112 Works

Free-Energy Surface Prediction by Flying Gaussian Method: Numerical Proof

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...

Emergence of hidden phases of methylammonium lead-iodide (CH3NH3PbI) upon compression

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...

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...

Intrinsic defects in amorphous TiO2

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.

Ab initio thermodynamics of liquid and solid water: supplemental materials

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...

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...

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

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...

TopoMat: a database of high-throughput first-principles calculations of topological materials

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...

Unified theory of thermal transport in crystals and disordered solids

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;...

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...

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...

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).

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....

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

Berend Smit, Kevin Maik Jablonka & Daniele Ongari
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

Berend Smit, Kevin Maik Jablonka & Daniele Ongari
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...

Generating carbon schwarzites via zeolite-templating

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...

Reducing the Number of Mean-Square Deviation Calculations with Floating Close Structure in Metadynamics

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...

Symmetry-Adapted Machine Learning for Tensorial Properties of Atomistic Systems

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.

Quantum Mechanical Static Dipole Polarizabilities in the QM7b and AlphaML Showcase Databases

Yang Yang, Ka Un Lao, David M. Wilkins, Andrea Grisafi, Michele Ceriotti & DiStasio Jr., Robert A.
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.

MD trajectories of bulk water and of the water-vacuum interface

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.

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...

TopoMat: a database of high-throughput first-principles calculations of topological materials

QuanSheng Wu, Gabriel Autès, 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...

Enhanced sampling of transition states

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,...

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

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,...

Reducing the Number of Mean-Square Deviation Calculations with Floating Close Structure in Metadynamics

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...

Registration Year

  • 2017
    7
  • 2018
    23
  • 2019
    82

Resource Types

  • Dataset
    112