6,147,452 Works

Free-Energy Surface Prediction by Flying Gaussian Method

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...

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

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...

BLOSOM - release

L. Sim, J. Vielma, R. Duran, R. Romeo, P. Wingo & Rose K
Link to BLOSOM release download site

Oxygen defects in amorphous Al2O3

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...

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,...

Supplementary Data for “Non-Abelian band topology in noninteracting metals”

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...

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

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).

EBDC Business Expectations Panel (2016)

Ralf Elsas, Oliver Falck & Joachim Winter
Das EBDC Business Expectations Panel, BEP, besteht aus den wichtigsten Variablen des ifo Konjunkturtests und den entsprechenden Bilanzdaten aus den Unternehmensdatenbanken Amadeus (Bureau van Dijk) und Hoppenstedt (Hoppenstedt Firmeninformationen GmbH). Der ifo Konjunkturtest wird monatlich vom ifo Institut erhoben. Er setzt sich aus den EInzelerhebungen für die Sektoren Bau, Dienstleister, Handel und Verarbeitendes Gewerbe zusammen. Kern des Fragenprogramms sind qualitative Urteile zu aktuellen ökonomischen Parametern der Unternehmen wie z.B. der allgemeinen Situation, dem Umsatz, der...

A Standard Solid State Pseudopotentials (SSSP) library optimized for precision and efficiency (Version 1.1, 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...

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....

Ocean colour and distribution of suspended particulates in the St. Lawrence Estuary.

Martin Montes-Hugo, Suzanne Roy, Jean Pierre Gagne, Serge Demers, Servet Cizmeli & Sebastien Mas
Distribution of total suspended particulate matter (SPM) in the St Lawrence estuary was investigated based on spaceborne ocean colour measurements. Biogeooptical models were constructed and validated with in situ biogeochemical and optical data obtained during spring of 2000 and 2001. The resulting remote sensing reflectance (Rrs) model was applied to derive SPM maps during spring and fall of two years with different river discharge (i.e., 'low' in 2001, 'high' in 2000). Uncertainty of SPM estimates...

MD trajectories of semiconductor-water interfaces and relaxed atomic structures of semiconductor surfaces

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...

Chemical Shifts in Molecular Solids by Machine Learning Datasets

Federico Paruzzo, Albert Hofstetter, Félix Musil, Michele Ceriotti, Lyndon Emsley & Sandip De
We present a database of energy and NMR chemical shifts DFT calculations of 2500 crystal organic solids. The structures contain only H/C/N/O atoms and were subject to all-atoms geometry optimisation. Calculations were carried out using Quantum Espresso and GIPAW.

Evaluating charge equilibration methods to generate electrostatic fields in nanoporous materials

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

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...

Hidden Beneath the Surface: Origin of the Observed Enantioselective Adsorption on PdGa(111)

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...

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...

Evaluating charge equilibration methods to generate electrostatic fields in nanoporous materials

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

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...

Multithermal-multibaric molecular simulations from a variational principle

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...

Picture of Wet Electron: A Localized Transient State in Liquid Water

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...

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

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

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

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,...

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...

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