Grisafi & David M. Wilkins
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.

Ab initio thermodynamics of liquid and solid water: supplemental materials

Christoph Dellago, Michele Ceriotti, Bingqing Cheng, Jörg Behler & Edgar Engel
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...

Evaluating charge equilibration methods to generate electrostatic fields in nanoporous materials

Amber K. Mace, Daniele Ongari, Berend Smit, Seda Keskin, Peter G. Boyd & Ozge Kadioglu
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...

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

Sondre Schnell, Wouter Thijssen, Joshua A. Thompson, Jihan Kim, Berend Smit, Alexander F. Zurhelle, Efrem Braun & Li-Chiang Lin
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....

The geometric blueprint of perovskites

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...

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

Berend Smit, Rueih-Sheng Fu, Rocio Mercado, Maciej Haranczyk, Aliaksandr V. Yakutovich & Leopold Talirz
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...

The Influence of Intrinsic Framework Flexibility on Adsorption in Nanoporous Materials (Data Download)

Ben Slater, Peter G. Boyd, Matthew Witman, Sanliang Ling, Berend Smit, Sudi Jawahery & Maciej Haranczyk
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...

Mapping uncharted territory in ice from zeolite networks to ice structures

Andrea Anelli, Richard J. Needs, Michele Ceriotti, Chris J. Pickard & Edgar A. Engel
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,...

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

Arunraj Chidambaram, Seyed Mohamad Moosavi, Richard Bounds, Thomas D. Daff, Berend Smit, Tom K. Woo, Pascal Schouwink, Jorge A. R. Navarro, Kyriakos C. Stylianou, Jeffrey A. Reimer, Peter George Boyd & Andrzej Gładysiak
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...

DORI reveals the influence of non-covalent interactions on covalent bonding patterns in molecular crystals under pressure

Benoit Guillot, Senja Barthel, Benjamin Meyer, Berend Smit, Amber Mace, Laurent Vannay & 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...

Atomic structures of semiconductor surfaces

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).

Double helix PBDT polymer - Submitted manuscript, simulations and other source data

Curt Zanelotti, Zhou Yu, Carla Slebodnick, Robert Moore, Gregory Fahs, Jianwei Gao, Bernd Ensing, Stephanie Brinck, Yadong He, Maruti Hegde, Louis Madsen, Rui Qiao, Ying Wang & Theo Dingemans
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).

Unified theory of thermal transport in crystals and disordered solids

Francesco Mauri, Nicola Marzari & Michele Simoncelli
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;...

Rational design and synthesis of metal-organic frameworks for carbon capture using adsorbaphore identification

Andrzej Gładysiak, Pascal Schouwink, Berend Smit, Tom K. Woo, Arunraj Chidambaram, Richard Bounds, Peter George Boyd, Seyed Mohamad Moosavi, Jorge A. R. Navarro, Kyriakos C. Stylianou, Thomas D. Daff & Jeffrey A. Reimer
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...

In Silico Design of Porous Polymer Networks: High Throughput Screening for Methane Storage Materials

Richard L. Martin, Berend Smit, Cory M. Simon & 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...

Ab initio electronic structure of liquid water: Molecular dynamics snapshots

Alfredo Pasquarello, Wei Chen, Francesco Ambrosio & Giacomo Miceli
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.

Adatom-Induced Local Melting

Francesca Baletto, Ngoc Linh Nguyen & 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...

Few layer 2D pnictogens catalyze the alkylation of soft nucleophiles with esters.

Bettina S. J. Heller, Stefan Wild, Florian Maier, Hans-Peter Steinrück, Vicent Lloret, Antonio Leyva–Pérez, Sunghwan Shin, Gonzalo Abellán, Maria Varela, Miguel Ángel Rivero–Crespo, Andreas Hirsch, Frank Hauke, José Alejandro Vidal–Moya & Antonio Doménech–Carbó
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...

Accurate Characterization of the Pore Volume in Microporous Crystalline Materials (Data Download)

Senja Barthel, Maciej Haranczyk, Peter G. Boyd, Berend Smit, Matthew Witman & Daniele Ongari
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...

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

Joshua A. Thompson, Alexander F. Zurhelle, Berend Smit, Jihan Kim, Li-Chiang Lin, Wouter Thijssen, Efrem Braun & Sondre Schnell
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....

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

Leopold Talirz, Berend Smit, Maciej Haranczyk, Rueih-Sheng Fu, Rocio Mercado & Aliaksandr V. Yakutovich
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...

Barcodes for nanoporous materials

Paweł Dłotko, Yongjin Lee, Senja D. Barthel, Kathryn Hess, S. Mohamad Moosavi & 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...

Isobaric-Isothermal Monte Carlo Simulations of Bulk Liquid Water from MP2 and RPA Theory (MC Trajectories Data Download)

Juerg Hutter, Joost VandeVondele & Mauro Del Ben
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,...

Machine learning meets volcano plots: Computational discovery of cross-coupling catalysts

Benjamin Meyer, Boodsarin Sawatlon, Clémence Corminboeuf, O. Anatole Von Lilienfeld & Stefan Niklaus Heinen
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...

Capturing chemical intuition in synthesis of metal-organic frameworks

Kyriakos C. Stylianou, Berend Smit, Arunraj Chidambaram, Seyed Mohamad Moosavi, Leopold Talirz & Maciej Haranczyk
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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